Citrus Sinensis ID: 041804

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400---
Protein Sequence
RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGEQSG
Secondary Structure (PSIPRED)
ccEEccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEccccHHHHHHHHHHHHHHcccccccEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHcccHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccEEEHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
RETLSCYANDWKRALEFFNWvetdchfthttdtYNSVIDILGKFFEFDLSWNLIhrmkdnpssipnhatFRIMFKRYVTAHLVNEAMgtfnkldefglkdeVSYCNLVDALCEYKHVIEAQElcfgenknvgfsglVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRemgcqpsvvTCNTVIKLLCENGRVREAYAVLAempkkgcvpdvitYHCFFRCLEKPREILGLFDRMiesgirpkMDTYVMLLRKfgrwgflrPVFVVWKKMeelgcspdefAYNALVDALIDKGMLDMARKYDEEMFAkglsakpreeLGTKLvqggldgeqsg
Flexible Loop (DISEMBL)
retlscyaNDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIravgvsegvDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAempkkgcvpDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKglsakpreelgtklvqggldgeqsg
Low Complexity Region (SEG)
RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGEQSG
Disordered region (IsUnstruct)
***LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYD*******************************
Disordered Region (DISOPRED)
RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGEQ**
Disordered Region (DISEMBL)
RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGEQSG
Disordered Region (DISPRO)
*ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGE***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGEQSG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	403	2.2.26 [Sep-21-2011]
Q9M8M3	448	Pentatricopeptide repeat-	yes	no	0.972	0.875	0.667	1e-161
Q9LFQ4	572	Pentatricopeptide repeat-	no	no	0.962	0.678	0.343	3e-56
Q9LIL5	523	Putative pentatricopeptid	no	no	0.940	0.724	0.292	2e-44
Q9SSR6	523	Pentatricopeptide repeat-	no	no	0.928	0.715	0.320	9e-43
Q9LN22	537	Pentatricopeptide repeat-	no	no	0.935	0.702	0.276	2e-41
Q9S7R4	482	Pentatricopeptide repeat-	no	no	0.883	0.738	0.297	2e-39
Q9FVX2	517	Pentatricopeptide repeat-	no	no	0.913	0.711	0.289	2e-38
Q9C9A2	510	Pentatricopeptide repeat-	no	no	0.950	0.750	0.286	4e-38
P0C8A0	638	Pentatricopeptide repeat-	no	no	0.893	0.564	0.263	3e-35
Q9FH87	637	Putative pentatricopeptid	no	no	0.883	0.558	0.268	6e-35

>sp|Q9M8M3|PP136_ARATH Pentatricopeptide repeat-containing protein At1g80550, mitochondrial OS=Arabidopsis thaliana GN=At1g80550 PE=2 SV=1

 Score =  568 bits (1463), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 265/397 (66%), Positives = 325/397 (81%), Gaps = 5/397 (1%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           E L+CY+NDW++ALEFFNWVE +  F HTT+T+N VIDILGK+FEF++SW LI+RM  N 
Sbjct: 52  EALTCYSNDWQKALEFFNWVERESGFRHTTETFNRVIDILGKYFEFEISWALINRMIGNT 111

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ 121
            S+PNH TFRI+FKRYVTAHLV EA+  ++KLD+F L+DE S+ NLVDALCE+KHV+EA+
Sbjct: 112 ESVPNHVTFRIVFKRYVTAHLVQEAIDAYDKLDDFNLRDETSFYNLVDALCEHKHVVEAE 171

Query: 122 ELCFGENK-NVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           ELCFG+N    GFS    ++ TKI+N+ILRGW K+ WWGKC+E+W++MD  GV KDL SY
Sbjct: 172 ELCFGKNVIGNGFS----VSNTKIHNLILRGWSKLGWWGKCKEYWKKMDTEGVTKDLFSY 227

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
           SIYMDIMCKSGKPWKAVKLYKEMK + +K+DVVAYNTVIRA+G S+GV+F +RV+REMRE
Sbjct: 228 SIYMDIMCKSGKPWKAVKLYKEMKSRRMKLDVVAYNTVIRAIGASQGVEFGIRVFREMRE 287

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG 300
            GC+P+V T NT+IKLLCE+GR+R+AY +L EMPK+GC PD ITY C F  LEKP EIL 
Sbjct: 288 RGCEPNVATHNTIIKLLCEDGRMRDAYRMLDEMPKRGCQPDSITYMCLFSRLEKPSEILS 347

Query: 301 LFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI 360
           LF RMI SG+RPKMDTYVML+RKF RWGFL+PV  VWK M+E G +PD  AYNA++DALI
Sbjct: 348 LFGRMIRSGVRPKMDTYVMLMRKFERWGFLQPVLYVWKTMKESGDTPDSAAYNAVIDALI 407

Query: 361 DKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGL 397
            KGMLDMAR+Y+EEM  +GLS + R EL  K +   L
Sbjct: 408 QKGMLDMAREYEEEMIERGLSPRRRPELVEKSLDETL 444

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LFQ4|PP383_ARATH Pentatricopeptide repeat-containing protein At5g15010, mitochondrial OS=Arabidopsis thaliana GN=At5g15010 PE=2 SV=2

 Score =  219 bits (557), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 139/405 (34%), Positives = 206/405 (50%), Gaps = 17/405 (4%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           E LS   NDW+ A  FF W      +  +   Y+S+I ILGK  +FD +W LI  M+   
Sbjct: 132 EILSRVRNDWETAFTFFVWAGKQQGYVRSVREYHSMISILGKMRKFDTAWTLIDEMRKFS 191

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVS-YCNLVDALCEYKHVIEA 120
            S+ N  T  IM ++Y   H V +A+ TF+    F L+  +  + +L+ ALC YK+V +A
Sbjct: 192 PSLVNSQTLLIMIRKYCAVHDVGKAINTFHAYKRFKLEMGIDDFQSLLSALCRYKNVSDA 251

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCRE---FWEEMDKRGVVKDL 177
             L F       F         K +N++L GW  +   G  RE    W EM   GV  D+
Sbjct: 252 GHLIFCNKDKYPFDA-------KSFNIVLNGWCNV--IGSPREAERVWMEMGNVGVKHDV 302

Query: 178 HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYRE 237
            SYS  +    K G   K +KL+  MKK+ I+ D   YN V+ A+  +  V  A  + + 
Sbjct: 303 VSYSSMISCYSKGGSLNKVLKLFDRMKKECIEPDRKVYNAVVHALAKASFVSEARNLMKT 362

Query: 238 MRE-MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPR 296
           M E  G +P+VVT N++IK LC+  +  EA  V  EM +KG  P + TYH F R L    
Sbjct: 363 MEEEKGIEPNVVTYNSLIKPLCKARKTEEAKQVFDEMLEKGLFPTIRTYHAFMRILRTGE 422

Query: 297 EILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALV 356
           E+  L  +M + G  P ++TY+ML+RK  RW     V ++W +M+E    PD  +Y  ++
Sbjct: 423 EVFELLAKMRKMGCEPTVETYIMLIRKLCRWRDFDNVLLLWDEMKEKTVGPDLSSYIVMI 482

Query: 357 DALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGEQ 401
             L   G ++ A  Y +EM  KG+  +P E +   ++Q    G+Q
Sbjct: 483 HGLFLNGKIEEAYGYYKEMKDKGM--RPNENV-EDMIQSWFSGKQ 524

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIL5|PP233_ARATH Putative pentatricopeptide repeat-containing protein At3g15200 OS=Arabidopsis thaliana GN=At3g15200 PE=3 SV=1

 Score =  180 bits (457), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 114/390 (29%), Positives = 193/390 (49%), Gaps = 11/390 (2%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           E ++   +DWK A      V        ++  YN ++D+LGK   F+    +   M    
Sbjct: 114 EVVNRNRSDWKPAYILSQLVVKQSVHLSSSMLYNEILDVLGKMRRFEEFHQVFDEMSKRD 173

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE-VSYCNLVDALCEYKHVIEA 120
             + N  T+ ++  RY  AH V+EA+G F +  EFG+ D+ V++  L+  LC YKHV  A
Sbjct: 174 GFV-NEKTYEVLLNRYAAAHKVDEAVGVFERRKEFGIDDDLVAFHGLLMWLCRYKHVEFA 232

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           + L     +  G          K  NMIL GW  +    + + FW+++       D+ SY
Sbjct: 233 ETLFCSRRREFGCD-------IKAMNMILNGWCVLGNVHEAKRFWKDIIASKCRPDVVSY 285

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
              ++ + K GK  KA++LY+ M       DV   N VI A+   + +  A+ V+RE+ E
Sbjct: 286 GTMINALTKKGKLGKAMELYRAMWDTRRNPDVKICNNVIDALCFKKRIPEALEVFREISE 345

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKG--CVPDVITYHCFFRCLEKPREI 298
            G  P+VVT N+++K LC+  R  + + ++ EM  KG  C P+ +T+    +  ++ +++
Sbjct: 346 KGPDPNVVTYNSLLKHLCKIRRTEKVWELVEEMELKGGSCSPNDVTFSYLLKYSQRSKDV 405

Query: 299 LGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDA 358
             + +RM ++      D Y ++ R + +W     V  +W +ME  G  PD+  Y   +  
Sbjct: 406 DIVLERMAKNKCEMTSDLYNLMFRLYVQWDKEEKVREIWSEMERSGLGPDQRTYTIRIHG 465

Query: 359 LIDKGMLDMARKYDEEMFAKGLSAKPREEL 388
           L  KG +  A  Y +EM +KG+  +PR E+
Sbjct: 466 LHTKGKIGEALSYFQEMMSKGMVPEPRTEM 495

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SSR6|PPR78_ARATH Pentatricopeptide repeat-containing protein At1g52640, mitochondrial OS=Arabidopsis thaliana GN=At1g52640 PE=2 SV=1

 Score =  174 bits (442), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 126/393 (32%), Positives = 202/393 (51%), Gaps = 19/393 (4%)

Query: 14  ALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIM 73
           A  FF W      F H+ ++Y+ +++ILG   +F L W+ +   ++      +   F I+
Sbjct: 85  AHRFFLWARRIPDFAHSLESYHILVEILGSSKQFALLWDFLIEAREYNYFEISSKVFWIV 144

Query: 74  FKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN-LVDALCEYKHVIEAQELCFGENKNVG 132
           F+ Y  A+L +EA   FN++ EFG+K  V   + L+ +LC+ KHV  AQE  FG+ K  G
Sbjct: 145 FRAYSRANLPSEACRAFNRMVEFGIKPCVDDLDQLLHSLCDKKHVNHAQEF-FGKAK--G 201

Query: 133 FSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK 192
           F G+V   KT  Y++++RGW ++      R+ ++EM +R  V DL +Y+  +D +CKSG 
Sbjct: 202 F-GIVPSAKT--YSILVRGWARIRDASGARKVFDEMLERNCVVDLLAYNALLDALCKSGD 258

Query: 193 PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNT 252
                K+++EM   G+K D  ++   I A   +  V  A +V   M+     P+V T N 
Sbjct: 259 VDGGYKMFQEMGNLGLKPDAYSFAIFIHAYCDAGDVHSAYKVLDRMKRYDLVPNVYTFNH 318

Query: 253 VIKLLCENGRVREAYAVLAEMPKKGCVPD------VITYHCFFRCLEKPREILGLFDRMI 306
           +IK LC+N +V +AY +L EM +KG  PD      ++ YHC    + +  ++L   DR  
Sbjct: 319 IIKTLCKNEKVDDAYLLLDEMIQKGANPDTWTYNSIMAYHCDHCEVNRATKLLSRMDR-- 376

Query: 307 ESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI-DKGML 365
            +   P   TY M+L+   R G       +W+ M E    P    Y  ++  L+  KG L
Sbjct: 377 -TKCLPDRHTYNMVLKLLIRIGRFDRATEIWEGMSERKFYPTVATYTVMIHGLVRKKGKL 435

Query: 366 DMARKYDEEMFAKGLS--AKPREELGTKLVQGG 396
           + A +Y E M  +G+   +   E L  +LV  G
Sbjct: 436 EEACRYFEMMIDEGIPPYSTTVEMLRNRLVGWG 468

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LN22|PPR54_ARATH Pentatricopeptide repeat-containing protein At1g20300, mitochondrial OS=Arabidopsis thaliana GN=At1g20300 PE=2 SV=1

 Score =  170 bits (431), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 113/409 (27%), Positives = 206/409 (50%), Gaps = 32/409 (7%)

Query: 13  RALEFFNWVETDCHFTH-TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFR 71
           ++L FFNW  +   + H +   YN +ID+ GK  +FDL+W+LI  MK     I +  TF 
Sbjct: 132 QSLAFFNWATSRDDYDHKSPHPYNEMIDLSGKVRQFDLAWHLIDLMKSRNVEI-SIETFT 190

Query: 72  IMFKRYVTAHLVNEAMGTFNKLDEFG-LKDEVSYCNLVDALCEYKHVIEAQELCFGENKN 130
           I+ +RYV A L +EA+  FN+++++G + D++++  ++  L   +   EAQ   F   K+
Sbjct: 191 ILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRKRRASEAQSF-FDSLKD 249

Query: 131 VGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS 190
                ++      +Y  ++RGW +     +  + ++EM   G+  ++++YSI +D +C+ 
Sbjct: 250 RFEPDVI------VYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDALCRC 303

Query: 191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTC 250
           G+  +A  ++ +M   G   + + +N ++R    +   +  ++VY +M+++GC+P  +T 
Sbjct: 304 GQISRAHDVFADMLDSGCAPNAITFNNLMRVHVKAGRTEKVLQVYNQMKKLGCEPDTITY 363

Query: 251 NTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG---LFDRMIE 307
           N +I+  C +  +  A  VL  M KK C  +  T++  FR +EK R++ G   ++ +M+E
Sbjct: 364 NFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIFRYIEKKRDVNGAHRMYSKMME 423

Query: 308 SGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDM 367
           +   P   TY +L+R F        V  + K+M++    P+   Y  LV      G  + 
Sbjct: 424 AKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFCGMGHWNN 483

Query: 368 ARKYDEEM-----FAKGLS--------------AKPREELGTKLVQGGL 397
           A K  +EM         LS               K  EEL  K++Q GL
Sbjct: 484 AYKLFKEMVEEKCLTPSLSLYEMVLAQLRRAGQLKKHEELVEKMIQKGL 532

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S7R4|PP125_ARATH Pentatricopeptide repeat-containing protein At1g74900, mitochondrial OS=Arabidopsis thaliana GN=OTP43 PE=2 SV=1

 Score =  163 bits (412), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 112/376 (29%), Positives = 182/376 (48%), Gaps = 20/376 (5%)

Query: 9   NDWKRALEFFNWVETDCH-FTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH 67
           N   +AL+FF++++     + H   +++  IDI  +       W+LIHRM+      P+ 
Sbjct: 68  NHGPKALQFFHFLDNHHREYVHDASSFDLAIDIAARLHLHPTVWSLIHRMRSLRIG-PSP 126

Query: 68  ATFRIMFKRYVTAHLVNEAMGTFNKLDEFG-LKDEVSYCNLVDALCEYKHVIEAQELCFG 126
            TF I+ +RY +A   ++A+  F  + E G  +D  S+  ++D LC+ K V +A EL   
Sbjct: 127 KTFAIVAERYASAGKPDKAVKLFLNMHEHGCFQDLASFNTILDVLCKSKRVEKAYELF-- 184

Query: 127 ENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI 186
                   G   ++ T  YN+IL GW  +    K  E  +EM +RG+  +L +Y+  +  
Sbjct: 185 ----RALRGRFSVD-TVTYNVILNGWCLIKRTPKALEVLKEMVERGINPNLTTYNTMLKG 239

Query: 187 MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS 246
             ++G+   A + + EMKK+  ++DVV Y TV+   GV+  +  A  V+ EM   G  PS
Sbjct: 240 FFRAGQIRHAWEFFLEMKKRDCEIDVVTYTTVVHGFGVAGEIKRARNVFDEMIREGVLPS 299

Query: 247 VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG---LFD 303
           V T N +I++LC+   V  A  +  EM ++G  P+V TY+   R L    E      L  
Sbjct: 300 VATYNAMIQVLCKKDNVENAVVMFEEMVRRGYEPNVTTYNVLIRGLFHAGEFSRGEELMQ 359

Query: 304 RMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKG 363
           RM   G  P   TY M++R +     +     +++KM    C P+   YN L+  +    
Sbjct: 360 RMENEGCEPNFQTYNMMIRYYSECSEVEKALGLFEKMGSGDCLPNLDTYNILISGMF--- 416

Query: 364 MLDMARKYDEEMFAKG 379
                RK  E+M   G
Sbjct: 417 ----VRKRSEDMVVAG 428

Required for the trans-splicing of intron 1 of the mitochondrial nad1 transcript encoding the ND1 subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I).

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FVX2|PP129_ARATH Pentatricopeptide repeat-containing protein At1g77360, mitochondrial OS=Arabidopsis thaliana GN=At1g77360 PE=2 SV=2

 Score =  160 bits (404), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 111/384 (28%), Positives = 188/384 (48%), Gaps = 16/384 (4%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           + L+ + N       FF W E   H+ H+   Y+ +I+   K  ++ L W+LI+ M+   
Sbjct: 105 DVLNRFRNAGLLTYRFFQWSEKQRHYEHSVRAYHMMIESTAKIRQYKLMWDLINAMRKK- 163

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE-VSYCNLVDALCEYKHVIEA 120
             + N  TF I+ ++Y  A  V+EA+  FN ++++ L    V++  L+ ALC+ K+V +A
Sbjct: 164 -KMLNVETFCIVMRKYARAQKVDEAIYAFNVMEKYDLPPNLVAFNGLLSALCKSKNVRKA 222

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           QE+   EN    F+       +K Y+++L GW K     K RE + EM   G   D+ +Y
Sbjct: 223 QEV--FENMRDRFTP-----DSKTYSILLEGWGKEPNLPKAREVFREMIDAGCHPDIVTY 275

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
           SI +DI+CK+G+  +A+ + + M     K     Y+ ++   G    ++ A+  + EM  
Sbjct: 276 SIMVDILCKAGRVDEALGIVRSMDPSICKPTTFIYSVLVHTYGTENRLEEAVDTFLEMER 335

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL----EKPR 296
            G +  V   N++I   C+  R++  Y VL EM  KG  P+  + +   R L    EK  
Sbjct: 336 SGMKADVAVFNSLIGAFCKANRMKNVYRVLKEMKSKGVTPNSKSCNIILRHLIERGEKD- 394

Query: 297 EILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALV 356
           E   +F +MI+    P  DTY M+++ F     +     VWK M + G  P    ++ L+
Sbjct: 395 EAFDVFRKMIKV-CEPDADTYTMVIKMFCEKKEMETADKVWKYMRKKGVFPSMHTFSVLI 453

Query: 357 DALIDKGMLDMARKYDEEMFAKGL 380
           + L ++     A    EEM   G+
Sbjct: 454 NGLCEERTTQKACVLLEEMIEMGI 477

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C9A2|PP112_ARATH Pentatricopeptide repeat-containing protein At1g71060, mitochondrial OS=Arabidopsis thaliana GN=At1g71060 PE=2 SV=1

 Score =  159 bits (402), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 115/402 (28%), Positives = 198/402 (49%), Gaps = 19/402 (4%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           E L   +N    AL  F W E    F HTT  YN++I+ LGK  +F L W+L+  MK   
Sbjct: 99  EVLKKLSNAGVLALSVFKWAENQKGFKHTTSNYNALIESLGKIKQFKLIWSLVDDMK--A 156

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN-LVDALCEYKHVIEA 120
             + +  TF ++ +RY  A  V EA+G F+K++EFG K E S  N ++D L + ++V +A
Sbjct: 157 KKLLSKETFALISRRYARARKVKEAIGAFHKMEEFGFKMESSDFNRMLDTLSKSRNVGDA 216

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           Q++ F + K   F   +     K Y ++L GW +     +  E   EM   G   D+ +Y
Sbjct: 217 QKV-FDKMKKKRFEPDI-----KSYTILLEGWGQELNLLRVDEVNREMKDEGFEPDVVAY 270

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
            I ++  CK+ K  +A++ + EM+++  K     + ++I  +G  + ++ A+  +   + 
Sbjct: 271 GIIINAHCKAKKYEEAIRFFNEMEQRNCKPSPHIFCSLINGLGSEKKLNDALEFFERSKS 330

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITY----HCFFRCLEKPR 296
            G      T N ++   C + R+ +AY  + EM  KG  P+  TY    H   R +++ +
Sbjct: 331 SGFPLEAPTYNALVGAYCWSQRMEDAYKTVDEMRLKGVGPNARTYDIILHHLIR-MQRSK 389

Query: 297 EILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALV 356
           E   ++  M      P + TY +++R F     L     +W +M+  G  P    +++L+
Sbjct: 390 EAYEVYQTM---SCEPTVSTYEIMVRMFCNKERLDMAIKIWDEMKGKGVLPGMHMFSSLI 446

Query: 357 DALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLD 398
            AL  +  LD A +Y  EM   G+  +P   + ++L Q  LD
Sbjct: 447 TALCHENKLDEACEYFNEMLDVGI--RPPGHMFSRLKQTLLD 486

Arabidopsis thaliana (taxid: 3702)

>sp|P0C8A0|PP275_ARATH Pentatricopeptide repeat-containing protein At3g49730 OS=Arabidopsis thaliana GN=At3g49730 PE=2 SV=1

 Score =  149 bits (377), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 99/376 (26%), Positives = 186/376 (49%), Gaps = 16/376 (4%)

Query: 17  FFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKR 76
           FF W      + H+ +   S++ IL K  +F   W LI  M+     +     F ++ +R
Sbjct: 117 FFLWATKQPGYFHSYEVCKSMVMILSKMRQFGAVWGLIEEMRKTNPELIEPELFVVLMRR 176

Query: 77  YVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSG 135
           + +A++V +A+   +++ ++GL+ DE  +  L+DALC+   V EA ++         F  
Sbjct: 177 FASANMVKKAVEVLDEMPKYGLEPDEYVFGCLLDALCKNGSVKEASKV---------FED 227

Query: 136 LVEM--NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKP 193
           + E      + +  +L GW +     + +E   +M + G+  D+  ++  +     +GK 
Sbjct: 228 MREKFPPNLRYFTSLLYGWCREGKLMEAKEVLVQMKEAGLEPDIVVFTNLLSGYAHAGKM 287

Query: 194 WKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG-VDFAMRVYREMREMGCQPSVVTCNT 252
             A  L  +M+K+G + +V  Y  +I+A+  +E  +D AMRV+ EM   GC+  +VT   
Sbjct: 288 ADAYDLMNDMRKRGFEPNVNCYTVLIQALCRTEKRMDEAMRVFVEMERYGCEADIVTYTA 347

Query: 253 VIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKP---REILGLFDRMIESG 309
           +I   C+ G + + Y+VL +M KKG +P  +TY       EK     E L L ++M   G
Sbjct: 348 LISGFCKWGMIDKGYSVLDDMRKKGVMPSQVTYMQIMVAHEKKEQFEECLELIEKMKRRG 407

Query: 310 IRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMAR 369
             P +  Y +++R   + G ++    +W +ME  G SP    +  +++    +G L  A 
Sbjct: 408 CHPDLLIYNVVIRLACKLGEVKEAVRLWNEMEANGLSPGVDTFVIMINGFTSQGFLIEAC 467

Query: 370 KYDEEMFAKGLSAKPR 385
            + +EM ++G+ + P+
Sbjct: 468 NHFKEMVSRGIFSAPQ 483

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FH87|PP447_ARATH Putative pentatricopeptide repeat-containing protein At5g65820 OS=Arabidopsis thaliana GN=At5g65820 PE=3 SV=1

 Score =  148 bits (374), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 99/369 (26%), Positives = 186/369 (50%), Gaps = 13/369 (3%)

Query: 17  FFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRM-KDNPSSIPNHATFRIMFK 75
           FF W      + H+ + Y S++ IL K  +F   W LI  M K+NP  I     F ++ +
Sbjct: 133 FFVWAAKQPRYCHSIEVYKSMVKILSKMRQFGAVWGLIEEMRKENPQLIEPE-LFVVLVQ 191

Query: 76  RYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFS 134
           R+ +A +V +A+   +++ +FG + DE  +  L+DALC++  V +A +L   E+  + F 
Sbjct: 192 RFASADMVKKAIEVLDEMPKFGFEPDEYVFGCLLDALCKHGSVKDAAKLF--EDMRMRFP 249

Query: 135 GLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPW 194
                   + +  +L GW ++    + +    +M++ G   D+  Y+  +     +GK  
Sbjct: 250 V-----NLRYFTSLLYGWCRVGKMMEAKYVLVQMNEAGFEPDIVDYTNLLSGYANAGKMA 304

Query: 195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVI 254
            A  L ++M+++G + +   Y  +I+A+   + ++ AM+V+ EM    C+  VVT   ++
Sbjct: 305 DAYDLLRDMRRRGFEPNANCYTVLIQALCKVDRMEEAMKVFVEMERYECEADVVTYTALV 364

Query: 255 KLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKP---REILGLFDRMIESGIR 311
              C+ G++ + Y VL +M KKG +P  +TY       EK     E L L ++M +    
Sbjct: 365 SGFCKWGKIDKCYIVLDDMIKKGLMPSELTYMHIMVAHEKKESFEECLELMEKMRQIEYH 424

Query: 312 PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKY 371
           P +  Y +++R   + G ++    +W +MEE G SP    +  +++ L  +G L  A  +
Sbjct: 425 PDIGIYNVVIRLACKLGEVKEAVRLWNEMEENGLSPGVDTFVIMINGLASQGCLLEASDH 484

Query: 372 DEEMFAKGL 380
            +EM  +GL
Sbjct: 485 FKEMVTRGL 493

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	403
224081867	439	predicted protein [Populus trichocarpa]	0.955	0.876	0.774	0.0
359487106	571	PREDICTED: pentatricopeptide repeat-cont	0.957	0.676	0.726	1e-175
449491189	450	PREDICTED: pentatricopeptide repeat-cont	0.970	0.868	0.719	1e-174
449436631	1559	PREDICTED: uncharacterized protein LOC10	0.940	0.243	0.721	1e-171
356547448	445	PREDICTED: pentatricopeptide repeat-cont	0.977	0.885	0.672	1e-163
357455405	520	Pentatricopeptide repeat-containing prot	0.970	0.751	0.656	1e-161
15220166	448	pentatricopeptide repeat-containing prot	0.972	0.875	0.667	1e-159
297839881	407	pentatricopeptide repeat-containing prot	0.972	0.963	0.667	1e-158
147827256	655	hypothetical protein VITISV_027954 [Viti	0.890	0.548	0.664	1e-152
255579214	391	pentatricopeptide repeat-containing prot	0.826	0.851	0.650	1e-146

>gi|224081867|ref|XP_002306508.1| predicted protein [Populus trichocarpa] gi|222855957|gb|EEE93504.1| predicted protein [Populus trichocarpa]

 Score =  644 bits (1662), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 302/390 (77%), Positives = 342/390 (87%), Gaps = 5/390 (1%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           +TLSCY NDWKRAL+FFNWVET+  F HTT+TYN +IDILGKFFEFDLSW+LI RM++NP
Sbjct: 51  QTLSCYNNDWKRALDFFNWVETESQFQHTTETYNRMIDILGKFFEFDLSWDLIQRMRNNP 110

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTF-NKLDEFGLKDEVSYCNLVDALCEYKHVIEA 120
            S PNH TFR++F RY++AHLVNEA+  + ++L EFGLKDE SYC LVDALCEYKHVIEA
Sbjct: 111 FSTPNHTTFRVLFHRYISAHLVNEAVSVYEDRLKEFGLKDETSYCILVDALCEYKHVIEA 170

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
            ELCFG N N      +    TKIYNMILRGWFKM WWGKCREFWEEMD++ V KDLHSY
Sbjct: 171 HELCFGNNNNSINVRNI----TKIYNMILRGWFKMGWWGKCREFWEEMDRKEVCKDLHSY 226

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
           SIYMDI+CKSGKPWKAVKLYKEMK KGIK+DVVAYNTVI A+G+SEGVDF +RVYREMRE
Sbjct: 227 SIYMDILCKSGKPWKAVKLYKEMKSKGIKLDVVAYNTVINAIGLSEGVDFVLRVYREMRE 286

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG 300
           +GCQP+VVTCNTVIKLLCENGR++EAY +L EMP+    PDV TYHCFFRCLEKP+EIL 
Sbjct: 287 LGCQPNVVTCNTVIKLLCENGRIKEAYKMLDEMPQSYIAPDVFTYHCFFRCLEKPKEILC 346

Query: 301 LFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI 360
           LFD+MIE+G+ P+MDTYVML+RKFGRWGFLRPVF+VWKKME+LGCSPDEFAYNAL+DALI
Sbjct: 347 LFDQMIENGVCPRMDTYVMLMRKFGRWGFLRPVFLVWKKMEKLGCSPDEFAYNALIDALI 406

Query: 361 DKGMLDMARKYDEEMFAKGLSAKPREELGT 390
            KGM+DMARKYDEEM AKGLSAKPR EL T
Sbjct: 407 QKGMVDMARKYDEEMMAKGLSAKPRVELNT 436

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487106|ref|XP_002274114.2| PREDICTED: pentatricopeptide repeat-containing protein At1g80550, mitochondrial-like [Vitis vinifera]

 Score =  622 bits (1603), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 284/391 (72%), Positives = 336/391 (85%), Gaps = 5/391 (1%)

Query: 1   RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN 60
           R+TLSCYANDWKRALEFF+WV+T C F HTTDTYN +IDILGKFFEFDL W LI RMK +
Sbjct: 182 RQTLSCYANDWKRALEFFDWVQTQCGFNHTTDTYNGMIDILGKFFEFDLIWVLIQRMKAD 241

Query: 61  PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEA 120
           P + PNH TFR +FKRY  AHLV EAM  + + +EF L+DE SY NL+DALCEYKHVIEA
Sbjct: 242 PVAYPNHVTFRFVFKRYAAAHLVEEAMNAYYRTEEFNLRDETSYSNLIDALCEYKHVIEA 301

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           +EL   E+K++ F+     +  KIYN+ILRGWFKM WW KCREFWEEMD+RGV K L+SY
Sbjct: 302 EELFLKESKDLVFN-----DDVKIYNIILRGWFKMGWWKKCREFWEEMDRRGVCKSLYSY 356

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
           SIYMDI CKSGKPW+AVKLYKEMKKKGI++DVVAYNTVIRA+G+SEGVDF++RV+REM+E
Sbjct: 357 SIYMDIQCKSGKPWRAVKLYKEMKKKGIRLDVVAYNTVIRAIGLSEGVDFSIRVFREMKE 416

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG 300
           +GC+P+VVT NT+IKLLCENGR+REAY V  +M +KG  P+VITYHCFF C+EKP++IL 
Sbjct: 417 VGCEPNVVTYNTIIKLLCENGRIREAYGVFDQMREKGYAPNVITYHCFFGCIEKPKQILR 476

Query: 301 LFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI 360
            FDRMI SG+RP+MDTYVML++KFGRWGFLRPVF+VWKKMEE GCSPD  AYNAL+DAL+
Sbjct: 477 TFDRMINSGVRPRMDTYVMLMKKFGRWGFLRPVFIVWKKMEEQGCSPDACAYNALIDALV 536

Query: 361 DKGMLDMARKYDEEMFAKGLSAKPREELGTK 391
            KGM+D+ARKY+EEM AKGLSAKPR +LGTK
Sbjct: 537 QKGMVDLARKYEEEMLAKGLSAKPRVDLGTK 567

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449491189|ref|XP_004158824.1| PREDICTED: pentatricopeptide repeat-containing protein At1g80550, mitochondrial-like [Cucumis sativus]

 Score =  616 bits (1589), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 285/396 (71%), Positives = 339/396 (85%), Gaps = 5/396 (1%)

Query: 1   RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN 60
           RE L  Y NDWKR+ EFFNWVE++C F HTT+TYN ++DILGKFFEFDLSW LI+RM+ +
Sbjct: 51  REALDSYCNDWKRSYEFFNWVESECKFDHTTETYNRMLDILGKFFEFDLSWVLINRMRQS 110

Query: 61  PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEA 120
           PS+ P+HATFRI+FKRY  AHLV+EA+  + +L EF L+DE S+CNL+DALCE +HV EA
Sbjct: 111 PSASPDHATFRILFKRYALAHLVSEAIAAYERLREFKLRDETSFCNLIDALCESRHVDEA 170

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           QELCFG+N+ +        + TKI+N+ILRGW KM WW KCR+FWEEMDK+GV KDLHSY
Sbjct: 171 QELCFGKNRKLDCD-----SSTKIHNLILRGWLKMGWWSKCRDFWEEMDKKGVRKDLHSY 225

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
           SIYMDI CKSGKPWKAVKLYKEMKKKG+K+DVVAYNTVI AVG+SEGVDFA RV+ EM+E
Sbjct: 226 SIYMDIQCKSGKPWKAVKLYKEMKKKGMKLDVVAYNTVIHAVGISEGVDFASRVFHEMKE 285

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG 300
           MGC+P+VVTCNTVIKL CENGR ++A+ +L +M K+ C P+VITYHCFFR LEKP+EIL 
Sbjct: 286 MGCKPNVVTCNTVIKLFCENGRFKDAHMMLDQMLKRDCQPNVITYHCFFRSLEKPKEILV 345

Query: 301 LFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI 360
           LFDRMI+ G+ PKMDTYVMLLRKFGRWGFLRPVF+VW KMEELGCSP+E AYNAL+DAL+
Sbjct: 346 LFDRMIKYGVHPKMDTYVMLLRKFGRWGFLRPVFLVWNKMEELGCSPNECAYNALIDALV 405

Query: 361 DKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGG 396
           +KGM+DMARKYDEEM AKGLS K R ELGT+++ GG
Sbjct: 406 EKGMIDMARKYDEEMVAKGLSPKLRVELGTQMMNGG 441

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449436631|ref|XP_004136096.1| PREDICTED: uncharacterized protein LOC101205322 [Cucumis sativus]

 Score =  606 bits (1563), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 277/384 (72%), Positives = 331/384 (86%), Gaps = 5/384 (1%)

Query: 13  RALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRI 72
           R+ EFFNWVE++C F HTT+TYN ++DILGKFFEFDLSW LI+RM+ +PS+ P+HATFRI
Sbjct: 614 RSYEFFNWVESECKFDHTTETYNRMLDILGKFFEFDLSWVLINRMRQSPSASPDHATFRI 673

Query: 73  MFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVG 132
           +FKRY  AHLV+EA+  + +L EF L+DE S+CNL+DALCE +HV EAQELCFG+N+ + 
Sbjct: 674 LFKRYALAHLVSEAIAAYERLREFKLRDETSFCNLIDALCESRHVDEAQELCFGKNRKLD 733

Query: 133 FSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK 192
                  + TKI+N+ILRGW KM WW KCR+FWEEMDK+GV KDLHSYSIYMDI CKSGK
Sbjct: 734 CD-----SSTKIHNLILRGWLKMGWWSKCRDFWEEMDKKGVRKDLHSYSIYMDIQCKSGK 788

Query: 193 PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNT 252
           PWKAVKLYKEMKKKG+K+DVVAYNTVI AVG+SEGVDFA RV+ EM+EMGC+P+VVTCNT
Sbjct: 789 PWKAVKLYKEMKKKGMKLDVVAYNTVIHAVGISEGVDFASRVFHEMKEMGCKPNVVTCNT 848

Query: 253 VIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRP 312
           VIKL CENGR ++A+ +L +M K+ C P+VITYHCFFR LEKP+EIL LFDRMI+ G+ P
Sbjct: 849 VIKLFCENGRFKDAHMMLDQMLKRDCQPNVITYHCFFRSLEKPKEILVLFDRMIKYGVHP 908

Query: 313 KMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYD 372
           KMDTYVMLLRKFGRWGFLRPVF+VW KMEELGCSP+E AYNAL+DAL++KGM+DMARKYD
Sbjct: 909 KMDTYVMLLRKFGRWGFLRPVFLVWNKMEELGCSPNECAYNALIDALVEKGMIDMARKYD 968

Query: 373 EEMFAKGLSAKPREELGTKLVQGG 396
           EEM AKGLS K R ELGT+++ GG
Sbjct: 969 EEMVAKGLSPKLRVELGTQMMNGG 992

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356547448|ref|XP_003542124.1| PREDICTED: pentatricopeptide repeat-containing protein At1g80550, mitochondrial-like [Glycine max]

 Score =  580 bits (1495), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 267/397 (67%), Positives = 327/397 (82%), Gaps = 3/397 (0%)

Query: 1   RETLSCYANDWKRALEFFNWVE-TDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKD 59
           R+TL  + NDWKRALEFFNWVE +   F H+TDT+N ++DILGKFFEF L W+LI RM  
Sbjct: 38  RQTLLSFNNDWKRALEFFNWVEESHSQFHHSTDTFNLMLDILGKFFEFKLCWDLIRRMNA 97

Query: 60  NPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIE 119
           +PSS PNHATFR+MFKRYV+AH VN+A+ TFN+L EF LKD  S+ NL+DALCEYKHV+E
Sbjct: 98  HPSSPPNHATFRLMFKRYVSAHSVNDAIDTFNRLGEFNLKDHTSFSNLLDALCEYKHVLE 157

Query: 120 AQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHS 179
           AQ+L FG +  V  S +  +  TKI+NM+LRGWFK+ WW KC EFWEEMDK+GV KDLHS
Sbjct: 158 AQDLLFGNDNRVTLS-VDPIGNTKIHNMVLRGWFKLGWWSKCNEFWEEMDKKGVHKDLHS 216

Query: 180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMR 239
           YSIYMDI+CK GKPWKAVKL+KE+KKKG K+DVV YN VIRA+G+S GVDF++RV+REM+
Sbjct: 217 YSIYMDILCKGGKPWKAVKLFKEIKKKGFKLDVVVYNIVIRAIGLSHGVDFSIRVFREMK 276

Query: 240 EMGCQPSVVTCNTVIKLLCENGRVREAYAVLAE-MPKKGCVPDVITYHCFFRCLEKPREI 298
           E+G +P+VVT NT+I+LLC+  R +EA A+L   MP  GC P  ++YHCFF  +EKP++I
Sbjct: 277 ELGIKPTVVTYNTLIRLLCDCYRHKEALALLRTIMPSDGCHPTAVSYHCFFASMEKPKQI 336

Query: 299 LGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDA 358
           L +FD M+ESG+RP MDTYVMLL KFGRWGFLRPVF+VW KM++LGCSPD  AYNAL+DA
Sbjct: 337 LAMFDEMVESGVRPTMDTYVMLLNKFGRWGFLRPVFMVWNKMKQLGCSPDAAAYNALIDA 396

Query: 359 LIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQG 395
           L+DK ++DMARKYDEEM AKGLS KPR+ELGTKL+  
Sbjct: 397 LVDKALIDMARKYDEEMLAKGLSPKPRKELGTKLLAA 433

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357455405|ref|XP_003597983.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355487031|gb|AES68234.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  574 bits (1479), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 262/399 (65%), Positives = 327/399 (81%), Gaps = 8/399 (2%)

Query: 1   RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN 60
           R TL+ + ND+KRALEFFNWVET   F H+T+TYN V+DILGKFFEF   WNLIHRM+ N
Sbjct: 80  RATLTSFNNDYKRALEFFNWVETKFKFQHSTETYNLVLDILGKFFEFQQCWNLIHRMRQN 139

Query: 61  PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEA 120
           P S+PNH TFR+MFKRYV+AH V +A+ TF +L+EF LKDE S+ NL+DALCEYKHV+EA
Sbjct: 140 PHSLPNHTTFRVMFKRYVSAHCVQDAVNTFQRLNEFNLKDETSFSNLIDALCEYKHVLEA 199

Query: 121 QELCFGENKNV-------GFSGLVEMNK-TKIYNMILRGWFKMSWWGKCREFWEEMDKRG 172
           Q+L FG+ KN        G  G V  +K TKI+N++LRGW+K+ WW KC EFW+EMD+RG
Sbjct: 200 QDLVFGDKKNQTLTWIVDGVDGFVASSKNTKIFNIVLRGWYKLGWWSKCWEFWDEMDRRG 259

Query: 173 VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAM 232
           V KDLHSYSIYMDI+ K GKPWKAVKL+KEMK+KGI++DVV YN VIRA+GVS+GVDF++
Sbjct: 260 VEKDLHSYSIYMDILSKGGKPWKAVKLFKEMKRKGIQLDVVVYNIVIRAIGVSQGVDFSI 319

Query: 233 RVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL 292
           R++ EM+++G  P+VVT NT+I+LLC++ R +EA  ++  M + GC P+ ++Y CFF CL
Sbjct: 320 RMFCEMKDLGLNPTVVTYNTIIRLLCDSYRYKEALTLIRTMRRDGCSPNAVSYQCFFACL 379

Query: 293 EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAY 352
           EKP+ I+ LFD MIESG+RP MDTYVMLL+KF RWGFLR VF+VW +MEELGCSPD  AY
Sbjct: 380 EKPKFIIELFDGMIESGVRPTMDTYVMLLKKFARWGFLRLVFLVWNRMEELGCSPDASAY 439

Query: 353 NALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTK 391
           NAL+DAL++KG++DMARKYDEEM AKGLS KPR+ELGTK
Sbjct: 440 NALIDALVEKGLIDMARKYDEEMLAKGLSPKPRKELGTK 478

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15220166|ref|NP_178170.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75264854|sp|Q9M8M3.1|PP136_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At1g80550, mitochondrial; Flags: Precursor gi|6730729|gb|AAF27119.1|AC018849_7 unknown protein; 31926-33272 [Arabidopsis thaliana] gi|332198297|gb|AEE36418.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  568 bits (1463), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 265/397 (66%), Positives = 325/397 (81%), Gaps = 5/397 (1%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           E L+CY+NDW++ALEFFNWVE +  F HTT+T+N VIDILGK+FEF++SW LI+RM  N 
Sbjct: 52  EALTCYSNDWQKALEFFNWVERESGFRHTTETFNRVIDILGKYFEFEISWALINRMIGNT 111

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ 121
            S+PNH TFRI+FKRYVTAHLV EA+  ++KLD+F L+DE S+ NLVDALCE+KHV+EA+
Sbjct: 112 ESVPNHVTFRIVFKRYVTAHLVQEAIDAYDKLDDFNLRDETSFYNLVDALCEHKHVVEAE 171

Query: 122 ELCFGENK-NVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           ELCFG+N    GFS    ++ TKI+N+ILRGW K+ WWGKC+E+W++MD  GV KDL SY
Sbjct: 172 ELCFGKNVIGNGFS----VSNTKIHNLILRGWSKLGWWGKCKEYWKKMDTEGVTKDLFSY 227

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
           SIYMDIMCKSGKPWKAVKLYKEMK + +K+DVVAYNTVIRA+G S+GV+F +RV+REMRE
Sbjct: 228 SIYMDIMCKSGKPWKAVKLYKEMKSRRMKLDVVAYNTVIRAIGASQGVEFGIRVFREMRE 287

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG 300
            GC+P+V T NT+IKLLCE+GR+R+AY +L EMPK+GC PD ITY C F  LEKP EIL 
Sbjct: 288 RGCEPNVATHNTIIKLLCEDGRMRDAYRMLDEMPKRGCQPDSITYMCLFSRLEKPSEILS 347

Query: 301 LFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI 360
           LF RMI SG+RPKMDTYVML+RKF RWGFL+PV  VWK M+E G +PD  AYNA++DALI
Sbjct: 348 LFGRMIRSGVRPKMDTYVMLMRKFERWGFLQPVLYVWKTMKESGDTPDSAAYNAVIDALI 407

Query: 361 DKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGL 397
            KGMLDMAR+Y+EEM  +GLS + R EL  K +   L
Sbjct: 408 QKGMLDMAREYEEEMIERGLSPRRRPELVEKSLDETL 444

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839881|ref|XP_002887822.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297333663|gb|EFH64081.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  562 bits (1449), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 265/397 (66%), Positives = 323/397 (81%), Gaps = 5/397 (1%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           E LSCY NDW++ALEFFNWVE +  F HTT+T+N +IDILGK+FEF+  W LI+RM  NP
Sbjct: 12  EALSCYINDWQKALEFFNWVEKESGFRHTTETFNRMIDILGKYFEFETCWALINRMIGNP 71

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ 121
            S+PNH TFRI+FKRYVTAHLV EA+  ++KLD+F L+D+ S+ NLVDALCE+KHV+EA+
Sbjct: 72  ESLPNHVTFRIVFKRYVTAHLVQEAIDAYDKLDDFNLRDDTSFYNLVDALCEHKHVVEAE 131

Query: 122 ELCFGENKNV-GFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           ELCFG+N    GFS    ++ TKI+N+ILRGW K+ WWGKC+E+W++MD  GV KDL SY
Sbjct: 132 ELCFGKNVIAHGFS----VSNTKIHNLILRGWSKLGWWGKCKEYWDKMDTEGVPKDLFSY 187

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
           SIYMDIMCKSGKPWKAVKLYKEMK + IK+DVVAYNTVIRA+G S+GV+F +RV+REMRE
Sbjct: 188 SIYMDIMCKSGKPWKAVKLYKEMKSRRIKLDVVAYNTVIRAIGASQGVEFGIRVFREMRE 247

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG 300
            GC+P+V T NT+IKLLCE+GR+R+AY +L EMPKKGC PD I+Y C F  LEKP EIL 
Sbjct: 248 RGCEPNVATHNTIIKLLCEDGRMRDAYRMLDEMPKKGCQPDSISYMCLFSRLEKPSEILS 307

Query: 301 LFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI 360
           LF RMI SG+RPKMDTYVML+RKF RWGFL+PV  VWK M+E G +PD  AYNA++DALI
Sbjct: 308 LFGRMIRSGVRPKMDTYVMLMRKFERWGFLQPVLYVWKTMKESGDTPDSAAYNAVIDALI 367

Query: 361 DKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGL 397
            KGMLDMAR+Y+EEM  +GLS + R EL  K +   L
Sbjct: 368 QKGMLDMAREYEEEMIERGLSPRRRPELVEKSLDETL 404

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147827256|emb|CAN64312.1| hypothetical protein VITISV_027954 [Vitis vinifera]

 Score =  545 bits (1405), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 260/391 (66%), Positives = 312/391 (79%), Gaps = 32/391 (8%)

Query: 1   RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN 60
           R+TLSCYANDWKRALEFF+WV+T C F HTTDTYN +IDILGKFFEFDL W LI RMK +
Sbjct: 293 RQTLSCYANDWKRALEFFDWVQTQCGFNHTTDTYNGMIDILGKFFEFDLIWVLIQRMKAD 352

Query: 61  PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEA 120
           P + PNH TFR +FKRY  AHLV EAM  + + +EF L+DE SY NL+DALCEYKHVIEA
Sbjct: 353 PVAYPNHVTFRFVFKRYAAAHLVEEAMNAYYRTEEFNLRDETSYSNLIDALCEYKHVIEA 412

Query: 121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
           +EL   E+K++ F+     +  KIYN+ILRGWFK                 GVV++    
Sbjct: 413 EELFLKESKDLVFN-----DDVKIYNIILRGWFK----------------NGVVEE---- 447

Query: 181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
                  CKSGKPW+AVKLYKEMKKKGI++DVVAYNTVIRA+G+SEGVDF++RV+RE +E
Sbjct: 448 -------CKSGKPWRAVKLYKEMKKKGIRLDVVAYNTVIRAIGLSEGVDFSIRVFREXKE 500

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG 300
           +GC+P+VVT NT+IKLLCENGR+REAY V  +M +KG  P+VITYHCFF C+EKP++IL 
Sbjct: 501 VGCEPNVVTYNTIIKLLCENGRIREAYGVFDQMREKGYAPNVITYHCFFGCIEKPKQILR 560

Query: 301 LFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI 360
            FDRMI SG+RP+MDTYVML++KFGRWGFLRPVF+VWKKMEE GCSPD  AYNAL+DAL+
Sbjct: 561 TFDRMINSGVRPRMDTYVMLMKKFGRWGFLRPVFIVWKKMEEQGCSPDACAYNALIDALV 620

Query: 361 DKGMLDMARKYDEEMFAKGLSAKPREELGTK 391
            KGM+D+ARKY+EEM AKGLSAKPR +LGTK
Sbjct: 621 QKGMVDLARKYEEEMLAKGLSAKPRVDLGTK 651

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579214|ref|XP_002530453.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223529998|gb|EEF31923.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  524 bits (1350), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 259/398 (65%), Positives = 301/398 (75%), Gaps = 65/398 (16%)

Query: 2   ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
           ETLSCY+NDWK AL+FFNWVE +C+F                                  
Sbjct: 54  ETLSCYSNDWKSALDFFNWVEKECNF---------------------------------- 79

Query: 62  SSIPNHATFRIMFKRYVTAHLVNEAMGTFNK----LDEFGLKDEVSYCNLVDALCEYKHV 117
               NH T                   TFN+    L++F LKDE S+CNL+DALCE+KHV
Sbjct: 80  ----NHTT------------------DTFNRMIDILEKFNLKDETSFCNLIDALCEHKHV 117

Query: 118 IEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL 177
           IE+QELCFG N     +G+  +NKTKIYNMILRGWFKM WW KCREFWEEMD++GV KDL
Sbjct: 118 IESQELCFGNN-----NGIDIVNKTKIYNMILRGWFKMGWWSKCREFWEEMDQKGVHKDL 172

Query: 178 HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYRE 237
           HSYSIYMDI+CK GKPWKAVKLYKEMK+KG+K+DVV+YN V+RAVG+SEGVDFAMRVYRE
Sbjct: 173 HSYSIYMDIVCKGGKPWKAVKLYKEMKRKGMKLDVVSYNIVVRAVGLSEGVDFAMRVYRE 232

Query: 238 MREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPRE 297
           M+E+GC P+VVT NT+IKLLCE GRV+EAY +L +M KKG V DVITYHCFFRCLEKP+E
Sbjct: 233 MKELGCMPNVVTYNTIIKLLCETGRVKEAYKMLDDMRKKGIVADVITYHCFFRCLEKPKE 292

Query: 298 ILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVD 357
           IL LFDRMIESG++P+MDTYVML+RKFGRWGFLRPV +VWKKMEE GCSPDEFAYNAL+D
Sbjct: 293 ILWLFDRMIESGVQPRMDTYVMLMRKFGRWGFLRPVLLVWKKMEEQGCSPDEFAYNALID 352

Query: 358 ALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQG 395
           AL+ KGML MAR+Y+EEM AKGLSAKPR EL  K+ +G
Sbjct: 353 ALVQKGMLHMARRYEEEMLAKGLSAKPRAELSKKVDEG 390

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	403
TAIR|locus:2198908	448	AT1G80550 [Arabidopsis thalian	0.960	0.863	0.676	5.4e-150
TAIR|locus:2083671	523	AT3G15200 [Arabidopsis thalian	0.940	0.724	0.292	4.8e-46
TAIR|locus:2035206	523	AT1G52640 [Arabidopsis thalian	0.933	0.718	0.332	3.1e-44
TAIR|locus:2012883	537	AT1G20300 [Arabidopsis thalian	0.878	0.659	0.287	4e-42
TAIR|locus:2026346	510	AT1G71060 [Arabidopsis thalian	0.950	0.750	0.286	1.1e-39
TAIR|locus:2025747	540	AT1G80880 [Arabidopsis thalian	0.890	0.664	0.295	3.2e-39
TAIR|locus:2156213	637	AT5G65820 [Arabidopsis thalian	0.883	0.558	0.273	8.5e-37
TAIR|locus:2097395	638	AT3G49730 [Arabidopsis thalian	0.895	0.565	0.277	5.3e-36
TAIR|locus:2094394	562	AT3G22670 [Arabidopsis thalian	0.945	0.677	0.265	1.2e-34
TAIR|locus:2139732	566	AT4G11690 [Arabidopsis thalian	0.920	0.655	0.251	1.1e-33

TAIR|locus:2198908 AT1G80550 [Arabidopsis thaliana (taxid:3702)]

 Score = 1464 (520.4 bits), Expect = 5.4e-150, P = 5.4e-150
 Identities = 264/390 (67%), Positives = 323/390 (82%)

Query:     2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
             E L+CY+NDW++ALEFFNWVE +  F HTT+T+N VIDILGK+FEF++SW LI+RM  N 
Sbjct:    52 EALTCYSNDWQKALEFFNWVERESGFRHTTETFNRVIDILGKYFEFEISWALINRMIGNT 111

Query:    62 SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ 121
              S+PNH TFRI+FKRYVTAHLV EA+  ++KLD+F L+DE S+ NLVDALCE+KHV+EA+
Sbjct:   112 ESVPNHVTFRIVFKRYVTAHLVQEAIDAYDKLDDFNLRDETSFYNLVDALCEHKHVVEAE 171

Query:   122 ELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYS 181
             ELCFG  KNV  +G   ++ TKI+N+ILRGW K+ WWGKC+E+W++MD  GV KDL SYS
Sbjct:   172 ELCFG--KNVIGNGF-SVSNTKIHNLILRGWSKLGWWGKCKEYWKKMDTEGVTKDLFSYS 228

Query:   182 IYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM 241
             IYMDIMCKSGKPWKAVKLYKEMK + +K+DVVAYNTVIRA+G S+GV+F +RV+REMRE 
Sbjct:   229 IYMDIMCKSGKPWKAVKLYKEMKSRRMKLDVVAYNTVIRAIGASQGVEFGIRVFREMRER 288

Query:   242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGL 301
             GC+P+V T NT+IKLLCE+GR+R+AY +L EMPK+GC PD ITY C F  LEKP EIL L
Sbjct:   289 GCEPNVATHNTIIKLLCEDGRMRDAYRMLDEMPKRGCQPDSITYMCLFSRLEKPSEILSL 348

Query:   302 FDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID 361
             F RMI SG+RPKMDTYVML+RKF RWGFL+PV  VWK M+E G +PD  AYNA++DALI 
Sbjct:   349 FGRMIRSGVRPKMDTYVMLMRKFERWGFLQPVLYVWKTMKESGDTPDSAAYNAVIDALIQ 408

Query:   362 KGMLDMARKYDEEMFAKGLSAKPREELGTK 391
             KGMLDMAR+Y+EEM  +GLS + R EL  K
Sbjct:   409 KGMLDMAREYEEEMIERGLSPRRRPELVEK 438

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2083671 AT3G15200 [Arabidopsis thaliana (taxid:3702)]

 Score = 483 (175.1 bits), Expect = 4.8e-46, P = 4.8e-46
 Identities = 114/390 (29%), Positives = 193/390 (49%)

Query:     2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
             E ++   +DWK A      V        ++  YN ++D+LGK   F+    +   M    
Sbjct:   114 EVVNRNRSDWKPAYILSQLVVKQSVHLSSSMLYNEILDVLGKMRRFEEFHQVFDEMSKRD 173

Query:    62 SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE-VSYCNLVDALCEYKHVIEA 120
               + N  T+ ++  RY  AH V+EA+G F +  EFG+ D+ V++  L+  LC YKHV  A
Sbjct:   174 GFV-NEKTYEVLLNRYAAAHKVDEAVGVFERRKEFGIDDDLVAFHGLLMWLCRYKHVEFA 232

Query:   121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
             + L     +  G          K  NMIL GW  +    + + FW+++       D+ SY
Sbjct:   233 ETLFCSRRREFGCD-------IKAMNMILNGWCVLGNVHEAKRFWKDIIASKCRPDVVSY 285

Query:   181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
                ++ + K GK  KA++LY+ M       DV   N VI A+   + +  A+ V+RE+ E
Sbjct:   286 GTMINALTKKGKLGKAMELYRAMWDTRRNPDVKICNNVIDALCFKKRIPEALEVFREISE 345

Query:   241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKG--CVPDVITYHCFFRCLEKPREI 298
              G  P+VVT N+++K LC+  R  + + ++ EM  KG  C P+ +T+    +  ++ +++
Sbjct:   346 KGPDPNVVTYNSLLKHLCKIRRTEKVWELVEEMELKGGSCSPNDVTFSYLLKYSQRSKDV 405

Query:   299 LGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDA 358
               + +RM ++      D Y ++ R + +W     V  +W +ME  G  PD+  Y   +  
Sbjct:   406 DIVLERMAKNKCEMTSDLYNLMFRLYVQWDKEEKVREIWSEMERSGLGPDQRTYTIRIHG 465

Query:   359 LIDKGMLDMARKYDEEMFAKGLSAKPREEL 388
             L  KG +  A  Y +EM +KG+  +PR E+
Sbjct:   466 LHTKGKIGEALSYFQEMMSKGMVPEPRTEM 495

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0022626 "cytosolic ribosome" evidence=IDA

TAIR|locus:2035206 AT1G52640 [Arabidopsis thaliana (taxid:3702)]

 Score = 466 (169.1 bits), Expect = 3.1e-44, P = 3.1e-44
 Identities = 130/391 (33%), Positives = 201/391 (51%)

Query:    14 ALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWN-LIHRMKDNPSSIPNHATFRI 72
             A  FF W      F H+ ++Y+ +++ILG   +F L W+ LI   + N   I +   F I
Sbjct:    85 AHRFFLWARRIPDFAHSLESYHILVEILGSSKQFALLWDFLIEAREYNYFEISSKV-FWI 143

Query:    73 MFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN-LVDALCEYKHVIEAQELCFGENKNV 131
             +F+ Y  A+L +EA   FN++ EFG+K  V   + L+ +LC+ KHV  AQE  FG+ K  
Sbjct:   144 VFRAYSRANLPSEACRAFNRMVEFGIKPCVDDLDQLLHSLCDKKHVNHAQEF-FGKAK-- 200

Query:   132 GFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSG 191
             GF G+V   KT  Y++++RGW ++      R+ ++EM +R  V DL +Y+  +D +CKSG
Sbjct:   201 GF-GIVPSAKT--YSILVRGWARIRDASGARKVFDEMLERNCVVDLLAYNALLDALCKSG 257

Query:   192 KPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCN 251
                   K+++EM   G+K D  ++   I A   +  V  A +V   M+     P+V T N
Sbjct:   258 DVDGGYKMFQEMGNLGLKPDAYSFAIFIHAYCDAGDVHSAYKVLDRMKRYDLVPNVYTFN 317

Query:   252 TVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCF--FRCLE-KPREILGLFDRMIES 308
              +IK LC+N +V +AY +L EM +KG  PD  TY+    + C   +      L  RM  +
Sbjct:   318 HIIKTLCKNEKVDDAYLLLDEMIQKGANPDTWTYNSIMAYHCDHCEVNRATKLLSRMDRT 377

Query:   309 GIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI-DKGMLDM 367
                P   TY M+L+   R G       +W+ M E    P    Y  ++  L+  KG L+ 
Sbjct:   378 KCLPDRHTYNMVLKLLIRIGRFDRATEIWEGMSERKFYPTVATYTVMIHGLVRKKGKLEE 437

Query:   368 ARKYDEEMFAKGLS--AKPREELGTKLVQGG 396
             A +Y E M  +G+   +   E L  +LV  G
Sbjct:   438 ACRYFEMMIDEGIPPYSTTVEMLRNRLVGWG 468

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2012883 AT1G20300 [Arabidopsis thaliana (taxid:3702)]

 Score = 446 (162.1 bits), Expect = 4.0e-42, P = 4.0e-42
 Identities = 106/369 (28%), Positives = 196/369 (53%)

Query:    13 RALEFFNWVETDCHFTHTTD-TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFR 71
             ++L FFNW  +   + H +   YN +ID+ GK  +FDL+W+LI  MK     I +  TF 
Sbjct:   132 QSLAFFNWATSRDDYDHKSPHPYNEMIDLSGKVRQFDLAWHLIDLMKSRNVEI-SIETFT 190

Query:    72 IMFKRYVTAHLVNEAMGTFNKLDEFG-LKDEVSYCNLVDALCEYKHVIEAQELCFGENKN 130
             I+ +RYV A L +EA+  FN+++++G + D++++  ++  L   +   EAQ   F   K+
Sbjct:   191 ILIRRYVRAGLASEAVHCFNRMEDYGCVPDKIAFSIVISNLSRKRRASEAQSF-FDSLKD 249

Query:   131 VGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS 190
                  ++      +Y  ++RGW +     +  + ++EM   G+  ++++YSI +D +C+ 
Sbjct:   250 RFEPDVI------VYTNLVRGWCRAGEISEAEKVFKEMKLAGIEPNVYTYSIVIDALCRC 303

Query:   191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG-VDFAMRVYREMREMGCQPSVVT 249
             G+  +A  ++ +M   G   + + +N ++R V V  G  +  ++VY +M+++GC+P  +T
Sbjct:   304 GQISRAHDVFADMLDSGCAPNAITFNNLMR-VHVKAGRTEKVLQVYNQMKKLGCEPDTIT 362

Query:   250 CNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG---LFDRMI 306
              N +I+  C +  +  A  VL  M KK C  +  T++  FR +EK R++ G   ++ +M+
Sbjct:   363 YNFLIEAHCRDENLENAVKVLNTMIKKKCEVNASTFNTIFRYIEKKRDVNGAHRMYSKMM 422

Query:   307 ESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLD 366
             E+   P   TY +L+R F        V  + K+M++    P+   Y  LV      G  +
Sbjct:   423 EAKCEPNTVTYNILMRMFVGSKSTDMVLKMKKEMDDKEVEPNVNTYRLLVTMFCGMGHWN 482

Query:   367 MARKYDEEM 375
              A K  +EM
Sbjct:   483 NAYKLFKEM 491

GO:0005739 "mitochondrion" evidence=ISM;IDA

TAIR|locus:2026346 AT1G71060 [Arabidopsis thaliana (taxid:3702)]

 Score = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 115/402 (28%), Positives = 198/402 (49%)

Query:     2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP 61
             E L   +N    AL  F W E    F HTT  YN++I+ LGK  +F L W+L+  MK   
Sbjct:    99 EVLKKLSNAGVLALSVFKWAENQKGFKHTTSNYNALIESLGKIKQFKLIWSLVDDMK--A 156

Query:    62 SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN-LVDALCEYKHVIEA 120
               + +  TF ++ +RY  A  V EA+G F+K++EFG K E S  N ++D L + ++V +A
Sbjct:   157 KKLLSKETFALISRRYARARKVKEAIGAFHKMEEFGFKMESSDFNRMLDTLSKSRNVGDA 216

Query:   121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY 180
             Q++ F + K   F   +     K Y ++L GW +     +  E   EM   G   D+ +Y
Sbjct:   217 QKV-FDKMKKKRFEPDI-----KSYTILLEGWGQELNLLRVDEVNREMKDEGFEPDVVAY 270

Query:   181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE 240
              I ++  CK+ K  +A++ + EM+++  K     + ++I  +G  + ++ A+  +   + 
Sbjct:   271 GIIINAHCKAKKYEEAIRFFNEMEQRNCKPSPHIFCSLINGLGSEKKLNDALEFFERSKS 330

Query:   241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITY----HCFFRCLEKPR 296
              G      T N ++   C + R+ +AY  + EM  KG  P+  TY    H   R +++ +
Sbjct:   331 SGFPLEAPTYNALVGAYCWSQRMEDAYKTVDEMRLKGVGPNARTYDIILHHLIR-MQRSK 389

Query:   297 EILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALV 356
             E   ++  M      P + TY +++R F     L     +W +M+  G  P    +++L+
Sbjct:   390 EAYEVYQTM---SCEPTVSTYEIMVRMFCNKERLDMAIKIWDEMKGKGVLPGMHMFSSLI 446

Query:   357 DALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLD 398
              AL  +  LD A +Y  EM   G+  +P   + ++L Q  LD
Sbjct:   447 TALCHENKLDEACEYFNEMLDVGI--RPPGHMFSRLKQTLLD 486

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2025747 AT1G80880 [Arabidopsis thaliana (taxid:3702)]

 Score = 398 (145.2 bits), Expect = 3.2e-39, Sum P(2) = 3.2e-39
 Identities = 113/383 (29%), Positives = 190/383 (49%)

Query:     9 NDWKRALEFFNWVET-DCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH 67
             ++W+ A   F W E   C    + D    +I +LG   +F+++W LI  M  N S     
Sbjct:   135 DEWRLAFLAFKWGEKRGCDDQKSCDL---MIWVLGNHQKFNIAWCLIRDMF-NVSKDTRK 190

Query:    68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--DEVSYCNLVDALCEYKHVIEAQELCF 125
             A F +M  RY  A+  ++A+ TF+ +D+F     DE ++  L+ ALC + H+ +A+E   
Sbjct:   191 AMF-LMMDRYAAANDTSQAIRTFDIMDKFKHTPYDE-AFQGLLCALCRHGHIEKAEEFML 248

Query:   126 GENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWG--KCREFWEEMDKRGVVKDLHSYSIY 183
                K   F   VE      +N+IL GW  + W    + +  W EM    +  +  SYS  
Sbjct:   249 ASKKL--FPVDVEG-----FNVILNGWCNI-WTDVTEAKRIWREMGNYCITPNKDSYSHM 300

Query:   184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC 243
             +    K G  + +++LY EMKK+G+   +  YN+++  +   +  D AM++ +++ E G 
Sbjct:   301 ISCFSKVGNLFDSLRLYDEMKKRGLAPGIEVYNSLVYVLTREDCFDEAMKLMKKLNEEGL 360

Query:   244 QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL--EKPREILGL 301
             +P  VT N++I+ LCE G++  A  VLA M  +   P V T+H F   +  EK  E+LG 
Sbjct:   361 KPDSVTYNSMIRPLCEAGKLDVARNVLATMISENLSPTVDTFHAFLEAVNFEKTLEVLG- 419

Query:   302 FDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID 361
               +M  S + P  +T++++L K  +         +W +M+      +   Y A +  L+ 
Sbjct:   420 --QMKISDLGPTEETFLLILGKLFKGKQPENALKIWAEMDRFEIVANPALYLATIQGLLS 477

Query:   362 KGMLDMARKYDEEMFAKGLSAKP 384
              G L+ AR+   EM +KG    P
Sbjct:   478 CGWLEKAREIYSEMKSKGFVGNP 500

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2156213 AT5G65820 [Arabidopsis thaliana (taxid:3702)]

 Score = 400 (145.9 bits), Expect = 8.5e-37, P = 8.5e-37
 Identities = 101/369 (27%), Positives = 189/369 (51%)

Query:    17 FFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRM-KDNPSSIPNHATFRIMFK 75
             FF W      + H+ + Y S++ IL K  +F   W LI  M K+NP  I     F ++ +
Sbjct:   133 FFVWAAKQPRYCHSIEVYKSMVKILSKMRQFGAVWGLIEEMRKENPQLIEPEL-FVVLVQ 191

Query:    76 RYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFS 134
             R+ +A +V +A+   +++ +FG + DE  +  L+DALC++  V +A +L F E+  + F 
Sbjct:   192 RFASADMVKKAIEVLDEMPKFGFEPDEYVFGCLLDALCKHGSVKDAAKL-F-EDMRMRFP 249

Query:   135 GLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPW 194
                 +N  + +  +L GW ++    + +    +M++ G   D+  Y+  +     +GK  
Sbjct:   250 ----VN-LRYFTSLLYGWCRVGKMMEAKYVLVQMNEAGFEPDIVDYTNLLSGYANAGKMA 304

Query:   195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVI 254
              A  L ++M+++G + +   Y  +I+A+   + ++ AM+V+ EM    C+  VVT   ++
Sbjct:   305 DAYDLLRDMRRRGFEPNANCYTVLIQALCKVDRMEEAMKVFVEMERYECEADVVTYTALV 364

Query:   255 KLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPR---EILGLFDRMIESGIR 311
                C+ G++ + Y VL +M KKG +P  +TY       EK     E L L ++M +    
Sbjct:   365 SGFCKWGKIDKCYIVLDDMIKKGLMPSELTYMHIMVAHEKKESFEECLELMEKMRQIEYH 424

Query:   312 PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKY 371
             P +  Y +++R   + G ++    +W +MEE G SP    +  +++ L  +G L  A  +
Sbjct:   425 PDIGIYNVVIRLACKLGEVKEAVRLWNEMEENGLSPGVDTFVIMINGLASQGCLLEASDH 484

Query:   372 DEEMFAKGL 380
              +EM  +GL
Sbjct:   485 FKEMVTRGL 493

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2097395 AT3G49730 [Arabidopsis thaliana (taxid:3702)]

 Score = 393 (143.4 bits), Expect = 5.3e-36, P = 5.3e-36
 Identities = 104/375 (27%), Positives = 189/375 (50%)

Query:    17 FFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRM-KDNPSSIPNHATFRIMFK 75
             FF W      + H+ +   S++ IL K  +F   W LI  M K NP  I     F ++ +
Sbjct:   117 FFLWATKQPGYFHSYEVCKSMVMILSKMRQFGAVWGLIEEMRKTNPELIEPEL-FVVLMR 175

Query:    76 RYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFS 134
             R+ +A++V +A+   +++ ++GL+ DE  +  L+DALC+   V EA ++ F E+    F 
Sbjct:   176 RFASANMVKKAVEVLDEMPKYGLEPDEYVFGCLLDALCKNGSVKEASKV-F-EDMREKFP 233

Query:   135 GLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPW 194
                     + +  +L GW +     + +E   +M + G+  D+  ++  +     +GK  
Sbjct:   234 P-----NLRYFTSLLYGWCREGKLMEAKEVLVQMKEAGLEPDIVVFTNLLSGYAHAGKMA 288

Query:   195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG-VDFAMRVYREMREMGCQPSVVTCNTV 253
              A  L  +M+K+G + +V  Y  +I+A+  +E  +D AMRV+ EM   GC+  +VT   +
Sbjct:   289 DAYDLMNDMRKRGFEPNVNCYTVLIQALCRTEKRMDEAMRVFVEMERYGCEADIVTYTAL 348

Query:   254 IKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPR---EILGLFDRMIESGI 310
             I   C+ G + + Y+VL +M KKG +P  +TY       EK     E L L ++M   G 
Sbjct:   349 ISGFCKWGMIDKGYSVLDDMRKKGVMPSQVTYMQIMVAHEKKEQFEECLELIEKMKRRGC 408

Query:   311 RPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARK 370
              P +  Y +++R   + G ++    +W +ME  G SP    +  +++    +G L  A  
Sbjct:   409 HPDLLIYNVVIRLACKLGEVKEAVRLWNEMEANGLSPGVDTFVIMINGFTSQGFLIEACN 468

Query:   371 YDEEMFAKGLSAKPR 385
             + +EM ++G+ + P+
Sbjct:   469 HFKEMVSRGIFSAPQ 483

GO:0005739 "mitochondrion" evidence=ISM

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

GO:0009691 "cytokinin biosynthetic process" evidence=RCA

TAIR|locus:2094394 AT3G22670 [Arabidopsis thaliana (taxid:3702)]

 Score = 377 (137.8 bits), Expect = 1.2e-34, P = 1.2e-34
 Identities = 107/403 (26%), Positives = 197/403 (48%)

Query:     2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRM-KDN 60
             + L  ++N W +A  FF W  +   + H+  TYN+++D+LGK   FDL W L++ M K+ 
Sbjct:   137 QVLRRFSNGWNQAYGFFIWANSQTGYVHSGHTYNAMVDVLGKCRNFDLMWELVNEMNKNE 196

Query:    61 PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDE-FGLK-DEVSYCNLVDALCEYKHVI 118
              S +    T   + +R   +   N+A+  F ++++ +G+K D ++  +L+DAL +   + 
Sbjct:   197 ESKLVTLDTMSKVMRRLAKSGKYNKAVDAFLEMEKSYGVKTDTIAMNSLMDALVKENSIE 256

Query:   119 EAQELCFGENKNVGFSGLVEMNK--TKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKD 176
              A E+         F  L +  K   + +N+++ G+ K   +   R   + M       D
Sbjct:   257 HAHEV---------FLKLFDTIKPDARTFNILIHGFCKARKFDDARAMMDLMKVTEFTPD 307

Query:   177 LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYR 236
             + +Y+ +++  CK G   +  ++ +EM++ G   +VV Y  V+ ++G S+ V  A+ VY 
Sbjct:   308 VVTYTSFVEAYCKEGDFRRVNEMLEEMRENGCNPNVVTYTIVMHSLGKSKQVAEALGVYE 367

Query:   237 EMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRC-LEKP 295
             +M+E GC P     +++I +L + GR ++A  +  +M  +G   DV+ Y+      L   
Sbjct:   368 KMKEDGCVPDAKFYSSLIHILSKTGRFKDAAEIFEDMTNQGVRRDVLVYNTMISAALHHS 427

Query:   296 RE--ILGLFDRMI-ESG--IRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEF 350
             R+   L L  RM  E G    P ++TY  LL+       ++ + ++   M +   S D  
Sbjct:   428 RDEMALRLLKRMEDEEGESCSPNVETYAPLLKMCCHKKKMKLLGILLHHMVKNDVSIDVS 487

Query:   351 AYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLV 393
              Y  L+  L   G ++ A  + EE   KG+   PR+     LV
Sbjct:   488 TYILLIRGLCMSGKVEEACLFFEEAVRKGMV--PRDSTCKMLV 528

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2139732 AT4G11690 [Arabidopsis thaliana (taxid:3702)]

 Score = 369 (135.0 bits), Expect = 1.1e-33, P = 1.1e-33
 Identities = 97/386 (25%), Positives = 190/386 (49%)

Query:    14 ALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIM 73
             ++ +FN +  D  F   ++ +N ++  +     F+  W+  +  K     + +  +F I+
Sbjct:   113 SISYFNEM-VDNGFVPGSNCFNYLLTFVVGSSSFNQWWSFFNENKSKV--VLDVYSFGIL 169

Query:    74 FKRYVTAHLVNEAMGTFNKLDEFGLKDEVS-YCNLVDALCEYKHVIEAQELCFGENKNVG 132
              K    A  + ++     +L EFG    V  Y  L+D  C+   + +A++L F     +G
Sbjct:   170 IKGCCEAGEIEKSFDLLIELTEFGFSPNVVIYTTLIDGCCKKGEIEKAKDLFF----EMG 225

Query:   133 FSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK 192
               GLV   +T  Y +++ G FK     +  E +E+M + GV  +L++Y+  M+ +CK G+
Sbjct:   226 KLGLVANERT--YTVLINGLFKNGVKKQGFEMYEKMQEDGVFPNLYTYNCVMNQLCKDGR 283

Query:   193 PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNT 252
                A +++ EM+++G+  ++V YNT+I  +     ++ A +V  +M+  G  P+++T NT
Sbjct:   284 TKDAFQVFDEMRERGVSCNIVTYNTLIGGLCREMKLNEANKVVDQMKSDGINPNLITYNT 343

Query:   253 VIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILG---LFDRMIESG 309
             +I   C  G++ +A ++  ++  +G  P ++TY+       +  +  G   +   M E G
Sbjct:   344 LIDGFCGVGKLGKALSLCRDLKSRGLSPSLVTYNILVSGFCRKGDTSGAAKMVKEMEERG 403

Query:   310 IRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMAR 369
             I+P   TY +L+  F R   +     +   MEELG  PD   Y+ L+     KG ++ A 
Sbjct:   404 IKPSKVTYTILIDTFARSDNMEKAIQLRLSMEELGLVPDVHTYSVLIHGFCIKGQMNEAS 463

Query:   370 KYDEEMFAKGLSAKPREELGTKLVQG 395
             +  + M  K  + +P E +   ++ G
Sbjct:   464 RLFKSMVEK--NCEPNEVIYNTMILG 487

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9M8M3	PP136_ARATH	No assigned EC number	0.6675	0.9727	0.875	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

Your Input: gw1.V.4375.1 hypothetical protein (397 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	403
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	5e-17
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	6e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-14
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	4e-12
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-11
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-10
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-08
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	5e-07
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-06
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-06
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-05
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-04
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-04
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-04
pfam01535	31	pfam01535, PPR, PPR repeat	3e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	5e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	6e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.001
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	0.001
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.002
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	0.002
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	0.003
pfam12854	34	pfam12854, PPR_1, PPR repeat	0.003

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

 Score = 83.0 bits (205), Expect = 5e-17
 Identities = 54/216 (25%), Positives = 106/216 (49%), Gaps = 9/216 (4%)

Query: 100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWG 159
           D ++   L+ A      V  A+E+    ++     G  E     +Y + +    +   W 
Sbjct: 578 DHITVGALMKACANAGQVDRAKEVYQMIHEY-NIKGTPE-----VYTIAVNSCSQKGDWD 631

Query: 160 KCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVI 219
                +++M K+GV  D   +S  +D+   +G   KA ++ ++ +K+GIK+  V+Y++++
Sbjct: 632 FALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM 691

Query: 220 RAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCV 279
            A   ++    A+ +Y +++ +  +P+V T N +I  LCE  ++ +A  VL+EM + G  
Sbjct: 692 GACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLC 751

Query: 280 PDVITYHCFFRCLEKPREI---LGLFDRMIESGIRP 312
           P+ ITY       E+  +    L L  +  E GI+P
Sbjct: 752 PNTITYSILLVASERKDDADVGLDLLSQAKEDGIKP 787

Length = 1060

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

 Score = 76.5 bits (188), Expect = 6e-15
 Identities = 53/223 (23%), Positives = 93/223 (41%), Gaps = 40/223 (17%)

Query: 163 EFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV 222
           E + EM   GV  ++H++   +D   ++G+  KA   Y  M+ K +K D V +N +I A 
Sbjct: 493 EVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISAC 552

Query: 223 GVSEGVDFAMRVYREMREMG--CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP 280
           G S  VD A  V  EM+       P  +T   ++K     G+V                 
Sbjct: 553 GQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQV----------------- 595

Query: 281 DVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLR---KFGRWGFLRPVFVVW 337
                       ++ +E+   +  + E  I+   + Y + +    + G W F   ++   
Sbjct: 596 ------------DRAKEV---YQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIY--- 637

Query: 338 KKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGL 380
             M++ G  PDE  ++ALVD     G LD A +  ++   +G+
Sbjct: 638 DDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGI 680

Length = 1060

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

 Score = 65.9 bits (162), Expect = 4e-14
 Identities = 21/48 (43%), Positives = 27/48 (56%)

Query: 245 PSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL 292
           P VVT NT+I   C+ G+V EA  +  EM K+G  P+V TY      L
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 67.6 bits (165), Expect = 4e-12
 Identities = 44/212 (20%), Positives = 87/212 (41%), Gaps = 11/212 (5%)

Query: 179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREM 238
           +    M     +G+  +A ++Y+ + +  IK     Y   + +       DFA+ +Y +M
Sbjct: 581 TVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDM 640

Query: 239 REMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYH------CFFRCL 292
           ++ G +P  V  + ++ +    G + +A+ +L +  K+G     ++Y          +  
Sbjct: 641 KKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNW 700

Query: 293 EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAY 352
           +K  E   L++ +    +RP + T   L+        L     V  +M+ LG  P+   Y
Sbjct: 701 KKALE---LYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY 757

Query: 353 NALVDALIDKGMLDMARKYDEEMFAKGLSAKP 384
           + L+ A   K   D+    D    AK    KP
Sbjct: 758 SILLVASERKDDADVG--LDLLSQAKEDGIKP 787

Length = 1060

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

 Score = 57.4 bits (140), Expect = 4e-11
 Identities = 20/47 (42%), Positives = 31/47 (65%)

Query: 175 KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRA 221
            D+ +Y+  +D  CK GK  +A+KL+ EMKK+GIK +V  Y+ +I  
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDG 47

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

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

 Score = 53.6 bits (130), Expect = 8e-10
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 211 DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLC 258
           DVV YNT+I        V+ A++++ EM++ G +P+V T + +I  LC
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLC 49

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|205109 pfam12854, PPR_1, PPR repeat

 Score = 50.0 bits (121), Expect = 1e-08
 Identities = 18/34 (52%), Positives = 21/34 (61%)

Query: 241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP 274
            G +P VVT NT+I  LC  GRV EA  +L EM 
Sbjct: 1   KGLKPDVVTYNTLIDGLCRAGRVDEAVELLDEME 34

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

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

 Score = 45.1 bits (108), Expect = 5e-07
 Identities = 18/35 (51%), Positives = 23/35 (65%)

Query: 248 VTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDV 282
           VT NT+I  LC+ GRV EA  +  EM ++G  PDV
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 49.5 bits (118), Expect = 2e-06
 Identities = 49/228 (21%), Positives = 98/228 (42%), Gaps = 12/228 (5%)

Query: 144 IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEM 203
           + N +++ +  +  WG+  + +  M+     KD  S++  +    K+G P KA++ Y  M
Sbjct: 325 VCNSLIQMYLSLGSWGEAEKVFSRME----TKDAVSWTAMISGYEKNGLPDKALETYALM 380

Query: 204 KKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRV 263
           ++  +  D +   +V+ A      +D  ++++      G    VV  N +I++  +   +
Sbjct: 381 EQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCI 440

Query: 264 REAYAVLAEMPKKGCVP--DVITYHCF-FRCLEKPREILGLFDRMIESGIRPKMDTYVML 320
            +A  V   +P+K  +    +I       RC E     L  F +M+ + ++P   T +  
Sbjct: 441 DKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEA----LIFFRQMLLT-LKPNSVTLIAA 495

Query: 321 LRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMA 368
           L    R G L     +   +   G   D F  NAL+D  +  G ++ A
Sbjct: 496 LSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYA 543

Length = 857

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

 Score = 48.3 bits (115), Expect = 4e-06
 Identities = 40/182 (21%), Positives = 84/182 (46%), Gaps = 8/182 (4%)

Query: 191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTC 250
           G   +A+ LY EM+  G+ +D   ++ +IR       ++ A + +  +   G    +V  
Sbjct: 304 GYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVAN 363

Query: 251 NTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCF---FRCLEKPREILGLFDRMIE 307
             ++ L  + GR+ +A  V   MP+K    ++I+++     +    +  + + +F+RMI 
Sbjct: 364 TALVDLYSKWGRMEDARNVFDRMPRK----NLISWNALIAGYGNHGRGTKAVEMFERMIA 419

Query: 308 SGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKM-EELGCSPDEFAYNALVDALIDKGMLD 366
            G+ P   T++ +L      G     + +++ M E     P    Y  +++ L  +G+LD
Sbjct: 420 EGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLD 479

Query: 367 MA 368
            A
Sbjct: 480 EA 481

Length = 697

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

 Score = 46.4 bits (110), Expect = 2e-05
 Identities = 48/229 (20%), Positives = 94/229 (41%), Gaps = 45/229 (19%)

Query: 184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC 243
           +++  K     KA++++  + +K    DV+++ ++I  + ++     A+  +R+M  +  
Sbjct: 431 IEMYSKCKCIDKALEVFHNIPEK----DVISWTSIIAGLRLNNRCFEALIFFRQML-LTL 485

Query: 244 QPSVVT-------CNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLE--- 293
           +P+ VT       C  +  L+C  G+   A+ +   +   G +P+ +    + RC     
Sbjct: 486 KPNSVTLIAALSACARIGALMC--GKEIHAHVLRTGIGFDGFLPNALL-DLYVRCGRMNY 542

Query: 294 --------------------------KPREILGLFDRMIESGIRPKMDTYVMLLRKFGRW 327
                                     K    + LF+RM+ESG+ P   T++ LL    R 
Sbjct: 543 AWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRS 602

Query: 328 GFLRPVFVVWKKMEE-LGCSPDEFAYNALVDALIDKGMLDMARKYDEEM 375
           G +      +  MEE    +P+   Y  +VD L   G L  A  +  +M
Sbjct: 603 GMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM 651

Length = 857

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

 Score = 45.6 bits (108), Expect = 3e-05
 Identities = 53/239 (22%), Positives = 97/239 (40%), Gaps = 11/239 (4%)

Query: 145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMK 204
            N +L    K       R  ++EM +R    +L S+   +  +  +G   +A  L++EM 
Sbjct: 161 MNRVLLMHVKCGMLIDARRLFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMW 216

Query: 205 KKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG-CQPSVVTCNTVIKLLCENGRV 263
           + G   +   +  ++RA           +++  + + G    + V+C  +I +  + G +
Sbjct: 217 EDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSC-ALIDMYSKCGDI 275

Query: 264 REAYAVLAEMPKKGCVP--DVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLL 321
            +A  V   MP+K  V    ++  +      E   E L L+  M +SG+     T+ +++
Sbjct: 276 EDARCVFDGMPEKTTVAWNSMLAGYALHGYSE---EALCLYYEMRDSGVSIDQFTFSIMI 332

Query: 322 RKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGL 380
           R F R   L         +   G   D  A  ALVD     G ++ AR   + M  K L
Sbjct: 333 RIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNL 391

Length = 697

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

 Score = 38.9 bits (92), Expect = 1e-04
 Identities = 15/45 (33%), Positives = 28/45 (62%)

Query: 145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK 189
           YN ++ G+ K     +  + + EM KRG+  ++++YSI +D +CK
Sbjct: 6   YNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 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 = 43.7 bits (103), Expect = 1e-04
 Identities = 34/142 (23%), Positives = 64/142 (45%), Gaps = 7/142 (4%)

Query: 187 MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS 246
           +C  G+  +A+KL + M++  + +D  AY  + R       V+   RV            
Sbjct: 61  LCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLG 120

Query: 247 VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKP---REILGLFD 303
           V   N ++ +    G +  A+ V  +MP++    D+ +++       K     E L L+ 
Sbjct: 121 VRLGNAMLSMFVRFGELVHAWYVFGKMPER----DLFSWNVLVGGYAKAGYFDEALCLYH 176

Query: 304 RMIESGIRPKMDTYVMLLRKFG 325
           RM+ +G+RP + T+  +LR  G
Sbjct: 177 RMLWAGVRPDVYTFPCVLRTCG 198

Length = 857

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

 Score = 38.5 bits (91), Expect = 2e-04
 Identities = 11/44 (25%), Positives = 24/44 (54%)

Query: 316 TYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDAL 359
           TY  L+  + + G +     ++ +M++ G  P+ + Y+ L+D L
Sbjct: 5   TYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 37.8 bits (89), Expect = 2e-04
 Identities = 13/30 (43%), Positives = 23/30 (76%)

Query: 179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGI 208
           +Y+  +   CK+GK  +A++L+KEMK+KG+
Sbjct: 2   TYNSLISGYCKAGKLEEALELFKEMKEKGV 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|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score = 42.6 bits (100), Expect = 3e-04
 Identities = 37/174 (21%), Positives = 69/174 (39%), Gaps = 15/174 (8%)

Query: 209 KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYA 268
            +    Y+ ++ A    + +     VY  +   G +P     N V+ +  + G + +A  
Sbjct: 120 TLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARR 179

Query: 269 VLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVMLLRKFG 325
           +  EMP++    ++ ++      L      RE   LF  M E G   +  T+V++LR   
Sbjct: 180 LFDEMPER----NLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASA 235

Query: 326 RWGFLRPVFVVWKKME----ELGCSPDEFAYNALVDALIDKGMLDMARKYDEEM 375
             G  R      +++     + G   D F   AL+D     G ++ AR   + M
Sbjct: 236 GLGSAR----AGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGM 285

Length = 697

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

 Score = 37.4 bits (88), Expect = 3e-04
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 248 VTCNTVIKLLCENGRVREAYAVLAEMPKKGC 278
           VT N++I   C+ G++ EA  +  EM +KG 
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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 36.8 bits (86), Expect = 5e-04
 Identities = 11/33 (33%), Positives = 20/33 (60%)

Query: 177 LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK 209
           L +Y+  +  + K+G P  A+ + +EMK  G+K
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLK 33

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

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

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 12/34 (35%), Positives = 16/34 (47%)

Query: 247 VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP 280
           + T N ++  L + G    A AVL EM   G  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

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

 Score = 36.6 bits (86), Expect = 0.001
 Identities = 13/35 (37%), Positives = 18/35 (51%)

Query: 347 PDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLS 381
           PD   YN L+D    KG ++ A K   EM  +G+ 
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIK 35

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

 Score = 40.6 bits (95), Expect = 0.001
 Identities = 51/229 (22%), Positives = 96/229 (41%), Gaps = 27/229 (11%)

Query: 163 EFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV 222
             + EM   GV  D  ++SI + I  +      A + +  + + G  +D+VA NT +   
Sbjct: 311 CLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVA-NTAL--- 366

Query: 223 GVSEGVDF-----AMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKG 277
                VD       M   R + +   + ++++ N +I     +GR  +A  +   M  +G
Sbjct: 367 -----VDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEG 421

Query: 278 CVPDVITY-----HCFFRCL-EKPREILGLFDRMIES-GIRPKMDTYVMLLRKFGRWGFL 330
             P+ +T+      C +  L E+  EI   F  M E+  I+P+   Y  ++   GR G L
Sbjct: 422 VAPNHVTFLAVLSACRYSGLSEQGWEI---FQSMSENHRIKPRAMHYACMIELLGREGLL 478

Query: 331 RPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKG 379
              + + ++       P    + AL+ A      L++ R   E+++  G
Sbjct: 479 DEAYAMIRRAP---FKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMG 524

Length = 697

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

 Score = 35.1 bits (82), Expect = 0.002
 Identities = 15/35 (42%), Positives = 28/35 (80%)

Query: 178 HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV 212
            +Y+  +D +CK+G+  +A++L+KEMK++GI+ DV
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

 Score = 39.9 bits (93), Expect = 0.002
 Identities = 29/125 (23%), Positives = 60/125 (48%), Gaps = 8/125 (6%)

Query: 156 SWWGK---CREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV 212
           S WG+    R  ++ M ++ ++    S++  +      G+  KAV++++ M  +G+  + 
Sbjct: 371 SKWGRMEDARNVFDRMPRKNLI----SWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNH 426

Query: 213 VAYNTVIRAVGVSEGVDFAMRVYREMRE-MGCQPSVVTCNTVIKLLCENGRVREAYAVLA 271
           V +  V+ A   S   +    +++ M E    +P  +    +I+LL   G + EAYA++ 
Sbjct: 427 VTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIR 486

Query: 272 EMPKK 276
             P K
Sbjct: 487 RAPFK 491

Length = 697

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

 Score = 39.5 bits (92), Expect = 0.003
 Identities = 20/99 (20%), Positives = 50/99 (50%)

Query: 158 WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNT 217
           W K  E +E++    +   + + +  +  +C+  +  KA+++  EMK+ G+  + + Y+ 
Sbjct: 700 WKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSI 759

Query: 218 VIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKL 256
           ++ A    +  D  + +  + +E G +P++V C  +  L
Sbjct: 760 LLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGL 798

Length = 1060

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

 Score = 35.0 bits (82), Expect = 0.003
 Identities = 13/32 (40%), Positives = 17/32 (53%)

Query: 344 GCSPDEFAYNALVDALIDKGMLDMARKYDEEM 375
           G  PD   YN L+D L   G +D A +  +EM
Sbjct: 2   GLKPDVVTYNTLIDGLCRAGRVDEAVELLDEM 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	403
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.96
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.96
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.94
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.93
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.91
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.91
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.9
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.9
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.89
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.88
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.88
PRK14574	822	hmsH outer membrane protein; Provisional	99.85
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.85
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.83
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.82
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.78
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.75
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.75
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.74
PRK14574	822	hmsH outer membrane protein; Provisional	99.74
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.73
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.73
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.72
KOG2076	895	consensus RNA polymerase III transcription factor	99.72
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.72
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.72
KOG2076	895	consensus RNA polymerase III transcription factor	99.71
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.69
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.69
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.68
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.68
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.68
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.68
KOG2003	840	consensus TPR repeat-containing protein [General f	99.67
KOG1126	638	consensus DNA-binding cell division cycle control	99.67
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.63
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.62
KOG1126	638	consensus DNA-binding cell division cycle control	99.62
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.59
KOG2003	840	consensus TPR repeat-containing protein [General f	99.59
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.59
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.58
PRK12370	553	invasion protein regulator; Provisional	99.57
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.57
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.56
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.55
PRK12370	553	invasion protein regulator; Provisional	99.55
KOG1129	478	consensus TPR repeat-containing protein [General f	99.54
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.53
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.46
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.44
PF13041	50	PPR_2: PPR repeat family	99.44
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.43
PF13041	50	PPR_2: PPR repeat family	99.43
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.41
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.41
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.4
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.39
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.38
KOG1129	478	consensus TPR repeat-containing protein [General f	99.37
PRK11189	296	lipoprotein NlpI; Provisional	99.36
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.33
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.33
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.32
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.31
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.31
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.29
PRK11189	296	lipoprotein NlpI; Provisional	99.28
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.28
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.25
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.24
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.24
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.22
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.21
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.19
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.17
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.15
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.12
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.08
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.07
PLN02789	320	farnesyltranstransferase	99.07
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.06
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.05
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.99
PRK04841	903	transcriptional regulator MalT; Provisional	98.98
KOG1125	579	consensus TPR repeat-containing protein [General f	98.97
PLN02789	320	farnesyltranstransferase	98.97
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.96
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.95
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.94
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.94
KOG1125	579	consensus TPR repeat-containing protein [General f	98.94
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.92
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.92
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.91
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.9
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.89
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.89
PF12854	34	PPR_1: PPR repeat	98.88
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.87
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.86
PF12854	34	PPR_1: PPR repeat	98.86
PRK04841	903	transcriptional regulator MalT; Provisional	98.82
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.79
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.78
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.75
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.74
PRK15359	144	type III secretion system chaperone protein SscB;	98.74
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.73
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.72
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.71
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.71
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.67
PRK15359	144	type III secretion system chaperone protein SscB;	98.67
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.66
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.66
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.66
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.66
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.61
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.6
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.57
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.56
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.54
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.54
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.52
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.52
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.49
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.49
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.48
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.47
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.46
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.43
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.42
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.39
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.34
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.33
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.3
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.3
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.24
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.18
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.18
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	98.17
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	98.15
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	98.15
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.14
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.13
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.13
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.12
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.11
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.11
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.1
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	98.1
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.08
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.08
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.06
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	98.04
KOG0553	304	consensus TPR repeat-containing protein [General f	98.0
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.99
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.99
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.97
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.96
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.96
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.94
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.92
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.91
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.88
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.84
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.81
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.81
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.81
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.8
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.77
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.74
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.74
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.74
KOG0553	304	consensus TPR repeat-containing protein [General f	97.73
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.73
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.7
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.66
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.64
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.62
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.6
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.59
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.58
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.58
PF12688	120	TPR_5: Tetratrico peptide repeat	97.57
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.57
PF12688	120	TPR_5: Tetratrico peptide repeat	97.57
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.55
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.52
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.44
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.41
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.4
PRK10803	263	tol-pal system protein YbgF; Provisional	97.4
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.35
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.29
PRK10803	263	tol-pal system protein YbgF; Provisional	97.28
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.27
PF13371	73	TPR_9: Tetratricopeptide repeat	97.21
PF13371	73	TPR_9: Tetratricopeptide repeat	97.14
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	97.01
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.99
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	96.97
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.96
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.95
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.94
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.89
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.89
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.88
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.82
PRK15331	165	chaperone protein SicA; Provisional	96.8
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	96.74
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.69
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	96.65
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.64
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.64
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.64
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.63
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.62
KOG1585	308	consensus Protein required for fusion of vesicles	96.62
PRK15331	165	chaperone protein SicA; Provisional	96.61
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.58
PF13512	142	TPR_18: Tetratricopeptide repeat	96.5
PF13428	44	TPR_14: Tetratricopeptide repeat	96.49
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.43
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.42
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.41
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	96.37
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.37
KOG3941	406	consensus Intermediate in Toll signal transduction	96.35
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.29
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.18
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	96.18
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.15
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.12
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	96.12
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.12
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.03
KOG4555	175	consensus TPR repeat-containing protein [Function	96.02
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.01
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.0
KOG3941	406	consensus Intermediate in Toll signal transduction	95.98
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.95
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.93
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	95.84
KOG4555	175	consensus TPR repeat-containing protein [Function	95.83
PRK11906	458	transcriptional regulator; Provisional	95.83
COG4105	254	ComL DNA uptake lipoprotein [General function pred	95.8
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.8
PRK11906	458	transcriptional regulator; Provisional	95.8
KOG2610	491	consensus Uncharacterized conserved protein [Funct	95.69
PF13428	44	TPR_14: Tetratricopeptide repeat	95.58
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	95.5
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	95.46
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.31
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.26
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.18
COG3629	280	DnrI DNA-binding transcriptional activator of the	95.17
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	94.9
PF13431	34	TPR_17: Tetratricopeptide repeat	94.86
KOG1585	308	consensus Protein required for fusion of vesicles	94.83
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	94.78
KOG1550	552	consensus Extracellular protein SEL-1 and related	94.7
COG0457	291	NrfG FOG: TPR repeat [General function prediction	94.58
COG4105	254	ComL DNA uptake lipoprotein [General function pred	94.56
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.42
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	94.29
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	94.27
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	94.23
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.19
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	93.88
PF13512	142	TPR_18: Tetratricopeptide repeat	93.62
COG0457	291	NrfG FOG: TPR repeat [General function prediction	93.56
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	93.55
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	93.45
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	93.3
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	93.27
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	93.18
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	93.05
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	93.04
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	93.01
PF13431	34	TPR_17: Tetratricopeptide repeat	92.97
KOG4570	418	consensus Uncharacterized conserved protein [Funct	92.64
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	92.37
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	92.23
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.11
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	91.91
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.87
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	91.6
KOG1941	518	consensus Acetylcholine receptor-associated protei	91.28
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	91.24
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	91.23
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	91.18
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	91.17
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	91.15
PF13929	292	mRNA_stabil: mRNA stabilisation	90.97
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	90.96
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	90.92
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	90.89
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	90.51
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	90.21
COG1747	711	Uncharacterized N-terminal domain of the transcrip	90.09
COG4455	273	ImpE Protein of avirulence locus involved in tempe	89.95
PF13929	292	mRNA_stabil: mRNA stabilisation	89.95
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	89.7
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	89.69
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	89.42
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	89.12
COG3947	361	Response regulator containing CheY-like receiver a	89.08
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	89.06
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	88.89
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	88.78
PF09477	116	Type_III_YscG: Bacterial type II secretion system	88.62
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	88.48
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	88.44
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	88.23
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	87.79
KOG4234	271	consensus TPR repeat-containing protein [General f	87.75
COG1747	711	Uncharacterized N-terminal domain of the transcrip	87.46
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	87.19
KOG4648	536	consensus Uncharacterized conserved protein, conta	87.19
KOG4648	536	consensus Uncharacterized conserved protein, conta	86.96
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	86.67
KOG4234	271	consensus TPR repeat-containing protein [General f	86.3
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	86.04
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	85.86
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	85.73
KOG1258	577	consensus mRNA processing protein [RNA processing	85.7
KOG1550	552	consensus Extracellular protein SEL-1 and related	85.66
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	85.42
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	84.97
KOG1258	577	consensus mRNA processing protein [RNA processing	84.95
COG4455	273	ImpE Protein of avirulence locus involved in tempe	84.85
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	84.61
PRK09687	280	putative lyase; Provisional	84.32
PF08424	321	NRDE-2: NRDE-2, necessary for RNA interference; In	84.23
COG3947	361	Response regulator containing CheY-like receiver a	84.12
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	84.08
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	83.84
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	83.81
PRK10941	269	hypothetical protein; Provisional	83.4
PRK09687	280	putative lyase; Provisional	83.04
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	82.92
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	82.79
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	82.73
PF13762	145	MNE1: Mitochondrial splicing apparatus component	82.18
PF14669	233	Asp_Glu_race_2: Putative aspartate racemase	81.89
KOG2300	629	consensus Uncharacterized conserved protein [Funct	81.66
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	81.65
PF11663	140	Toxin_YhaV: Toxin with endonuclease activity YhaV;	81.61
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	81.1
PF14689	62	SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical do	80.31

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.3e-61  Score=456.33  Aligned_cols=381  Identities=17%  Similarity=0.215  Sum_probs=275.7

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVN   84 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   84 (403)
                      +++.|+++.|.++|+.|.+ .|+.||..+|+.+|.+|++.|++++|.++|++|.+.+ +.||..+|+.+|.+|++.|+++
T Consensus       447 ~~k~g~~e~A~~lf~~M~~-~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~G-v~PdvvTynaLI~gy~k~G~~e  524 (1060)
T PLN03218        447 CASSQDIDGALRVLRLVQE-AGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAG-VEANVHTFGALIDGCARAGQVA  524 (1060)
T ss_pred             HHhCcCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHHCcCHH
Confidence            4456777777777777764 6777777777777777777777777777777777766 5677777777777777777777


Q ss_pred             HHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHH
Q 041804           85 EAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCRE  163 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  163 (403)
                      +|.++|++|.+.|.. |..+|+.++.+|++.|++++|.++|.+|....    .+..||..+|+.++.+|++.|++++|.+
T Consensus       525 eAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~----~gi~PD~vTynaLI~ay~k~G~ldeA~e  600 (1060)
T PLN03218        525 KAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET----HPIDPDHITVGALMKACANAGQVDRAKE  600 (1060)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhc----CCCCCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            777777777777765 77777777777777777777777777765420    0556777777777777777777777777


Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          164 FWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      +|+.|.+.|+.|+..+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++|+.|.+.|+
T Consensus       601 lf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~  680 (1060)
T PLN03218        601 VYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGI  680 (1060)
T ss_pred             HHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence            77777777777777777777777777777777777777777777777777777777777777777777777777777777


Q ss_pred             CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHH
Q 041804          244 QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVML  320 (403)
Q Consensus       244 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (403)
                      .|+..+|+++|.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|   ++.++|.++|++|.+.|+.||..||+++
T Consensus       681 ~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sL  760 (1060)
T PLN03218        681 KLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSIL  760 (1060)
T ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            7777777777777777777777777777777777777777777777766   5567777777777777777777777777


Q ss_pred             HHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----c-------------------CCHHHHHHHHHHHHH
Q 041804          321 LRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID----K-------------------GMLDMARKYDEEMFA  377 (403)
Q Consensus       321 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~-------------------g~~~~a~~~~~~m~~  377 (403)
                      +.+|++.|++++|.+++++|.+.|+.||..+|++++..|.+    .                   +..++|..+|++|++
T Consensus       761 L~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~  840 (1060)
T PLN03218        761 LVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETIS  840 (1060)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHH
Confidence            77777777777777777777777777777777777654331    1                   123567777777777


Q ss_pred             cCCCCChhhHHHHH
Q 041804          378 KGLSAKPREELGTK  391 (403)
Q Consensus       378 ~~~~p~~~~~~~~~  391 (403)
                      .|+.||..|+....
T Consensus       841 ~Gi~Pd~~T~~~vL  854 (1060)
T PLN03218        841 AGTLPTMEVLSQVL  854 (1060)
T ss_pred             CCCCCCHHHHHHHH
Confidence            77777777665544

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.5e-61  Score=454.49  Aligned_cols=372  Identities=15%  Similarity=0.242  Sum_probs=350.3

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHH
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEA   86 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a   86 (403)
                      +.|.+++|+++|+.|.     .||..+|+.++.+|++.|++++|.++|+.|.+.+ ..||..+|+.+|.+|++.|++++|
T Consensus       418 ~~g~~~eAl~lf~~M~-----~pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~G-l~pD~~tynsLI~~y~k~G~vd~A  491 (1060)
T PLN03218        418 KQRAVKEAFRFAKLIR-----NPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAG-LKADCKLYTTLISTCAKSGKVDAM  491 (1060)
T ss_pred             HCCCHHHHHHHHHHcC-----CCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhCcCHHHH
Confidence            3455555555555554     2889999999999999999999999999999988 789999999999999999999999


Q ss_pred             HHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           87 MGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        87 ~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      .++|++|.+.|+. |..+|+.++.+|++.|++++|.++|++|...      +..||..+|+.++.+|++.|++++|.++|
T Consensus       492 ~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~------Gv~PD~vTYnsLI~a~~k~G~~deA~~lf  565 (1060)
T PLN03218        492 FEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK------NVKPDRVVFNALISACGQSGAVDRAFDVL  565 (1060)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHc------CCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            9999999999987 9999999999999999999999999999887      88999999999999999999999999999


Q ss_pred             HHHHh--CCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          166 EEMDK--RGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       166 ~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      ++|..  .|+.||..+|+.+|.+|++.|++++|.++|+.|.+.|+.|+..+|+.+|.+|++.|++++|.++|++|.+.|+
T Consensus       566 ~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv  645 (1060)
T PLN03218        566 AEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGV  645 (1060)
T ss_pred             HHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Confidence            99976  6789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHH
Q 041804          244 QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVML  320 (403)
Q Consensus       244 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (403)
                      .||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+++|.+|   ++.++|.++|++|.+.|+.||..+|+++
T Consensus       646 ~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~L  725 (1060)
T PLN03218        646 KPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNAL  725 (1060)
T ss_pred             CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            9999999999999999999999999999999999999999999999988   6789999999999999999999999999


Q ss_pred             HHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhhHHHH
Q 041804          321 LRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGT  390 (403)
Q Consensus       321 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~~  390 (403)
                      |.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|+.++|.+++++|.+.|+.||..++...
T Consensus       726 I~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsL  795 (1060)
T PLN03218        726 ITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCI  795 (1060)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999998877654

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

Probab=100.00  E-value=1.6e-55  Score=412.26  Aligned_cols=370  Identities=17%  Similarity=0.269  Sum_probs=321.9

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVN   84 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   84 (403)
                      +.+.|++++|+++|++|....+..||..+|+.++.+|++.++++.+..++..|...| ..||..+|+.++.+|++.|+++
T Consensus        97 l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g-~~~~~~~~n~Li~~y~k~g~~~  175 (697)
T PLN03081         97 LVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSG-FEPDQYMMNRVLLMHVKCGMLI  175 (697)
T ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHhcCCCHH
Confidence            356788888888888887645577888888888888888888888888888888877 6788888888888888888888


Q ss_pred             HHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccc-----------------------------cc
Q 041804           85 EAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGF-----------------------------SG  135 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----------------------------~~  135 (403)
                      .|.++|++|.+   +|..+|+.++.+|++.|++++|.++|++|......                             ..
T Consensus       176 ~A~~lf~~m~~---~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~  252 (697)
T PLN03081        176 DARRLFDEMPE---RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLK  252 (697)
T ss_pred             HHHHHHhcCCC---CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence            88888888865   57788888888888888888888888887654110                             01


Q ss_pred             cccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhH
Q 041804          136 LVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAY  215 (403)
Q Consensus       136 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  215 (403)
                      .+..++..+|+.|+.+|++.|++++|.++|++|..    +|..+|+.||.+|++.|++++|+++|++|.+.|+.||..||
T Consensus       253 ~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~  328 (697)
T PLN03081        253 TGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE----KTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTF  328 (697)
T ss_pred             hCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC----CChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            14566777888999999999999999999999964    58889999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---
Q 041804          216 NTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---  292 (403)
Q Consensus       216 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---  292 (403)
                      ++++.+|++.|+++.|.+++..|.+.|+.|+..+|++|+.+|++.|++++|.++|++|.+    ||..+|+++|.+|   
T Consensus       329 ~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----~d~~t~n~lI~~y~~~  404 (697)
T PLN03081        329 SIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----KNLISWNALIAGYGNH  404 (697)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----CCeeeHHHHHHHHHHc
Confidence            999999999999999999999999999999999999999999999999999999999974    6899999999988   


Q ss_pred             CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHh-cCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 041804          293 EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEE-LGCSPDEFAYNALVDALIDKGMLDMARKY  371 (403)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  371 (403)
                      ++.++|.++|++|.+.|+.||..||++++.+|++.|++++|.++|+.|.+ .|+.|+..+|++++++|++.|++++|.++
T Consensus       405 G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~  484 (697)
T PLN03081        405 GRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAM  484 (697)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHH
Confidence            67899999999999999999999999999999999999999999999976 58999999999999999999999999999


Q ss_pred             HHHHHHcCCCCChhhHHH
Q 041804          372 DEEMFAKGLSAKPREELG  389 (403)
Q Consensus       372 ~~~m~~~~~~p~~~~~~~  389 (403)
                      +++|   ++.|+..++..
T Consensus       485 ~~~~---~~~p~~~~~~~  499 (697)
T PLN03081        485 IRRA---PFKPTVNMWAA  499 (697)
T ss_pred             HHHC---CCCCCHHHHHH
Confidence            8765   67787766433

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

Probab=100.00  E-value=1.5e-54  Score=405.85  Aligned_cols=347  Identities=14%  Similarity=0.207  Sum_probs=248.1

Q ss_pred             CcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHH
Q 041804           27 FTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYC  105 (403)
Q Consensus        27 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~  105 (403)
                      ...+...|+.+|..+.+.|++++|+++|+.|...++..||..+|+.++.+|.+.++++.+.+++..|.+.|.. |..+|+
T Consensus        83 ~~~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n  162 (697)
T PLN03081         83 IRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN  162 (697)
T ss_pred             CCCCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHH
Confidence            4566778999999999999999999999999987657799999999999999999999999999999999987 999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHH
Q 041804          106 NLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMD  185 (403)
Q Consensus       106 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  185 (403)
                      .++.+|++.|+++.|.++|+++..          ||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++.
T Consensus       163 ~Li~~y~k~g~~~~A~~lf~~m~~----------~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~  232 (697)
T PLN03081        163 RVLLMHVKCGMLIDARRLFDEMPE----------RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLR  232 (697)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcCCC----------CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHH
Confidence            999999999999999999999853          6889999999999999999999999999998888777766655555


Q ss_pred             HHHHcCChhHHHHHHHHHHHcCCCC-------------------------------ChhhHHHHHHHHhhcCCHHHHHHH
Q 041804          186 IMCKSGKPWKAVKLYKEMKKKGIKM-------------------------------DVVAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       186 ~~~~~~~~~~a~~~~~~~~~~~~~~-------------------------------~~~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      +|+..|+.+.+.+++..+.+.|+.|                               |..+|++++.+|++.|++++|.++
T Consensus       233 a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~l  312 (697)
T PLN03081        233 ASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCL  312 (697)
T ss_pred             HHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHH
Confidence            4444444444444444444444444                               455555555555555555555555


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCC
Q 041804          235 YREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIR  311 (403)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~  311 (403)
                      |++|.+.|+.||..||+.++.+|++.|++++|.+++..|.+.|+.||..+|++++..|   ++.++|.++|++|.    .
T Consensus       313 f~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~  388 (697)
T PLN03081        313 YYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----R  388 (697)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----C
Confidence            5555555555555555555555555555555555555555555555555555555544   44555555555553    2


Q ss_pred             CchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCChhhH
Q 041804          312 PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA-KGLSAKPREE  387 (403)
Q Consensus       312 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~~~~p~~~~~  387 (403)
                      ||..+|+++|.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|+.++|.++|+.|.+ .|+.|+..++
T Consensus       389 ~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y  465 (697)
T PLN03081        389 KNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHY  465 (697)
T ss_pred             CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccch
Confidence            455566666666666666666666666666666666666666666666666666666666666654 3666665444

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=6.4e-54  Score=410.72  Aligned_cols=368  Identities=17%  Similarity=0.237  Sum_probs=251.9

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHh-----------------------------------HHHHHHHHHccCChhH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDT-----------------------------------YNSVIDILGKFFEFDL   49 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~-----------------------------------~~~li~~~~~~~~~~~   49 (403)
                      +.+.|++++|+++|+.|.. .|+.||..+                                   |+.+|.+|+++|++++
T Consensus       162 ~~~~g~~~~A~~~f~~M~~-~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~  240 (857)
T PLN03077        162 YAKAGYFDEALCLYHRMLW-AGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVS  240 (857)
T ss_pred             HHhCCCHHHHHHHHHHHHH-cCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHH
Confidence            4556777777777777764 455555444                                   4556666777777777


Q ss_pred             HHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhccc
Q 041804           50 SWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGEN  128 (403)
Q Consensus        50 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  128 (403)
                      |.++|++|..     ||..+||.+|.+|++.|++++|+++|++|.+.|+. |..+|+.++.+|++.|+.+.+.+++..+.
T Consensus       241 A~~lf~~m~~-----~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~  315 (857)
T PLN03077        241 ARLVFDRMPR-----RDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVV  315 (857)
T ss_pred             HHHHHhcCCC-----CCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHH
Confidence            7777777754     67777888888888888888888888888877766 77788888888888888888877777777


Q ss_pred             ccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC
Q 041804          129 KNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI  208 (403)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  208 (403)
                      ..      +..||..+|+.++.+|++.|++++|.++|++|..    ||..+|+.+|.+|++.|++++|+++|++|.+.|+
T Consensus       316 ~~------g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~  385 (857)
T PLN03077        316 KT------GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----KDAVSWTAMISGYEKNGLPDKALETYALMEQDNV  385 (857)
T ss_pred             Hh------CCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC----CCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCC
Confidence            66      7778888888888888888888888888888763    5777888888888888888888888888888888


Q ss_pred             CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc------------
Q 041804          209 KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK------------  276 (403)
Q Consensus       209 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~------------  276 (403)
                      .||..||+.++.+|++.|+++.|.++++.+.+.|+.|+..+|++|+.+|++.|++++|.++|++|.+.            
T Consensus       386 ~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~  465 (857)
T PLN03077        386 SPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGL  465 (857)
T ss_pred             CCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHH
Confidence            88888888888888888888888888888888888888888888888888877777777777776542            


Q ss_pred             ------------------CCCCChhhHHHHHHhhC---CHHHHHHHHHHHHHcCC-------------------------
Q 041804          277 ------------------GCVPDVITYHCFFRCLE---KPREILGLFDRMIESGI-------------------------  310 (403)
Q Consensus       277 ------------------~~~p~~~~~~~l~~~~~---~~~~a~~~~~~~~~~~~-------------------------  310 (403)
                                        ++.||..||+.++.+|.   ..+.+.+++..+.+.|+                         
T Consensus       466 ~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~  545 (857)
T PLN03077        466 RLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWN  545 (857)
T ss_pred             HHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHH
Confidence                              23444444444333221   11111122111111111                         


Q ss_pred             -----CCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCCCh
Q 041804          311 -----RPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMF-AKGLSAKP  384 (403)
Q Consensus       311 -----~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~-~~~~~p~~  384 (403)
                           .||..+|+++|.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|++++|.++|+.|. ..|+.|+.
T Consensus       546 ~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~  625 (857)
T PLN03077        546 QFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNL  625 (857)
T ss_pred             HHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCch
Confidence                 234444555555555566666666666666666666666666666666666666666666666665 34666655


Q ss_pred             hhHH
Q 041804          385 REEL  388 (403)
Q Consensus       385 ~~~~  388 (403)
                      .++.
T Consensus       626 ~~y~  629 (857)
T PLN03077        626 KHYA  629 (857)
T ss_pred             HHHH
Confidence            4443

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.6e-53  Score=406.58  Aligned_cols=359  Identities=18%  Similarity=0.187  Sum_probs=222.9

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      .+.|++++|.++|+.|.     .||..+||.+|.+|++.|++++|+++|++|...+ ..||..+|+.++.+|++.|+.+.
T Consensus       233 ~k~g~~~~A~~lf~~m~-----~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g-~~Pd~~ty~~ll~a~~~~g~~~~  306 (857)
T PLN03077        233 VKCGDVVSARLVFDRMP-----RRDCISWNAMISGYFENGECLEGLELFFTMRELS-VDPDLMTITSVISACELLGDERL  306 (857)
T ss_pred             hcCCCHHHHHHHHhcCC-----CCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcC-CCCChhHHHHHHHHHHhcCChHH
Confidence            44455555555555554     2444555555555555555555555555555444 44555555555555555444444


Q ss_pred             HHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHH
Q 041804           86 AMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREF  164 (403)
Q Consensus        86 a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  164 (403)
                      |.+++..|.+.|.. |..+|+.++.+|++.|++++|.++|++|..          ||..+|+.++.+|++.|++++|.++
T Consensus       307 a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~----------~d~~s~n~li~~~~~~g~~~~A~~l  376 (857)
T PLN03077        307 GREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET----------KDAVSWTAMISGYEKNGLPDKALET  376 (857)
T ss_pred             HHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC----------CCeeeHHHHHHHHHhCCCHHHHHHH
Confidence            44444444444444 444444444444444444444444444321          2333444444444444444444444


Q ss_pred             HHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC-------------------------------------
Q 041804          165 WEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG-------------------------------------  207 (403)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-------------------------------------  207 (403)
                      |++|.+.|+.||..||+.++.+|++.|+++.|.++++.+.+.|                                     
T Consensus       377 f~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~v  456 (857)
T PLN03077        377 YALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVI  456 (857)
T ss_pred             HHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCee
Confidence            4444444444444444444433333333333333333333333                                     


Q ss_pred             ----------------------------CCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 041804          208 ----------------------------IKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCE  259 (403)
Q Consensus       208 ----------------------------~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  259 (403)
                                                  +.||..||+.++.+|++.|+++.+.+++..+.+.|+.++..++++|+.+|++
T Consensus       457 s~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k  536 (857)
T PLN03077        457 SWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVR  536 (857)
T ss_pred             eHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHH
Confidence                                        3444444444444444444444444444444445555555555666677777


Q ss_pred             cCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHH
Q 041804          260 NGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVV  336 (403)
Q Consensus       260 ~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  336 (403)
                      +|++++|.++|+.+     .||..+|+++|.+|   |+.++|.++|++|.+.|+.||..||+.++.+|++.|++++|.++
T Consensus       537 ~G~~~~A~~~f~~~-----~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~  611 (857)
T PLN03077        537 CGRMNYAWNQFNSH-----EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEY  611 (857)
T ss_pred             cCCHHHHHHHHHhc-----CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHH
Confidence            77777777777776     57899999999988   77899999999999999999999999999999999999999999


Q ss_pred             HHHHH-hcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhhHH
Q 041804          337 WKKME-ELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREEL  388 (403)
Q Consensus       337 ~~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  388 (403)
                      |+.|. +.|+.|+..+|++++++|.+.|++++|.+++++|   .++||..++-
T Consensus       612 f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m---~~~pd~~~~~  661 (857)
T PLN03077        612 FHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM---PITPDPAVWG  661 (857)
T ss_pred             HHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHC---CCCCCHHHHH
Confidence            99998 6799999999999999999999999999999998   3788877543

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

Probab=99.96  E-value=1.1e-25  Score=220.52  Aligned_cols=374  Identities=11%  Similarity=0.020  Sum_probs=290.5

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      .++...|++++|++.|+.+...  .+.+..++..+...+.+.|++++|..+++++...+  +.+...+..+...+...|+
T Consensus       507 ~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~  582 (899)
T TIGR02917       507 RIDIQEGNPDDAIQRFEKVLTI--DPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN--PQEIEPALALAQYYLGKGQ  582 (899)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--ccchhHHHHHHHHHHHCCC
Confidence            4556778999999999888742  34567788888889989999999999999887765  4566778888888999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCR  162 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  162 (403)
                      +++|..+++.+.+..+.+...|..+..++...|++++|...++++...       .+.+...+..+...+.+.|++++|.
T Consensus       583 ~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~A~  655 (899)
T TIGR02917       583 LKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLAL-------QPDSALALLLLADAYAVMKNYAKAI  655 (899)
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-------CCCChHHHHHHHHHHHHcCCHHHHH
Confidence            999999999988877678888899999999999999999988887763       3456677888888888899999999


Q ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          163 EFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      .+|+++.+..+. +..++..+...+...|++++|.++++.+.+.. +.+...+..+...+...|++++|...|+.+.+.+
T Consensus       656 ~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  733 (899)
T TIGR02917       656 TSLKRALELKPD-NTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA  733 (899)
T ss_pred             HHHHHHHhcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC
Confidence            999888876554 67788888888888999999999998888774 4566777788888888899999999998888764


Q ss_pred             CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHh---hCCHHHHHHHHHHHHHcCCCCchhhHHH
Q 041804          243 CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRC---LEKPREILGLFDRMIESGIRPKMDTYVM  319 (403)
Q Consensus       243 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (403)
                        |+..++..+..++.+.|++++|.+.+..+.+.. +.+...+..+...   .++.++|.++|+++.+... .+..+++.
T Consensus       734 --~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p-~~~~~~~~  809 (899)
T TIGR02917       734 --PSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAP-DNAVVLNN  809 (899)
T ss_pred             --CCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCC-CCHHHHHH
Confidence              444667778888888888888888888887652 2234444443333   3778888888888887654 36777888


Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCChhhHHHHHHHhC
Q 041804          320 LLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGL-SAKPREELGTKLVQG  395 (403)
Q Consensus       320 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~-~p~~~~~~~~~~~~~  395 (403)
                      +...+...|+ .+|+..++++.+.. +.++.++..+..++.+.|++++|.++++++++.+. .|.....++..++..
T Consensus       810 l~~~~~~~~~-~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~  884 (899)
T TIGR02917       810 LAWLYLELKD-PRALEYAEKALKLA-PNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPEAAAIRYHLALALLAT  884 (899)
T ss_pred             HHHHHHhcCc-HHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHc
Confidence            8888888888 77888888887753 44566777888888888888888888888888643 333333444444443

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=99.96  E-value=6.5e-25  Score=215.10  Aligned_cols=356  Identities=11%  Similarity=0.030  Sum_probs=206.6

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVN   84 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   84 (403)
                      +...|++++|+++++.+..  ..++++.++..+..++...|++++|...|+++.+..  +.+...+..+...+...|+++
T Consensus       441 ~~~~~~~~~A~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~g~~~  516 (899)
T TIGR02917       441 YLRSGQFDKALAAAKKLEK--KQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE--PDFFPAAANLARIDIQEGNPD  516 (899)
T ss_pred             HHhcCCHHHHHHHHHHHHH--hCCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC--CCcHHHHHHHHHHHHHCCCHH
Confidence            4456777777777777663  234556677777777777777777777777776654  234555666666777777777


Q ss_pred             HHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHH
Q 041804           85 EAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREF  164 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  164 (403)
                      +|.+.|+++...++.+..++..+...+.+.|+.++|...+.++..       ..+.+...+..+...|.+.|++++|.++
T Consensus       517 ~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~A~~~  589 (899)
T TIGR02917       517 DAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAE-------LNPQEIEPALALAQYYLGKGQLKKALAI  589 (899)
T ss_pred             HHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCccchhHHHHHHHHHHHCCCHHHHHHH
Confidence            777777777666655666666667777677777777776666554       2234445555666666666666666666


Q ss_pred             HHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC
Q 041804          165 WEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ  244 (403)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  244 (403)
                      ++.+.+.... +..+|..+..++...|++++|...|+.+.+.. +.+...+..+..++...|++++|..+++.+.+.. +
T Consensus       590 ~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~  666 (899)
T TIGR02917       590 LNEAADAAPD-SPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-P  666 (899)
T ss_pred             HHHHHHcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-C
Confidence            6666554333 45566666666666666666666666665542 2344455555666666666666666666665542 2


Q ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHh---hCCHHHHHHHHHHHHHcCCCCchhhHHHHH
Q 041804          245 PSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRC---LEKPREILGLFDRMIESGIRPKMDTYVMLL  321 (403)
Q Consensus       245 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  321 (403)
                      .+..++..+...+...|++++|..+++.+.+.+. ++...+..+...   .++.++|.+.++.+....  |+..++..+.
T Consensus       667 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l~  743 (899)
T TIGR02917       667 DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHP-KAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKLH  743 (899)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc-CChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHHH
Confidence            2345555555556666666666666655554421 122222222221   245555555555555433  2224444455


Q ss_pred             HHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          322 RKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       322 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .++.+.|++++|.+.++++.+.. +.+...+..+...|.+.|++++|..+|+++.+.
T Consensus       744 ~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  799 (899)
T TIGR02917       744 RALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKK  799 (899)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence            55555555555555555555432 334555555555555555555555555555543

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.

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.94  E-value=2.4e-23  Score=183.73  Aligned_cols=303  Identities=14%  Similarity=0.015  Sum_probs=182.2

Q ss_pred             HHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC----cHHHHHHHHHHHHhc
Q 041804           39 DILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK----DEVSYCNLVDALCEY  114 (403)
Q Consensus        39 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~l~~~~~~~  114 (403)
                      ..+...|++++|...|+++.+.+  +.+..++..+...+...|++++|..+++.+...+..    ...++..+...|...
T Consensus        43 ~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~  120 (389)
T PRK11788         43 LNFLLNEQPDKAIDLFIEMLKVD--PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKA  120 (389)
T ss_pred             HHHHhcCChHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHC
Confidence            34455566666666666666654  233445666666666666666666666666554322    123455556666666


Q ss_pred             CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH----HHHHHHHHHHHHc
Q 041804          115 KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL----HSYSIYMDIMCKS  190 (403)
Q Consensus       115 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~  190 (403)
                      |++++|...|.++..       ..+.+..+++.++..+.+.|++++|.+.++.+.+.+..++.    ..+..+...+...
T Consensus       121 g~~~~A~~~~~~~l~-------~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~  193 (389)
T PRK11788        121 GLLDRAEELFLQLVD-------EGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALAR  193 (389)
T ss_pred             CCHHHHHHHHHHHHc-------CCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhC
Confidence            666666666665554       22344555566666666666666666666666554433211    1233444455555


Q ss_pred             CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHH
Q 041804          191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVL  270 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  270 (403)
                      |++++|.+.|+++.+.. +.+...+..+...+.+.|++++|.++++++.+.+......+++.++.+|...|++++|...+
T Consensus       194 ~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l  272 (389)
T PRK11788        194 GDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFL  272 (389)
T ss_pred             CCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            66666666666655542 22333445555555556666666666665555422222334455555555555555555555


Q ss_pred             HhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHH
Q 041804          271 AEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEF  350 (403)
Q Consensus       271 ~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  350 (403)
                      +++.                                +.  .|+...+..++..+.+.|++++|..+++++.+.  .|+..
T Consensus       273 ~~~~--------------------------------~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~  316 (389)
T PRK11788        273 RRAL--------------------------------EE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLR  316 (389)
T ss_pred             HHHH--------------------------------Hh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHH
Confidence            5544                                32  245556677888889999999999999988775  58888


Q ss_pred             HHHHHHHHHHh---cCCHHHHHHHHHHHHHcCCCCChhhH
Q 041804          351 AYNALVDALID---KGMLDMARKYDEEMFAKGLSAKPREE  387 (403)
Q Consensus       351 ~~~~l~~~~~~---~g~~~~a~~~~~~m~~~~~~p~~~~~  387 (403)
                      .++.++..+..   .|+.+++..++++|..+++.|+|...
T Consensus       317 ~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~~~  356 (389)
T PRK11788        317 GFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPRYR  356 (389)
T ss_pred             HHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCCEE
Confidence            88888877664   55888999999999998888888743

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.93  E-value=8.6e-23  Score=180.25  Aligned_cols=300  Identities=13%  Similarity=0.090  Sum_probs=244.6

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC--CHHHHHHHHHHHHhcC
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP--NHATFRIMFKRYVTAH   81 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~   81 (403)
                      .....|++++|++.|+.+...  .+.+..++..+...+...|++++|..+++.+...+...+  ....+..+...|.+.|
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g  121 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKV--DPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAG  121 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhc--CcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCC
Confidence            345668999999999999852  345677899999999999999999999999988542111  1356888999999999


Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc---chHHHHHHHHHHHhcCCh
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN---KTKIYNMILRGWFKMSWW  158 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~  158 (403)
                      ++++|+.+|+++.+..+.+..++..++..+...|++++|...+..+....     ...+   ....+..+...+.+.|++
T Consensus       122 ~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-----~~~~~~~~~~~~~~la~~~~~~~~~  196 (389)
T PRK11788        122 LLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLG-----GDSLRVEIAHFYCELAQQALARGDL  196 (389)
T ss_pred             CHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhc-----CCcchHHHHHHHHHHHHHHHhCCCH
Confidence            99999999999998876688899999999999999999999999887642     1111   123456788889999999


Q ss_pred             hHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHH
Q 041804          159 GKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREM  238 (403)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  238 (403)
                      ++|.+.|+++.+.... +...+..+...+.+.|++++|.++|+++.+.+......++..+..+|...|++++|...++.+
T Consensus       197 ~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  275 (389)
T PRK11788        197 DAARALLKKALAADPQ-CVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRA  275 (389)
T ss_pred             HHHHHHHHHHHhHCcC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999999999887544 567888899999999999999999999998643333467888999999999999999999999


Q ss_pred             HHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh------CCHHHHHHHHHHHHHcCCCC
Q 041804          239 REMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL------EKPREILGLFDRMIESGIRP  312 (403)
Q Consensus       239 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~------~~~~~a~~~~~~~~~~~~~~  312 (403)
                      .+.  .|+...+..++..+.+.|++++|..+++++.+.  .|+..++..++...      ++..++..+++.+.+.++.|
T Consensus       276 ~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~  351 (389)
T PRK11788        276 LEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKR  351 (389)
T ss_pred             HHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhC
Confidence            886  456666788999999999999999999998875  57777777666542      25667888888888766666


Q ss_pred             chh
Q 041804          313 KMD  315 (403)
Q Consensus       313 ~~~  315 (403)
                      ++.
T Consensus       352 ~p~  354 (389)
T PRK11788        352 KPR  354 (389)
T ss_pred             CCC
Confidence            655

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.91  E-value=5.6e-20  Score=170.21  Aligned_cols=323  Identities=10%  Similarity=-0.030  Sum_probs=132.9

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV  117 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (403)
                      +..+.+.|++++|..+++......  +-+...+..++.+....|+++.|+..|+++.+..+.+...+..+...+...|++
T Consensus        49 ~~~~~~~g~~~~A~~l~~~~l~~~--p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~  126 (656)
T PRK15174         49 AIACLRKDETDVGLTLLSDRVLTA--KNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLKSKQY  126 (656)
T ss_pred             HHHHHhcCCcchhHHHhHHHHHhC--CCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCH
Confidence            344444444444444444444432  122233333334444444444444444444444444444444444444444444


Q ss_pred             HHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHH
Q 041804          118 IEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAV  197 (403)
Q Consensus       118 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  197 (403)
                      ++|...+++...       ..+.+...+..+...+...|++++|...++.+....+.+ ...+..+ ..+...|++++|.
T Consensus       127 ~~Ai~~l~~Al~-------l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~-~~a~~~~-~~l~~~g~~~eA~  197 (656)
T PRK15174        127 ATVADLAEQAWL-------AFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPR-GDMIATC-LSFLNKSRLPEDH  197 (656)
T ss_pred             HHHHHHHHHHHH-------hCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCC-HHHHHHH-HHHHHcCCHHHHH
Confidence            444444444443       123333444444444444444444444444443332221 1122111 1234444444444


Q ss_pred             HHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHH----HHHHHHhc
Q 041804          198 KLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVRE----AYAVLAEM  273 (403)
Q Consensus       198 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~----a~~~~~~~  273 (403)
                      ..++.+......++......+..++...|++++|...++.+.+... .+...+..+...+...|++++    |...|++.
T Consensus       198 ~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p-~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~A  276 (656)
T PRK15174        198 DLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGL-DGAALRRSLGLAYYQSGRSREAKLQAAEHWRHA  276 (656)
T ss_pred             HHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHH
Confidence            4444444332112222223333344444444444444444444321 133344444444444444443    44444444


Q ss_pred             hhcCCCCC-hhhHHH---HHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCH
Q 041804          274 PKKGCVPD-VITYHC---FFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDE  349 (403)
Q Consensus       274 ~~~~~~p~-~~~~~~---l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  349 (403)
                      .+.  .|+ ...+..   ++...++.++|...+++..+.... +...+..+..++.+.|++++|...++++.+.  .|+.
T Consensus       277 l~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~-~~~a~~~La~~l~~~G~~~eA~~~l~~al~~--~P~~  351 (656)
T PRK15174        277 LQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPD-LPYVRAMYARALRQVGQYTAASDEFVQLARE--KGVT  351 (656)
T ss_pred             Hhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--Cccc
Confidence            432  222 111111   112224444444444444443221 2233334444444445555555444444433  1221


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          350 -FAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       350 -~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                       ..+..+..++...|+.++|...|++..+
T Consensus       352 ~~~~~~~a~al~~~G~~deA~~~l~~al~  380 (656)
T PRK15174        352 SKWNRYAAAALLQAGKTSEAESVFEHYIQ  380 (656)
T ss_pred             hHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             1222223344444555555544444443

>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=99.91  E-value=1.3e-19  Score=168.25  Aligned_cols=361  Identities=12%  Similarity=-0.016  Sum_probs=274.8

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+....   ..|++..|..+..+|.+.|++++|+..++...+..  +.+..+|..+..+|...|+
T Consensus       135 ~~~~~~~~~~~Ai~~y~~al~---~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~--p~~~~a~~~~a~a~~~lg~  209 (615)
T TIGR00990       135 NKAYRNKDFNKAIKLYSKAIE---CKPDPVYYSNRAACHNALGDWEKVVEDTTAALELD--PDYSKALNRRANAYDGLGK  209 (615)
T ss_pred             HHHHHcCCHHHHHHHHHHHHh---cCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHcCC
Confidence            456678999999999999875   46788889999999999999999999999999875  3457789999999999999


Q ss_pred             hHHHHHHHHHHhhcCCC-cH-----------------------------HHHHHHHH-----------------------
Q 041804           83 VNEAMGTFNKLDEFGLK-DE-----------------------------VSYCNLVD-----------------------  109 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~-~~-----------------------------~~~~~l~~-----------------------  109 (403)
                      +++|+.-|......+.. +.                             ..+..+..                       
T Consensus       210 ~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  289 (615)
T TIGR00990       210 YADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEE  289 (615)
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccccccc
Confidence            99998776554332211 10                             00000000                       


Q ss_pred             -------HH------HhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCc
Q 041804          110 -------AL------CEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKD  176 (403)
Q Consensus       110 -------~~------~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  176 (403)
                             ..      ...+.+++|...|++......    ..+.....++.+...+...|++++|...|++..+..+. +
T Consensus       290 ~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~----~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~-~  364 (615)
T TIGR00990       290 TGNGQLQLGLKSPESKADESYEEAARAFEKALDLGK----LGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPR-V  364 (615)
T ss_pred             cccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCC----CChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-c
Confidence                   00      112467788888887765310    12345667888889999999999999999999887554 5


Q ss_pred             HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 041804          177 LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKL  256 (403)
Q Consensus       177 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  256 (403)
                      ...|..+..++...|++++|...|+...+.. +.+..++..+...+...|++++|...|+...+... .+...+..+...
T Consensus       365 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P-~~~~~~~~la~~  442 (615)
T TIGR00990       365 TQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDP-DFIFSHIQLGVT  442 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCc-cCHHHHHHHHHH
Confidence            6788899999999999999999999998874 44577888899999999999999999999998743 356778888899


Q ss_pred             HHhcCcHHHHHHHHHhchhcCCCCC-hhhHHH---HHHhhCCHHHHHHHHHHHHHcCCCCchh------hHHHHHHHHHh
Q 041804          257 LCENGRVREAYAVLAEMPKKGCVPD-VITYHC---FFRCLEKPREILGLFDRMIESGIRPKMD------TYVMLLRKFGR  326 (403)
Q Consensus       257 ~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~---l~~~~~~~~~a~~~~~~~~~~~~~~~~~------~~~~li~~~~~  326 (403)
                      +.+.|++++|+..|++..+.  .|+ ...++.   ++...++.++|.+.|++........+..      .++.....+..
T Consensus       443 ~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~  520 (615)
T TIGR00990       443 QYKEGSIASSMATFRRCKKN--FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQW  520 (615)
T ss_pred             HHHCCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHH
Confidence            99999999999999998764  343 333333   3344588999999999988753321111      12222223344


Q ss_pred             cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          327 WGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       327 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .|++++|.+++++..+.. +.+...+..+...+.+.|++++|.++|++..+.
T Consensus       521 ~~~~~eA~~~~~kAl~l~-p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       521 KQDFIEAENLCEKALIID-PECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             hhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            699999999999988764 345567889999999999999999999998774

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.90  E-value=2.4e-19  Score=166.08  Aligned_cols=320  Identities=9%  Similarity=-0.005  Sum_probs=260.7

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      .++|++++|+.+++.....  .+.+...+..++.++...|++++|...++++....  +.+...+..+...+...|++++
T Consensus        53 ~~~g~~~~A~~l~~~~l~~--~p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~--P~~~~a~~~la~~l~~~g~~~~  128 (656)
T PRK15174         53 LRKDETDVGLTLLSDRVLT--AKNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVN--VCQPEDVLLVASVLLKSKQYAT  128 (656)
T ss_pred             HhcCCcchhHHHhHHHHHh--CCCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHH
Confidence            4579999999999998853  34456677778888889999999999999999976  3556788899999999999999


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      |+..|++..+..+.+...+..+..++...|++++|...+..+...       .+.+...+..+ ..+...|++++|...+
T Consensus       129 Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~-------~P~~~~a~~~~-~~l~~~g~~~eA~~~~  200 (656)
T PRK15174        129 VADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQE-------VPPRGDMIATC-LSFLNKSRLPEDHDLA  200 (656)
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHh-------CCCCHHHHHHH-HHHHHcCCHHHHHHHH
Confidence            999999999998889999999999999999999999999877653       23333444443 3478899999999999


Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHH----HHHHHHHHHHc
Q 041804          166 EEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDF----AMRVYREMREM  241 (403)
Q Consensus       166 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~----a~~~~~~~~~~  241 (403)
                      +.+.+....++...+..+..++...|++++|...++++.... +.+...+..+...+...|++++    |...|+.+.+.
T Consensus       201 ~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l  279 (656)
T PRK15174        201 RALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF  279 (656)
T ss_pred             HHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh
Confidence            999887654455566667788999999999999999999874 4466788889999999999985    89999999987


Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhh-HHH---HHHhhCCHHHHHHHHHHHHHcCCCCch-hh
Q 041804          242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVIT-YHC---FFRCLEKPREILGLFDRMIESGIRPKM-DT  316 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~-~~~---l~~~~~~~~~a~~~~~~~~~~~~~~~~-~~  316 (403)
                      .+ .+...+..+...+.+.|++++|...+++..+.  .|+... +..   +....++.++|...++.+....  |+. ..
T Consensus       280 ~P-~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l--~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~--P~~~~~  354 (656)
T PRK15174        280 NS-DNVRIVTLYADALIRTGQNEKAIPLLQQSLAT--HPDLPYVRAMYARALRQVGQYTAASDEFVQLAREK--GVTSKW  354 (656)
T ss_pred             CC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--ccchHH
Confidence            43 36778999999999999999999999998875  455332 222   2334589999999999998764  343 33


Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          317 YVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       317 ~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      +..+..++...|++++|...|++..+.
T Consensus       355 ~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        355 NRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            444567889999999999999999875

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.90  E-value=2.3e-19  Score=177.22  Aligned_cols=357  Identities=10%  Similarity=-0.004  Sum_probs=232.8

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHH------------
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFR------------   71 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~------------   71 (403)
                      .+...|++++|+..|+...+.  .+.+..++..+..++.+.|++++|+..|++..+..+..+....|.            
T Consensus       278 ~~~~~g~~~~A~~~l~~aL~~--~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~  355 (1157)
T PRK11447        278 AAVDSGQGGKAIPELQQAVRA--NPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLI  355 (1157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHH
Confidence            345679999999999998852  244788999999999999999999999999988652222222222            


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHH
Q 041804           72 IMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG  151 (403)
Q Consensus        72 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (403)
                      .....+.+.|++++|+..|+++.+..+.+...+..+..++...|++++|++.|++.....       +.+..++..+...
T Consensus       356 ~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-------p~~~~a~~~L~~l  428 (1157)
T PRK11447        356 QQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-------PGNTNAVRGLANL  428 (1157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-------CCCHHHHHHHHHH
Confidence            224567789999999999999999988788899999999999999999999999887632       3333334333333


Q ss_pred             ------------------------------------------HHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          152 ------------------------------------------WFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       152 ------------------------------------------~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                                                                +...|++++|.+.|++..+..+. +...+..+...|.+
T Consensus       429 ~~~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P~-~~~~~~~LA~~~~~  507 (1157)
T PRK11447        429 YRQQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDPG-SVWLTYRLAQDLRQ  507 (1157)
T ss_pred             HHhcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence                                                      34456666666666666555443 44555555566666


Q ss_pred             cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHH---------HHHHHHHHHHhc
Q 041804          190 SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVV---------TCNTVIKLLCEN  260 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---------~~~~li~~~~~~  260 (403)
                      .|++++|...++++.+.. +.+...+..+...+...++.++|...++.+......++..         .+..+...+...
T Consensus       508 ~G~~~~A~~~l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~  586 (1157)
T PRK11447        508 AGQRSQADALMRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDS  586 (1157)
T ss_pred             cCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHC
Confidence            666666666666655432 1122233333333444555555555555443221111111         112234455566


Q ss_pred             CcHHHHHHHHHhchhcCCCCChhhHH---HHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHH
Q 041804          261 GRVREAYAVLAEMPKKGCVPDVITYH---CFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVW  337 (403)
Q Consensus       261 g~~~~a~~~~~~~~~~~~~p~~~~~~---~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  337 (403)
                      |+.++|..+++.-     .++...+.   .+....++.++|++.|+...+.... +...+..+...+...|++++|.+.+
T Consensus       587 G~~~eA~~~l~~~-----p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~-~~~a~~~la~~~~~~g~~~eA~~~l  660 (1157)
T PRK11447        587 GKEAEAEALLRQQ-----PPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPG-NADARLGLIEVDIAQGDLAAARAQL  660 (1157)
T ss_pred             CCHHHHHHHHHhC-----CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            6666666666521     11222222   2223337788888888888876433 5677888888888888888888888


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          338 KKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       338 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      +.+.+.. +.+...+..+..++...|++++|.++++++...
T Consensus       661 ~~ll~~~-p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        661 AKLPATA-NDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             HHHhccC-CCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            8777642 335566677777888888888888888888765

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.89  E-value=5.4e-19  Score=174.62  Aligned_cols=364  Identities=10%  Similarity=0.013  Sum_probs=270.9

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhH------------HHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHH
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTY------------NSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHAT   69 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~------------~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~   69 (403)
                      +.++.+.|++++|++.|+...+.....+....+            ......+.+.|++++|+..|+++.+..  +.+...
T Consensus       310 g~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~--P~~~~a  387 (1157)
T PRK11447        310 GQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVD--NTDSYA  387 (1157)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHH
Confidence            456678899999999999887532222222212            122456778999999999999999875  345677


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH----------------------------------------
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD----------------------------------------  109 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~----------------------------------------  109 (403)
                      +..+..++...|++++|++.|++..+..+.+...+..+..                                        
T Consensus       388 ~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~  467 (1157)
T PRK11447        388 VLGLGDVAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYRQQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQ  467 (1157)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHH
Confidence            8888999999999999999999999887665555443333                                        


Q ss_pred             --HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHH
Q 041804          110 --ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIM  187 (403)
Q Consensus       110 --~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  187 (403)
                        .+...|++++|...+++...       ..+.+..++..+...|.+.|++++|...++++.+..+. +...+..+...+
T Consensus       468 a~~~~~~g~~~eA~~~~~~Al~-------~~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~P~-~~~~~~a~al~l  539 (1157)
T PRK11447        468 AEALENQGKWAQAAELQRQRLA-------LDPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQKPN-DPEQVYAYGLYL  539 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHH
Confidence              34456888888888888776       33556778889999999999999999999999886554 555565666667


Q ss_pred             HHcCChhHHHHHHHHHHHcCCCCChh---------hHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 041804          188 CKSGKPWKAVKLYKEMKKKGIKMDVV---------AYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLC  258 (403)
Q Consensus       188 ~~~~~~~~a~~~~~~~~~~~~~~~~~---------~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  258 (403)
                      ...+++++|+..++.+......++..         .+..+...+...|+.++|..+++.     .+.+...+..+...+.
T Consensus       540 ~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~-----~p~~~~~~~~La~~~~  614 (1157)
T PRK11447        540 SGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQ-----QPPSTRIDLTLADWAQ  614 (1157)
T ss_pred             HhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHh-----CCCCchHHHHHHHHHH
Confidence            78999999999998765432222221         123456678889999999999872     2446667788899999


Q ss_pred             hcCcHHHHHHHHHhchhcCCCCC-hhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHH
Q 041804          259 ENGRVREAYAVLAEMPKKGCVPD-VITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVF  334 (403)
Q Consensus       259 ~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  334 (403)
                      +.|++++|+..|++..+.  .|+ ...+..+...+   ++.++|.+.++.+.+... .+..++..+..++...|++++|.
T Consensus       615 ~~g~~~~A~~~y~~al~~--~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p-~~~~~~~~la~~~~~~g~~~eA~  691 (1157)
T PRK11447        615 QRGDYAAARAAYQRVLTR--EPGNADARLGLIEVDIAQGDLAAARAQLAKLPATAN-DSLNTQRRVALAWAALGDTAAAQ  691 (1157)
T ss_pred             HcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCC-CChHHHHHHHHHHHhCCCHHHHH
Confidence            999999999999999876  343 44444444433   889999999998876432 24556777888899999999999


Q ss_pred             HHHHHHHhcCC--CC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCCCC
Q 041804          335 VVWKKMEELGC--SP---DEFAYNALVDALIDKGMLDMARKYDEEMFA-KGLSAK  383 (403)
Q Consensus       335 ~~~~~~~~~~~--~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~~~~p~  383 (403)
                      ++++++....-  +|   +...+..+...+...|++++|...|++.+. .|+.|+
T Consensus       692 ~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~~~~~~~~  746 (1157)
T PRK11447        692 RTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMVASGITPT  746 (1157)
T ss_pred             HHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcCCCCC
Confidence            99999986531  22   234666678889999999999999999865 355443

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

Probab=99.88  E-value=6.3e-20  Score=156.65  Aligned_cols=360  Identities=13%  Similarity=0.084  Sum_probs=291.3

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcC-CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHH-HHHHHHHHHhc
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTH-TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHAT-FRIMFKRYVTA   80 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~   80 (403)
                      .++..+|++++|+..++.+..   .+| ....|..+..++...|+.+.|...|.+..+.+   |+... ...+...+...
T Consensus       124 N~~kerg~~~~al~~y~~aie---l~p~fida~inla~al~~~~~~~~a~~~~~~alqln---P~l~ca~s~lgnLlka~  197 (966)
T KOG4626|consen  124 NILKERGQLQDALALYRAAIE---LKPKFIDAYINLAAALVTQGDLELAVQCFFEALQLN---PDLYCARSDLGNLLKAE  197 (966)
T ss_pred             HHHHHhchHHHHHHHHHHHHh---cCchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcC---cchhhhhcchhHHHHhh
Confidence            345667888889998888874   344 46788888888889999999998888888855   66543 44455566667


Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhH
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGK  160 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  160 (403)
                      |+..+|...|.+..+..+.-..+|+.|...+-.+|+...|+..|++...-       .+.-..+|-.|...|...+.++.
T Consensus       198 Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl-------dP~f~dAYiNLGnV~ke~~~~d~  270 (966)
T KOG4626|consen  198 GRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL-------DPNFLDAYINLGNVYKEARIFDR  270 (966)
T ss_pred             cccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcC-------CCcchHHHhhHHHHHHHHhcchH
Confidence            88889999888888877767778889999999999999999999888763       34455678899999999999999


Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC-hhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          161 CREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD-VVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      |...+.+.....+. ....+..|...|..+|..+.|++.|++.++.  .|+ ...|+.|..++-..|++.+|.+.+.+..
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 AVSCYLRALNLRPN-HAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAVDCYNKAL  347 (966)
T ss_pred             HHHHHHHHHhcCCc-chhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHHHHHHHHH
Confidence            99999988876555 6678888888999999999999999999886  444 5689999999999999999999999998


Q ss_pred             HcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChh----hHHHHHHhhCCHHHHHHHHHHHHHcCCCCch-
Q 041804          240 EMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVI----TYHCFFRCLEKPREILGLFDRMIESGIRPKM-  314 (403)
Q Consensus       240 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~----~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~-  314 (403)
                      ..... .....+.|...|...|.++.|..+|....+-  .|...    ...+++..-++.++|+..|++.++  +.|+. 
T Consensus       348 ~l~p~-hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fA  422 (966)
T KOG4626|consen  348 RLCPN-HADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFA  422 (966)
T ss_pred             HhCCc-cHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHH
Confidence            87432 4667888999999999999999999987764  44422    233455566899999999999887  45654 


Q ss_pred             hhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhh
Q 041804          315 DTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPRE  386 (403)
Q Consensus       315 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~  386 (403)
                      ..|+.+...|-..|+.+.|.+.+.+....+ +.-...++.|...|-..|+..+|+.-+++.++  ++||...
T Consensus       423 da~~NmGnt~ke~g~v~~A~q~y~rAI~~n-Pt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDfpd  491 (966)
T KOG4626|consen  423 DALSNMGNTYKEMGDVSAAIQCYTRAIQIN-PTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDFPD  491 (966)
T ss_pred             HHHHhcchHHHHhhhHHHHHHHHHHHHhcC-cHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCCch
Confidence            688999999999999999999999998753 22467889999999999999999999999887  5566543

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.88  E-value=6.2e-18  Score=160.02  Aligned_cols=370  Identities=11%  Similarity=-0.015  Sum_probs=247.5

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      |....|+.++|++++.....  ..+.+...+..+...+...|++++|..+|++..+..  +.+...+..+..++...|++
T Consensus        24 ia~~~g~~~~A~~~~~~~~~--~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~l~~~g~~   99 (765)
T PRK10049         24 IALWAGQDAEVITVYNRYRV--HMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE--PQNDDYQRGLILTLADAGQY   99 (765)
T ss_pred             HHHHcCCHHHHHHHHHHHHh--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCH
Confidence            44556777777777776653  123345557777777777777777777777776654  34455666677777777777


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhH---
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGK---  160 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---  160 (403)
                      ++|+..++++.+..+.+.. +..+..++...|+.++|...++++..       ..+.+...+..+...+...+..+.   
T Consensus       100 ~eA~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~-------~~P~~~~~~~~la~~l~~~~~~e~Al~  171 (765)
T PRK10049        100 DEALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALP-------RAPQTQQYPTEYVQALRNNRLSAPALG  171 (765)
T ss_pred             HHHHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHCCChHHHHH
Confidence            7777777777777666666 77777777777777777777777666       234444444445555544444443   


Q ss_pred             -------------------------------------------HHHHHHHHHhC-CCCCcHH-HH----HHHHHHHHHcC
Q 041804          161 -------------------------------------------CREFWEEMDKR-GVVKDLH-SY----SIYMDIMCKSG  191 (403)
Q Consensus       161 -------------------------------------------a~~~~~~~~~~-~~~~~~~-~~----~~l~~~~~~~~  191 (403)
                                                                 |++.++.+.+. ...|+.. .+    ...+..+...|
T Consensus       172 ~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g  251 (765)
T PRK10049        172 AIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARD  251 (765)
T ss_pred             HHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhh
Confidence                                                       44444444432 1122211 11    11133456778


Q ss_pred             ChhHHHHHHHHHHHcCCC-CChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHhcCcHHHHH
Q 041804          192 KPWKAVKLYKEMKKKGIK-MDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQP---SVVTCNTVIKLLCENGRVREAY  267 (403)
Q Consensus       192 ~~~~a~~~~~~~~~~~~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~a~  267 (403)
                      ++++|+..|+.+.+.+.+ |+. ....+..+|...|++++|..+|+.+.+.....   .......+..++...|++++|.
T Consensus       252 ~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~  330 (765)
T PRK10049        252 RYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGAL  330 (765)
T ss_pred             hHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHH
Confidence            999999999999887532 332 22335678889999999999999987653221   1345566777888999999999


Q ss_pred             HHHHhchhcCC-----------CCChh------hHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCc
Q 041804          268 AVLAEMPKKGC-----------VPDVI------TYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFL  330 (403)
Q Consensus       268 ~~~~~~~~~~~-----------~p~~~------~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  330 (403)
                      .+++.+.+...           .|+..      ....++...++.++|++.++++...... +...+..+...+...|++
T Consensus       331 ~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~-n~~l~~~lA~l~~~~g~~  409 (765)
T PRK10049        331 TVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPG-NQGLRIDYASVLQARGWP  409 (765)
T ss_pred             HHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCCH
Confidence            99998876521           12211      1122333448899999999999876433 567888888999999999


Q ss_pred             chHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhhHHHH
Q 041804          331 RPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGT  390 (403)
Q Consensus       331 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~~  390 (403)
                      ++|++.+++..... +.+...+......+.+.|++++|..+++++++.  .|+.......
T Consensus       410 ~~A~~~l~~al~l~-Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~--~Pd~~~~~~~  466 (765)
T PRK10049        410 RAAENELKKAEVLE-PRNINLEVEQAWTALDLQEWRQMDVLTDDVVAR--EPQDPGVQRL  466 (765)
T ss_pred             HHHHHHHHHHHhhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CCCCHHHHHH
Confidence            99999999988764 344677777778899999999999999999884  3555544433

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.85  E-value=1.4e-16  Score=148.37  Aligned_cols=172  Identities=6%  Similarity=-0.072  Sum_probs=126.4

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCH--HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhc
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTT--DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTA   80 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   80 (403)
                      .+..++|+++.|++.|+.+.+   ..|+.  .++ .++..+...|+.++|+.++++.....  +........+...+...
T Consensus        42 ii~~r~Gd~~~Al~~L~qaL~---~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~--n~~~~~llalA~ly~~~  115 (822)
T PRK14574         42 IIRARAGDTAPVLDYLQEESK---AGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSM--NISSRGLASAARAYRNE  115 (822)
T ss_pred             HHHHhCCCHHHHHHHHHHHHh---hCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCC--CCCHHHHHHHHHHHHHc
Confidence            456788999999999999885   23442  344 88888899999999999999998321  23444555557788899


Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhH
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGK  160 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  160 (403)
                      |++++|+++|+++.+..+.++..+..++..+...++.++|+..+.++...        .|+...+..++..+...++..+
T Consensus       116 gdyd~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--------dp~~~~~l~layL~~~~~~~~~  187 (822)
T PRK14574        116 KRWDQALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAER--------DPTVQNYMTLSYLNRATDRNYD  187 (822)
T ss_pred             CCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--------CcchHHHHHHHHHHHhcchHHH
Confidence            99999999999999999888888888899999999999999999988764        3444445444444444556656


Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          161 CREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                      |++.++++.+..+. +...+..+..++.+
T Consensus       188 AL~~~ekll~~~P~-n~e~~~~~~~~l~~  215 (822)
T PRK14574        188 ALQASSEAVRLAPT-SEEVLKNHLEILQR  215 (822)
T ss_pred             HHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence            88888888776543 33333443333333

>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=99.85  E-value=1.6e-16  Score=147.76  Aligned_cols=339  Identities=10%  Similarity=-0.049  Sum_probs=253.7

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      .+......+.+.|++++|+..|++.....   |+...|..+..+|.+.|++++|+..++...+.++.+..++..+..+|.
T Consensus       129 ~~k~~G~~~~~~~~~~~Ai~~y~~al~~~---p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~a~a~~  205 (615)
T TIGR00990       129 KLKEKGNKAYRNKDFNKAIKLYSKAIECK---PDPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKALNRRANAYD  205 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcC---CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            35567788899999999999999998854   888899999999999999999999999999998889999999999999


Q ss_pred             hcCCHHHHHHHHhccccccccccc--------------------------ccCcchHHHHHH------------------
Q 041804          113 EYKHVIEAQELCFGENKNVGFSGL--------------------------VEMNKTKIYNMI------------------  148 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~l------------------  148 (403)
                      ..|++++|..-+.......++...                          ...|........                  
T Consensus       206 ~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  285 (615)
T TIGR00990       206 GLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNE  285 (615)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccc
Confidence            999999998655433211100000                          000000000000                  


Q ss_pred             ---------HHHH------HhcCChhHHHHHHHHHHhCC-CCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC
Q 041804          149 ---------LRGW------FKMSWWGKCREFWEEMDKRG-VVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD  211 (403)
Q Consensus       149 ---------~~~~------~~~~~~~~a~~~~~~~~~~~-~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  211 (403)
                               +..+      ...+++++|.+.|+...+.+ ..| ....|..+...+...|++++|+..|++..+.. +-+
T Consensus       286 ~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~-P~~  364 (615)
T TIGR00990       286 LDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD-PRV  364 (615)
T ss_pred             cccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCc
Confidence                     0000      12357889999999998765 222 45678888889999999999999999998863 223


Q ss_pred             hhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCCh-hhHHHH--
Q 041804          212 VVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDV-ITYHCF--  288 (403)
Q Consensus       212 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~-~~~~~l--  288 (403)
                      ...|..+...+...|++++|...|+.+.+... .+...|..+...+...|++++|...|++..+.  .|+. ..+..+  
T Consensus       365 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P~~~~~~~~la~  441 (615)
T TIGR00990       365 TQSYIKRASMNLELGDPDKAEEDFDKALKLNS-EDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DPDFIFSHIQLGV  441 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CccCHHHHHHHHH
Confidence            55788888899999999999999999988743 36788899999999999999999999998875  4543 333322  


Q ss_pred             -HHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCH------HHHHHHHHHHHh
Q 041804          289 -FRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDE------FAYNALVDALID  361 (403)
Q Consensus       289 -~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~~~  361 (403)
                       ....++.++|+..++....... -+...++.+...+...|++++|++.|++.....-..+.      ..++.....+..
T Consensus       442 ~~~~~g~~~eA~~~~~~al~~~P-~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~  520 (615)
T TIGR00990       442 TQYKEGSIASSMATFRRCKKNFP-EAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQW  520 (615)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHH
Confidence             2234889999999999987543 25678889999999999999999999998875311111      112222333445


Q ss_pred             cCCHHHHHHHHHHHHHcC
Q 041804          362 KGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       362 ~g~~~~a~~~~~~m~~~~  379 (403)
                      .|++++|.+++++....+
T Consensus       521 ~~~~~eA~~~~~kAl~l~  538 (615)
T TIGR00990       521 KQDFIEAENLCEKALIID  538 (615)
T ss_pred             hhhHHHHHHHHHHHHhcC
Confidence            799999999999988753

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.83  E-value=1e-15  Score=145.01  Aligned_cols=342  Identities=9%  Similarity=-0.027  Sum_probs=257.0

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      +.++....-.+.+....|+.++|++++.+.....  +.+...+..+...+...|++++|..+|++..+..+.+...+..+
T Consensus        12 ~~~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~--~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~l   89 (765)
T PRK10049         12 ALSNNQIADWLQIALWAGQDAEVITVYNRYRVHM--QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGL   89 (765)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            4556666677888899999999999999998733  35666799999999999999999999999999988888888999


Q ss_pred             HHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHH
Q 041804          108 VDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIM  187 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  187 (403)
                      ..++...|+.++|...++++..       ..+.+.. +..+...+...|+.++|...++++.+..+. +...+..+..++
T Consensus        90 a~~l~~~g~~~eA~~~l~~~l~-------~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~-~~~~~~~la~~l  160 (765)
T PRK10049         90 ILTLADAGQYDEALVKAKQLVS-------GAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQ-TQQYPTEYVQAL  160 (765)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH-------hCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            9999999999999999999887       3455666 888999999999999999999999998766 666666677777


Q ss_pred             HHcCChhHHHHHHH----------------------------------------------HHHHc-CCCCChh-hHH---
Q 041804          188 CKSGKPWKAVKLYK----------------------------------------------EMKKK-GIKMDVV-AYN---  216 (403)
Q Consensus       188 ~~~~~~~~a~~~~~----------------------------------------------~~~~~-~~~~~~~-~~~---  216 (403)
                      ...+..++|++.++                                              .+.+. ...|+.. .+.   
T Consensus       161 ~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~  240 (765)
T PRK10049        161 RNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRAR  240 (765)
T ss_pred             HHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHH
Confidence            66666665554443                                              33322 1122211 111   


Q ss_pred             -HHHHHHhhcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC---ChhhHHHHHH-
Q 041804          217 -TVIRAVGVSEGVDFAMRVYREMREMGCQ-PSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP---DVITYHCFFR-  290 (403)
Q Consensus       217 -~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p---~~~~~~~l~~-  290 (403)
                       ..+.++...+++++|...|+.+.+.+.+ |+. ....+...|...|++++|...|+++.......   .......+.. 
T Consensus       241 ~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a  319 (765)
T PRK10049        241 IDRLGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYS  319 (765)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHH
Confidence             1133455778999999999999887532 332 22235778999999999999999987542111   0122333332 


Q ss_pred             --hhCCHHHHHHHHHHHHHcCC-----------CCc---hhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHH
Q 041804          291 --CLEKPREILGLFDRMIESGI-----------RPK---MDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNA  354 (403)
Q Consensus       291 --~~~~~~~a~~~~~~~~~~~~-----------~~~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  354 (403)
                        ..++.++|..+++.+.+...           .|+   ...+..+...+...|++++|+++++++.... +.+...+..
T Consensus       320 ~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~  398 (765)
T PRK10049        320 LLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA-PGNQGLRID  398 (765)
T ss_pred             HHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHH
Confidence              33889999999999887531           123   1245567778889999999999999998763 567888999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCh
Q 041804          355 LVDALIDKGMLDMARKYDEEMFAKGLSAKP  384 (403)
Q Consensus       355 l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~  384 (403)
                      +...+...|++++|++.+++....  .|+.
T Consensus       399 lA~l~~~~g~~~~A~~~l~~al~l--~Pd~  426 (765)
T PRK10049        399 YASVLQARGWPRAAENELKKAEVL--EPRN  426 (765)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHhh--CCCC
Confidence            999999999999999999998884  4664

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

Probab=99.82  E-value=3.1e-17  Score=140.45  Aligned_cols=328  Identities=15%  Similarity=0.097  Sum_probs=269.3

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      -.++|..+..++-..|++++|+.+++.+.+..  +.....|-.+..++...|+.+.|.+.|......++...-..+.+..
T Consensus       115 ~ae~ysn~aN~~kerg~~~~al~~y~~aiel~--p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgn  192 (966)
T KOG4626|consen  115 GAEAYSNLANILKERGQLQDALALYRAAIELK--PKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLGN  192 (966)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHHHHHHHHhcC--chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhH
Confidence            35678888888889999999999999999865  3456789999999999999999999999998887765555666677


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                      .+...|+.++|..-+.+....       .+--..+|+.|...+-..|++..|+..|++....++. -...|-.|...|..
T Consensus       193 Llka~Grl~ea~~cYlkAi~~-------qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~-f~dAYiNLGnV~ke  264 (966)
T KOG4626|consen  193 LLKAEGRLEEAKACYLKAIET-------QPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPN-FLDAYINLGNVYKE  264 (966)
T ss_pred             HHHhhcccchhHHHHHHHHhh-------CCceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCc-chHHHhhHHHHHHH
Confidence            777789999998888877763       2444567889999999999999999999999887654 45688899999999


Q ss_pred             cCChhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCcHHHHH
Q 041804          190 SGKPWKAVKLYKEMKKKGIKM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS-VVTCNTVIKLLCENGRVREAY  267 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~  267 (403)
                      .+.++.|...|.+....  .| ....+..+...|...|.+|.|+..+++..+.  .|+ +..|+.|..++-..|++.+|.
T Consensus       265 ~~~~d~Avs~Y~rAl~l--rpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~G~V~ea~  340 (966)
T KOG4626|consen  265 ARIFDRAVSCYLRALNL--RPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDKGSVTEAV  340 (966)
T ss_pred             HhcchHHHHHHHHHHhc--CCcchhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhccchHHHH
Confidence            99999999999888775  44 4567888888899999999999999999986  444 678999999999999999999


Q ss_pred             HHHHhchhcCCCCC-hhhHHHH---HHhhCCHHHHHHHHHHHHHcCCCCc-hhhHHHHHHHHHhcCCcchHHHHHHHHHh
Q 041804          268 AVLAEMPKKGCVPD-VITYHCF---FRCLEKPREILGLFDRMIESGIRPK-MDTYVMLLRKFGRWGFLRPVFVVWKKMEE  342 (403)
Q Consensus       268 ~~~~~~~~~~~~p~-~~~~~~l---~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  342 (403)
                      +.+......  .|+ ....+.+   -.-.++.++|..+|....+-  .|. ...++.|...|-+.|++++|+..+++..+
T Consensus       341 ~cYnkaL~l--~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr  416 (966)
T KOG4626|consen  341 DCYNKALRL--CPNHADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR  416 (966)
T ss_pred             HHHHHHHHh--CCccHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh
Confidence            999998765  332 2222323   33447889999999988874  333 45788999999999999999999999987


Q ss_pred             cCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          343 LGCSPD-EFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       343 ~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                        ++|+ ...|+.+...|-..|+.+.|.+.+.+.+.
T Consensus       417 --I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~  450 (966)
T KOG4626|consen  417 --IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQ  450 (966)
T ss_pred             --cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHh
Confidence              4565 67899999999999999999999998876

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.78  E-value=1.4e-14  Score=119.10  Aligned_cols=274  Identities=13%  Similarity=0.184  Sum_probs=195.4

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccC--ChhH-HHHHHHHhhhCC------------------CCCCC
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFF--EFDL-SWNLIHRMKDNP------------------SSIPN   66 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~--~~~~-a~~~~~~~~~~~------------------~~~~~   66 (403)
                      +|..+++.-+|+.|.+ .+++.+...-..|+...+-.+  ++.- -++.|-.|...+                  ..+.+
T Consensus       128 ~~EvKDs~ilY~~m~~-e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~vAdL~~E~~PKT  206 (625)
T KOG4422|consen  128 SREVKDSCILYERMRS-ENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAVADLLFETLPKT  206 (625)
T ss_pred             hcccchhHHHHHHHHh-cCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccHHHHHHhhcCCC
Confidence            5778888889999985 777777777666665433221  1111 112222222111                  02345


Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      ..++..||.+.++--..+.|.++|++..+...+ +..+||.+|.+-.-..+    .+++.+|...      ...||..|+
T Consensus       207 ~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisq------km~Pnl~Tf  276 (625)
T KOG4422|consen  207 DETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQ------KMTPNLFTF  276 (625)
T ss_pred             chhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHh------hcCCchHhH
Confidence            668999999999999999999999999888777 99999999987654433    6677777776      889999999


Q ss_pred             HHHHHHHHhcCChhHH----HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhH-HHHHHHHHHHc--C--CC----CCh
Q 041804          146 NMILRGWFKMSWWGKC----REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWK-AVKLYKEMKKK--G--IK----MDV  212 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~--~--~~----~~~  212 (403)
                      |+++.+..+.|+++.|    .+++.+|++.|+.|...+|..+|..+++.+++.+ |..++.+....  |  ++    -|.
T Consensus       277 NalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~  356 (625)
T KOG4422|consen  277 NALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDN  356 (625)
T ss_pred             HHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchh
Confidence            9999999999988765    5678889999999999999999999999988865 44455554432  2  22    245


Q ss_pred             hhHHHHHHHHhhcCCHHHHHHHHHHHHHcC----CCCC---HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhH
Q 041804          213 VAYNTVIRAVGVSEGVDFAMRVYREMREMG----CQPS---VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITY  285 (403)
Q Consensus       213 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~  285 (403)
                      ..|...+..|.+..+.+.|.++..-+....    +.|+   ..-|..+....++....+.-...|+.|.-.-+-|+..+.
T Consensus       357 ~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m  436 (625)
T KOG4422|consen  357 KFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTM  436 (625)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhH
Confidence            567888888888899888888776554321    2222   223555666667777777777777777766666777666


Q ss_pred             HHHHHhh
Q 041804          286 HCFFRCL  292 (403)
Q Consensus       286 ~~l~~~~  292 (403)
                      ..++++.
T Consensus       437 ~~~lrA~  443 (625)
T KOG4422|consen  437 IHLLRAL  443 (625)
T ss_pred             HHHHHHH
Confidence            6666654

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.75  E-value=1.5e-14  Score=126.76  Aligned_cols=283  Identities=11%  Similarity=0.037  Sum_probs=216.1

Q ss_pred             cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH--HHHHHHHHhcCC
Q 041804           80 AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY--NMILRGWFKMSW  157 (403)
Q Consensus        80 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~  157 (403)
                      .|+++.|++.+....+........+.....+..+.|+++.|...+.++.+.        .|+....  ......+...|+
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--------~~~~~~~~~l~~a~l~l~~g~  168 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--------ADNDQLPVEITRVRIQLARNE  168 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CCcchHHHHHHHHHHHHHCCC
Confidence            599999998888765543223333444455557899999999999988764        3443322  234678889999


Q ss_pred             hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh-------hhHHHHHHHHhhcCCHHH
Q 041804          158 WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV-------VAYNTVIRAVGVSEGVDF  230 (403)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~ll~~~~~~~~~~~  230 (403)
                      ++.|.+.++++.+..+. +......+...|.+.|++++|.+++..+.+.+..++.       .+|..++.......+.+.
T Consensus       169 ~~~Al~~l~~~~~~~P~-~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~  247 (398)
T PRK10747        169 NHAARHGVDKLLEVAPR-HPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEG  247 (398)
T ss_pred             HHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHH
Confidence            99999999999998876 7888999999999999999999999999988654322       123333444444556666


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH-hhCCHHHHHHHHHHHHHcC
Q 041804          231 AMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR-CLEKPREILGLFDRMIESG  309 (403)
Q Consensus       231 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~-~~~~~~~a~~~~~~~~~~~  309 (403)
                      ..++++.+.+. .+.++.....+...+...|+.++|.+++++..+.  .|+......... ..++.+++.+..+...+..
T Consensus       248 l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~~l~~~l~~~~~~~al~~~e~~lk~~  324 (398)
T PRK10747        248 LKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLVLLIPRLKTNNPEQLEKVLRQQIKQH  324 (398)
T ss_pred             HHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHhhccCCChHHHHHHHHHHHhhC
Confidence            67777666443 3457788888999999999999999999998875  444432221111 1167888999999988765


Q ss_pred             CCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          310 IRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       310 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      .. |...+..+.+.|.+.+++++|.+.|+...+.  .|+...+..+..++.+.|+.++|.+++++-..
T Consensus       325 P~-~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        325 GD-TPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             CC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44 6677889999999999999999999999985  69999999999999999999999999998755

>TIGR00540 hemY_coli hemY protein

Probab=99.75  E-value=1.4e-14  Score=127.53  Aligned_cols=296  Identities=10%  Similarity=-0.039  Sum_probs=218.4

Q ss_pred             HHHHHHHHH--hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcch--HHH
Q 041804           70 FRIMFKRYV--TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKT--KIY  145 (403)
Q Consensus        70 ~~~l~~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~--~~~  145 (403)
                      ...+..+..  ..|+++.|.+.+.+..+..+.....+-....+....|+.+.|...+.+..+.        .|+.  .+.
T Consensus        85 ~~~~~~glla~~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~--------~p~~~l~~~  156 (409)
T TIGR00540        85 QKQTEEALLKLAEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAEL--------AGNDNILVE  156 (409)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCcCchHHH
Confidence            344444443  5799999999999888776545666667778888999999999999987653        2332  334


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHH---
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV---  222 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~---  222 (403)
                      -.....+...|+++.|.+.++.+.+..+. +...+..+...+...|++++|.+.+..+.+.++.++......-..++   
T Consensus       157 ~~~a~l~l~~~~~~~Al~~l~~l~~~~P~-~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~  235 (409)
T TIGR00540       157 IARTRILLAQNELHAARHGVDKLLEMAPR-HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGL  235 (409)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            44588889999999999999999998866 77889999999999999999999999999987543332212112222   


Q ss_pred             hhcCCHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhh-----HHHHHHh-hC
Q 041804          223 GVSEGVDFAMRVYREMREMGC---QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVIT-----YHCFFRC-LE  293 (403)
Q Consensus       223 ~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~-----~~~l~~~-~~  293 (403)
                      ...+..+.....+..+.+...   +.+...+..+...+...|+.++|.+++++..+.  .||...     +...... -+
T Consensus       236 l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~  313 (409)
T TIGR00540       236 LDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPE  313 (409)
T ss_pred             HHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCC
Confidence            222333333445555554422   137888899999999999999999999999876  344432     2222111 14


Q ss_pred             CHHHHHHHHHHHHHcCCCCch--hhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 041804          294 KPREILGLFDRMIESGIRPKM--DTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKY  371 (403)
Q Consensus       294 ~~~~a~~~~~~~~~~~~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  371 (403)
                      +.+.+.+.++...+.... |+  ....++.+.+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|.++
T Consensus       314 ~~~~~~~~~e~~lk~~p~-~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~  392 (409)
T TIGR00540       314 DNEKLEKLIEKQAKNVDD-KPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAM  392 (409)
T ss_pred             ChHHHHHHHHHHHHhCCC-ChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            567788888877765322 34  567789999999999999999999654444579999999999999999999999999


Q ss_pred             HHHHHH
Q 041804          372 DEEMFA  377 (403)
Q Consensus       372 ~~~m~~  377 (403)
                      +++...
T Consensus       393 ~~~~l~  398 (409)
T TIGR00540       393 RQDSLG  398 (409)
T ss_pred             HHHHHH
Confidence            998644

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

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

Probab=99.74  E-value=1.8e-17  Score=138.79  Aligned_cols=258  Identities=12%  Similarity=0.053  Sum_probs=65.9

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      ++.+.|++++|++++.........+.++..|..+.......++++.|...++++...+  +-+...+..++.. ...+++
T Consensus        17 ~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~--~~~~~~~~~l~~l-~~~~~~   93 (280)
T PF13429_consen   17 LLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD--KANPQDYERLIQL-LQDGDP   93 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccc--ccccccccccccc-cccccc
Confidence            3444455555555553322111012233333344444444555555555555555443  1123334444443 455555


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHH
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCRE  163 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  163 (403)
                      ++|.+++....+.. +++..+..++..+...++++++..++..+....     ..+.+...|..+...+.+.|++++|.+
T Consensus        94 ~~A~~~~~~~~~~~-~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~~~~~~~~a~~~~~~G~~~~A~~  167 (280)
T PF13429_consen   94 EEALKLAEKAYERD-GDPRYLLSALQLYYRLGDYDEAEELLEKLEELP-----AAPDSARFWLALAEIYEQLGDPDKALR  167 (280)
T ss_dssp             -------------------------H-HHHTT-HHHHHHHHHHHHH-T--------T-HHHHHHHHHHHHHCCHHHHHHH
T ss_pred             cccccccccccccc-cccchhhHHHHHHHHHhHHHHHHHHHHHHHhcc-----CCCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            55555554443322 234444445555555555555555555443221     223444455555555555555555555


Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          164 FWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      .+++..+..+. |....+.++..+...|+.+++.++++...+.. +.|...+..+..+|...|+.++|..+|+...+.. 
T Consensus       168 ~~~~al~~~P~-~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-  244 (280)
T PF13429_consen  168 DYRKALELDPD-DPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-  244 (280)
T ss_dssp             HHHHHHHH-TT--HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHcCCC-CHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-
Confidence            55555554333 44445555555555555555555555544442 3333444455555555555555555555555432 


Q ss_pred             CCCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          244 QPSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       244 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      +.|+.....+..++.+.|+.++|..+..+.
T Consensus       245 p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  245 PDDPLWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             TT-HHHHHHHHHHHT---------------
T ss_pred             cccccccccccccccccccccccccccccc
Confidence            124444455555555555555555554443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.74  E-value=1.1e-13  Score=129.25  Aligned_cols=362  Identities=10%  Similarity=0.034  Sum_probs=267.2

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      .++...|++++|+++|+.+...  .+.++..+..++..+...++.++|++.++++....   |+...+..++..+...++
T Consensus       110 ~ly~~~gdyd~Aiely~kaL~~--dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~d---p~~~~~l~layL~~~~~~  184 (822)
T PRK14574        110 RAYRNEKRWDQALALWQSSLKK--DPTNPDLISGMIMTQADAGRGGVVLKQATELAERD---PTVQNYMTLSYLNRATDR  184 (822)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccC---cchHHHHHHHHHHHhcch
Confidence            3566778999999999998853  34456777788888899999999999999988865   666666445444445666


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH------HHHHHHH---H
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY------NMILRGW---F  153 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~------~~l~~~~---~  153 (403)
                      ..+|++.++++.+..+.+...+..++.+..+.|-...|.++..+...-       ..+....+      ..+++.-   .
T Consensus       185 ~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~-------f~~~~~~~l~~~~~a~~vr~a~~~~  257 (822)
T PRK14574        185 NYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNL-------VSAEHYRQLERDAAAEQVRMAVLPT  257 (822)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccc-------cCHHHHHHHHHHHHHHHHhhccccc
Confidence            666999999999988778888899999999999988888887665431       11211111      1111111   0


Q ss_pred             --hcCC---hhHHHHHHHHHHh-CCCCCc-----HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHH
Q 041804          154 --KMSW---WGKCREFWEEMDK-RGVVKD-----LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV  222 (403)
Q Consensus       154 --~~~~---~~~a~~~~~~~~~-~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~  222 (403)
                        ....   .+.|+.-++.+.. .+..|.     ....--.+-++...+++.+|++.|+.+...+.+....+-..+..+|
T Consensus       258 ~~~~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~aday  337 (822)
T PRK14574        258 RSETERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAY  337 (822)
T ss_pred             ccchhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHH
Confidence              1112   3445555555544 233332     2233345668889999999999999999998776777899999999


Q ss_pred             hhcCCHHHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcC-------------CCCChhh
Q 041804          223 GVSEGVDFAMRVYREMREMG-----CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKG-------------CVPDVIT  284 (403)
Q Consensus       223 ~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-------------~~p~~~~  284 (403)
                      ...+++++|..+++.+....     ..++......|..+|...+++++|..+++.+.+..             ..||-..
T Consensus       338 l~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~  417 (822)
T PRK14574        338 IDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIE  417 (822)
T ss_pred             HhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHH
Confidence            99999999999999997653     23344456789999999999999999999998631             2233333


Q ss_pred             HHHHHH----hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHH
Q 041804          285 YHCFFR----CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI  360 (403)
Q Consensus       285 ~~~l~~----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  360 (403)
                      +..+..    ..++..+|.+.++.+....+. |......+...+...|.+.+|.+.++...... +-+..+....+.++.
T Consensus       418 ~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~-n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~-P~~~~~~~~~~~~al  495 (822)
T PRK14574        418 GQTLLVQSLVALNDLPTAQKKLEDLSSTAPA-NQNLRIALASIYLARDLPRKAEQELKAVESLA-PRSLILERAQAETAM  495 (822)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhC-CccHHHHHHHHHHHH
Confidence            333222    238899999999999876544 88899999999999999999999997776652 446777888889999


Q ss_pred             hcCCHHHHHHHHHHHHHc
Q 041804          361 DKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       361 ~~g~~~~a~~~~~~m~~~  378 (403)
                      ..|++.+|..+.+.+.+.
T Consensus       496 ~l~e~~~A~~~~~~l~~~  513 (822)
T PRK14574        496 ALQEWHQMELLTDDVISR  513 (822)
T ss_pred             hhhhHHHHHHHHHHHHhh
Confidence            999999999999988774

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.73  E-value=5.2e-13  Score=127.47  Aligned_cols=356  Identities=8%  Similarity=-0.032  Sum_probs=252.2

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      ++..+++++.|.++.. .      .|.......-.......+...++...++.|.+..  +-+......+.-...+.|+.
T Consensus       322 ~~~~~~~~~~~~~~~~-~------~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~y~~~--~~~~~~l~q~~~~~~~~~~~  392 (987)
T PRK09782        322 VLLKEGQYDAAQKLLA-T------LPANEMLEERYAVSVATRNKAEALRLARLLYQQE--PANLTRLDQLTWQLMQNGQS  392 (987)
T ss_pred             HHHhccHHHHHHHHhc-C------CCcchHHHHHHhhccccCchhHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHcccH
Confidence            3456677776665533 2      2222222222222334577888888888888863  24666666777777889999


Q ss_pred             HHHHHHHHHHhhcCCC---cHHHHHHHHHHHHhcCC---HHHHHHHHh------------ccccccc-----cccc-ccC
Q 041804           84 NEAMGTFNKLDEFGLK---DEVSYCNLVDALCEYKH---VIEAQELCF------------GENKNVG-----FSGL-VEM  139 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~---~~~a~~~~~------------~~~~~~~-----~~~~-~~~  139 (403)
                      ++|.++|+........   +......++..|.+.+.   ..++..+..            +......     .... ..+
T Consensus       393 ~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p  472 (987)
T PRK09782        393 REAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMS  472 (987)
T ss_pred             HHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCC
Confidence            9999999998774221   45566688888888776   333433311            1100000     0000 123


Q ss_pred             c--chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHH
Q 041804          140 N--KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNT  217 (403)
Q Consensus       140 ~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  217 (403)
                      +  +...|..+..++.. ++.++|...+.+.....  |+......+...+...|++++|...|+++...  +|+...+..
T Consensus       473 ~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~  547 (987)
T PRK09782        473 PSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLA  547 (987)
T ss_pred             CCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHH
Confidence            4  67778888888877 88889999888877664  55544444555667899999999999998655  455556667


Q ss_pred             HHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH---hhCC
Q 041804          218 VIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR---CLEK  294 (403)
Q Consensus       218 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~---~~~~  294 (403)
                      +..++.+.|+++.|...++...+... .+...+..+.....+.|++++|...+++..+.  .|+...+..+-.   ..++
T Consensus       548 la~all~~Gd~~eA~~~l~qAL~l~P-~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~  624 (987)
T PRK09782        548 AANTAQAAGNGAARDRWLQQAEQRGL-GDNALYWWLHAQRYIPGQPELALNDLTRSLNI--APSANAYVARATIYRQRHN  624 (987)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCC
Confidence            77888999999999999999988642 23333334444555669999999999999876  456555554433   4488


Q ss_pred             HHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 041804          295 PREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEE  374 (403)
Q Consensus       295 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  374 (403)
                      .++|...+++....... +...++.+..++...|++++|+..+++..+.. +-+...+..+..++...|++++|...+++
T Consensus       625 ~deA~~~l~~AL~l~Pd-~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~-P~~~~a~~nLA~al~~lGd~~eA~~~l~~  702 (987)
T PRK09782        625 VPAAVSDLRAALELEPN-NSNYQAALGYALWDSGDIAQSREMLERAHKGL-PDDPALIRQLAYVNQRLDDMAATQHYARL  702 (987)
T ss_pred             HHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            99999999999987544 56788888889999999999999999998864 45788899999999999999999999999


Q ss_pred             HHHc
Q 041804          375 MFAK  378 (403)
Q Consensus       375 m~~~  378 (403)
                      ..+.
T Consensus       703 Al~l  706 (987)
T PRK09782        703 VIDD  706 (987)
T ss_pred             HHhc
Confidence            9874

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.73  E-value=5.5e-13  Score=127.30  Aligned_cols=351  Identities=7%  Similarity=-0.053  Sum_probs=252.1

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhC-CCCCCCHHHHHHHHHHHHhcCC---hH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN-PSSIPNHATFRIMFKRYVTAHL---VN   84 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~---~~   84 (403)
                      +...++...+..+-++  .+-+......+-....+.|+.++|.++|+..... +...++....+-++..|.+.+.   ..
T Consensus       356 ~~~~~~~~~~~~~y~~--~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~  433 (987)
T PRK09782        356 RNKAEALRLARLLYQQ--EPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPA  433 (987)
T ss_pred             CchhHHHHHHHHHHhc--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchH
Confidence            4445555555555532  2346667777777788889999999999888762 2122344455566677766655   22


Q ss_pred             HH-------------------------HHHHHHHhhcCCC--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccc
Q 041804           85 EA-------------------------MGTFNKLDEFGLK--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLV  137 (403)
Q Consensus        85 ~a-------------------------~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  137 (403)
                      ++                         ...+.......+.  +...|..+..++.. ++.++|...+.+....       
T Consensus       434 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~-------  505 (987)
T PRK09782        434 KVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR-------  505 (987)
T ss_pred             HHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh-------
Confidence            22                         2233333444445  67788888888877 7888899977776653       


Q ss_pred             cCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHH
Q 041804          138 EMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNT  217 (403)
Q Consensus       138 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  217 (403)
                       .|+......+...+...|++++|...|+++...  .|+...+..+..++.+.|++++|...+++..+.. +.+...+..
T Consensus       506 -~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~  581 (987)
T PRK09782        506 -QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWW  581 (987)
T ss_pred             -CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHH
Confidence             244444444455557899999999999998665  3344556777888999999999999999998874 223333333


Q ss_pred             HHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHH----HHHhhC
Q 041804          218 VIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHC----FFRCLE  293 (403)
Q Consensus       218 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~----l~~~~~  293 (403)
                      +.......|++++|...+++..+.  .|+...+..+...+.+.|+.++|...|++....  .|+...+..    ++...+
T Consensus       582 La~~l~~~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G  657 (987)
T PRK09782        582 LHAQRYIPGQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSG  657 (987)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCC
Confidence            444445669999999999999986  457888999999999999999999999998876  465443322    333448


Q ss_pred             CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 041804          294 KPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDE  373 (403)
Q Consensus       294 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  373 (403)
                      +.++|+..+++..+.... +...+..+..++...|++++|...+++..+.. +-+..+.........+..+++.|.+-++
T Consensus       658 ~~eeAi~~l~~AL~l~P~-~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~-P~~a~i~~~~g~~~~~~~~~~~a~~~~~  735 (987)
T PRK09782        658 DIAQSREMLERAHKGLPD-DPALIRQLAYVNQRLDDMAATQHYARLVIDDI-DNQALITPLTPEQNQQRFNFRRLHEEVG  735 (987)
T ss_pred             CHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCchhhhhhhHHHHHHHHHHHHHHHHH
Confidence            899999999999986543 67788999999999999999999999998763 2234566666777777888888888777


Q ss_pred             HHHHcC
Q 041804          374 EMFAKG  379 (403)
Q Consensus       374 ~m~~~~  379 (403)
                      +-...+
T Consensus       736 r~~~~~  741 (987)
T PRK09782        736 RRWTFS  741 (987)
T ss_pred             HHhhcC
Confidence            766533

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.72  E-value=5.5e-14  Score=123.17  Aligned_cols=255  Identities=9%  Similarity=0.011  Sum_probs=192.0

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHH-HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHH--HHHHHHHhcC
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSV-IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFR--IMFKRYVTAH   81 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l-i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~   81 (403)
                      ....|+++.|.+.+.....   ..+++..+..+ ..+..+.|+++.|...+.++.+..   |+.....  .....+...|
T Consensus        94 a~~eGd~~~A~k~l~~~~~---~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~---~~~~~~~~l~~a~l~l~~g  167 (398)
T PRK10747         94 KLAEGDYQQVEKLMTRNAD---HAEQPVVNYLLAAEAAQQRGDEARANQHLERAAELA---DNDQLPVEITRVRIQLARN  167 (398)
T ss_pred             HHhCCCHHHHHHHHHHHHh---cccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC---CcchHHHHHHHHHHHHHCC
Confidence            3446999999988887653   12334444444 445589999999999999998854   6654332  3367889999


Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcch------HHHHHHHHHHHhc
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKT------KIYNMILRGWFKM  155 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~------~~~~~l~~~~~~~  155 (403)
                      +++.|...++++.+..+.++.....+...|.+.|++++|..++..+.+..     ...+..      .+|..++......
T Consensus       168 ~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~-----~~~~~~~~~l~~~a~~~l~~~~~~~  242 (398)
T PRK10747        168 ENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAH-----VGDEEHRAMLEQQAWIGLMDQAMAD  242 (398)
T ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcC-----CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999998899999999999999999999999999988763     111111      2344445444555


Q ss_pred             CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHH
Q 041804          156 SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVY  235 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  235 (403)
                      .+.+...++++.+.+.- +.+......+...+...|+.++|.+++++..+.  +|+....  ++.+....++.+.+.+..
T Consensus       243 ~~~~~l~~~w~~lp~~~-~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~~l~~~~~~~al~~~  317 (398)
T PRK10747        243 QGSEGLKRWWKNQSRKT-RHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIPRLKTNNPEQLEKVL  317 (398)
T ss_pred             cCHHHHHHHHHhCCHHH-hCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHhhccCCChHHHHHHH
Confidence            56677777777765442 237778888999999999999999999998874  5555322  334444568999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          236 REMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       236 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      +...+..+ -|...+..+...+.+.+++++|.+.|+...+.
T Consensus       318 e~~lk~~P-~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~  357 (398)
T PRK10747        318 RQQIKQHG-DTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ  357 (398)
T ss_pred             HHHHhhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            98887743 36677888899999999999999999988764

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

Probab=99.72  E-value=2.9e-13  Score=121.31  Aligned_cols=365  Identities=10%  Similarity=0.061  Sum_probs=273.1

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      .-+|+.++|.+++.++.++  .+.+...|.+|..+|-..|+.+++...+-......  +.|...|..+.......|++++
T Consensus       150 farg~~eeA~~i~~EvIkq--dp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~--p~d~e~W~~ladls~~~~~i~q  225 (895)
T KOG2076|consen  150 FARGDLEEAEEILMEVIKQ--DPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN--PKDYELWKRLADLSEQLGNINQ  225 (895)
T ss_pred             HHhCCHHHHHHHHHHHHHh--CccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC--CCChHHHHHHHHHHHhcccHHH
Confidence            3459999999999999853  45678899999999999999999988777666654  4677899999999999999999


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      |.-+|.+..+..+++....-.-...|-+.|+...|..-|.++....+  .............++..+...++-+.|.+.+
T Consensus       226 A~~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p--~~d~er~~d~i~~~~~~~~~~~~~e~a~~~l  303 (895)
T KOG2076|consen  226 ARYCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDP--PVDIERIEDLIRRVAHYFITHNERERAAKAL  303 (895)
T ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCC--chhHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            99999999999988888888888889999999999999888877421  0000112223345567777888889999988


Q ss_pred             HHHHhC-CCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC---------------------------CCCChhhHHH
Q 041804          166 EEMDKR-GVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG---------------------------IKMDVVAYNT  217 (403)
Q Consensus       166 ~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------------------~~~~~~~~~~  217 (403)
                      +..... +-..+...+++++..+.+...++.+......+....                           +.++..++ -
T Consensus       304 e~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~-r  382 (895)
T KOG2076|consen  304 EGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVI-R  382 (895)
T ss_pred             HHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhH-h
Confidence            887662 222356678899999999999999998888877621                           12222221 2


Q ss_pred             HHHHHhhcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---
Q 041804          218 VIRAVGVSEGVDFAMRVYREMREMG--CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---  292 (403)
Q Consensus       218 ll~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---  292 (403)
                      ++-++...+..+....+.....+..  +.-+...|.-+..+|.+.|++..|+.+|..+......-+...|-.+-+++   
T Consensus       383 l~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l  462 (895)
T KOG2076|consen  383 LMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMEL  462 (895)
T ss_pred             HhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHH
Confidence            2334445555566666666666665  33356678889999999999999999999998764444455555554444   


Q ss_pred             CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHH--------hcCCCCCHHHHHHHHHHHHhcCC
Q 041804          293 EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKME--------ELGCSPDEFAYNALVDALIDKGM  364 (403)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~g~  364 (403)
                      +..++|.+.|+..+..... +...-.+|...+-+.|+.++|.+++..+.        ..+..|+....-...+.+.+.|+
T Consensus       463 ~e~e~A~e~y~kvl~~~p~-~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk  541 (895)
T KOG2076|consen  463 GEYEEAIEFYEKVLILAPD-NLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGK  541 (895)
T ss_pred             hhHHHHHHHHHHHHhcCCC-chhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhh
Confidence            7789999999999875432 44555667778889999999999999853        23456777777777888999999


Q ss_pred             HHHHHHHHHHHHHc
Q 041804          365 LDMARKYDEEMFAK  378 (403)
Q Consensus       365 ~~~a~~~~~~m~~~  378 (403)
                      .++-+.+...|+..
T Consensus       542 ~E~fi~t~~~Lv~~  555 (895)
T KOG2076|consen  542 REEFINTASTLVDD  555 (895)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99888777777764

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

Probab=99.72  E-value=7.9e-17  Score=134.97  Aligned_cols=257  Identities=16%  Similarity=0.086  Sum_probs=73.2

Q ss_pred             HHHHHhcCChHHHHHHHHHHhhcC-CC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHH
Q 041804           74 FKRYVTAHLVNEAMGTFNKLDEFG-LK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG  151 (403)
Q Consensus        74 ~~~~~~~~~~~~a~~~~~~~~~~~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (403)
                      ...+.+.|++++|+++++...... ++ +...|..+...+...++.+.|...++++...       .+.+...+..++..
T Consensus        15 A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~-------~~~~~~~~~~l~~l   87 (280)
T PF13429_consen   15 ARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLAS-------DKANPQDYERLIQL   87 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-------cccccccccccccc
Confidence            445555555555555553332222 22 4455555555555555555555555555442       12233334444444


Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC-CCCChhhHHHHHHHHhhcCCHHH
Q 041804          152 WFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG-IKMDVVAYNTVIRAVGVSEGVDF  230 (403)
Q Consensus       152 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~ll~~~~~~~~~~~  230 (403)
                       ...+++++|.++++...+..  ++...+..++..+...++++++.++++.+.... .+.+...|..+...+.+.|+.++
T Consensus        88 -~~~~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~  164 (280)
T PF13429_consen   88 -LQDGDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDK  164 (280)
T ss_dssp             ---------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHH
T ss_pred             -cccccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHH
Confidence             45555555555555443332  233444555555556666666666665554331 23344455555555556666666


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCC
Q 041804          231 AMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGI  310 (403)
Q Consensus       231 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~  310 (403)
                      |.+.+++..+..+. +....+.++..+...|+.+++.+++....+..                                 
T Consensus       165 A~~~~~~al~~~P~-~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~---------------------------------  210 (280)
T PF13429_consen  165 ALRDYRKALELDPD-DPDARNALAWLLIDMGDYDEAREALKRLLKAA---------------------------------  210 (280)
T ss_dssp             HHHHHHHHHHH-TT--HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH----------------------------------
T ss_pred             HHHHHHHHHHcCCC-CHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC---------------------------------
Confidence            66666666554221 34455555555655666655555555544321                                 


Q ss_pred             CCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 041804          311 RPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEM  375 (403)
Q Consensus       311 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  375 (403)
                      +.|+..+..+..++...|++++|...+++..+.. +.|+.+...+.+++...|+.++|.++.++.
T Consensus       211 ~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  211 PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPLWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHT---------------
T ss_pred             cCHHHHHHHHHHHhcccccccccccccccccccc-cccccccccccccccccccccccccccccc
Confidence            1233445556666666666666666666665542 345666666666666666666666665544

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

Probab=99.72  E-value=5.7e-14  Score=111.37  Aligned_cols=222  Identities=13%  Similarity=0.001  Sum_probs=102.4

Q ss_pred             CChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC----cHHHHHHHHHHHHhcCCHHHH
Q 041804           45 FEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK----DEVSYCNLVDALCEYKHVIEA  120 (403)
Q Consensus        45 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a  120 (403)
                      ++.++|.++|-+|.+.+  +.+..+.-+|.+.|-+.|..++|+++...+.++.--    ...+...|.+-|...|-++.|
T Consensus        49 ~Q~dKAvdlF~e~l~~d--~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRA  126 (389)
T COG2956          49 NQPDKAVDLFLEMLQED--PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRA  126 (389)
T ss_pred             cCcchHHHHHHHHHhcC--chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHH
Confidence            44455555555555432  222334444555555555555555555554443221    112233344445555555555


Q ss_pred             HHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH----HHHHHHHHHHHHcCChhHH
Q 041804          121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL----HSYSIYMDIMCKSGKPWKA  196 (403)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a  196 (403)
                      +.+|..+....       .--..+...|+..|-...+|++|+++-+++.+.+..+..    ..|.-+...+....+.+.|
T Consensus       127 E~~f~~L~de~-------efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A  199 (389)
T COG2956         127 EDIFNQLVDEG-------EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRA  199 (389)
T ss_pred             HHHHHHHhcch-------hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHH
Confidence            55555544421       112233445555555555555555555555444433221    2344444444444555555


Q ss_pred             HHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          197 VKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      ..++.+..+.+ +-....--.+-+.....|+++.|.+.++.+.+.+..--..+...|..+|.+.|+.++....+.++.+.
T Consensus       200 ~~~l~kAlqa~-~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~  278 (389)
T COG2956         200 RELLKKALQAD-KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET  278 (389)
T ss_pred             HHHHHHHHhhC-ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence            55555554442 11222222333444455555555555555555443333444455555555555555555555554443

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

Probab=99.71  E-value=2.2e-13  Score=122.03  Aligned_cols=332  Identities=12%  Similarity=0.014  Sum_probs=259.0

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      .-.....+.-.|++++|..++.++....  +.+...|.+|...|-..|+.+++...+-..-...+.|...|..+.....+
T Consensus       142 ll~eAN~lfarg~~eeA~~i~~EvIkqd--p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~  219 (895)
T KOG2076|consen  142 LLGEANNLFARGDLEEAEEILMEVIKQD--PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQ  219 (895)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhC--ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHh
Confidence            3334444555599999999999999986  56788999999999999999999999988888888899999999999999


Q ss_pred             cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHH----HHHHHH
Q 041804          114 YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIY----MDIMCK  189 (403)
Q Consensus       114 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l----~~~~~~  189 (403)
                      .|++..|.-.|.+..+       -.+++...+-.-...|-+.|+...|.+.|.++....++.|..-+..+    +..+..
T Consensus       220 ~~~i~qA~~cy~rAI~-------~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~  292 (895)
T KOG2076|consen  220 LGNINQARYCYSRAIQ-------ANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFIT  292 (895)
T ss_pred             cccHHHHHHHHHHHHh-------cCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHH
Confidence            9999999999999988       45777777778889999999999999999999988664444444443    455666


Q ss_pred             cCChhHHHHHHHHHHHc-CCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC-------------------------
Q 041804          190 SGKPWKAVKLYKEMKKK-GIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC-------------------------  243 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~-~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-------------------------  243 (403)
                      .++.+.|.+.++..... +-..+...++.++..+.+...++.+......+.....                         
T Consensus       293 ~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~  372 (895)
T KOG2076|consen  293 HNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGK  372 (895)
T ss_pred             hhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCC
Confidence            77778999998887763 2345666788999999999999999988887776211                         


Q ss_pred             --CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC--ChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhh
Q 041804          244 --QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP--DVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDT  316 (403)
Q Consensus       244 --~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p--~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~  316 (403)
                        .++..++ .+.-++......+....+.....+.++.|  +...|.-+..++   +++.+|+.++..+......-+...
T Consensus       373 ~~s~~l~v~-rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~v  451 (895)
T KOG2076|consen  373 ELSYDLRVI-RLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFV  451 (895)
T ss_pred             CCCccchhH-hHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhh
Confidence              1222221 22334445555555555555555555333  445565555565   789999999999998655557788


Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 041804          317 YVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMF  376 (403)
Q Consensus       317 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  376 (403)
                      |--+.++|...|.+++|.+.+++..... +-+...--.|...+.+.|+.++|.+.++.+.
T Consensus       452 w~~~a~c~~~l~e~e~A~e~y~kvl~~~-p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~  510 (895)
T KOG2076|consen  452 WYKLARCYMELGEYEEAIEFYEKVLILA-PDNLDARITLASLYQQLGNHEKALETLEQII  510 (895)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCchhhhhhHHHHHHhcCCHHHHHHHHhccc
Confidence            9999999999999999999999998863 4456667778888999999999999999875

>TIGR00540 hemY_coli hemY protein

Probab=99.69  E-value=1.5e-13  Score=121.18  Aligned_cols=49  Identities=10%  Similarity=0.014  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHH
Q 041804          293 EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKME  341 (403)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  341 (403)
                      +++++|.+.|+........|+...+..+...+.+.|+.++|.++|++..
T Consensus       349 ~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l  397 (409)
T TIGR00540       349 GEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSL  397 (409)
T ss_pred             ccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4445555555533332335667677777778888888888888877653

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.

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

Probab=99.69  E-value=1.1e-13  Score=124.72  Aligned_cols=362  Identities=10%  Similarity=0.076  Sum_probs=210.5

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcC-CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH--HHHHHHHHHHHhc
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTH-TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH--ATFRIMFKRYVTA   80 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~   80 (403)
                      -+...|+++.+..+...+.......+ -...|..+.++|-..|++++|..+|-+..+..   |+.  ..+.-+...|.+.
T Consensus       279 ~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~---~d~~~l~~~GlgQm~i~~  355 (1018)
T KOG2002|consen  279 HFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKAD---NDNFVLPLVGLGQMYIKR  355 (1018)
T ss_pred             HHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccC---CCCccccccchhHHHHHh
Confidence            34456888888888877765221111 24567888888999999999999888877754   444  3445577888899


Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC----CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK----HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS  156 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  156 (403)
                      |+.+.+...|+.+.+..+.+..+...|...|+..+    ..+.|..++.+...       ..+.+...|-.+...+-...
T Consensus       356 ~dle~s~~~fEkv~k~~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~-------~~~~d~~a~l~laql~e~~d  428 (1018)
T KOG2002|consen  356 GDLEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLE-------QTPVDSEAWLELAQLLEQTD  428 (1018)
T ss_pred             chHHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHh-------cccccHHHHHHHHHHHHhcC
Confidence            99999999999998888778888888888887764    45666666666655       33566777777766666554


Q ss_pred             ChhHHHHHHHH----HHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc---CCCCChh------hHHHHHHHHh
Q 041804          157 WWGKCREFWEE----MDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK---GIKMDVV------AYNTVIRAVG  223 (403)
Q Consensus       157 ~~~~a~~~~~~----~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~------~~~~ll~~~~  223 (403)
                      -+.. +.+|..    +...+..+.+...|.+...+...|++.+|...|......   ...+|..      +--.+....-
T Consensus       429 ~~~s-L~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E  507 (1018)
T KOG2002|consen  429 PWAS-LDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLE  507 (1018)
T ss_pred             hHHH-HHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHH
Confidence            4433 555544    334555567778888888888888888888888877654   1222221      1122333334


Q ss_pred             hcCCHHHHHHHHHHHHHcCC---------------------------------CCCHHHHHHHHHHHHhcCcHHHHHHHH
Q 041804          224 VSEGVDFAMRVYREMREMGC---------------------------------QPSVVTCNTVIKLLCENGRVREAYAVL  270 (403)
Q Consensus       224 ~~~~~~~a~~~~~~~~~~~~---------------------------------~~~~~~~~~li~~~~~~g~~~~a~~~~  270 (403)
                      ..++.+.|.+.|..+.+..+                                 ..++..++.+...+.....+..|.+-|
T Consensus       508 ~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f  587 (1018)
T KOG2002|consen  508 ELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKF  587 (1018)
T ss_pred             hhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHH
Confidence            44555555555555544311                                 112222222222333333333333322


Q ss_pred             Hhchhc-CCCCChhhHHHH----HHhhC-----------CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHH
Q 041804          271 AEMPKK-GCVPDVITYHCF----FRCLE-----------KPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVF  334 (403)
Q Consensus       271 ~~~~~~-~~~p~~~~~~~l----~~~~~-----------~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  334 (403)
                      ..+... ...+|.+...+|    +.++.           ..++|+++|.+.++..+. |...-|-+.-.++..|++.+|.
T Consensus       588 ~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpk-N~yAANGIgiVLA~kg~~~~A~  666 (1018)
T KOG2002|consen  588 ETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPK-NMYAANGIGIVLAEKGRFSEAR  666 (1018)
T ss_pred             HHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcc-hhhhccchhhhhhhccCchHHH
Confidence            222211 011222221111    11111           124566666666655433 4445555555566666666666


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          335 VVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .+|.+..+.. ..+..+|-.+..+|..+|++..|++.|+...++
T Consensus       667 dIFsqVrEa~-~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkk  709 (1018)
T KOG2002|consen  667 DIFSQVREAT-SDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKK  709 (1018)
T ss_pred             HHHHHHHHHH-hhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666543 223445556666666666666666666665554

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.68  E-value=1.2e-12  Score=108.06  Aligned_cols=303  Identities=18%  Similarity=0.248  Sum_probs=209.7

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHH--HHhcCChH-HHHHHHHHHhhcC---------
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKR--YVTAHLVN-EAMGTFNKLDEFG---------   97 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~-~a~~~~~~~~~~~---------   97 (403)
                      .+.+-|.|+.. ...|.+.++.-+|+.|.+.+ .+.+...-..|++.  |-...++. .-.+.|-.|...|         
T Consensus       115 ~V~~E~nL~km-IS~~EvKDs~ilY~~m~~e~-~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~  192 (625)
T KOG4422|consen  115 QVETENNLLKM-ISSREVKDSCILYERMRSEN-VDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKS  192 (625)
T ss_pred             hhcchhHHHHH-HhhcccchhHHHHHHHHhcC-CCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhcccccccccccccc
Confidence            34566666654 56789999999999999988 55555554444432  22222221 1122333332222         


Q ss_pred             -----------CCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHH
Q 041804           98 -----------LKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWE  166 (403)
Q Consensus        98 -----------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  166 (403)
                                 +++..++.++|.+.++.-..+.|.+++++....      ....+..+||.++.+-.-..    -.+++.
T Consensus       193 G~vAdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~------k~kv~~~aFN~lI~~~S~~~----~K~Lv~  262 (625)
T KOG4422|consen  193 GAVADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAA------KGKVYREAFNGLIGASSYSV----GKKLVA  262 (625)
T ss_pred             ccHHHHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHh------hheeeHHhhhhhhhHHHhhc----cHHHHH
Confidence                       237789999999999999999999999988776      66788889999987765432    278889


Q ss_pred             HHHhCCCCCcHHHHHHHHHHHHHcCChhH----HHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHH-HHHHHHHHHHc
Q 041804          167 EMDKRGVVKDLHSYSIYMDIMCKSGKPWK----AVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDF-AMRVYREMREM  241 (403)
Q Consensus       167 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~-a~~~~~~~~~~  241 (403)
                      +|....+.||..|+|+++++..+.|+++.    |.+++.+|++.|+.|...+|..+|..+++.++..+ +..++.++...
T Consensus       263 EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~  342 (625)
T KOG4422|consen  263 EMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNS  342 (625)
T ss_pred             HHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHh
Confidence            99999999999999999999999998764    56778889999999999999999999998888754 44444444432


Q ss_pred             --C--CCC----CHHHHHHHHHHHHhcCcHHHHHHHHHhchhc----CCCCC--hhhH-HHH---HHhhCCHHHHHHHHH
Q 041804          242 --G--CQP----SVVTCNTVIKLLCENGRVREAYAVLAEMPKK----GCVPD--VITY-HCF---FRCLEKPREILGLFD  303 (403)
Q Consensus       242 --~--~~~----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~p~--~~~~-~~l---~~~~~~~~~a~~~~~  303 (403)
                        |  ++|    +...|...+..|.+..+.+-|..+..-+...    -+.|+  ...| ..+   +......+....+|+
T Consensus       343 ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~  422 (625)
T KOG4422|consen  343 LTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYE  422 (625)
T ss_pred             hccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              1  222    3455667777788888888888877655421    12222  1112 222   222244566777888


Q ss_pred             HHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcC
Q 041804          304 RMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELG  344 (403)
Q Consensus       304 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  344 (403)
                      .|.-.-.-|+..+...++++....|.++-.-.+|..++..|
T Consensus       423 ~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~g  463 (625)
T KOG4422|consen  423 DLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYG  463 (625)
T ss_pred             HhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhh
Confidence            88776667788888888888888888777777776665444

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

Probab=99.68  E-value=1.4e-12  Score=106.70  Aligned_cols=297  Identities=12%  Similarity=0.062  Sum_probs=234.2

Q ss_pred             HHHHHH--hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804           73 MFKRYV--TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus        73 l~~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      +..+..  -.|++.+|+++..+-.+.+......|..-..+--..|+.+.+-.++.+..+.      ...++..+.-+..+
T Consensus        88 ~~egl~~l~eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~------~~~~~l~v~ltrar  161 (400)
T COG3071          88 LNEGLLKLFEGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAEL------AGDDTLAVELTRAR  161 (400)
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhcc------CCCchHHHHHHHHH
Confidence            444444  3699999999999988877667777888888888899999999999888775      34567777888888


Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh-------hhHHHHHHHHh
Q 041804          151 GWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV-------VAYNTVIRAVG  223 (403)
Q Consensus       151 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~ll~~~~  223 (403)
                      .....|+++.|..-++++.+.++. ++........+|.+.|+++.+..++..+.+.|.-.|.       .+|..+++-..
T Consensus       162 lll~~~d~~aA~~~v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~  240 (400)
T COG3071         162 LLLNRRDYPAARENVDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQAR  240 (400)
T ss_pred             HHHhCCCchhHHHHHHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999998877 7778999999999999999999999999999865554       45677777766


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh--CCHHHHHHH
Q 041804          224 VSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL--EKPREILGL  301 (403)
Q Consensus       224 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~--~~~~~a~~~  301 (403)
                      ..+..+.-...++..... .+-++..-.+++.-+.++|+.++|.++..+..+++..|.   ...++...  ++.+.-++.
T Consensus       241 ~~~~~~gL~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~---L~~~~~~l~~~d~~~l~k~  316 (400)
T COG3071         241 DDNGSEGLKTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR---LCRLIPRLRPGDPEPLIKA  316 (400)
T ss_pred             ccccchHHHHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh---HHHHHhhcCCCCchHHHHH
Confidence            666666666666665543 344566677888889999999999999999998877666   33333332  344444444


Q ss_pred             HHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 041804          302 FDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLS  381 (403)
Q Consensus       302 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~  381 (403)
                      .+.-...... ++-.+.+|...|.+.+.+.+|.+.|+...+.  .|+..+|+.+..++.+.|+.++|.+..++....-.+
T Consensus       317 ~e~~l~~h~~-~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~  393 (400)
T COG3071         317 AEKWLKQHPE-DPLLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGEPEEAEQVRREALLLTRQ  393 (400)
T ss_pred             HHHHHHhCCC-ChhHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcC
Confidence            5544443222 4478889999999999999999999987765  799999999999999999999999999988765444


Q ss_pred             CC
Q 041804          382 AK  383 (403)
Q Consensus       382 p~  383 (403)
                      |+
T Consensus       394 ~~  395 (400)
T COG3071         394 PN  395 (400)
T ss_pred             CC
Confidence            44

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

Probab=99.68  E-value=3.3e-13  Score=107.16  Aligned_cols=298  Identities=13%  Similarity=0.120  Sum_probs=226.2

Q ss_pred             hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCCh
Q 041804           79 TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWW  158 (403)
Q Consensus        79 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  158 (403)
                      -.++.++|..+|-+|.+.++.+..+..+|.+.|-+.|..+.|+.+.+.+..+.+.   .......+...|..-|...|-+
T Consensus        47 Ls~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdl---T~~qr~lAl~qL~~Dym~aGl~  123 (389)
T COG2956          47 LSNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDL---TFEQRLLALQQLGRDYMAAGLL  123 (389)
T ss_pred             hhcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCC---chHHHHHHHHHHHHHHHHhhhh
Confidence            3578999999999999988778899999999999999999999998888775321   2223345567788889999999


Q ss_pred             hHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh----hhHHHHHHHHhhcCCHHHHHHH
Q 041804          159 GKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV----VAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      +.|+++|..+.+.+.- -..+...|+..|-...+|++|+++-+++.+.+-.+..    ..|.-+...+....+++.|..+
T Consensus       124 DRAE~~f~~L~de~ef-a~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~  202 (389)
T COG2956         124 DRAEDIFNQLVDEGEF-AEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRAREL  202 (389)
T ss_pred             hHHHHHHHHHhcchhh-hHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            9999999999886543 4567889999999999999999999999887644433    2455666666678899999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCC
Q 041804          235 YREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIR  311 (403)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~  311 (403)
                      +.+..+.+.+ .+..--.+.+.+...|++++|.+.++...+.+..--..+...+..+|   ++.++....+.++.+....
T Consensus       203 l~kAlqa~~~-cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g  281 (389)
T COG2956         203 LKKALQADKK-CVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTG  281 (389)
T ss_pred             HHHHHhhCcc-ceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCC
Confidence            9999987433 44455566788999999999999999999874333345555666666   7888888888888875433


Q ss_pred             CchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh---cCCHHHHHHHHHHHHHcCCCCChh
Q 041804          312 PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID---KGMLDMARKYDEEMFAKGLSAKPR  385 (403)
Q Consensus       312 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~a~~~~~~m~~~~~~p~~~  385 (403)
                        ...-..+...-....-.+.|...+.+-...  +|+...+..+++.-..   .|.+.+....+++|+...++.++.
T Consensus       282 --~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge~l~~~~~  354 (389)
T COG2956         282 --ADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGEQLRRKPR  354 (389)
T ss_pred             --ccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHHHHhhcCC
Confidence              334444444444455566666665555543  6999999999987654   456778888899998875554444

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

Probab=99.68  E-value=9.2e-12  Score=104.14  Aligned_cols=355  Identities=12%  Similarity=0.091  Sum_probs=268.0

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      -|+...|.++|+....   ..|+...|++.|..=.+.+.++.|..++++..-   +.|++.+|---...-.+.|+...|.
T Consensus       154 LgNi~gaRqiferW~~---w~P~eqaW~sfI~fElRykeieraR~IYerfV~---~HP~v~~wikyarFE~k~g~~~~aR  227 (677)
T KOG1915|consen  154 LGNIAGARQIFERWME---WEPDEQAWLSFIKFELRYKEIERARSIYERFVL---VHPKVSNWIKYARFEEKHGNVALAR  227 (677)
T ss_pred             hcccHHHHHHHHHHHc---CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe---ecccHHHHHHHHHHHHhcCcHHHHH
Confidence            3778888898865442   689999999999999999999999999999887   5699999988888888899999999


Q ss_pred             HHHHHHhhcCCC---cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHH
Q 041804           88 GTFNKLDEFGLK---DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREF  164 (403)
Q Consensus        88 ~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  164 (403)
                      ++|+...+.-..   +...+.+....-.++..++.|.-+|.-...+.     ........|..+...=-+.|+.....+.
T Consensus       228 ~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~-----pk~raeeL~k~~~~fEKqfGd~~gIEd~  302 (677)
T KOG1915|consen  228 SVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHI-----PKGRAEELYKKYTAFEKQFGDKEGIEDA  302 (677)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CcccHHHHHHHHHHHHHHhcchhhhHHH
Confidence            999887664322   44455666666667888888888888776642     1122245566666666667776555443


Q ss_pred             --------HHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh-------hhHHHHHHHH---hhcC
Q 041804          165 --------WEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV-------VAYNTVIRAV---GVSE  226 (403)
Q Consensus       165 --------~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~ll~~~---~~~~  226 (403)
                              ++.+.+.++. |-.+|-..++.-...|+.+...++|+..+.. ++|-.       .+|-.+=-++   ....
T Consensus       303 Iv~KRk~qYE~~v~~np~-nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~e  380 (677)
T KOG1915|consen  303 IVGKRKFQYEKEVSKNPY-NYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAE  380 (677)
T ss_pred             HhhhhhhHHHHHHHhCCC-CchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence                    3455555554 7778888888888899999999999999976 55532       1222221122   3578


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH----HhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH---hhCCHHHHH
Q 041804          227 GVDFAMRVYREMREMGCQPSVVTCNTVIKLL----CENGRVREAYAVLAEMPKKGCVPDVITYHCFFR---CLEKPREIL  299 (403)
Q Consensus       227 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~----~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~---~~~~~~~a~  299 (403)
                      +++.+.++++...+. ++....||.-+--.|    .++.++..|.+++.....  ..|-..+|...|.   .+..++.+.
T Consensus       381 d~ertr~vyq~~l~l-IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG--~cPK~KlFk~YIelElqL~efDRcR  457 (677)
T KOG1915|consen  381 DVERTRQVYQACLDL-IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIG--KCPKDKLFKGYIELELQLREFDRCR  457 (677)
T ss_pred             hHHHHHHHHHHHHhh-cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhc--cCCchhHHHHHHHHHHHHhhHHHHH
Confidence            999999999999985 555666666554444    467899999999988764  4788888777665   457889999


Q ss_pred             HHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          300 GLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELG-CSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .++++.++.++. |..+|......-...|+.+.|..+|+...+.. +.-....|.+.|+.=...|.++.|..+++++++.
T Consensus       458 kLYEkfle~~Pe-~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  458 KLYEKFLEFSPE-NCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             HHHHHHHhcChH-hhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh
Confidence            999999998755 77889888888889999999999999998742 2234567778888888999999999999999986


Q ss_pred             C
Q 041804          379 G  379 (403)
Q Consensus       379 ~  379 (403)
                      .
T Consensus       537 t  537 (677)
T KOG1915|consen  537 T  537 (677)
T ss_pred             c
Confidence            3

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

Probab=99.67  E-value=1.2e-12  Score=108.95  Aligned_cols=205  Identities=12%  Similarity=0.102  Sum_probs=154.7

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHH
Q 041804          154 KMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMR  233 (403)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  233 (403)
                      ..|++++|.+.+++....+.. .+...-.+.-.+-..|+.++|++.|-++... +.-+..+...+...|-...+..+|.+
T Consensus       502 ~ngd~dka~~~ykeal~ndas-c~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie  579 (840)
T KOG2003|consen  502 ANGDLDKAAEFYKEALNNDAS-CTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIE  579 (840)
T ss_pred             ecCcHHHHHHHHHHHHcCchH-HHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHH
Confidence            357888999999888876433 2222222334567789999999998877554 23467778888889999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCC---HHHHHHHHHHHHHcCC
Q 041804          234 VYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEK---PREILGLFDRMIESGI  310 (403)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~---~~~a~~~~~~~~~~~~  310 (403)
                      ++-+.... ++.|+...+-|...|-+.|+-..|+..+-+--+. ++-+..+...+-..|-.   +++++.+|++..-  +
T Consensus       580 ~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~ekai~y~ekaal--i  655 (840)
T KOG2003|consen  580 LLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSEKAINYFEKAAL--I  655 (840)
T ss_pred             HHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHh--c
Confidence            98877665 5667889999999999999999999887654432 23355566655555532   5778888887654  6


Q ss_pred             CCchhhHHHHHHHHH-hcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCH
Q 041804          311 RPKMDTYVMLLRKFG-RWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGML  365 (403)
Q Consensus       311 ~~~~~~~~~li~~~~-~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  365 (403)
                      .|+..-|..++..|. +.|++++|.++++...+. ++.|.....-|++.+...|..
T Consensus       656 qp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~dlgl~  710 (840)
T KOG2003|consen  656 QPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAGDLGLK  710 (840)
T ss_pred             CccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhccccch
Confidence            899999999887664 789999999999998765 678889999999998887753

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

Probab=99.67  E-value=2.5e-14  Score=123.96  Aligned_cols=288  Identities=12%  Similarity=0.072  Sum_probs=206.4

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCC-CCCHHHHHHHHHHHHhcCChHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSS-IPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      =++++|+..|..+..  .+..+..+...+..+|...+++++|.++|+.+.+..+. ..+...|.+.+..+-+.   -+--
T Consensus       333 y~~~~A~~~~~klp~--h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~---v~Ls  407 (638)
T KOG1126|consen  333 YNCREALNLFEKLPS--HHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDE---VALS  407 (638)
T ss_pred             HHHHHHHHHHHhhHH--hcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhh---HHHH
Confidence            367899999998553  23344578889999999999999999999999886522 22456677666544322   1222


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHH
Q 041804           88 GTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEE  167 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  167 (403)
                      -+-+.+.+.++..+.+|..+..+|.-+++.+.|++.|++..+       ..+....+|+.+..-+....++|.|...|+.
T Consensus       408 ~Laq~Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQ-------ldp~faYayTLlGhE~~~~ee~d~a~~~fr~  480 (638)
T KOG1126|consen  408 YLAQDLIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQ-------LDPRFAYAYTLLGHESIATEEFDKAMKSFRK  480 (638)
T ss_pred             HHHHHHHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhc-------cCCccchhhhhcCChhhhhHHHHhHHHHHHh
Confidence            233445555555888899998888888888999888888877       3355777888888888888888888888888


Q ss_pred             HHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCH
Q 041804          168 MDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSV  247 (403)
Q Consensus       168 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  247 (403)
                      .+...+. +-.+|--+...|.+.++++.|+-.|+...+.+ +.+.+....+...+-+.|+.|+|+++++++.....+ |+
T Consensus       481 Al~~~~r-hYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~  557 (638)
T KOG1126|consen  481 ALGVDPR-HYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NP  557 (638)
T ss_pred             hhcCCch-hhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-Cc
Confidence            8776444 44555566778888888888888888888764 335566667777788888888898888888876544 33


Q ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH----hhCCHHHHHHHHHHHHHcCCCCc
Q 041804          248 VTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR----CLEKPREILGLFDRMIESGIRPK  313 (403)
Q Consensus       248 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~----~~~~~~~a~~~~~~~~~~~~~~~  313 (403)
                      ..--..+..+...++.++|+..++++++.  .|+..+...++.    .+++.+.|+.-|--+.+...+++
T Consensus       558 l~~~~~~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~  625 (638)
T KOG1126|consen  558 LCKYHRASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGA  625 (638)
T ss_pred             hhHHHHHHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccc
Confidence            33334456666788888888888888875  676655555443    33667777777777766544443

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

Probab=99.63  E-value=5.2e-12  Score=114.31  Aligned_cols=363  Identities=10%  Similarity=0.021  Sum_probs=238.3

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCC--HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC---
Q 041804            7 YANDWKRALEFFNWVETDCHFTHT--TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH---   81 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---   81 (403)
                      .+|+++.|...|....+.   .++  +..+--+.+.+.+.|+++.+...|+.+....  +.+..+...|...|...+   
T Consensus       319 a~Gd~ekA~~yY~~s~k~---~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~--p~~~etm~iLG~Lya~~~~~~  393 (1018)
T KOG2002|consen  319 AQGDFEKAFKYYMESLKA---DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL--PNNYETMKILGCLYAHSAKKQ  393 (1018)
T ss_pred             hhccHHHHHHHHHHHHcc---CCCCccccccchhHHHHHhchHHHHHHHHHHHHHhC--cchHHHHHHHHhHHHhhhhhh
Confidence            456666666666655531   122  2334455566666666666666666666543  222334444444444332   


Q ss_pred             -ChHHH---------------------------------HHHHHHH----hhcCCC-cHHHHHHHHHHHHhcCCHHHHHH
Q 041804           82 -LVNEA---------------------------------MGTFNKL----DEFGLK-DEVSYCNLVDALCEYKHVIEAQE  122 (403)
Q Consensus        82 -~~~~a---------------------------------~~~~~~~----~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~  122 (403)
                       ..+.|                                 +..|...    ...+.+ .+...|.+...+...|+++.|..
T Consensus       394 ~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e~~d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~  473 (1018)
T KOG2002|consen  394 EKRDKASNVLGKVLEQTPVDSEAWLELAQLLEQTDPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALE  473 (1018)
T ss_pred             HHHHHHHHHHHHHHhcccccHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHH
Confidence             22223                                 3333322    222333 66677777777888888999988


Q ss_pred             HHhccccccc-ccc--cccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHH
Q 041804          123 LCFGENKNVG-FSG--LVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKL  199 (403)
Q Consensus       123 ~~~~~~~~~~-~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  199 (403)
                      .|........ ...  .+..++..+--.+....-..++++.|.+.|..+.+..+. -+..|.-++......+...+|...
T Consensus       474 ~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkehp~-YId~ylRl~~ma~~k~~~~ea~~~  552 (1018)
T KOG2002|consen  474 HFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEHPG-YIDAYLRLGCMARDKNNLYEASLL  552 (1018)
T ss_pred             HHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHCch-hHHHHHHhhHHHHhccCcHHHHHH
Confidence            8887665411 011  112244444445666667778999999999999886433 233444444333345778899999


Q ss_pred             HHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHh------------cCcHHHH
Q 041804          200 YKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG-CQPSVVTCNTVIKLLCE------------NGRVREA  266 (403)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~li~~~~~------------~g~~~~a  266 (403)
                      +++....+ ..+...++.+-..+.+...+..|.+-|..+.+.- ..+|+.+.-+|...|.+            .+..++|
T Consensus       553 lk~~l~~d-~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KA  631 (1018)
T KOG2002|consen  553 LKDALNID-SSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKA  631 (1018)
T ss_pred             HHHHHhcc-cCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHH
Confidence            99988763 4455666666668888888888888777776542 23566666666665553            2356788


Q ss_pred             HHHHHhchhcCCCCChhh---HHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          267 YAVLAEMPKKGCVPDVIT---YHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       267 ~~~~~~~~~~~~~p~~~~---~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      +.+|....+.... +...   ..+++...+++.+|..+|....+.... ...+|..+.++|...|++..|+++|+...+.
T Consensus       632 lq~y~kvL~~dpk-N~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~-~~dv~lNlah~~~e~~qy~~AIqmYe~~lkk  709 (1018)
T KOG2002|consen  632 LQLYGKVLRNDPK-NMYAANGIGIVLAEKGRFSEARDIFSQVREATSD-FEDVWLNLAHCYVEQGQYRLAIQMYENCLKK  709 (1018)
T ss_pred             HHHHHHHHhcCcc-hhhhccchhhhhhhccCchHHHHHHHHHHHHHhh-CCceeeeHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999888765211 2222   335566669999999999999987553 5568899999999999999999999988664


Q ss_pred             -CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          344 -GCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       344 -~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                       .-..+..+...|.+++.+.|.+.+|.+.+......
T Consensus       710 f~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~  745 (1018)
T KOG2002|consen  710 FYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHL  745 (1018)
T ss_pred             hcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence             44557889999999999999999999998877764

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

Probab=99.62  E-value=4.5e-12  Score=105.62  Aligned_cols=246  Identities=10%  Similarity=0.048  Sum_probs=168.5

Q ss_pred             CChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHHHHHHHhcCCH-HHH
Q 041804           45 FEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNLVDALCEYKHV-IEA  120 (403)
Q Consensus        45 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~-~~a  120 (403)
                      ...+++..=.+...+.| .+.+...-+....+.-...++++|+.+|+++.+.+|-   |..+|+.++-+-...... --|
T Consensus       241 ~q~~e~~~k~e~l~~~g-f~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA  319 (559)
T KOG1155|consen  241 HQHEEALQKKERLSSVG-FPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLA  319 (559)
T ss_pred             HHHHHHHHHHHHHHhcc-CCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHH
Confidence            34555555555555554 3333333444445555677888888888888887654   777777776554332221 122


Q ss_pred             HHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHH
Q 041804          121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLY  200 (403)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  200 (403)
                      ..+++           ..+-.+.|+..+.+.|+-.++.++|...|++..+.++. ....|+.|..-|...++...|..-|
T Consensus       320 ~~v~~-----------idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~-~~~aWTLmGHEyvEmKNt~AAi~sY  387 (559)
T KOG1155|consen  320 QNVSN-----------IDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPK-YLSAWTLMGHEYVEMKNTHAAIESY  387 (559)
T ss_pred             HHHHH-----------hccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcc-hhHHHHHhhHHHHHhcccHHHHHHH
Confidence            22221           11233446777788888888899999999999888777 6778888889999999999999999


Q ss_pred             HHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC
Q 041804          201 KEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP  280 (403)
Q Consensus       201 ~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p  280 (403)
                      +...+-. +.|-..|-.|-++|.-.+.+.-|+-.|++..+.. +.|...|.+|..+|.+.++.++|++.|.+....|-. 
T Consensus       388 RrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-  464 (559)
T KOG1155|consen  388 RRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-  464 (559)
T ss_pred             HHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-
Confidence            9888874 5577888889999998898888999998888763 337888999999999999999999999887765422 


Q ss_pred             ChhhHHHHHHhh---CCHHHHHHHHHHHH
Q 041804          281 DVITYHCFFRCL---EKPREILGLFDRMI  306 (403)
Q Consensus       281 ~~~~~~~l~~~~---~~~~~a~~~~~~~~  306 (403)
                      +...+..+-..+   .+.++|...|++-+
T Consensus       465 e~~~l~~LakLye~l~d~~eAa~~yek~v  493 (559)
T KOG1155|consen  465 EGSALVRLAKLYEELKDLNEAAQYYEKYV  493 (559)
T ss_pred             chHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            223333333332   44555555555444

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

Probab=99.62  E-value=6.4e-13  Score=115.45  Aligned_cols=280  Identities=10%  Similarity=0.034  Sum_probs=140.2

Q ss_pred             ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHHHHHHHhcCCHHHHHH
Q 041804           46 EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNLVDALCEYKHVIEAQE  122 (403)
Q Consensus        46 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~  122 (403)
                      +..+|...|..+.+.-  .-+......+..+|...+++++|+++|+.+.+..+-   +.++|.+.+.-+-+.-    ++.
T Consensus       334 ~~~~A~~~~~klp~h~--~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v----~Ls  407 (638)
T KOG1126|consen  334 NCREALNLFEKLPSHH--YNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEV----ALS  407 (638)
T ss_pred             HHHHHHHHHHhhHHhc--CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhH----HHH
Confidence            4456666666654432  122244455666666666666666666666665543   5566666655443211    111


Q ss_pred             HH-hcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHH
Q 041804          123 LC-FGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYK  201 (403)
Q Consensus       123 ~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  201 (403)
                      .+ +.+..       ..+..+.+|.++.++|.-.++.+.|++.|++....++. ...+|+.+..-+.....+|.|...|+
T Consensus       408 ~Laq~Li~-------~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~-faYayTLlGhE~~~~ee~d~a~~~fr  479 (638)
T KOG1126|consen  408 YLAQDLID-------TDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPR-FAYAYTLLGHESIATEEFDKAMKSFR  479 (638)
T ss_pred             HHHHHHHh-------hCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCc-cchhhhhcCChhhhhHHHHhHHHHHH
Confidence            11 12222       22344455666666666666666666666666655433 55566666666666666666666666


Q ss_pred             HHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC
Q 041804          202 EMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD  281 (403)
Q Consensus       202 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~  281 (403)
                      ..+... +-+...|--+...|.+.++++.|+-.|+.+.+.++. +.+....+...+-+.|+.++|+.++++......+--
T Consensus       480 ~Al~~~-~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~-nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~  557 (638)
T KOG1126|consen  480 KALGVD-PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPS-NSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNP  557 (638)
T ss_pred             hhhcCC-chhhHHHHhhhhheeccchhhHHHHHHHhhhcCCcc-chhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCc
Confidence            554331 111223333444556666666666666666654332 444445555555566666666666665543321111


Q ss_pred             hhhH--HHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHh
Q 041804          282 VITY--HCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEE  342 (403)
Q Consensus       282 ~~~~--~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  342 (403)
                      ..-|  ..++-..++.++|+..++++.+.-++ +...|..+...|-+.|+.+.|+.-|..+.+
T Consensus       558 l~~~~~~~il~~~~~~~eal~~LEeLk~~vP~-es~v~~llgki~k~~~~~~~Al~~f~~A~~  619 (638)
T KOG1126|consen  558 LCKYHRASILFSLGRYVEALQELEELKELVPQ-ESSVFALLGKIYKRLGNTDLALLHFSWALD  619 (638)
T ss_pred             hhHHHHHHHHHhhcchHHHHHHHHHHHHhCcc-hHHHHHHHHHHHHHHccchHHHHhhHHHhc
Confidence            1111  12233334445555555544443111 233344444445555555555444444443

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

Probab=99.59  E-value=1.3e-10  Score=101.21  Aligned_cols=353  Identities=9%  Similarity=-0.021  Sum_probs=269.4

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHH
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEA   86 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a   86 (403)
                      ..+.++-|+.+|....+  -++-+...|...+..--..|..++...+|++....-  +.....|-....-+-..|+...|
T Consensus       528 k~~~~~carAVya~alq--vfp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~--pkae~lwlM~ake~w~agdv~~a  603 (913)
T KOG0495|consen  528 KRPAIECARAVYAHALQ--VFPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQC--PKAEILWLMYAKEKWKAGDVPAA  603 (913)
T ss_pred             hcchHHHHHHHHHHHHh--hccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC--CcchhHHHHHHHHHHhcCCcHHH
Confidence            44566777778877774  234456677777777777888888888998888863  45666777777888888999999


Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHH
Q 041804           87 MGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWE  166 (403)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  166 (403)
                      ..++....+..+.+...|...++....+.+++.|..+|.+....        .|+..+|.--+..---.++.++|.++++
T Consensus       604 r~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~~--------sgTeRv~mKs~~~er~ld~~eeA~rllE  675 (913)
T KOG0495|consen  604 RVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARSI--------SGTERVWMKSANLERYLDNVEEALRLLE  675 (913)
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--------CCcchhhHHHhHHHHHhhhHHHHHHHHH
Confidence            99999998888778899999999999999999999998887654        5667777777777777788999999998


Q ss_pred             HHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCC
Q 041804          167 EMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS  246 (403)
Q Consensus       167 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  246 (403)
                      +..+.-+. -...|..+...+-+.++.+.|.+.|..-.+. ++-....|-.+...=-+.|.+-.|..+++...-.++. +
T Consensus       676 e~lk~fp~-f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ipLWllLakleEk~~~~~rAR~ildrarlkNPk-~  752 (913)
T KOG0495|consen  676 EALKSFPD-FHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKNPK-N  752 (913)
T ss_pred             HHHHhCCc-hHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCCC-c
Confidence            88775322 3456777888888888888888888776654 3444556777777777888999999999998877544 7


Q ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHh
Q 041804          247 VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGR  326 (403)
Q Consensus       247 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  326 (403)
                      ...|-..|++-.+.|+.+.|..+..+..+. ++.+...|.--|....+.+.--...+.+.+.  .-|+.....+...|..
T Consensus       753 ~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~~~rkTks~DALkkc--e~dphVllaia~lfw~  829 (913)
T KOG0495|consen  753 ALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPRPQRKTKSIDALKKC--EHDPHVLLAIAKLFWS  829 (913)
T ss_pred             chhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccCcccchHHHHHHHhc--cCCchhHHHHHHHHHH
Confidence            888999999999999999999888877654 2334556666665554433322223333332  3466777788888999


Q ss_pred             cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          327 WGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       327 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      ..++++|.+.|.+..+.+ +.+-.+|..+...+.++|.-++-.+++.+....
T Consensus       830 e~k~~kar~Wf~Ravk~d-~d~GD~wa~fykfel~hG~eed~kev~~~c~~~  880 (913)
T KOG0495|consen  830 EKKIEKAREWFERAVKKD-PDNGDAWAWFYKFELRHGTEEDQKEVLKKCETA  880 (913)
T ss_pred             HHHHHHHHHHHHHHHccC-CccchHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            999999999999999875 445678888889999999999888999888763

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

Probab=99.59  E-value=9.7e-12  Score=103.57  Aligned_cols=378  Identities=10%  Similarity=0.032  Sum_probs=221.8

Q ss_pred             cccccccccHHHHHHhhhhhcccC-CCcCC--HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHH
Q 041804            2 ETLSCYANDWKRALEFFNWVETDC-HFTHT--TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYV   78 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~-~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~   78 (403)
                      +.++.+++.+.+|+++|+....+- .+..+  ..+.+.+.-.+.+.|+++.|+..|+...+..   |+..+-..|+-++.
T Consensus       244 gni~~kkr~fskaikfyrmaldqvpsink~~rikil~nigvtfiq~gqy~dainsfdh~m~~~---pn~~a~~nl~i~~f  320 (840)
T KOG2003|consen  244 GNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILNNIGVTFIQAGQYDDAINSFDHCMEEA---PNFIAALNLIICAF  320 (840)
T ss_pred             cceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHhhcCeeEEecccchhhHhhHHHHHHhC---ccHHhhhhhhhhhe
Confidence            567778889999999998776421 11111  2345555556779999999999999998865   99887777777788


Q ss_pred             hcCChHHHHHHHHHHhhcCCC-------------cHHHHHHH-----HHHHHhcC--CHHHHHHHHhccccccccccccc
Q 041804           79 TAHLVNEAMGTFNKLDEFGLK-------------DEVSYCNL-----VDALCEYK--HVIEAQELCFGENKNVGFSGLVE  138 (403)
Q Consensus        79 ~~~~~~~a~~~~~~~~~~~~~-------------~~~~~~~l-----~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~  138 (403)
                      .-|+.++..+.|.+|......             +....+..     ++-.-+.+  +.+++.-.--++...      .+
T Consensus       321 ~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiap------vi  394 (840)
T KOG2003|consen  321 AIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAP------VI  394 (840)
T ss_pred             ecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhcc------cc
Confidence            889999999999998765431             11111111     11111111  112221111111111      11


Q ss_pred             CcchH---------------------HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHH-----------
Q 041804          139 MNKTK---------------------IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI-----------  186 (403)
Q Consensus       139 ~~~~~---------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-----------  186 (403)
                      .|+..                     .--.-..-+.+.|+++.|.+++.-+.+.+-+.-...-+.|-..           
T Consensus       395 ~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~  474 (840)
T KOG2003|consen  395 APDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFAD  474 (840)
T ss_pred             ccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhH
Confidence            11110                     0112235678899999998888877655322111111111111           


Q ss_pred             -------------------------HHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          187 -------------------------MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       187 -------------------------~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                                               ...+|++++|.+.|++.+...-......|++ --.+-..|+.++|+..|-++...
T Consensus       475 aqqyad~aln~dryn~~a~~nkgn~~f~ngd~dka~~~ykeal~ndasc~ealfni-glt~e~~~~ldeald~f~klh~i  553 (840)
T KOG2003|consen  475 AQQYADIALNIDRYNAAALTNKGNIAFANGDLDKAAEFYKEALNNDASCTEALFNI-GLTAEALGNLDEALDCFLKLHAI  553 (840)
T ss_pred             HHHHHHHHhcccccCHHHhhcCCceeeecCcHHHHHHHHHHHHcCchHHHHHHHHh-cccHHHhcCHHHHHHHHHHHHHH
Confidence                                     1224667777777777765532222222222 22344667777777777665443


Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHH
Q 041804          242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYV  318 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~  318 (403)
                       +..+..+...+...|--..+...|++++.+.... ++.|+...+.+-.-|   |+..+|.+.+-.--+ -++.+..+..
T Consensus       554 -l~nn~evl~qianiye~led~aqaie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~ie  630 (840)
T KOG2003|consen  554 -LLNNAEVLVQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIE  630 (840)
T ss_pred             -HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHH
Confidence             2235556666667777777777777777655432 222455555555544   333344443322211 1345667777


Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHH-HhcCCHHHHHHHHHHHHHcCCCCChhhHHHHHHHhC
Q 041804          319 MLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDAL-IDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQG  395 (403)
Q Consensus       319 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~~~~~~~  395 (403)
                      .|...|....-+++++..|++..-  +.|+..-|..++..| .+.|++.+|..+++..-.+ +.-+....-.+.++.+
T Consensus       631 wl~ayyidtqf~ekai~y~ekaal--iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~  705 (840)
T KOG2003|consen  631 WLAAYYIDTQFSEKAINYFEKAAL--IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAG  705 (840)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHh--cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhc
Confidence            777788888888889998887654  589999999887654 5699999999999987654 4334444444444443

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.59  E-value=2.8e-12  Score=104.91  Aligned_cols=198  Identities=12%  Similarity=-0.027  Sum_probs=91.5

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHH
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNM  147 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (403)
                      ..+..+...+...|++++|...+++..+..+.+...+..+...+...|++++|.+.+++....       .+.+...+..
T Consensus        32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~-------~~~~~~~~~~  104 (234)
T TIGR02521        32 KIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTL-------NPNNGDVLNN  104 (234)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-------CCCCHHHHHH
Confidence            334444444444444444444444444444334444444444444444444444444444331       1223334444


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcC
Q 041804          148 ILRGWFKMSWWGKCREFWEEMDKRGVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSE  226 (403)
Q Consensus       148 l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  226 (403)
                      +...+...|++++|.+.+++....... .....+..+..++...|++++|...+++..... +.+...+..+...+...|
T Consensus       105 ~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  183 (234)
T TIGR02521       105 YGTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRG  183 (234)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcC
Confidence            444444455555555555444432111 122334444445555555555555555554432 223334445555555555


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          227 GVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       227 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      ++++|...+++..+. .+.+...+..+...+...|+.+.|..+.+.+.
T Consensus       184 ~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  230 (234)
T TIGR02521       184 QYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQ  230 (234)
T ss_pred             CHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            555555555555544 22234444444555555555555555554443

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.

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

Probab=99.58  E-value=2.7e-10  Score=99.30  Aligned_cols=354  Identities=11%  Similarity=0.016  Sum_probs=244.8

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhh----hCCCCCCCHH----------------
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMK----DNPSSIPNHA----------------   68 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~----~~~~~~~~~~----------------   68 (403)
                      ..|+.|.++++...  ..++.+..+|.+-...=-.+|+.+...++.++-.    ..| +..+..                
T Consensus       420 etYenAkkvLNkaR--e~iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ng-v~i~rdqWl~eAe~~e~agsv~  496 (913)
T KOG0495|consen  420 ETYENAKKVLNKAR--EIIPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANG-VEINRDQWLKEAEACEDAGSVI  496 (913)
T ss_pred             HHHHHHHHHHHHHH--hhCCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcc-eeecHHHHHHHHHHHhhcCChh
Confidence            34566666666665  3355566666666666666666666655554322    122 333333                


Q ss_pred             ---------------------HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcc
Q 041804           69 ---------------------TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGE  127 (403)
Q Consensus        69 ---------------------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  127 (403)
                                           +|+.-...|.+.+.++-|..+|....+..+.+...|......--..|..+....+|+++
T Consensus       497 TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqka  576 (913)
T KOG0495|consen  497 TCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQKA  576 (913)
T ss_pred             hHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence                                 44455555666666677777777776666666677777766666677777777777777


Q ss_pred             cccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC
Q 041804          128 NKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG  207 (403)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  207 (403)
                      ..       ..+.....|-.....+-..|+...|..++.+..+..+. +...|..-+.....+..++.|..+|.+.... 
T Consensus       577 v~-------~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-seeiwlaavKle~en~e~eraR~llakar~~-  647 (913)
T KOG0495|consen  577 VE-------QCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVKLEFENDELERARDLLAKARSI-  647 (913)
T ss_pred             HH-------hCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHHHhhccccHHHHHHHHHHHhcc-
Confidence            66       33455556666677777778888888888888877666 7778888888888888888888888877764 


Q ss_pred             CCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHH
Q 041804          208 IKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHC  287 (403)
Q Consensus       208 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~  287 (403)
                       .|+..+|.--+..---.++.++|.+++++..+. ++.-...|-.+.+.+-+.++++.|.+.|..-.+.  .|+....=.
T Consensus       648 -sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~-fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~--cP~~ipLWl  723 (913)
T KOG0495|consen  648 -SGTERVWMKSANLERYLDNVEEALRLLEEALKS-FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKK--CPNSIPLWL  723 (913)
T ss_pred             -CCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh-CCchHHHHHHHhHHHHHHHHHHHHHHHHHhcccc--CCCCchHHH
Confidence             567777766666666678888888888888775 2223456777778888888888888888765543  555444434


Q ss_pred             HHHhh----CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc----C---------------
Q 041804          288 FFRCL----EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL----G---------------  344 (403)
Q Consensus       288 l~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~---------------  344 (403)
                      ++..+    +..-.|..++++..-.+.+ +...|...|+.-.+.|+.+.|..+..+..+.    |               
T Consensus       724 lLakleEk~~~~~rAR~ildrarlkNPk-~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~~~r  802 (913)
T KOG0495|consen  724 LLAKLEEKDGQLVRARSILDRARLKNPK-NALLWLESIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPRPQR  802 (913)
T ss_pred             HHHHHHHHhcchhhHHHHHHHHHhcCCC-cchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccCccc
Confidence            44333    4567888899888877655 7788999999999999999888777655432    1               


Q ss_pred             ----------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          345 ----------CSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       345 ----------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                                ...|+...-.+...+....+++.|.+.|.+.++.+
T Consensus       803 kTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d  847 (913)
T KOG0495|consen  803 KTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKD  847 (913)
T ss_pred             chHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence                      23566677777788888889999999999988754

>PRK12370 invasion protein regulator; Provisional

Probab=99.57  E-value=8.4e-12  Score=114.33  Aligned_cols=248  Identities=13%  Similarity=0.074  Sum_probs=137.4

Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh---------cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE---------YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      +.++|+..|++..+.++.+...|..+..++..         .+++++|...+++...       ..+.+..++..+...+
T Consensus       276 ~~~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~-------ldP~~~~a~~~lg~~~  348 (553)
T PRK12370        276 SLQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE-------LDHNNPQALGLLGLIN  348 (553)
T ss_pred             HHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh-------cCCCCHHHHHHHHHHH
Confidence            34567777777777666666666655554432         2335667776666665       3345556666666666


Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHH
Q 041804          153 FKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAM  232 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~  232 (403)
                      ...|++++|...|++..+.++. +...+..+..++...|++++|...+++..+.... +...+..++..+...|++++|.
T Consensus       349 ~~~g~~~~A~~~~~~Al~l~P~-~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~-~~~~~~~~~~~~~~~g~~eeA~  426 (553)
T PRK12370        349 TIHSEYIVGSLLFKQANLLSPI-SADIKYYYGWNLFMAGQLEEALQTINECLKLDPT-RAAAGITKLWITYYHTGIDDAI  426 (553)
T ss_pred             HHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHhccCHHHHH
Confidence            7777777777777777666544 5556666666777777777777777777665321 2222223333445566777777


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHH-Hh-hCCHHHHHHHHHHHHHc-C
Q 041804          233 RVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFF-RC-LEKPREILGLFDRMIES-G  309 (403)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~-~~-~~~~~~a~~~~~~~~~~-~  309 (403)
                      ..++++.+...+-+...+..+..++...|+.++|...+.++...  .|+.......+ .. +...+++...++.+.+. .
T Consensus       427 ~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~a~~~l~~ll~~~~  504 (553)
T PRK12370        427 RLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEYCQNSERALPTIREFLESEQ  504 (553)
T ss_pred             HHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHHhccHHHHHHHHHHHHHHhh
Confidence            77776665432223444555666666777777777777665443  33333222222 22 23334555555555431 1


Q ss_pred             CCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          310 IRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       310 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      ..+....+  +-..+.-.|+.+.+... +++.+.
T Consensus       505 ~~~~~~~~--~~~~~~~~g~~~~~~~~-~~~~~~  535 (553)
T PRK12370        505 RIDNNPGL--LPLVLVAHGEAIAEKMW-NKFKNE  535 (553)
T ss_pred             HhhcCchH--HHHHHHHHhhhHHHHHH-HHhhcc
Confidence            12222222  23334445555555544 666543

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

Probab=99.57  E-value=6e-11  Score=97.34  Aligned_cols=297  Identities=11%  Similarity=0.019  Sum_probs=221.8

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      +....|+|..|.+....... ++-.| ...|..-+.+-.+.|+.+.+-.++.+..+.. ..++....-+........|+.
T Consensus        93 ~~l~eG~~~qAEkl~~rnae-~~e~p-~l~~l~aA~AA~qrgd~~~an~yL~eaae~~-~~~~l~v~ltrarlll~~~d~  169 (400)
T COG3071          93 LKLFEGDFQQAEKLLRRNAE-HGEQP-VLAYLLAAEAAQQRGDEDRANRYLAEAAELA-GDDTLAVELTRARLLLNRRDY  169 (400)
T ss_pred             HHHhcCcHHHHHHHHHHhhh-cCcch-HHHHHHHHHHHHhcccHHHHHHHHHHHhccC-CCchHHHHHHHHHHHHhCCCc
Confidence            34457999999999987653 43332 4456666778889999999999999999864 246677778888899999999


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhccccccccccc-ccCcchHHHHHHHHHHHhcCChhHHH
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGL-VEMNKTKIYNMILRGWFKMSWWGKCR  162 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~  162 (403)
                      +.|..-+.++.+.++.++.......++|.+.|++.....++.++.+..-..+. -......+|+.++.-....+..+.-.
T Consensus       170 ~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~  249 (400)
T COG3071         170 PAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLK  249 (400)
T ss_pred             hhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHH
Confidence            99999999999999889999999999999999999999999998876321110 01123345777777777777777766


Q ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          163 EFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      ..|+..... ..-++..-..++.-+.+.|+.++|.++.++..+.+..|+..    ..-.+.+.++...-.+..+.-.+..
T Consensus       250 ~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~~~~l~~~d~~~l~k~~e~~l~~h  324 (400)
T COG3071         250 TWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RLIPRLRPGDPEPLIKAAEKWLKQH  324 (400)
T ss_pred             HHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HHHhhcCCCCchHHHHHHHHHHHhC
Confidence            777776543 22255667778888889999999999999888886665521    1223456777777777777666552


Q ss_pred             CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHH
Q 041804          243 CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLR  322 (403)
Q Consensus       243 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  322 (403)
                       +-++..+.+|...|.+.+.|.+|...|+...+.                                  .|+..+|+.+..
T Consensus       325 -~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~----------------------------------~~s~~~~~~la~  369 (400)
T COG3071         325 -PEDPLLLSTLGRLALKNKLWGKASEALEAALKL----------------------------------RPSASDYAELAD  369 (400)
T ss_pred             -CCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhc----------------------------------CCChhhHHHHHH
Confidence             235578888899999999999999888865543                                  467777777778


Q ss_pred             HHHhcCCcchHHHHHHHHHhc
Q 041804          323 KFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       323 ~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      ++.+.|+..+|.+..++....
T Consensus       370 ~~~~~g~~~~A~~~r~e~L~~  390 (400)
T COG3071         370 ALDQLGEPEEAEQVRREALLL  390 (400)
T ss_pred             HHHHcCChHHHHHHHHHHHHH
Confidence            888888888888777776543

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

Probab=99.56  E-value=7.1e-11  Score=99.30  Aligned_cols=360  Identities=13%  Similarity=0.035  Sum_probs=230.0

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCC-HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH-HHHHHHHHHHHhcCC
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHT-TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH-ATFRIMFKRYVTAHL   82 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~   82 (403)
                      +.+++++++|++.|.+...   ..|+ +..|.....+|...|++++..+--....+..   |+- .++..-.+++-..|+
T Consensus       125 ~f~~kkY~eAIkyY~~AI~---l~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~---P~Y~KAl~RRA~A~E~lg~  198 (606)
T KOG0547|consen  125 FFRNKKYDEAIKYYTQAIE---LCPDEPIFYSNRAACYESLGDWEKVIEDCTKALELN---PDYVKALLRRASAHEQLGK  198 (606)
T ss_pred             hhhcccHHHHHHHHHHHHh---cCCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcC---cHHHHHHHHHHHHHHhhcc
Confidence            4567999999999999985   5777 8889999999999999999998888887754   653 455555666666666


Q ss_pred             hHHHHHHHHH-------------------------------HhhcCCC---cHHHHHHHHHHHHh--------c---C--
Q 041804           83 VNEAMGTFNK-------------------------------LDEFGLK---DEVSYCNLVDALCE--------Y---K--  115 (403)
Q Consensus        83 ~~~a~~~~~~-------------------------------~~~~~~~---~~~~~~~l~~~~~~--------~---~--  115 (403)
                      +++|+.=..-                               +.+.+++   ......+....+..        .   +  
T Consensus       199 ~~eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~~~~~~ksDa  278 (606)
T KOG0547|consen  199 FDEALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLFDNKSDKSDA  278 (606)
T ss_pred             HHHHHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccccCCCccchh
Confidence            6655432111                               1112222   22222222222210        0   0  


Q ss_pred             CHHHHHHHHhcccccc----------cccccccCc--c---------hHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC
Q 041804          116 HVIEAQELCFGENKNV----------GFSGLVEMN--K---------TKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV  174 (403)
Q Consensus       116 ~~~~a~~~~~~~~~~~----------~~~~~~~~~--~---------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  174 (403)
                      ...++.+.+.......          ...+....+  +         ..+.......+.-.|+.-.|..-|+..++....
T Consensus       279 ~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~~~~I~l~~~  358 (606)
T KOG0547|consen  279 ALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDFDAAIKLDPA  358 (606)
T ss_pred             hHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhHHHHHhcCcc
Confidence            0111111111110000          000000011  1         122222233344568888888888888887766


Q ss_pred             CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 041804          175 KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVI  254 (403)
Q Consensus       175 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  254 (403)
                      ++. .|--+...|....+.++..+.|....+.+ +-|..+|..=.+.+.-.++++.|..-|++....... +...|-.+.
T Consensus       359 ~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~ld-p~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~pe-~~~~~iQl~  435 (606)
T KOG0547|consen  359 FNS-LYIKRAAAYADENQSEKMWKDFNKAEDLD-PENPDVYYHRGQMRFLLQQYEEAIADFQKAISLDPE-NAYAYIQLC  435 (606)
T ss_pred             cch-HHHHHHHHHhhhhccHHHHHHHHHHHhcC-CCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcChh-hhHHHHHHH
Confidence            433 37777778889999999999999988875 446667777777777888999999999988876332 556666666


Q ss_pred             HHHHhcCcHHHHHHHHHhchhcCCCCC-hhhHHHHHHhh---CCHHHHHHHHHHHHHcCCC-----Cch--hhHHHHHHH
Q 041804          255 KLLCENGRVREAYAVLAEMPKKGCVPD-VITYHCFFRCL---EKPREILGLFDRMIESGIR-----PKM--DTYVMLLRK  323 (403)
Q Consensus       255 ~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~-----~~~--~~~~~li~~  323 (403)
                      .+..+.+.++++...|++..++  -|+ +..|+..-..+   ++++.|.+.|+..++....     .+.  .+.-.++..
T Consensus       436 ~a~Yr~~k~~~~m~~Fee~kkk--FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~  513 (606)
T KOG0547|consen  436 CALYRQHKIAESMKTFEEAKKK--FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVL  513 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHh--CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhh
Confidence            6677888999999999998765  233 33444443333   6688899999888764221     121  122222222


Q ss_pred             HHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          324 FGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       324 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      - -.+++..|.+++++..+.+ +-....|..|...-.+.|+.++|+++|++...
T Consensus       514 q-wk~d~~~a~~Ll~KA~e~D-pkce~A~~tlaq~~lQ~~~i~eAielFEksa~  565 (606)
T KOG0547|consen  514 Q-WKEDINQAENLLRKAIELD-PKCEQAYETLAQFELQRGKIDEAIELFEKSAQ  565 (606)
T ss_pred             c-hhhhHHHHHHHHHHHHccC-chHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            2 2388999999999998764 34567889999999999999999999997654

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

Probab=99.55  E-value=1.1e-11  Score=103.28  Aligned_cols=252  Identities=9%  Similarity=0.017  Sum_probs=163.8

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC-CHHHHHHHHHHHHhcCCh-HHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP-NHATFRIMFKRYVTAHLV-NEA   86 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~-~~a   86 (403)
                      .+.++++.-.+.... .|++.+...-+....+.-...++++|+.+|+++..+++... |..+|..++-.-...... -.|
T Consensus       241 ~q~~e~~~k~e~l~~-~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA  319 (559)
T KOG1155|consen  241 HQHEEALQKKERLSS-VGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLA  319 (559)
T ss_pred             HHHHHHHHHHHHHHh-ccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHH
Confidence            356667666666663 77777777777777788888999999999999998863322 455666555332221111 111


Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHH
Q 041804           87 MGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWE  166 (403)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  166 (403)
                      ..++    ..+--.+.|...+.+-|+-.++.++|...|++..+       -.+....+|+.+..-|....+...|.+.++
T Consensus       320 ~~v~----~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALk-------LNp~~~~aWTLmGHEyvEmKNt~AAi~sYR  388 (559)
T KOG1155|consen  320 QNVS----NIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALK-------LNPKYLSAWTLMGHEYVEMKNTHAAIESYR  388 (559)
T ss_pred             HHHH----HhccCCccceeeehhHHHHHHhHHHHHHHHHHHHh-------cCcchhHHHHHhhHHHHHhcccHHHHHHHH
Confidence            1111    11112566666667777777777777777776665       335556667777777777777777777777


Q ss_pred             HHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCC
Q 041804          167 EMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS  246 (403)
Q Consensus       167 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  246 (403)
                      ...+.++. |-..|-.|..+|.-.+.+.-|+-.|++..... +-|...|.+|..+|.+.++.++|.+.|......|- .+
T Consensus       389 rAvdi~p~-DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d-te  465 (559)
T KOG1155|consen  389 RAVDINPR-DYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD-TE  465 (559)
T ss_pred             HHHhcCch-hHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc-cc
Confidence            77766655 66777777777777777777777777766652 34566777777777777777777777777766542 24


Q ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          247 VVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       247 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      ...+..|.+.|-+.++..+|...|....+
T Consensus       466 ~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  466 GSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             hHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            56666777777777777777766665443

>PRK12370 invasion protein regulator; Provisional

Probab=99.55  E-value=7.3e-12  Score=114.71  Aligned_cols=248  Identities=10%  Similarity=0.029  Sum_probs=168.6

Q ss_pred             hHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh---------cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH
Q 041804           48 DLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT---------AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI  118 (403)
Q Consensus        48 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  118 (403)
                      ++|...|++..+..  +.+...|..+..++..         .+++++|...+++..+.++.+..++..+..++...|+++
T Consensus       278 ~~A~~~~~~Al~ld--P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~~~  355 (553)
T PRK12370        278 QQALKLLTQCVNMS--PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINTIHSEYI  355 (553)
T ss_pred             HHHHHHHHHHHhcC--CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccCHH
Confidence            67888888888765  2334556666555442         244788899999888888778888888888888888999


Q ss_pred             HHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHH
Q 041804          119 EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVK  198 (403)
Q Consensus       119 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  198 (403)
                      +|...+++...       ..+.+...+..+...+...|++++|...+++..+.++. +...+..++..+...|++++|..
T Consensus       356 ~A~~~~~~Al~-------l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~-~~~~~~~~~~~~~~~g~~eeA~~  427 (553)
T PRK12370        356 VGSLLFKQANL-------LSPISADIKYYYGWNLFMAGQLEEALQTINECLKLDPT-RAAAGITKLWITYYHTGIDDAIR  427 (553)
T ss_pred             HHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHhccCHHHHHH
Confidence            99988888776       33556677888888888889999999999988887655 33333444555667888888998


Q ss_pred             HHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc-C
Q 041804          199 LYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK-G  277 (403)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~  277 (403)
                      .++++.....+-+...+..+..++...|+.++|...+..+.... +.+....+.+...|...|  ++|...++.+.+. .
T Consensus       428 ~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~~~  504 (553)
T PRK12370        428 LGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQE-ITGLIAVNLLYAEYCQNS--ERALPTIREFLESEQ  504 (553)
T ss_pred             HHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhcc-chhHHHHHHHHHHHhccH--HHHHHHHHHHHHHhh
Confidence            88887765322234456667777788899999999888876542 123344455556666666  4777767665532 2


Q ss_pred             CCCChhhHHHHHHhh-CCHHHHHHHHHHHHHcC
Q 041804          278 CVPDVITYHCFFRCL-EKPREILGLFDRMIESG  309 (403)
Q Consensus       278 ~~p~~~~~~~l~~~~-~~~~~a~~~~~~~~~~~  309 (403)
                      ..|....+..++.++ ++.+.+..+ +++.+.+
T Consensus       505 ~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        505 RIDNNPGLLPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             HhhcCchHHHHHHHHHhhhHHHHHH-HHhhccc
Confidence            233333444555544 455444444 7776654

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

Probab=99.54  E-value=1.1e-12  Score=104.42  Aligned_cols=230  Identities=10%  Similarity=-0.025  Sum_probs=196.0

Q ss_pred             HHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhc
Q 041804           35 NSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEY  114 (403)
Q Consensus        35 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~  114 (403)
                      +.+..+|.+.|-+.+|.+.|+.....-   |-+.||..|-++|.+..++..|+.+|.+-.+.-+.+........+.+-..
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~---~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam  303 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQF---PHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAM  303 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcC---CchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHH
Confidence            577889999999999999999888754   88889999999999999999999999998887766888888888899999


Q ss_pred             CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChh
Q 041804          115 KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPW  194 (403)
Q Consensus       115 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  194 (403)
                      ++.++|.++++...+       ..+.++.....+...|.-.++++.|.++++++.+.|+. +...|+.+.-+|...++++
T Consensus       304 ~~~~~a~~lYk~vlk-------~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D  375 (478)
T KOG1129|consen  304 EQQEDALQLYKLVLK-------LHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQID  375 (478)
T ss_pred             HhHHHHHHHHHHHHh-------cCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchh
Confidence            999999999988877       44667777788888888999999999999999999988 8889999999999999999


Q ss_pred             HHHHHHHHHHHcCCCCCh--hhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHh
Q 041804          195 KAVKLYKEMKKKGIKMDV--VAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAE  272 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  272 (403)
                      -++.-|.+....--.|+.  .+|-.+-......||+..|.+.|+-...++.. +...+|.|.-.-.+.|++++|..++..
T Consensus       376 ~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ealnNLavL~~r~G~i~~Arsll~~  454 (478)
T KOG1129|consen  376 LVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEALNNLAVLAARSGDILGARSLLNA  454 (478)
T ss_pred             hhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHHHHhHHHHHhhcCchHHHHHHHHH
Confidence            999999988876444443  46767777778889999999999988877543 667888888888899999999999988


Q ss_pred             chhc
Q 041804          273 MPKK  276 (403)
Q Consensus       273 ~~~~  276 (403)
                      ....
T Consensus       455 A~s~  458 (478)
T KOG1129|consen  455 AKSV  458 (478)
T ss_pred             hhhh
Confidence            7654

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.53  E-value=1.6e-11  Score=100.37  Aligned_cols=203  Identities=8%  Similarity=-0.004  Sum_probs=170.2

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      ....+..+...+...|++++|...+++..+..  +.+...+..+...+...|++++|.+.+++..+..+.+...+..+..
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  107 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHD--PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGT  107 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHH
Confidence            46678888999999999999999999988765  3456788889999999999999999999999988778888899999


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                      .+...|++++|...+.+.....     ..+.....+..+...+...|++++|.+.+++..+.... +...+..+...+..
T Consensus       108 ~~~~~g~~~~A~~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~  181 (234)
T TIGR02521       108 FLCQQGKYEQAMQQFEQAIEDP-----LYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ-RPESLLELAELYYL  181 (234)
T ss_pred             HHHHcccHHHHHHHHHHHHhcc-----ccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-ChHHHHHHHHHHHH
Confidence            9999999999999999887642     22334556777888999999999999999999887544 56788889999999


Q ss_pred             cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          190 SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      .|++++|...+++..+. .+.+...+..+...+...|+.+.|..+.+.+...
T Consensus       182 ~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       182 RGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             cCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            99999999999998877 3446667777888888899999999988877653

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.

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

Probab=99.46  E-value=1.8e-10  Score=87.60  Aligned_cols=201  Identities=9%  Similarity=-0.044  Sum_probs=169.3

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL  111 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  111 (403)
                      .+...|.-.|...|++..|.+-+++..+.+  +.+..+|..+...|-+.|+.+.|.+.|++..+..+.+..+.|+....+
T Consensus        36 ~arlqLal~YL~~gd~~~A~~nlekAL~~D--Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FL  113 (250)
T COG3063          36 KARLQLALGYLQQGDYAQAKKNLEKALEHD--PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFL  113 (250)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHH
Confidence            356677778999999999999999999976  345678999999999999999999999999999988999999999999


Q ss_pred             HhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcC
Q 041804          112 CEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSG  191 (403)
Q Consensus       112 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  191 (403)
                      |..|.+++|...|++.....     ....-..+|..+.-+..+.|+.+.|...|++..+.... ...+...+.....+.|
T Consensus       114 C~qg~~~eA~q~F~~Al~~P-----~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~~~  187 (250)
T COG3063         114 CAQGRPEEAMQQFERALADP-----AYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYKAG  187 (250)
T ss_pred             HhCCChHHHHHHHHHHHhCC-----CCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHhcc
Confidence            99999999999999888764     44455667888888889999999999999998887766 5567778888888999


Q ss_pred             ChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          192 KPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       192 ~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ++-.|...++.....+. ++..+.-..|+.--..|+.+.+-++=..+...
T Consensus       188 ~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~  236 (250)
T COG3063         188 DYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL  236 (250)
T ss_pred             cchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            99999999988888764 78888888888888889988888877666654

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

Probab=99.44  E-value=9.3e-10  Score=97.80  Aligned_cols=313  Identities=13%  Similarity=0.086  Sum_probs=194.4

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH-HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH-ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL  111 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  111 (403)
                      ..-....++...|++++|++.++.-...   .+|. .........+.+.|+.++|..+|..+.+.++.+..-|..+..+.
T Consensus         6 ~lLY~~~il~e~g~~~~AL~~L~~~~~~---I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~   82 (517)
T PF12569_consen    6 LLLYKNSILEEAGDYEEALEHLEKNEKQ---ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEAL   82 (517)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhhhhh---CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHH
Confidence            3334456777888999998888776554   2554 45556678888889999999999999888887777777777776


Q ss_pred             Hhc-----CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCCh-hHHHHHHHHHHhCCCCCcHHHHHHHHH
Q 041804          112 CEY-----KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWW-GKCREFWEEMDKRGVVKDLHSYSIYMD  185 (403)
Q Consensus       112 ~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~  185 (403)
                      .-.     .+.+....+++++....        |...+...+.-.+..-..+ ..+..++..+...|+++   +|+.+-.
T Consensus        83 g~~~~~~~~~~~~~~~~y~~l~~~y--------p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~  151 (517)
T PF12569_consen   83 GLQLQLSDEDVEKLLELYDELAEKY--------PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKP  151 (517)
T ss_pred             hhhcccccccHHHHHHHHHHHHHhC--------ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHH
Confidence            332     24566677777665531        2222222221111111122 34455666777777663   6667766


Q ss_pred             HHHHcCChhHHHHHHHHHHHc----C----------CCCChh--hHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCC-HH
Q 041804          186 IMCKSGKPWKAVKLYKEMKKK----G----------IKMDVV--AYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS-VV  248 (403)
Q Consensus       186 ~~~~~~~~~~a~~~~~~~~~~----~----------~~~~~~--~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~  248 (403)
                      .|....+..-..+++......    +          -+|+..  ++..+.+.|...|+++.|+.+++...++  .|+ +.
T Consensus       152 Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~e  229 (517)
T PF12569_consen  152 LYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVE  229 (517)
T ss_pred             HHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHH
Confidence            666555555555555555432    1          123332  3455677788889999999999988887  344 66


Q ss_pred             HHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH---hhCCHHHHHHHHHHHHHcCCCCchhhH--------
Q 041804          249 TCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR---CLEKPREILGLFDRMIESGIRPKMDTY--------  317 (403)
Q Consensus       249 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~--------  317 (403)
                      .|..-.+.+-..|++.+|.+.++........ |...-+-...   ..++.++|.+++......+..|....+        
T Consensus       230 ly~~KarilKh~G~~~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~  308 (517)
T PF12569_consen  230 LYMTKARILKHAGDLKEAAEAMDEARELDLA-DRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFE  308 (517)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHH
Confidence            7777888888899999999988887765211 2222222222   226777777777777665543322211        


Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHhc--CCCCCHHHHHHHHHHHHhcCCH
Q 041804          318 VMLLRKFGRWGFLRPVFVVWKKMEEL--GCSPDEFAYNALVDALIDKGML  365 (403)
Q Consensus       318 ~~li~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~  365 (403)
                      .-...+|.+.|++..|++-|..+.+.  .+.-|..-|...   |.|.|.+
T Consensus       309 ~e~a~a~~r~~~~~~ALk~~~~v~k~f~~~~~DQfDFH~Y---c~RK~t~  355 (517)
T PF12569_consen  309 TECAEAYLRQGDYGLALKRFHAVLKHFDDFEEDQFDFHSY---CLRKMTL  355 (517)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcccccHHHH---HHhhccH
Confidence            23345677888888888887777653  334444444433   5566544

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>PF13041 PPR_2: PPR repeat family

Probab=99.44  E-value=4.1e-13  Score=79.37  Aligned_cols=49  Identities=43%  Similarity=0.675  Sum_probs=27.7

Q ss_pred             CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHh
Q 041804          175 KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVG  223 (403)
Q Consensus       175 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  223 (403)
                      ||..+||++|++|++.|++++|.++|++|.+.|+.||..||+.++++|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            4555555555555555555555555555555555555555555555554

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

Probab=99.43  E-value=2.2e-09  Score=95.43  Aligned_cols=264  Identities=13%  Similarity=0.078  Sum_probs=188.7

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHH-HHHHHHHHHHhc--
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHA-TFRIMFKRYVTA--   80 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~--   80 (403)
                      |....|++++|++.++.-.  ..+.............+.+.|+.++|..++..+...+   |+.. -|..+..+..-.  
T Consensus        13 il~e~g~~~~AL~~L~~~~--~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN---Pdn~~Yy~~L~~~~g~~~~   87 (517)
T PF12569_consen   13 ILEEAGDYEEALEHLEKNE--KQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN---PDNYDYYRGLEEALGLQLQ   87 (517)
T ss_pred             HHHHCCCHHHHHHHHHhhh--hhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC---CCcHHHHHHHHHHHhhhcc
Confidence            5567899999999998766  3355557778888999999999999999999999987   5554 455555555222  


Q ss_pred             ---CChHHHHHHHHHHhhcCCC------------c--------------------HHHHHHHHHHHHhcCCHHHHHHHHh
Q 041804           81 ---HLVNEAMGTFNKLDEFGLK------------D--------------------EVSYCNLVDALCEYKHVIEAQELCF  125 (403)
Q Consensus        81 ---~~~~~a~~~~~~~~~~~~~------------~--------------------~~~~~~l~~~~~~~~~~~~a~~~~~  125 (403)
                         .+.+...++|+++...-+.            +                    +.+|+.+-..|.......-...++.
T Consensus        88 ~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~  167 (517)
T PF12569_consen   88 LSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVE  167 (517)
T ss_pred             cccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHH
Confidence               2467777788776554431            1                    1233334344443333334444444


Q ss_pred             cccccc----cccc----cccCcchH--HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhH
Q 041804          126 GENKNV----GFSG----LVEMNKTK--IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWK  195 (403)
Q Consensus       126 ~~~~~~----~~~~----~~~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  195 (403)
                      ......    .+..    ...+|+..  ++..+...|...|++++|++++++.++..+. .+..|..-.+.+-+.|++.+
T Consensus       168 ~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt-~~ely~~KarilKh~G~~~~  246 (517)
T PF12569_consen  168 EYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPT-LVELYMTKARILKHAGDLKE  246 (517)
T ss_pred             HHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHCCCHHH
Confidence            433221    1111    12355553  4567788899999999999999999998655 57889999999999999999


Q ss_pred             HHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHH--------HHHHHHHHHHhcCcHHHHH
Q 041804          196 AVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVV--------TCNTVIKLLCENGRVREAY  267 (403)
Q Consensus       196 a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--------~~~~li~~~~~~g~~~~a~  267 (403)
                      |.+.++.....+ .-|...-+-.+..+.+.|++++|.+++....+.+..|...        .......+|.+.|++..|+
T Consensus       247 Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~AL  325 (517)
T PF12569_consen  247 AAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLAL  325 (517)
T ss_pred             HHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            999999999886 3477788888889999999999999999988776433221        1244578899999999888


Q ss_pred             HHHHhch
Q 041804          268 AVLAEMP  274 (403)
Q Consensus       268 ~~~~~~~  274 (403)
                      +.|..+.
T Consensus       326 k~~~~v~  332 (517)
T PF12569_consen  326 KRFHAVL  332 (517)
T ss_pred             HHHHHHH
Confidence            7776554

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>PF13041 PPR_2: PPR repeat family

Probab=99.43  E-value=3.8e-13  Score=79.54  Aligned_cols=50  Identities=28%  Similarity=0.598  Sum_probs=48.1

Q ss_pred             CchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 041804          312 PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID  361 (403)
Q Consensus       312 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (403)
                      ||..+||++|.+|++.|++++|.++|++|.+.|++||..||+.++++|++
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            79999999999999999999999999999999999999999999999875

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

Probab=99.41  E-value=2.7e-08  Score=83.88  Aligned_cols=355  Identities=12%  Similarity=0.022  Sum_probs=239.4

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH-HHHHHHHHHHHhcCChHH
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH-ATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~   85 (403)
                      .++++..|..+|+....  +...+...|-..+.+=.++..+..|..++++....-   |-+ ..|---+..--..|++..
T Consensus        85 sq~e~~RARSv~ERALd--vd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~l---PRVdqlWyKY~ymEE~LgNi~g  159 (677)
T KOG1915|consen   85 SQKEIQRARSVFERALD--VDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTIL---PRVDQLWYKYIYMEEMLGNIAG  159 (677)
T ss_pred             hHHHHHHHHHHHHHHHh--cccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhc---chHHHHHHHHHHHHHHhcccHH
Confidence            45788889999988873  335566778888888888999999999998888753   544 345555566667788888


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      |.++|++..+.. |+..+|.+.++.-.+.+.++.|..++++.+-        +.|++.+|--....=-++|+...|..+|
T Consensus       160 aRqiferW~~w~-P~eqaW~sfI~fElRykeieraR~IYerfV~--------~HP~v~~wikyarFE~k~g~~~~aR~Vy  230 (677)
T KOG1915|consen  160 ARQIFERWMEWE-PDEQAWLSFIKFELRYKEIERARSIYERFVL--------VHPKVSNWIKYARFEEKHGNVALARSVY  230 (677)
T ss_pred             HHHHHHHHHcCC-CcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--------ecccHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            888888877654 4778888888888888888888888888764        3588888888888888888888888888


Q ss_pred             HHHHhCCC--CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc-------------------------------------
Q 041804          166 EEMDKRGV--VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-------------------------------------  206 (403)
Q Consensus       166 ~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------------------------------------  206 (403)
                      +...+.=-  ..+...+++....-.++..++.|.-+|+-.+..                                     
T Consensus       231 erAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~q  310 (677)
T KOG1915|consen  231 ERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQ  310 (677)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhH
Confidence            77654210  012223333333333333444444433333221                                     


Q ss_pred             ------CCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCH--HHHHH--------HHHHHHhcCcHHHHHHHH
Q 041804          207 ------GIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSV--VTCNT--------VIKLLCENGRVREAYAVL  270 (403)
Q Consensus       207 ------~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~--------li~~~~~~g~~~~a~~~~  270 (403)
                            .-+-|-.+|--.++.-...|+.+...++|+.+... ++|-.  ..|..        .+..-....+.+.+.++|
T Consensus       311 YE~~v~~np~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vy  389 (677)
T KOG1915|consen  311 YEKEVSKNPYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVY  389 (677)
T ss_pred             HHHHHHhCCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence                  01335556666666666778888888888877765 33321  11111        111122467778888888


Q ss_pred             HhchhcCCCCChhhHHHHHHhh-------CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          271 AEMPKKGCVPDVITYHCFFRCL-------EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       271 ~~~~~~~~~p~~~~~~~l~~~~-------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      +...+. ++....||.-+--.+       .+...|.+++...+  |.-|-..+|...|..-.+.++++.+..++++..+.
T Consensus       390 q~~l~l-IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~  466 (677)
T KOG1915|consen  390 QACLDL-IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEF  466 (677)
T ss_pred             HHHHhh-cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            877762 223455555432222       34556666666544  45677788888888888889999999999999887


Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 041804          344 GCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGL  380 (403)
Q Consensus       344 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~  380 (403)
                      + +-|..+|......=...|+++.|..+|+-.++...
T Consensus       467 ~-Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~  502 (677)
T KOG1915|consen  467 S-PENCYAWSKYAELETSLGDTDRARAIFELAISQPA  502 (677)
T ss_pred             C-hHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcc
Confidence            5 55778888888888888999999999988877643

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

Probab=99.41  E-value=5.2e-11  Score=106.92  Aligned_cols=253  Identities=14%  Similarity=0.046  Sum_probs=143.7

Q ss_pred             hhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhc
Q 041804           17 FFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEF   96 (403)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   96 (403)
                      ++..+. ..|+.||..+|..+|.-|+..|+++.|- +|.-|.-.. .+.+...++.++.+....++.+.+.         
T Consensus        12 fla~~e-~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ks-Lpv~e~vf~~lv~sh~~And~Enpk---------   79 (1088)
T KOG4318|consen   12 FLALHE-ISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKS-LPVREGVFRGLVASHKEANDAENPK---------   79 (1088)
T ss_pred             HHHHHH-HhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhccc-ccccchhHHHHHhcccccccccCCC---------
Confidence            344444 4788899999999999999999998888 888877765 5567778888888888888777665         


Q ss_pred             CCCcHHHHHHHHHHHHhcCCHHH---HHHHHhcccccccccccccCcchHHH--------------HHHHHHHHhcCChh
Q 041804           97 GLKDEVSYCNLVDALCEYKHVIE---AQELCFGENKNVGFSGLVEMNKTKIY--------------NMILRGWFKMSWWG  159 (403)
Q Consensus        97 ~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~l~~~~~~~~~~~  159 (403)
                       .+.+.+|..|..+|...||...   .++.+..........  |+.....-+              ...+....-.|-++
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~--Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwa  156 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDH--GVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWA  156 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhh--ccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHH
Confidence             3577888888888888887654   222111111111101  110000000              11111122222333


Q ss_pred             HHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          160 KCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       160 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      .+.+++..+...... .  ++...++-+..  ......++.......--.|+..+|..++.+-...|+.+.|..++..|.
T Consensus       157 qllkll~~~Pvsa~~-~--p~~vfLrqnv~--~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emk  231 (1088)
T KOG4318|consen  157 QLLKLLAKVPVSAWN-A--PFQVFLRQNVV--DNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMK  231 (1088)
T ss_pred             HHHHHHhhCCccccc-c--hHHHHHHHhcc--CCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHH
Confidence            333333222211111 0  00001111111  122233333222222114677777777777777777777777777777


Q ss_pred             HcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh
Q 041804          240 EMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL  292 (403)
Q Consensus       240 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  292 (403)
                      +.|++.+..-|..|+-+   .++...+..+++-|.+.|+.|+..|+...+..+
T Consensus       232 e~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~  281 (1088)
T KOG4318|consen  232 EKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQ  281 (1088)
T ss_pred             HcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhh
Confidence            77777777666666654   666667777777777777777777776554443

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

Probab=99.40  E-value=2.6e-10  Score=97.68  Aligned_cols=269  Identities=11%  Similarity=0.012  Sum_probs=174.7

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHH
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEA   86 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a   86 (403)
                      ..+++++..++++.+..  ..++....+..-|.++...|+..+-..+=.++.+..  |....+|-.+.--|...|+..+|
T Consensus       256 ~~c~f~~c~kit~~lle--~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y--P~~a~sW~aVg~YYl~i~k~seA  331 (611)
T KOG1173|consen  256 YGCRFKECLKITEELLE--KDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY--PSKALSWFAVGCYYLMIGKYSEA  331 (611)
T ss_pred             HcChHHHHHHHhHHHHh--hCCCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC--CCCCcchhhHHHHHHHhcCcHHH
Confidence            34567777777776663  234455555555667777777777777767776654  33456777777777777777777


Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHH
Q 041804           87 MGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWE  166 (403)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  166 (403)
                      .+.|.+....++.-...|......++-.+..+.|...+....+-       .+-....+--+.--|.+.++++.|.++|.
T Consensus       332 Rry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl-------~~G~hlP~LYlgmey~~t~n~kLAe~Ff~  404 (611)
T KOG1173|consen  332 RRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-------MPGCHLPSLYLGMEYMRTNNLKLAEKFFK  404 (611)
T ss_pred             HHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-------ccCCcchHHHHHHHHHHhccHHHHHHHHH
Confidence            77777777766666667777777777777777777776655442       12222223444555667777777777777


Q ss_pred             HHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc--CCC----CChhhHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          167 EMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK--GIK----MDVVAYNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       167 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~----~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      +.....+. |+...+-+.-.....+.+.+|..+|+..+..  .+.    .-..+++.|..+|.+.+..++|+..++....
T Consensus       405 ~A~ai~P~-Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~  483 (611)
T KOG1173|consen  405 QALAIAPS-DPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALL  483 (611)
T ss_pred             HHHhcCCC-cchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHH
Confidence            77766555 6666777766666677777777777766522  011    1223466677777777777777777777776


Q ss_pred             cCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH
Q 041804          241 MGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR  290 (403)
Q Consensus       241 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  290 (403)
                      .. +-+..++.++.-.|...|+++.|.+.|.+..-  +.|+..+...++.
T Consensus       484 l~-~k~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~  530 (611)
T KOG1173|consen  484 LS-PKDASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLK  530 (611)
T ss_pred             cC-CCchhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHH
Confidence            53 33677777777777777777777777776654  3566655554444

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.39  E-value=1.7e-09  Score=85.53  Aligned_cols=326  Identities=16%  Similarity=0.116  Sum_probs=215.3

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      -+++.+..+.+..++..|++++..-.+..  +.+......+..+|.+..++..|-.+|+++-...+.-..--.--.+.+.
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~--p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY   89 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERS--PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLY   89 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcC--ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHH
Confidence            46677777788889999999988887765  3477778888889999999999999999888776652222222344555


Q ss_pred             hcCCHHHHHHHHhcccccccccccccCcchHHHHHHH--HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          113 EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL--RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      +.+.+.+|+.+...+...         ++...-..-+  ......+++..+..++++....|   +..+.+.......+.
T Consensus        90 ~A~i~ADALrV~~~~~D~---------~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllyke  157 (459)
T KOG4340|consen   90 KACIYADALRVAFLLLDN---------PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKE  157 (459)
T ss_pred             HhcccHHHHHHHHHhcCC---------HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeecc
Confidence            677888888887776542         2222111122  23345678888888888877543   333445555556788


Q ss_pred             CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC-------------CH----------
Q 041804          191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQP-------------SV----------  247 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-------------~~----------  247 (403)
                      |+++.|.+-|+...+-+--.....|+..+..| +.++.+.|+++..++.++|++.             |+          
T Consensus       158 gqyEaAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh  236 (459)
T KOG4340|consen  158 GQYEAAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLH  236 (459)
T ss_pred             ccHHHHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHH
Confidence            89999999888887764343556777666555 6788888999888888876541             11          


Q ss_pred             -----HHHHHHHHHHHhcCcHHHHHHHHHhchhc-CCCCChhhHHHH--HHhhCCHHHHHHHHHHHHHcCCCCchhhHHH
Q 041804          248 -----VTCNTVIKLLCENGRVREAYAVLAEMPKK-GCVPDVITYHCF--FRCLEKPREILGLFDRMIESGIRPKMDTYVM  319 (403)
Q Consensus       248 -----~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~p~~~~~~~l--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (403)
                           ..+|.-...+.+.|+++.|.+.+-.|..+ ....|++|...+  ...-+++.+..+-+.-+....+ ....||..
T Consensus       237 ~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~~~~p~~g~~KLqFLL~~nP-fP~ETFAN  315 (459)
T KOG4340|consen  237 QSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNMDARPTEGFEKLQFLLQQNP-FPPETFAN  315 (459)
T ss_pred             HHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcccCCccccHHHHHHHHhcCC-CChHHHHH
Confidence                 11222233456789999999999999733 334577776643  3444667776666666666544 35689999


Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhcCCC-CCHHHHHHHHHHHHh-cCCHHHHHHHHHHH
Q 041804          320 LLRKFGRWGFLRPVFVVWKKMEELGCS-PDEFAYNALVDALID-KGMLDMARKYDEEM  375 (403)
Q Consensus       320 li~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~-~g~~~~a~~~~~~m  375 (403)
                      ++-.||+..-++.|-.++-+-.....+ .+...|+.| ++++- .-..++|.+-++.+
T Consensus       316 lLllyCKNeyf~lAADvLAEn~~lTyk~L~~Yly~LL-daLIt~qT~pEea~KKL~~L  372 (459)
T KOG4340|consen  316 LLLLYCKNEYFDLAADVLAENAHLTYKFLTPYLYDLL-DALITCQTAPEEAFKKLDGL  372 (459)
T ss_pred             HHHHHhhhHHHhHHHHHHhhCcchhHHHhhHHHHHHH-HHHHhCCCCHHHHHHHHHHH
Confidence            999999999999999887764433221 244555543 33332 34555555544433

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.38  E-value=1.7e-08  Score=88.27  Aligned_cols=229  Identities=13%  Similarity=0.094  Sum_probs=151.1

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMG   88 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~   88 (403)
                      ++++..+++.+.+.+  +.+-...+.....-.+...|+.++|.+..+.-...+  ..+.+.|+.+.-.+-...++++|++
T Consensus        21 kQYkkgLK~~~~iL~--k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d--~~S~vCwHv~gl~~R~dK~Y~eaiK   96 (700)
T KOG1156|consen   21 KQYKKGLKLIKQILK--KFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRND--LKSHVCWHVLGLLQRSDKKYDEAIK   96 (700)
T ss_pred             HHHHhHHHHHHHHHH--hCCccchhHHhccchhhcccchHHHHHHHHHHhccC--cccchhHHHHHHHHhhhhhHHHHHH
Confidence            567777777777764  233334555555556667788899988888877765  4677888888888888889999999


Q ss_pred             HHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHH
Q 041804           89 TFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEM  168 (403)
Q Consensus        89 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  168 (403)
                      +|......++.|...+.-+.-.-++.++++.....-..+.+       ..+.....|..+..++.-.|++..|..++++.
T Consensus        97 cy~nAl~~~~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLq-------l~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef  169 (700)
T KOG1156|consen   97 CYRNALKIEKDNLQILRDLSLLQIQMRDYEGYLETRNQLLQ-------LRPSQRASWIGFAVAQHLLGEYKMALEILEEF  169 (700)
T ss_pred             HHHHHHhcCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHH-------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999888877888887776666677777766665555554       33445566777888888888888888888887


Q ss_pred             HhCC-CCCcHHHHHHHHH------HHHHcCChhHHHHHHHHHHHcCCCCChh-hHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          169 DKRG-VVKDLHSYSIYMD------IMCKSGKPWKAVKLYKEMKKKGIKMDVV-AYNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       169 ~~~~-~~~~~~~~~~l~~------~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      .+.. -.|+...|.....      ...+.|..++|++.+..-...  ..|.. .-.+-...+.+.+++++|..++..+..
T Consensus       170 ~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~--i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~  247 (700)
T KOG1156|consen  170 EKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ--IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLE  247 (700)
T ss_pred             HHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH--HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHh
Confidence            7654 2455555544332      234456666666665544332  11222 222334455667777777777777776


Q ss_pred             cCCCCCHHHHHH
Q 041804          241 MGCQPSVVTCNT  252 (403)
Q Consensus       241 ~~~~~~~~~~~~  252 (403)
                      .  .||..-|..
T Consensus       248 r--nPdn~~Yy~  257 (700)
T KOG1156|consen  248 R--NPDNLDYYE  257 (700)
T ss_pred             h--CchhHHHHH
Confidence            5  344444433

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

Probab=99.37  E-value=3.3e-10  Score=90.61  Aligned_cols=226  Identities=12%  Similarity=0.013  Sum_probs=145.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHH
Q 041804          104 YCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIY  183 (403)
Q Consensus       104 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  183 (403)
                      -+-+.++|.+.|.+.+|.+.++.....        .|-+.+|-.|-..|.+..++..|+.++.+-.+.-+. |+....-+
T Consensus       226 k~Q~gkCylrLgm~r~AekqlqssL~q--------~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~-~VT~l~g~  296 (478)
T KOG1129|consen  226 KQQMGKCYLRLGMPRRAEKQLQSSLTQ--------FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPF-DVTYLLGQ  296 (478)
T ss_pred             HHHHHHHHHHhcChhhhHHHHHHHhhc--------CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCc-hhhhhhhh
Confidence            356778888888888888887766654        456667788888888888888888888877765322 55445556


Q ss_pred             HHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 041804          184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRV  263 (403)
Q Consensus       184 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  263 (403)
                      .+.+...++.++|.++|+...+.. +.++.....+...|.-.++++.|+++++.+.+.|+. ++..|+.+.-+|.-.+++
T Consensus       297 ARi~eam~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~  374 (478)
T KOG1129|consen  297 ARIHEAMEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQI  374 (478)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcch
Confidence            677777888888888888877763 445566666666777788888888888888888876 777788888888888888


Q ss_pred             HHHHHHHHhchhcCCCCChh---hHH--HHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHH
Q 041804          264 REAYAVLAEMPKKGCVPDVI---TYH--CFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWK  338 (403)
Q Consensus       264 ~~a~~~~~~~~~~~~~p~~~---~~~--~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  338 (403)
                      +.++..|.+....--.|+..   -||  .+....|+..-|.+.|+-...+... +...++.|.-.-.+.|+++.|..+++
T Consensus       375 D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ealnNLavL~~r~G~i~~Arsll~  453 (478)
T KOG1129|consen  375 DLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEALNNLAVLAARSGDILGARSLLN  453 (478)
T ss_pred             hhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHHHHhHHHHHhhcCchHHHHHHHH
Confidence            88887777765432223211   111  1111224444444444444433222 33444444444444455555554444


Q ss_pred             HHH
Q 041804          339 KME  341 (403)
Q Consensus       339 ~~~  341 (403)
                      ...
T Consensus       454 ~A~  456 (478)
T KOG1129|consen  454 AAK  456 (478)
T ss_pred             Hhh
Confidence            443

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.36  E-value=1.3e-09  Score=91.69  Aligned_cols=120  Identities=8%  Similarity=-0.082  Sum_probs=61.5

Q ss_pred             CChhHHHHHHHHhhhCCCCCCC--HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHH
Q 041804           45 FEFDLSWNLIHRMKDNPSSIPN--HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQE  122 (403)
Q Consensus        45 ~~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  122 (403)
                      +..+.++.-+.++.......|+  ...|..+...|...|+.++|...|++..+..+.+...|+.+...+...|++++|..
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~  119 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYE  119 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            3444444444444433211122  23344555555555555555555555555555555555555555555555555555


Q ss_pred             HHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          123 LCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      .|++..+       ..+.+..++..+...+...|++++|.+.|++..+.
T Consensus       120 ~~~~Al~-------l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~  161 (296)
T PRK11189        120 AFDSVLE-------LDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD  161 (296)
T ss_pred             HHHHHHH-------hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            5555544       22333445555555555555555555555555554

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

Probab=99.33  E-value=4.9e-09  Score=90.09  Aligned_cols=278  Identities=10%  Similarity=0.043  Sum_probs=186.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      ....-..-+-..+++.+..++++.+.+..+.....+..-|.++...|+..+-..+-.+++.       ..|....+|.++
T Consensus       246 ll~~~ad~~y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~-------~yP~~a~sW~aV  318 (611)
T KOG1173|consen  246 LLAEKADRLYYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVD-------LYPSKALSWFAV  318 (611)
T ss_pred             HHHHHHHHHHHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhcccchHHHHHHHHHH-------hCCCCCcchhhH
Confidence            3444455566778888888888888888877777777777778888887777766666666       556677788888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCH
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGV  228 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  228 (403)
                      .-.|.-.|++++|.+.|.+....+.. =...|......|+-.+..++|...|...-+. ++-....+--+---|.+.++.
T Consensus       319 g~YYl~i~k~seARry~SKat~lD~~-fgpaWl~fghsfa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~  396 (611)
T KOG1173|consen  319 GCYYLMIGKYSEARRYFSKATTLDPT-FGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNL  396 (611)
T ss_pred             HHHHHHhcCcHHHHHHHHHHhhcCcc-ccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccH
Confidence            88888888888888888887665444 3347888888888888888888888776654 111222233344456778888


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc--CCCCChhhHH-------HHHHhhCCHHHHH
Q 041804          229 DFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK--GCVPDVITYH-------CFFRCLEKPREIL  299 (403)
Q Consensus       229 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~--~~~p~~~~~~-------~l~~~~~~~~~a~  299 (403)
                      ..|.++|.+..... +.|+...+-+.-.....+.+.+|..+|+.....  .+.+...+|.       ...+.+++.++|+
T Consensus       397 kLAe~Ff~~A~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI  475 (611)
T KOG1173|consen  397 KLAEKFFKQALAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAI  475 (611)
T ss_pred             HHHHHHHHHHHhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHH
Confidence            88888888877653 346677777776666778888888888765521  1111111222       2223335566777


Q ss_pred             HHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 041804          300 GLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDAL  359 (403)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  359 (403)
                      ..+++.+....+ +..++.++.-.|...|+++.|.+.|.+...  +.|+-.+-..++..+
T Consensus       476 ~~~q~aL~l~~k-~~~~~asig~iy~llgnld~Aid~fhKaL~--l~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  476 DYYQKALLLSPK-DASTHASIGYIYHLLGNLDKAIDHFHKALA--LKPDNIFISELLKLA  532 (611)
T ss_pred             HHHHHHHHcCCC-chhHHHHHHHHHHHhcChHHHHHHHHHHHh--cCCccHHHHHHHHHH
Confidence            777776665433 666777777777777777777777776664  356655555555433

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.33  E-value=1.3e-07  Score=82.78  Aligned_cols=344  Identities=10%  Similarity=0.115  Sum_probs=199.4

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL  111 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  111 (403)
                      ..|-..+..+.++|++......|++....-++......|...+......+-++-++++|++.++..|.   .-...+..+
T Consensus       103 RIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~~P~---~~eeyie~L  179 (835)
T KOG2047|consen  103 RIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKVAPE---AREEYIEYL  179 (835)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhcCHH---HHHHHHHHH
Confidence            46677777888899999999999888876544455667888888888889999999999998875544   355566667


Q ss_pred             HhcCCHHHHHHHHhccccccccccc------------------------------------ccCcc--hHHHHHHHHHHH
Q 041804          112 CEYKHVIEAQELCFGENKNVGFSGL------------------------------------VEMNK--TKIYNMILRGWF  153 (403)
Q Consensus       112 ~~~~~~~~a~~~~~~~~~~~~~~~~------------------------------------~~~~~--~~~~~~l~~~~~  153 (403)
                      +..+++++|.+.+........+.+.                                    +.-+|  ...|.+|...|.
T Consensus       180 ~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYI  259 (835)
T KOG2047|consen  180 AKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYI  259 (835)
T ss_pred             HhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHH
Confidence            7888888888887776655421111                                    01111  134789999999


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH--------------------------------------------
Q 041804          154 KMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK--------------------------------------------  189 (403)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--------------------------------------------  189 (403)
                      +.|.+++|..+|++....-  .+..-|+.+.++|+.                                            
T Consensus       260 r~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~l  337 (835)
T KOG2047|consen  260 RSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLL  337 (835)
T ss_pred             HhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHH
Confidence            9999999999988765431  122222222222211                                            


Q ss_pred             ----------------------cCChhHHHHHHHHHHHcCCCCC------hhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          190 ----------------------SGKPWKAVKLYKEMKKKGIKMD------VVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       190 ----------------------~~~~~~a~~~~~~~~~~~~~~~------~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                                            .|+..+....|.+.... +.|.      ...|..+...|-..|+++.|..+|++..+.
T Consensus       338 NsVlLRQn~~nV~eW~kRV~l~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V  416 (835)
T KOG2047|consen  338 NSVLLRQNPHNVEEWHKRVKLYEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKV  416 (835)
T ss_pred             HHHHHhcCCccHHHHHhhhhhhcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcC
Confidence                                  12222333333333332 2221      134666777788888899999998888775


Q ss_pred             CCCCC---HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCC-----------CCChhhHHH---------HHHhhCCHHHH
Q 041804          242 GCQPS---VVTCNTVIKLLCENGRVREAYAVLAEMPKKGC-----------VPDVITYHC---------FFRCLEKPREI  298 (403)
Q Consensus       242 ~~~~~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-----------~p~~~~~~~---------l~~~~~~~~~a  298 (403)
                      ..+--   ..+|..-...-.+..+++.|+++.+......-           ++....+++         +..++|-++..
T Consensus       417 ~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfest  496 (835)
T KOG2047|consen  417 PYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFEST  496 (835)
T ss_pred             CccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHH
Confidence            43311   34555555666667778888887776543211           111122222         22345666666


Q ss_pred             HHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCC-HHHHHHHHHHHHh---cCCHHHHHHHHHH
Q 041804          299 LGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPD-EFAYNALVDALID---KGMLDMARKYDEE  374 (403)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~---~g~~~~a~~~~~~  374 (403)
                      ..+|+++++..+. ++.........+-.+.-++++.+++++-...--.|+ ...|+..+.-+.+   .-..+.|..+|++
T Consensus       497 k~vYdriidLria-TPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEq  575 (835)
T KOG2047|consen  497 KAVYDRIIDLRIA-TPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQ  575 (835)
T ss_pred             HHHHHHHHHHhcC-CHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence            7777777765554 222211122222233345555555554443321232 2345544444332   2245566666666


Q ss_pred             HHHcCCCCC
Q 041804          375 MFAKGLSAK  383 (403)
Q Consensus       375 m~~~~~~p~  383 (403)
                      .++ |..|.
T Consensus       576 aL~-~Cpp~  583 (835)
T KOG2047|consen  576 ALD-GCPPE  583 (835)
T ss_pred             HHh-cCCHH
Confidence            665 44443

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.32  E-value=1.4e-08  Score=89.40  Aligned_cols=253  Identities=11%  Similarity=0.105  Sum_probs=161.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH-HHHHHHHHHHhcCChhHHHHHHHHHHhC-----CC
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK-IYNMILRGWFKMSWWGKCREFWEEMDKR-----GV  173 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~  173 (403)
                      -..+...+...|...|+++.|..++........-......|... ..+.+...|...+++.+|..+|+++...     |.
T Consensus       198 ~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~  277 (508)
T KOG1840|consen  198 RLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGE  277 (508)
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCC
Confidence            34444556666666666666666665544321000001122222 2344667777788888888888776542     21


Q ss_pred             --CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc-----CCC-CCh-hhHHHHHHHHhhcCCHHHHHHHHHHHHHc---
Q 041804          174 --VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-----GIK-MDV-VAYNTVIRAVGVSEGVDFAMRVYREMREM---  241 (403)
Q Consensus       174 --~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~-~~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---  241 (403)
                        +.-..+++.|..+|.+.|++++|...++...+-     |.. |.. ..++.+...|+..+++++|..+++...+.   
T Consensus       278 ~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~  357 (508)
T KOG1840|consen  278 DHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLD  357 (508)
T ss_pred             CCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHh
Confidence              112356666777888889988888777765432     211 222 24566667788889999999888876543   


Q ss_pred             CCCC----CHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhH
Q 041804          242 GCQP----SVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTY  317 (403)
Q Consensus       242 ~~~~----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  317 (403)
                      -+.+    -..+++.|...|...|++++|.++++.....                         .+........-....+
T Consensus       358 ~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~-------------------------~~~~~~~~~~~~~~~l  412 (508)
T KOG1840|consen  358 APGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQI-------------------------LRELLGKKDYGVGKPL  412 (508)
T ss_pred             hccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHH-------------------------HHhcccCcChhhhHHH
Confidence            1112    2357888999999999999999998876542                         1111111111124567


Q ss_pred             HHHHHHHHhcCCcchHHHHHHHHHh----cC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          318 VMLLRKFGRWGFLRPVFVVWKKMEE----LG--CSPDEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       318 ~~li~~~~~~g~~~~a~~~~~~~~~----~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      +.+...|.+.+++.+|.++|.+...    .|  .+-...+|..|...|.+.|+++.|.++.+....
T Consensus       413 ~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  413 NQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence            7888889999999999998887643    22  223457889999999999999999999888773

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

Probab=99.31  E-value=4.2e-10  Score=101.28  Aligned_cols=269  Identities=15%  Similarity=0.132  Sum_probs=164.6

Q ss_pred             HHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhccccc
Q 041804           52 NLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      .++-.+...| ..|+..||..+|.-|+..|+.+.|- +|.-|.-...+ +...++.++.+....++.+.+.         
T Consensus        11 nfla~~e~~g-i~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk---------   79 (1088)
T KOG4318|consen   11 NFLALHEISG-ILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK---------   79 (1088)
T ss_pred             hHHHHHHHhc-CCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC---------
Confidence            4566677777 7899999999999999999999888 89888888888 8888898888888877766543         


Q ss_pred             ccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH-cCCC
Q 041804          131 VGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK-KGIK  209 (403)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~  209 (403)
                              .|...+|..|..+|..+||...    |+...+        ....+...+...|.-.....++..+.- .+.-
T Consensus        80 --------ep~aDtyt~Ll~ayr~hGDli~----fe~veq--------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~l  139 (1088)
T KOG4318|consen   80 --------EPLADTYTNLLKAYRIHGDLIL----FEVVEQ--------DLESINQSFSDHGVGSPERWFLMKIHCCPHSL  139 (1088)
T ss_pred             --------CCchhHHHHHHHHHHhccchHH----HHHHHH--------HHHHHHhhhhhhccCcHHHHHHhhcccCcccc
Confidence                    5677788899999998888766    222222        122344455566665555555544322 2334


Q ss_pred             CChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHh-cCcHHHHHHHHHhchhcCCCCChhhHHH
Q 041804          210 MDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ-PSVVTCNTVIKLLCE-NGRVREAYAVLAEMPKKGCVPDVITYHC  287 (403)
Q Consensus       210 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li~~~~~-~g~~~~a~~~~~~~~~~~~~p~~~~~~~  287 (403)
                      ||..+   ++....-.|-++.+.+++..+...... |..+    +++-+.. ...+++-..+.+...+   .|+..+|.+
T Consensus       140 pda~n---~illlv~eglwaqllkll~~~Pvsa~~~p~~v----fLrqnv~~ntpvekLl~~cksl~e---~~~s~~l~a  209 (1088)
T KOG4318|consen  140 PDAEN---AILLLVLEGLWAQLLKLLAKVPVSAWNAPFQV----FLRQNVVDNTPVEKLLNMCKSLVE---APTSETLHA  209 (1088)
T ss_pred             hhHHH---HHHHHHHHHHHHHHHHHHhhCCcccccchHHH----HHHHhccCCchHHHHHHHHHHhhc---CCChHHHHH
Confidence            45433   333334456666666666554332111 1111    1222222 1223333333333332   466666666


Q ss_pred             HHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC
Q 041804          288 FFRCL---EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGM  364 (403)
Q Consensus       288 l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  364 (403)
                      ++.+.   |+.+.|..++..|.+.|++.+..-|..|+-+   .++..-+..+++-|.+.|+.|+..|+.-.+..+.++|.
T Consensus       210 ~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  210 VLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             HHHHHHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            65533   5666677777777777766666666665544   56666666666666677777777777666666655444

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.31  E-value=2.3e-09  Score=94.29  Aligned_cols=244  Identities=14%  Similarity=0.052  Sum_probs=179.2

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhC-----CCCCCCHHH-HHHHHHHHHhcCChHHHHHHHHHHhhc-----CCC
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDN-----PSSIPNHAT-FRIMFKRYVTAHLVNEAMGTFNKLDEF-----GLK   99 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~   99 (403)
                      ..+...+...|...|+++.|..++....+.     |...|...+ .+.+...|...+++++|..+|+++...     |..
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            456777999999999999999999987764     212355443 445788899999999999999998653     222


Q ss_pred             ---cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcch-HHHHHHHHHHHhcCChhHHHHHHHHHHhC---C
Q 041804          100 ---DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKT-KIYNMILRGWFKMSWWGKCREFWEEMDKR---G  172 (403)
Q Consensus       100 ---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~  172 (403)
                         -..+++.|..+|.+.|++++|...++....-.........|.+ ..++.+...+...+++++|..++....+.   -
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               4567888889999999999998887765543211000112222 34677778888899999999988765432   1


Q ss_pred             CCC----cHHHHHHHHHHHHHcCChhHHHHHHHHHHHc----CCC---CChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          173 VVK----DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK----GIK---MDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       173 ~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      +.+    -..+++.|...|...|++++|.++++.....    +..   -....++.+...|.+.++.+.|.++|.+....
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            111    2467899999999999999999999987654    111   12346778888999999999898888865532


Q ss_pred             ----CCC--CCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          242 ----GCQ--PSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       242 ----~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                          |+.  -...+|..|...|.+.|+++.|.++.+...
T Consensus       439 ~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  439 MKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence                322  235688999999999999999999888765

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

Probab=99.29  E-value=8.8e-09  Score=78.65  Aligned_cols=206  Identities=11%  Similarity=-0.086  Sum_probs=171.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      +...|.-.|...|+...|..-+++.++.++.+..+|..+...|.+.|+.+.|.+.|++...       ..+.+..+.|..
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAls-------l~p~~GdVLNNY  109 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALS-------LAPNNGDVLNNY  109 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHh-------cCCCccchhhhh
Confidence            4566778899999999999999999999988999999999999999999999999999887       457778889999


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCC
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRG-VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG  227 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  227 (403)
                      ...+|..|.+++|...|++....- ..-...+|..+.-+..+.|+++.|.+.|++..+.. +-...+...+.....+.|+
T Consensus       110 G~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~  188 (250)
T COG3063         110 GAFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGD  188 (250)
T ss_pred             hHHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhccc
Confidence            999999999999999999987653 12234588888889999999999999999998874 3345567778888889999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhH
Q 041804          228 VDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITY  285 (403)
Q Consensus       228 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~  285 (403)
                      +-.|..+++.....+. ++..+.-..|+.--..|+.+.+.+.=..+.+.  .|...-|
T Consensus       189 y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~--fP~s~e~  243 (250)
T COG3063         189 YAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL--FPYSEEY  243 (250)
T ss_pred             chHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCcHHH
Confidence            9999999999888765 78888888888888899988888776666654  4544443

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.28  E-value=5.9e-09  Score=87.74  Aligned_cols=218  Identities=11%  Similarity=-0.065  Sum_probs=126.8

Q ss_pred             ccHHHHHHhhhhhcccCCCcCC--HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHT--TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEA   86 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a   86 (403)
                      ++.+.++..+..+.......|+  ...|..+...+...|+.++|...|++..+..  +.+..+|+.+...+...|++++|
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~~~~~g~~~~A  117 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR--PDMADAYNYLGIYLTQAGNFDAA  117 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHCCCHHHH
Confidence            4556677777666642223332  3456667777777788888888777777754  34567777777778888888888


Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHH
Q 041804           87 MGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWE  166 (403)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  166 (403)
                      +..|++..+..+.+..++..+..++...|++++|.+.+++....        .|+..........+...+++++|...|.
T Consensus       118 ~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--------~P~~~~~~~~~~l~~~~~~~~~A~~~l~  189 (296)
T PRK11189        118 YEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--------DPNDPYRALWLYLAESKLDPKQAKENLK  189 (296)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--------CCCCHHHHHHHHHHHccCCHHHHHHHHH
Confidence            88888877777667777777777777778888888777776653        1222111222222344566777777775


Q ss_pred             HHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC---C--C-CChhhHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          167 EMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG---I--K-MDVVAYNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       167 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~--~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      +..... .|+...+ .  ......|+...+ +.+..+.+.-   +  . .....|..+...+.+.|++++|...|+...+
T Consensus       190 ~~~~~~-~~~~~~~-~--~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~  264 (296)
T PRK11189        190 QRYEKL-DKEQWGW-N--IVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALA  264 (296)
T ss_pred             HHHhhC-CccccHH-H--HHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            544322 2222211 1  222334554443 2344443220   0  0 1123455555666666666666666666665


Q ss_pred             c
Q 041804          241 M  241 (403)
Q Consensus       241 ~  241 (403)
                      .
T Consensus       265 ~  265 (296)
T PRK11189        265 N  265 (296)
T ss_pred             h
Confidence            4

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

Probab=99.28  E-value=9.6e-08  Score=83.46  Aligned_cols=202  Identities=6%  Similarity=-0.134  Sum_probs=123.9

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHH-HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHH---
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHA-TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN---  106 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---  106 (403)
                      ...|..+...+...|+.+.+.+.+....+.....++.. ........+...|++++|.+.+++..+..+.+...+..   
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~~~~   85 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDYPRDLLALKLHLG   85 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHhHH
Confidence            45666677777777888887777776665442223322 22233445667888999999998888877666655542   


Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHH
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI  186 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  186 (403)
                      ........+....+.+.+.....       ..+........+...+...|++++|.+.+++..+..+. +...+..+..+
T Consensus        86 ~~~~~~~~~~~~~~~~~l~~~~~-------~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~-~~~~~~~la~i  157 (355)
T cd05804          86 AFGLGDFSGMRDHVARVLPLWAP-------ENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELNPD-DAWAVHAVAHV  157 (355)
T ss_pred             HHHhcccccCchhHHHHHhccCc-------CCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CcHHHHHHHHH
Confidence            11111223444555555443111       22333444555666777778888888888887776544 55667777777


Q ss_pred             HHHcCChhHHHHHHHHHHHcCC-CCCh--hhHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          187 MCKSGKPWKAVKLYKEMKKKGI-KMDV--VAYNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~~~~-~~~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      +...|++++|...+++...... .|+.  ..|..+...+...|++++|..+++....
T Consensus       158 ~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~  214 (355)
T cd05804         158 LEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIA  214 (355)
T ss_pred             HHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            7778888888887777765421 1222  2344566666777777777777777643

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.

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

Probab=99.25  E-value=1.4e-07  Score=82.46  Aligned_cols=300  Identities=8%  Similarity=-0.109  Sum_probs=189.5

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--c-HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--D-EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      ...|..+...+...|+.+.+...+.........  + ..........+...|++++|.+.+++....       .|.+..
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~-------~P~~~~   78 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDD-------YPRDLL   78 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-------CCCcHH
Confidence            456777777788888898888888777665554  2 233333445566789999999999988763       344444


Q ss_pred             HHHHHHHHHH----hcCChhHHHHHHHHHHhCCCCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHH
Q 041804          144 IYNMILRGWF----KMSWWGKCREFWEEMDKRGVVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTV  218 (403)
Q Consensus       144 ~~~~l~~~~~----~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  218 (403)
                      .+.. ...+.    ..+..+.+.+.+...  ....| .......+...+...|++++|...+++..+.. +.+...+..+
T Consensus        79 a~~~-~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~l  154 (355)
T cd05804          79 ALKL-HLGAFGLGDFSGMRDHVARVLPLW--APENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAV  154 (355)
T ss_pred             HHHH-hHHHHHhcccccCchhHHHHHhcc--CcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHH
Confidence            4442 22222    244555555555541  11223 33445566678899999999999999999874 4456677888


Q ss_pred             HHHHhhcCCHHHHHHHHHHHHHcCCC-CCH--HHHHHHHHHHHhcCcHHHHHHHHHhchhcCC-CCChhhH-HH--HHHh
Q 041804          219 IRAVGVSEGVDFAMRVYREMREMGCQ-PSV--VTCNTVIKLLCENGRVREAYAVLAEMPKKGC-VPDVITY-HC--FFRC  291 (403)
Q Consensus       219 l~~~~~~~~~~~a~~~~~~~~~~~~~-~~~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~p~~~~~-~~--l~~~  291 (403)
                      ...+...|++++|...++...+.... |+.  ..|..+...+...|++++|..++++...... .+..... +.  ++..
T Consensus       155 a~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  234 (355)
T cd05804         155 AHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWR  234 (355)
T ss_pred             HHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHH
Confidence            88999999999999999998875321 232  3455788899999999999999999764322 1222111 11  1111


Q ss_pred             h---CCHHHHHHHHHHHHH---cCC--CCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCC------C--CHHHHHHH
Q 041804          292 L---EKPREILGLFDRMIE---SGI--RPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCS------P--DEFAYNAL  355 (403)
Q Consensus       292 ~---~~~~~a~~~~~~~~~---~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~------~--~~~~~~~l  355 (403)
                      +   +....+.. ++.+..   ...  ............++...|+.+.|..+++.+......      .  .....-..
T Consensus       235 ~~~~g~~~~~~~-w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~  313 (355)
T cd05804         235 LELAGHVDVGDR-WEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAE  313 (355)
T ss_pred             HHhcCCCChHHH-HHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHH
Confidence            1   22221211 121211   111  111122235667788999999999999988653211      0  12222233


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHc
Q 041804          356 VDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       356 ~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      ..++...|++++|.+.+......
T Consensus       314 A~~~~~~g~~~~A~~~L~~al~~  336 (355)
T cd05804         314 ALYAFAEGNYATALELLGPVRDD  336 (355)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH
Confidence            34566899999999999987764

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.

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

Probab=99.24  E-value=4.4e-09  Score=88.82  Aligned_cols=223  Identities=12%  Similarity=0.084  Sum_probs=174.1

Q ss_pred             HHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHH
Q 041804           40 ILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIE  119 (403)
Q Consensus        40 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  119 (403)
                      .+.-.|+...|..-|+........  +...|--+...|....+..+-.+.|++..+.++.++.+|..-.+.+.-.+++++
T Consensus       335 F~fL~g~~~~a~~d~~~~I~l~~~--~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~  412 (606)
T KOG0547|consen  335 FHFLKGDSLGAQEDFDAAIKLDPA--FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEE  412 (606)
T ss_pred             hhhhcCCchhhhhhHHHHHhcCcc--cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHH
Confidence            344568888999999988887622  222277777888999999999999999999998899999988888888899999


Q ss_pred             HHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHH
Q 041804          120 AQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKL  199 (403)
Q Consensus       120 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  199 (403)
                      |..=|++...       -.+.+...|--+.-+..+.+.++++...|++.++.=+. .+..|+.....+..++++++|.+.
T Consensus       413 A~aDF~Kai~-------L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~-~~Evy~~fAeiLtDqqqFd~A~k~  484 (606)
T KOG0547|consen  413 AIADFQKAIS-------LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKKFPN-CPEVYNLFAEILTDQQQFDKAVKQ  484 (606)
T ss_pred             HHHHHHHHhh-------cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CchHHHHHHHHHhhHHhHHHHHHH
Confidence            9999988876       44667778888888888899999999999998887444 778899999999999999999999


Q ss_pred             HHHHHHcCCC-----CChhhH--HHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHh
Q 041804          200 YKEMKKKGIK-----MDVVAY--NTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAE  272 (403)
Q Consensus       200 ~~~~~~~~~~-----~~~~~~--~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  272 (403)
                      |+..++....     .+..++  ..++.. .-.+++..|..++++..+..++ ....|..|...-.+.|+.++|+++|++
T Consensus       485 YD~ai~LE~~~~~~~v~~~plV~Ka~l~~-qwk~d~~~a~~Ll~KA~e~Dpk-ce~A~~tlaq~~lQ~~~i~eAielFEk  562 (606)
T KOG0547|consen  485 YDKAIELEPREHLIIVNAAPLVHKALLVL-QWKEDINQAENLLRKAIELDPK-CEQAYETLAQFELQRGKIDEAIELFEK  562 (606)
T ss_pred             HHHHHhhccccccccccchhhhhhhHhhh-chhhhHHHHHHHHHHHHccCch-HHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            9988765211     111111  111111 1248899999999999886543 567788899999999999999999987


Q ss_pred             ch
Q 041804          273 MP  274 (403)
Q Consensus       273 ~~  274 (403)
                      -.
T Consensus       563 sa  564 (606)
T KOG0547|consen  563 SA  564 (606)
T ss_pred             HH
Confidence            54

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.24  E-value=2.1e-07  Score=77.36  Aligned_cols=299  Identities=11%  Similarity=0.024  Sum_probs=189.4

Q ss_pred             CCHHHHHHHHHHHHh--cCChHHHHHHHHHHhhcC-CC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           65 PNHATFRIMFKRYVT--AHLVNEAMGTFNKLDEFG-LK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                      |+..+...-+.+++.  .++...|..++-.+.... ++ +......+.+++...|+..+|...|++....       .+-
T Consensus       192 ~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~-------dpy  264 (564)
T KOG1174|consen  192 DHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA-------NPD  264 (564)
T ss_pred             CCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC-------Chh
Confidence            333333333444433  344444444444333322 23 7777888888888888888888888776542       233


Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHH
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIR  220 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  220 (403)
                      +........-.+.+.|+.+....+...+....-. ....|-.-.......+++..|+.+-++.++.+ +-+...+-.--.
T Consensus       265 ~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~~-ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~-~r~~~alilKG~  342 (564)
T KOG1174|consen  265 NVEAMDLYAVLLGQEGGCEQDSALMDYLFAKVKY-TASHWFVHAQLLYDEKKFERALNFVEKCIDSE-PRNHEALILKGR  342 (564)
T ss_pred             hhhhHHHHHHHHHhccCHhhHHHHHHHHHhhhhc-chhhhhhhhhhhhhhhhHHHHHHHHHHHhccC-cccchHHHhccH
Confidence            3333333444455677777777777766554211 33344444455566777888888877777653 223334443444


Q ss_pred             HHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHH---HHhh--CCH
Q 041804          221 AVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCF---FRCL--EKP  295 (403)
Q Consensus       221 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l---~~~~--~~~  295 (403)
                      .+...+++++|.-.|+...... +.+...|.-|+.+|...|.+.+|...-+...+. ...+..+.+.+   +...  .--
T Consensus       343 lL~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~r  420 (564)
T KOG1174|consen  343 LLIALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMR  420 (564)
T ss_pred             HHHhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhH
Confidence            6667788888888888877652 246778888888888888888887666554332 11122333322   1111  124


Q ss_pred             HHHHHHHHHHHHcCCCCc-hhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 041804          296 REILGLFDRMIESGIRPK-MDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEE  374 (403)
Q Consensus       296 ~~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  374 (403)
                      ++|..++++-...  .|+ ....+.+...|...|..+.++.+++.....  .||....+.|.+.+...+.+++|.+.|..
T Consensus       421 EKAKkf~ek~L~~--~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~  496 (564)
T KOG1174|consen  421 EKAKKFAEKSLKI--NPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYK  496 (564)
T ss_pred             HHHHHHHHhhhcc--CCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            6677777766653  333 356677778888999999999999988764  68999999999999999999999999988


Q ss_pred             HHHc
Q 041804          375 MFAK  378 (403)
Q Consensus       375 m~~~  378 (403)
                      ....
T Consensus       497 ALr~  500 (564)
T KOG1174|consen  497 ALRQ  500 (564)
T ss_pred             HHhc
Confidence            7764

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.22  E-value=5.4e-07  Score=79.14  Aligned_cols=203  Identities=14%  Similarity=0.020  Sum_probs=142.6

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+..-|+-++|.+....-.+  +...+...|+.+.-.+....++++|++.|......+  +.|...|.-+.-.-++.|+
T Consensus        49 L~L~~lg~~~ea~~~vr~glr--~d~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~--~dN~qilrDlslLQ~QmRd  124 (700)
T KOG1156|consen   49 LTLNCLGKKEEAYELVRLGLR--NDLKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE--KDNLQILRDLSLLQIQMRD  124 (700)
T ss_pred             chhhcccchHHHHHHHHHHhc--cCcccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC--CCcHHHHHHHHHHHHHHHh
Confidence            345556888999988887763  345567788888888888899999999999999876  4567788888888889999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH------HHHHhcC
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL------RGWFKMS  156 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~------~~~~~~~  156 (403)
                      ++.....-..+.+..+.....|..+..++.-.|+...|..+++...+..     ...|+...+....      ....+.|
T Consensus       125 ~~~~~~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~-----~~~~s~~~~e~se~~Ly~n~i~~E~g  199 (700)
T KOG1156|consen  125 YEGYLETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQ-----NTSPSKEDYEHSELLLYQNQILIEAG  199 (700)
T ss_pred             hhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-----ccCCCHHHHHHHHHHHHHHHHHHHcc
Confidence            9999999888888877788889999999999999999999988887753     2245554444333      2334556


Q ss_pred             ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHH
Q 041804          157 WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNT  217 (403)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  217 (403)
                      ..+.|.+.+..-...-+. ....-.+-...+.+.+++++|..++..++..  .||..-|..
T Consensus       200 ~~q~ale~L~~~e~~i~D-kla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Yy~  257 (700)
T KOG1156|consen  200 SLQKALEHLLDNEKQIVD-KLAFEETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDYYE  257 (700)
T ss_pred             cHHHHHHHHHhhhhHHHH-HHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHHHH
Confidence            666666665544332111 1122233345566777777777777777766  345544433

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.21  E-value=6e-08  Score=80.45  Aligned_cols=287  Identities=9%  Similarity=-0.049  Sum_probs=198.8

Q ss_pred             cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHH
Q 041804           44 FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQEL  123 (403)
Q Consensus        44 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  123 (403)
                      .++-..|..++-.+......+-|......+..++...|+.++|+-.|++....++.+........-.+.+.|+.+....+
T Consensus       209 ~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~~~L  288 (564)
T KOG1174|consen  209 NFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQDSAL  288 (564)
T ss_pred             hcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhHHHH
Confidence            34444455544444444335667788888899999999999999999998887766555555555556677887777777


Q ss_pred             HhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 041804          124 CFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEM  203 (403)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  203 (403)
                      ...+..       ...-....|..-+.......+++.|+.+-++..+.+.. +...|-.-...+...+++++|.-.|+..
T Consensus       289 ~~~Lf~-------~~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r-~~~alilKG~lL~~~~R~~~A~IaFR~A  360 (564)
T KOG1174|consen  289 MDYLFA-------KVKYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPR-NHEALILKGRLLIALERHTQAVIAFRTA  360 (564)
T ss_pred             HHHHHh-------hhhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcc-cchHHHhccHHHHhccchHHHHHHHHHH
Confidence            666544       22233444555566666778888998888888876555 5566666667888889999999889888


Q ss_pred             HHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-HHHH-hcCcHHHHHHHHHhchhcCCCCC
Q 041804          204 KKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVI-KLLC-ENGRVREAYAVLAEMPKKGCVPD  281 (403)
Q Consensus       204 ~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li-~~~~-~~g~~~~a~~~~~~~~~~~~~p~  281 (403)
                      .... +-+...|.-|+.+|...|++.+|.-+-+...+. .+-+..+.+.+. ..+. ...--++|.++++.-...  .|+
T Consensus       361 q~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~--~P~  436 (564)
T KOG1174|consen  361 QMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKI--NPI  436 (564)
T ss_pred             Hhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhcc--CCc
Confidence            7652 456788999999999999998888777666554 233445544442 2222 223357888888876653  454


Q ss_pred             hhh----HHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcC
Q 041804          282 VIT----YHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELG  344 (403)
Q Consensus       282 ~~~----~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  344 (403)
                      ..-    ..-+...-++.++++.++++....  .||....+.|...+...+.+++|.+.|....+.+
T Consensus       437 Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~d  501 (564)
T KOG1174|consen  437 YTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQD  501 (564)
T ss_pred             cHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence            322    222233337788888888887763  5788888899999999999999999988887653

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

Probab=99.19  E-value=6.8e-07  Score=77.72  Aligned_cols=358  Identities=13%  Similarity=0.050  Sum_probs=199.4

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      ..++++++|.+....+..  ..+.+...+..-+-++.+.+.+++|+.+.+.-....   .+..-+-.=..+..+.+..++
T Consensus        23 ~~~~e~e~a~k~~~Kil~--~~pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~---~~~~~~fEKAYc~Yrlnk~De   97 (652)
T KOG2376|consen   23 GKNGEYEEAVKTANKILS--IVPDDEDAIRCKVVALIQLDKYEDALKLIKKNGALL---VINSFFFEKAYCEYRLNKLDE   97 (652)
T ss_pred             ccchHHHHHHHHHHHHHh--cCCCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhh---hcchhhHHHHHHHHHcccHHH
Confidence            456889999999999883  445667778888888899999999986655433211   111111122334447788888


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccc----------------------cccccCc--c
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGF----------------------SGLVEMN--K  141 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----------------------~~~~~~~--~  141 (403)
                      |+..++-..   ..+..+...-.+.+.+.+++++|.++|+.+.++..-                      ......|  +
T Consensus        98 alk~~~~~~---~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v~~v~e~s  174 (652)
T KOG2376|consen   98 ALKTLKGLD---RLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSVPEVPEDS  174 (652)
T ss_pred             HHHHHhccc---ccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhccCCCcch
Confidence            888877221   125556667777788888888888888877544300                      0001111  2


Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHhCC--------CC-----CcH-HHHHHHHHHHHHcCChhHHHHHHHHHHHcC
Q 041804          142 TKIYNMILRGWFKMSWWGKCREFWEEMDKRG--------VV-----KDL-HSYSIYMDIMCKSGKPWKAVKLYKEMKKKG  207 (403)
Q Consensus       142 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~-----~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  207 (403)
                      ...+......+...|++.+|+++++...+.+        ..     -.. ..-..|.-.+...|+.++|..+|...++..
T Consensus       175 yel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~~~  254 (652)
T KOG2376|consen  175 YELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIKRN  254 (652)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhc
Confidence            2223334455677899999999998873211        11     000 122334556778899999999999988764


Q ss_pred             CCCChhhH----HHHH-----------------------------------------------HHHhhcC----------
Q 041804          208 IKMDVVAY----NTVI-----------------------------------------------RAVGVSE----------  226 (403)
Q Consensus       208 ~~~~~~~~----~~ll-----------------------------------------------~~~~~~~----------  226 (403)
                       ++|....    |.|+                                               ..|...+          
T Consensus       255 -~~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~tnk~~q~r~~~a~l  333 (652)
T KOG2376|consen  255 -PADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALFTNKMDQVRELSASL  333 (652)
T ss_pred             -CCCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhC
Confidence             2333111    1111                                               1110000          


Q ss_pred             ----------------------CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHH--------hchhc
Q 041804          227 ----------------------GVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLA--------EMPKK  276 (403)
Q Consensus       227 ----------------------~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~--------~~~~~  276 (403)
                                            ....+..++...-+....-...+.-.++......|+++.|.+++.        .+.+.
T Consensus       334 p~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~  413 (652)
T KOG2376|consen  334 PGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEA  413 (652)
T ss_pred             CccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhh
Confidence                                  011122222222222111123344455566677888888888888        55555


Q ss_pred             CCCCChhhHHHHH-HhhCCHHHHHHHHHHHHHc--CCCCchh----hHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCH
Q 041804          277 GCVPDVITYHCFF-RCLEKPREILGLFDRMIES--GIRPKMD----TYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDE  349 (403)
Q Consensus       277 ~~~p~~~~~~~l~-~~~~~~~~a~~~~~~~~~~--~~~~~~~----~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  349 (403)
                      +..|..+.+...+ ...+..+.|..++...+..  ...+...    ++.-+...-.+.|+-++|..+++++.+.. ++|.
T Consensus       414 ~~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~  492 (652)
T KOG2376|consen  414 KHLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDT  492 (652)
T ss_pred             ccChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchH
Confidence            5555544333222 2222222233333333210  0011112    23333334456788888888888888754 6788


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHH
Q 041804          350 FAYNALVDALIDKGMLDMARKYDEE  374 (403)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~a~~~~~~  374 (403)
                      .+...++.+|++. +.+.|..+-+.
T Consensus       493 ~~l~~lV~a~~~~-d~eka~~l~k~  516 (652)
T KOG2376|consen  493 DLLVQLVTAYARL-DPEKAESLSKK  516 (652)
T ss_pred             HHHHHHHHHHHhc-CHHHHHHHhhc
Confidence            8888888888865 45666655443

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

Probab=99.17  E-value=1e-06  Score=79.01  Aligned_cols=359  Identities=11%  Similarity=0.004  Sum_probs=214.1

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHH-hcCChHH
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYV-TAHLVNE   85 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~   85 (403)
                      +.|+++.+.+.|+...  .+.-...+.|+.+...|...|.-..|..+++.-......+++...+-..-..|. +.+..++
T Consensus       335 ~~g~f~~lae~fE~~~--~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmasklc~e~l~~~ee  412 (799)
T KOG4162|consen  335 RCGQFEVLAEQFEQAL--PFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMASKLCIERLKLVEE  412 (799)
T ss_pred             HHHHHHHHHHHHHHHh--HhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHHHHHHhchhhhhh
Confidence            3466666777776665  333444566677777777777777777766655443311223333333333333 3455666


Q ss_pred             HHHHHHHHhhc--CC---CcHHHHHHHHHHHHh-----------cCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           86 AMGTFNKLDEF--GL---KDEVSYCNLVDALCE-----------YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        86 a~~~~~~~~~~--~~---~~~~~~~~l~~~~~~-----------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      ++..-.+....  +.   -.+..+..+.-+|..           .....++.+.+++..+.       .+.|..+...+.
T Consensus       413 gldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~-------d~~dp~~if~la  485 (799)
T KOG4162|consen  413 GLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQF-------DPTDPLVIFYLA  485 (799)
T ss_pred             HHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhc-------CCCCchHHHHHH
Confidence            66655555541  11   144455555555442           11234455555655542       233444455556


Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc-CCC------------------C
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-GIK------------------M  210 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~------------------~  210 (403)
                      --|+..++++.|.+...+..+.+..-+...|..+.-.+...+++.+|+.+.+...+. |..                  -
T Consensus       486 lq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~~~~~~e~  565 (799)
T KOG4162|consen  486 LQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIELTFNDREE  565 (799)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhhhhcccHHH
Confidence            667788899999999999998866668889999999999999999999998876654 210                  0


Q ss_pred             ChhhHHHHHHHHhhc-----------------------CCHHHHHHHHHHHH--------HcC---------CC--CC--
Q 041804          211 DVVAYNTVIRAVGVS-----------------------EGVDFAMRVYREMR--------EMG---------CQ--PS--  246 (403)
Q Consensus       211 ~~~~~~~ll~~~~~~-----------------------~~~~~a~~~~~~~~--------~~~---------~~--~~--  246 (403)
                      ...|+..++..+-..                       ++..++.+..+.+.        ..|         ..  |+  
T Consensus       566 ~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~~~~~~~~  645 (799)
T KOG4162|consen  566 ALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSSTVLPGPDSL  645 (799)
T ss_pred             HHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCcccccCCCCch
Confidence            011222222222100                       01111111111110        001         00  11  


Q ss_pred             ----HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC-hhhHH---HHHHhhCCHHHHHHHHHHHHHcCCCCchhhHH
Q 041804          247 ----VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD-VITYH---CFFRCLEKPREILGLFDRMIESGIRPKMDTYV  318 (403)
Q Consensus       247 ----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~---~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  318 (403)
                          ...|......+.+.+..++|...+.+....  .|- ...|.   .+...-+..++|.+.|.......+. ++....
T Consensus       646 ~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~--~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~-hv~s~~  722 (799)
T KOG4162|consen  646 WYLLQKLWLLAADLFLLSGNDDEARSCLLEASKI--DPLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPD-HVPSMT  722 (799)
T ss_pred             HHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhc--chhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCC-CcHHHH
Confidence                112334455666677777777666665543  121 11111   1122236678888888887765433 456788


Q ss_pred             HHHHHHHhcCCcchHHH--HHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          319 MLLRKFGRWGFLRPVFV--VWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       319 ~li~~~~~~g~~~~a~~--~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      ++..++.+.|+..-|..  ++..+.+.+ +.+...|-.+...+.+.|+.++|.+.|.....-
T Consensus       723 Ala~~lle~G~~~la~~~~~L~dalr~d-p~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qL  783 (799)
T KOG4162|consen  723 ALAELLLELGSPRLAEKRSLLSDALRLD-PLNHEAWYYLGEVFKKLGDSKQAAECFQAALQL  783 (799)
T ss_pred             HHHHHHHHhCCcchHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHccchHHHHHHHHHHHhh
Confidence            89999999999888888  999999876 678999999999999999999999999987763

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.15  E-value=6.7e-07  Score=72.98  Aligned_cols=179  Identities=6%  Similarity=-0.039  Sum_probs=103.6

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      ++++..|+.+++.-.. .+-.....+--.+..++.+.|++++|...+..+.+..  .|+...+-.|.-++.-.|.+.+|.
T Consensus        35 ~rDytGAislLefk~~-~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~--~~~~el~vnLAcc~FyLg~Y~eA~  111 (557)
T KOG3785|consen   35 NRDYTGAISLLEFKLN-LDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKD--DAPAELGVNLACCKFYLGQYIEAK  111 (557)
T ss_pred             cccchhHHHHHHHhhc-cchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccC--CCCcccchhHHHHHHHHHHHHHHH
Confidence            4677888888776552 2222222333346677778899999999888877754  467777777777777788888887


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHH
Q 041804           88 GTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEE  167 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  167 (403)
                      ++-.+..+    ++..-..++....+.++-++-..+-..+...           ..---+|.........+++|.+++.+
T Consensus       112 ~~~~ka~k----~pL~~RLlfhlahklndEk~~~~fh~~LqD~-----------~EdqLSLAsvhYmR~HYQeAIdvYkr  176 (557)
T KOG3785|consen  112 SIAEKAPK----TPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-----------LEDQLSLASVHYMRMHYQEAIDVYKR  176 (557)
T ss_pred             HHHhhCCC----ChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-----------HHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            76654432    4444444555555556555544443332221           11123344444444556777777777


Q ss_pred             HHhCCCCCcHHHHHHHH-HHHHHcCChhHHHHHHHHHHHc
Q 041804          168 MDKRGVVKDLHSYSIYM-DIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       168 ~~~~~~~~~~~~~~~l~-~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ....+  |.-...|..+ -+|.+..-++-+.++++...+.
T Consensus       177 vL~dn--~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q  214 (557)
T KOG3785|consen  177 VLQDN--PEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ  214 (557)
T ss_pred             HHhcC--hhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh
Confidence            76553  2333333333 3455555566666666665554

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.12  E-value=3.2e-06  Score=74.45  Aligned_cols=212  Identities=16%  Similarity=0.187  Sum_probs=138.5

Q ss_pred             HHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC---hhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC----------CC
Q 041804          178 HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD---VVAYNTVIRAVGVSEGVDFAMRVYREMREMG----------CQ  244 (403)
Q Consensus       178 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----------~~  244 (403)
                      ..|..+.+.|-..|+.+.|..+|++..+...+--   ..+|......=.+..+++.|+++++.....-          ..
T Consensus       388 ~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~  467 (835)
T KOG2047|consen  388 TLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSE  467 (835)
T ss_pred             hHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCC
Confidence            4678888999999999999999999887643321   2355555555567788999999888765321          11


Q ss_pred             C-------CHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCC-CC-hhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCch-
Q 041804          245 P-------SVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCV-PD-VITYHCFFRCLEKPREILGLFDRMIESGIRPKM-  314 (403)
Q Consensus       245 ~-------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~-p~-~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~-  314 (403)
                      |       +...|+..++.--..|-++....+++++.+..+. |. ...|..++.-..-++++.+.|++=+..-..|+. 
T Consensus       468 pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~  547 (835)
T KOG2047|consen  468 PVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVY  547 (835)
T ss_pred             cHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHH
Confidence            1       3345666677667788999999999999876543 32 234445555555577888888766554334444 


Q ss_pred             hhHHHHHHHHHh---cCCcchHHHHHHHHHhcCCCCCHHH--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhhHHH
Q 041804          315 DTYVMLLRKFGR---WGFLRPVFVVWKKMEELGCSPDEFA--YNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELG  389 (403)
Q Consensus       315 ~~~~~li~~~~~---~g~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~  389 (403)
                      ..|+..+.-+.+   ...++.|..+|++..+ |.+|...-  |-.....=-+.|....|+.++++.. .++.+.....+-
T Consensus       548 diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat-~~v~~a~~l~my  625 (835)
T KOG2047|consen  548 DIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERAT-SAVKEAQRLDMY  625 (835)
T ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH-hcCCHHHHHHHH
Confidence            467766665543   2368999999999998 66654322  2222333345788888999998854 345555544443


Q ss_pred             HH
Q 041804          390 TK  391 (403)
Q Consensus       390 ~~  391 (403)
                      ..
T Consensus       626 ni  627 (835)
T KOG2047|consen  626 NI  627 (835)
T ss_pred             HH
Confidence            33

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

Probab=99.08  E-value=3.3e-08  Score=82.03  Aligned_cols=245  Identities=11%  Similarity=0.054  Sum_probs=134.9

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      .|++..++.-.+ ... .....+......+.+++...|+++.+   +.++....  .|.......+...+...++-+.++
T Consensus        14 ~G~Y~~~i~e~~-~~~-~~~~~~~e~~~~~~Rs~iAlg~~~~v---l~ei~~~~--~~~l~av~~la~y~~~~~~~e~~l   86 (290)
T PF04733_consen   14 LGNYQQCINEAS-LKS-FSPENKLERDFYQYRSYIALGQYDSV---LSEIKKSS--SPELQAVRLLAEYLSSPSDKESAL   86 (290)
T ss_dssp             TT-HHHHCHHHH-CHT-STCHHHHHHHHHHHHHHHHTT-HHHH---HHHS-TTS--SCCCHHHHHHHHHHCTSTTHHCHH
T ss_pred             hhhHHHHHHHhh-ccC-CCchhHHHHHHHHHHHHHHcCChhHH---HHHhccCC--ChhHHHHHHHHHHHhCccchHHHH
Confidence            477777776555 221 11222344555667777777776643   34443332  455555555554444434455555


Q ss_pred             HHHHHHhhcCCC--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           88 GTFNKLDEFGLK--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        88 ~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      .-+++.......  ++.........+...|++++|+++++..            .+.......+..|.+.++++.|.+.+
T Consensus        87 ~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------------~~lE~~al~Vqi~L~~~R~dlA~k~l  154 (290)
T PF04733_consen   87 EELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------------GSLELLALAVQILLKMNRPDLAEKEL  154 (290)
T ss_dssp             HHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------------TCHHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             HHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------------CcccHHHHHHHHHHHcCCHHHHHHHH
Confidence            555544433322  2223333334455567777777665432            23445566677777777888888777


Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          166 EEMDKRGVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       166 ~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      +.|.+.+   +..+...+..++..    ...+++|..+|+++.+. ..++..+.+.+..+....|++++|.+++.+..+.
T Consensus       155 ~~~~~~~---eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~  230 (290)
T PF04733_consen  155 KNMQQID---EDSILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEK  230 (290)
T ss_dssp             HHHHCCS---CCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC
T ss_pred             HHHHhcC---CcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            7777653   22334444444433    23577777777776554 4566677777777777777777777777776654


Q ss_pred             CCCCCHHHHHHHHHHHHhcCcH-HHHHHHHHhchhc
Q 041804          242 GCQPSVVTCNTVIKLLCENGRV-REAYAVLAEMPKK  276 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~-~~a~~~~~~~~~~  276 (403)
                      +.. ++.+...++-+....|+. +.+.+.+.++...
T Consensus       231 ~~~-~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  231 DPN-DPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             -CC-HHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             ccC-CHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            322 445555566665666665 5566777776654

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.

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.07  E-value=5.1e-07  Score=73.64  Aligned_cols=364  Identities=10%  Similarity=0.021  Sum_probs=184.7

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCC----------CCCHH---H--
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSS----------IPNHA---T--   69 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~----------~~~~~---~--   69 (403)
                      +..-|++++|+..+..+..  .-.++...+-.|.-++.-.|.+.+|..+-....+..-.          -.|..   +  
T Consensus        67 ~fhLgdY~~Al~~Y~~~~~--~~~~~~el~vnLAcc~FyLg~Y~eA~~~~~ka~k~pL~~RLlfhlahklndEk~~~~fh  144 (557)
T KOG3785|consen   67 YFHLGDYEEALNVYTFLMN--KDDAPAELGVNLACCKFYLGQYIEAKSIAEKAPKTPLCIRLLFHLAHKLNDEKRILTFH  144 (557)
T ss_pred             HHhhccHHHHHHHHHHHhc--cCCCCcccchhHHHHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCcHHHHHHHH
Confidence            3456999999999998874  34566666666766666778888888776665432100          00000   0  


Q ss_pred             ---------HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           70 ---------FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        70 ---------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                               --+|.......-.+.+|+.+|.+....++.-...-..+.-+|.+..-++-+.+++.-...       ..+.
T Consensus       145 ~~LqD~~EdqLSLAsvhYmR~HYQeAIdvYkrvL~dn~ey~alNVy~ALCyyKlDYydvsqevl~vYL~-------q~pd  217 (557)
T KOG3785|consen  145 SSLQDTLEDQLSLASVHYMRMHYQEAIDVYKRVLQDNPEYIALNVYMALCYYKLDYYDVSQEVLKVYLR-------QFPD  217 (557)
T ss_pred             HHHhhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcChhhhhhHHHHHHHHHhcchhhhHHHHHHHHHH-------hCCC
Confidence                     011222222333456677777766654433222222233455566666666666555544       3344


Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHH--------------HHHhCCC------------CC-----cHHHHHHHHHHHHH
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWE--------------EMDKRGV------------VK-----DLHSYSIYMDIMCK  189 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~--------------~~~~~~~------------~~-----~~~~~~~l~~~~~~  189 (403)
                      ++.+.|..+....+.=+-..|++-..              .+.+.+.            -|     -+.+-..|+-.|.+
T Consensus       218 StiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~~~l~rHNLVvFrngEgALqVLP~L~~~IPEARlNL~iYyL~  297 (557)
T KOG3785|consen  218 STIAKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFIEYLCRHNLVVFRNGEGALQVLPSLMKHIPEARLNLIIYYLN  297 (557)
T ss_pred             cHHHHHHHHHHHhhhhccchhHHHHHHHHhcccccchhHHHHHHcCeEEEeCCccHHHhchHHHhhChHhhhhheeeecc
Confidence            44444444433333211111111111              1111110            01     11223334445667


Q ss_pred             cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHH-----hhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCcH
Q 041804          190 SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV-----GVSEGVDFAMRVYREMREMGCQPSV-VTCNTVIKLLCENGRV  263 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~-----~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~li~~~~~~g~~  263 (403)
                      +++.++|..+.+++.-  ..|-......+..+-     .......-|.+.|+..-+.+..-|. ..-.++...+.-..++
T Consensus       298 q~dVqeA~~L~Kdl~P--ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qF  375 (557)
T KOG3785|consen  298 QNDVQEAISLCKDLDP--TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQF  375 (557)
T ss_pred             cccHHHHHHHHhhcCC--CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHH
Confidence            7777777776655431  122222222222211     1122244455555444433332221 2223344444445567


Q ss_pred             HHHHHHHHhchhcCCCCChhhHHHHH--HhhCCHHHHHHHHHHHHHcCCCCchhhHHH-HHHHHHhcCCcchHHHHHHHH
Q 041804          264 REAYAVLAEMPKKGCVPDVITYHCFF--RCLEKPREILGLFDRMIESGIRPKMDTYVM-LLRKFGRWGFLRPVFVVWKKM  340 (403)
Q Consensus       264 ~~a~~~~~~~~~~~~~p~~~~~~~l~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-li~~~~~~g~~~~a~~~~~~~  340 (403)
                      ++.+..+..+..--..-|...+|..-  .+.+...+|.++|-.+....++ |..+|.+ |.++|.+.+.++.|++++-++
T Consensus       376 ddVl~YlnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~  454 (557)
T KOG3785|consen  376 DDVLTYLNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKT  454 (557)
T ss_pred             HHHHHHHHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhc
Confidence            77777776666543344555555332  2347778888888777655555 5555554 446778888888887765443


Q ss_pred             HhcCCCCCHHHH-HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChh
Q 041804          341 EELGCSPDEFAY-NALVDALIDKGMLDMARKYDEEMFAKGLSAKPR  385 (403)
Q Consensus       341 ~~~~~~~~~~~~-~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~  385 (403)
                      .   -+.+..+. ..+..-|.+.+.+--|-+.|+.+...  .|+|.
T Consensus       455 ~---t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~l--DP~pE  495 (557)
T KOG3785|consen  455 N---TPSERFSLLQLIANDCYKANEFYYAAKAFDELEIL--DPTPE  495 (557)
T ss_pred             C---CchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHcc--CCCcc
Confidence            3   22233333 33345677788777777777777653  34444

>PLN02789 farnesyltranstransferase

Probab=99.07  E-value=4.2e-07  Score=76.52  Aligned_cols=216  Identities=9%  Similarity=-0.006  Sum_probs=164.6

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC-ChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH-LVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      .++..+-.++...+..++|+.+.+.+.+..  +-+..+|+....++...| ++++++..++++.+..+.+..+|+....+
T Consensus        38 ~a~~~~ra~l~~~e~serAL~lt~~aI~ln--P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~  115 (320)
T PLN02789         38 EAMDYFRAVYASDERSPRALDLTADVIRLN--PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWL  115 (320)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHH
Confidence            355566667778889999999999999865  234557877777777777 67999999999999998888888877777


Q ss_pred             HHhcCCH--HHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          111 LCEYKHV--IEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       111 ~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      +.+.+..  +++...++++..       ..+.|..+|+.....+...|+++++++.++++.+.++. |..+|+.....+.
T Consensus       116 l~~l~~~~~~~el~~~~kal~-------~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~  187 (320)
T PLN02789        116 AEKLGPDAANKELEFTRKILS-------LDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVIT  187 (320)
T ss_pred             HHHcCchhhHHHHHHHHHHHH-------hCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHH
Confidence            7676653  667777777776       55788899999999999999999999999999998877 7788888777666


Q ss_pred             Hc---CCh----hHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 041804          189 KS---GKP----WKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS----EGVDFAMRVYREMREMGCQPSVVTCNTVIKLL  257 (403)
Q Consensus       189 ~~---~~~----~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  257 (403)
                      +.   |..    ++.++...+++... +-|...|+.+...+...    ++..+|...+.+..+.++ .+......|+..|
T Consensus       188 ~~~~l~~~~~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~-~s~~al~~l~d~~  265 (320)
T PLN02789        188 RSPLLGGLEAMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDS-NHVFALSDLLDLL  265 (320)
T ss_pred             hccccccccccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccC-CcHHHHHHHHHHH
Confidence            54   222    45677776777663 44677888888777663    344568788777766543 3667777788888


Q ss_pred             Hh
Q 041804          258 CE  259 (403)
Q Consensus       258 ~~  259 (403)
                      +.
T Consensus       266 ~~  267 (320)
T PLN02789        266 CE  267 (320)
T ss_pred             Hh
Confidence            75

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

Probab=99.06  E-value=1.8e-08  Score=83.65  Aligned_cols=246  Identities=11%  Similarity=0.064  Sum_probs=156.3

Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      +.-.|++..++.-.+ ....      ...........+.+++...|+++.+.   .++.... .|.......+...+...
T Consensus        11 ~fy~G~Y~~~i~e~~-~~~~------~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~   79 (290)
T PF04733_consen   11 QFYLGNYQQCINEAS-LKSF------SPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSP   79 (290)
T ss_dssp             HHCTT-HHHHCHHHH-CHTS------TCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTS
T ss_pred             HHHhhhHHHHHHHhh-ccCC------CchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCc
Confidence            334677777765444 1111      22334455667778888888876543   3443333 56666666665555443


Q ss_pred             CChhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHH
Q 041804          191 GKPWKAVKLYKEMKKKGIKM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAV  269 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  269 (403)
                      ++-+.++.-+++.......+ +..........+...|+++.|++++...      .+.......+..|.+.++++.|.+.
T Consensus        80 ~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~  153 (290)
T PF04733_consen   80 SDKESALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKE  153 (290)
T ss_dssp             TTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             cchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHH
Confidence            44555555554443333232 2233333334566788999998887642      3667777788999999999999999


Q ss_pred             HHhchhcCCCCChhhHHHHHHhh-------CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHh
Q 041804          270 LAEMPKKGCVPDVITYHCFFRCL-------EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEE  342 (403)
Q Consensus       270 ~~~~~~~~~~p~~~~~~~l~~~~-------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  342 (403)
                      ++.|.+.  ..|. +...+..++       .+.++|..+|+++.+. ..+++.+.+.+..++...|++++|.+++++..+
T Consensus       154 l~~~~~~--~eD~-~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~  229 (290)
T PF04733_consen  154 LKNMQQI--DEDS-ILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALE  229 (290)
T ss_dssp             HHHHHCC--SCCH-HHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCC
T ss_pred             HHHHHhc--CCcH-HHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            9998864  3343 333333322       4578999999997654 557888899999999999999999999999876


Q ss_pred             cCCCCCHHHHHHHHHHHHhcCCH-HHHHHHHHHHHHc
Q 041804          343 LGCSPDEFAYNALVDALIDKGML-DMARKYDEEMFAK  378 (403)
Q Consensus       343 ~~~~~~~~~~~~l~~~~~~~g~~-~~a~~~~~~m~~~  378 (403)
                      .+ +-++.+...++.+....|+. +.+.+++.++...
T Consensus       230 ~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  230 KD-PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             C--CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             hc-cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            54 45677888888888888888 6677888888764

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.05  E-value=4.8e-06  Score=71.86  Aligned_cols=361  Identities=12%  Similarity=-0.008  Sum_probs=195.7

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCC
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHL   82 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~   82 (403)
                      ..+..|+++.|+..|..... . .++|...|..-..+|++.|++++|++=-.+-.+..   |+ ...|+-...++.-.|+
T Consensus        11 aa~s~~d~~~ai~~~t~ai~-l-~p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~---p~w~kgy~r~Gaa~~~lg~   85 (539)
T KOG0548|consen   11 AAFSSGDFETAIRLFTEAIM-L-SPTNHVLYSNRSAAYASLGSYEKALKDATKTRRLN---PDWAKGYSRKGAALFGLGD   85 (539)
T ss_pred             hhcccccHHHHHHHHHHHHc-c-CCCccchhcchHHHHHHHhhHHHHHHHHHHHHhcC---CchhhHHHHhHHHHHhccc
Confidence            35678999999999988874 2 35578889999999999999999988777777654   55 5689999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH-------------------------HHHHHHhcccccccccccc
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI-------------------------EAQELCFGENKNVGFSGLV  137 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-------------------------~a~~~~~~~~~~~~~~~~~  137 (403)
                      +++|+.-|.+-++..+.+...+..+..++.......                         .-..++.........-  +
T Consensus        86 ~~eA~~ay~~GL~~d~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l--~  163 (539)
T KOG0548|consen   86 YEEAILAYSEGLEKDPSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSL--K  163 (539)
T ss_pred             HHHHHHHHHHHhhcCCchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhh--h
Confidence            999999999999988878888888887772210000                         0000011111000000  0


Q ss_pred             cCcchHHHHHHHHHHHhc-----------CC--------hh----HHHHHHHHHHh-CCCCCcHHHHHHHHHHHHHcCCh
Q 041804          138 EMNKTKIYNMILRGWFKM-----------SW--------WG----KCREFWEEMDK-RGVVKDLHSYSIYMDIMCKSGKP  193 (403)
Q Consensus       138 ~~~~~~~~~~l~~~~~~~-----------~~--------~~----~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~  193 (403)
                      ...+   ...++.+....           |.        +.    ........+.+ .....-..-...+.++..+..++
T Consensus       164 ~~l~---d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f  240 (539)
T KOG0548|consen  164 LYLN---DPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDF  240 (539)
T ss_pred             cccc---cHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhH
Confidence            0000   00011111000           00        00    00000000000 00000112234455555556666


Q ss_pred             hHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHH-------HHHHHHHhcCcHHHH
Q 041804          194 WKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCN-------TVIKLLCENGRVREA  266 (403)
Q Consensus       194 ~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-------~li~~~~~~g~~~~a  266 (403)
                      ..+++.+....+..  -+..-++....+|...|.+..+...-....+.|-. ...-|+       .+..+|.+.++.+.+
T Consensus       241 ~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~r~g~a~~k~~~~~~a  317 (539)
T KOG0548|consen  241 ETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRE-LRADYKLIAKALARLGNAYTKREDYEGA  317 (539)
T ss_pred             HHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHHHhhhhhhhHHhHHHH
Confidence            66666666555543  23333444444555555555555554444444322 111111       122344445556666


Q ss_pred             HHHHHhchhcCCCCChhhHHHH--------------------------HHh--hCCHHHHHHHHHHHHHcCCCCchhhHH
Q 041804          267 YAVLAEMPKKGCVPDVITYHCF--------------------------FRC--LEKPREILGLFDRMIESGIRPKMDTYV  318 (403)
Q Consensus       267 ~~~~~~~~~~~~~p~~~~~~~l--------------------------~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~  318 (403)
                      +..|.+.......|+..+-...                          ..+  .+++..|+..|.+++..... |...|.
T Consensus       318 i~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~P~-Da~lYs  396 (539)
T KOG0548|consen  318 IKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRDPE-DARLYS  396 (539)
T ss_pred             HHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCc-hhHHHH
Confidence            6666555443333332211110                          001  14566777777777766533 667777


Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          319 MLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       319 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                      .-.-+|.+.|.+..|+.=.+...+.. ++....|..=..++....+++.|.+.|++.++.+
T Consensus       397 NRAac~~kL~~~~~aL~Da~~~ieL~-p~~~kgy~RKg~al~~mk~ydkAleay~eale~d  456 (539)
T KOG0548|consen  397 NRAACYLKLGEYPEALKDAKKCIELD-PNFIKAYLRKGAALRAMKEYDKALEAYQEALELD  456 (539)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHhcC-chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            77777777777777777766666653 3334444444455555666777777777666543

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.99  E-value=5.8e-06  Score=67.40  Aligned_cols=208  Identities=11%  Similarity=-0.015  Sum_probs=134.5

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH-HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH-ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      .++.-...+...+...|++..|+.-|....+-+   |+. .++-.-...|...|+..-|+.=+.+..+..+.-..+..--
T Consensus        36 advekhlElGk~lla~~Q~sDALt~yHaAve~d---p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlelKpDF~~ARiQR  112 (504)
T KOG0624|consen   36 ADVEKHLELGKELLARGQLSDALTHYHAAVEGD---PNNYQAIFRRATVYLAMGKSKAALQDLSRVLELKPDFMAARIQR  112 (504)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC---chhHHHHHHHHHHHhhhcCCccchhhHHHHHhcCccHHHHHHHh
Confidence            345556677788888899999999998888754   433 3444455678888888888888888888766533344444


Q ss_pred             HHHHHhcCCHHHHHHHHhcccccccccccccC------c--chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHH
Q 041804          108 VDALCEYKHVIEAQELCFGENKNVGFSGLVEM------N--KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHS  179 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~------~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  179 (403)
                      ...+.+.|.++.|..=|+....+.+..+....      +  ........+..+.-.|+...|+.....+.+..+= |...
T Consensus       113 g~vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~W-da~l  191 (504)
T KOG0624|consen  113 GVVLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQPW-DASL  191 (504)
T ss_pred             chhhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCcc-hhHH
Confidence            55677889999999888887776422211100      0  0111223344555667777777777777765433 6666


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       180 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      |..-..+|...|++..|+.=++..-+.. ..+..++--+-..+...|+.+.++...++..+.
T Consensus       192 ~~~Rakc~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl  252 (504)
T KOG0624|consen  192 RQARAKCYIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECLKL  252 (504)
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc
Confidence            6666777777777777776666555442 224444445555666777777777777777664

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.98  E-value=4.6e-06  Score=82.47  Aligned_cols=337  Identities=10%  Similarity=-0.039  Sum_probs=208.7

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC-------C--cHHHHHHHH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL-------K--DEVSYCNLV  108 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-------~--~~~~~~~l~  108 (403)
                      .......|++..+..+++.+.... ...+..........+...|+++++..++......-.       +  .......+.
T Consensus       381 a~~l~~~g~~~~l~~~l~~lp~~~-~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a  459 (903)
T PRK04841        381 GWSLFNQGELSLLEECLNALPWEV-LLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRA  459 (903)
T ss_pred             HHHHHhcCChHHHHHHHHhCCHHH-HhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHH
Confidence            344556778888777777663221 111222233445556678999999999887654311       1  112223344


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccCc-chHHHHHHHHHHHhcCChhHHHHHHHHHHhCC----C-CCcHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEMN-KTKIYNMILRGWFKMSWWGKCREFWEEMDKRG----V-VKDLHSYSI  182 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~-~~~~~~~~~  182 (403)
                      ..+...|++++|...+++.......   .... .....+.+...+...|++++|...+++.....    . .+...++..
T Consensus       460 ~~~~~~g~~~~A~~~~~~al~~~~~---~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~  536 (903)
T PRK04841        460 QVAINDGDPEEAERLAELALAELPL---TWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQ  536 (903)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhcCCC---ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHH
Confidence            5566799999999998876542110   1111 22345667777888999999999998876421    1 112234556


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHc----CCC--C-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC--CCC--CHHHHH
Q 041804          183 YMDIMCKSGKPWKAVKLYKEMKKK----GIK--M-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMG--CQP--SVVTCN  251 (403)
Q Consensus       183 l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~--~~~~~~  251 (403)
                      +...+...|++++|...+++....    +..  + ....+..+...+...|+++.|...+.+.....  ..+  ....+.
T Consensus       537 la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~  616 (903)
T PRK04841        537 QSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLA  616 (903)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHH
Confidence            677788999999999998886553    211  1 12334455556677899999999998876531  112  233445


Q ss_pred             HHHHHHHhcCcHHHHHHHHHhchhcCC-CCChhhHH--------HHHHhhCCHHHHHHHHHHHHHcCCCCc---hhhHHH
Q 041804          252 TVIKLLCENGRVREAYAVLAEMPKKGC-VPDVITYH--------CFFRCLEKPREILGLFDRMIESGIRPK---MDTYVM  319 (403)
Q Consensus       252 ~li~~~~~~g~~~~a~~~~~~~~~~~~-~p~~~~~~--------~l~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~  319 (403)
                      .+...+...|+.+.|.+.+........ ......+.        ......++.+.+..++...........   ...+..
T Consensus       617 ~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~  696 (903)
T PRK04841        617 MLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRN  696 (903)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHH
Confidence            566778889999999999888753210 01111110        111123667777777665443211111   111345


Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhc----CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          320 LLRKFGRWGFLRPVFVVWKKMEEL----GCSPD-EFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       320 li~~~~~~g~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      +..++...|++++|...+++....    |..++ ..+...+..++.+.|+.++|...+.+..+.
T Consensus       697 ~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~l  760 (903)
T PRK04841        697 IARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKL  760 (903)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            667788999999999999988653    32222 345667778889999999999999998875

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.97  E-value=3.4e-08  Score=85.33  Aligned_cols=230  Identities=13%  Similarity=0.007  Sum_probs=171.5

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV  117 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (403)
                      ...+.+.|++.+|.-.|+.....+  +-+..+|..|.......++-..|+..+++..+.++.+..+.-.|.-.|...|.-
T Consensus       292 G~~lm~nG~L~~A~LafEAAVkqd--P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q  369 (579)
T KOG1125|consen  292 GCNLMKNGDLSEAALAFEAAVKQD--PQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQ  369 (579)
T ss_pred             HHHHHhcCCchHHHHHHHHHHhhC--hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhH
Confidence            345678999999999999998876  456789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccccccccccccC--cchHHHHHHHHHHHhcCChhHHHHHHHHHHh-CCCCCcHHHHHHHHHHHHHcCChh
Q 041804          118 IEAQELCFGENKNVGFSGLVEM--NKTKIYNMILRGWFKMSWWGKCREFWEEMDK-RGVVKDLHSYSIYMDIMCKSGKPW  194 (403)
Q Consensus       118 ~~a~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~  194 (403)
                      ..|.+.++..............  ++...-+.  ..+.....+....++|-++.. .+..+|...+..|.-.|.-.|+++
T Consensus       370 ~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efd  447 (579)
T KOG1125|consen  370 NQALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFD  447 (579)
T ss_pred             HHHHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHH
Confidence            9999999887543200000000  00000000  111112223444555555544 444467778888888888999999


Q ss_pred             HHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS-VVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      +|.+.|+..+... +-|...||-|-..++...+..+|...|.++++.  .|+ +.+...|.-+|...|.+++|.+.|-+.
T Consensus       448 raiDcf~~AL~v~-Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~A  524 (579)
T KOG1125|consen  448 RAVDCFEAALQVK-PNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHLLEA  524 (579)
T ss_pred             HHHHHHHHHHhcC-CchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHHHHH
Confidence            9999999998863 346678999999999999999999999999986  454 334455667888999999999888765


Q ss_pred             h
Q 041804          274 P  274 (403)
Q Consensus       274 ~  274 (403)
                      .
T Consensus       525 L  525 (579)
T KOG1125|consen  525 L  525 (579)
T ss_pred             H
Confidence            4

>PLN02789 farnesyltranstransferase

Probab=98.97  E-value=3.3e-07  Score=77.14  Aligned_cols=209  Identities=8%  Similarity=-0.037  Sum_probs=158.7

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccC-ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFF-EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      .++...++.++|+...+.+...  .+-+..+|+..-.++...| ++++++..++.+.+..  +.+..+|+.....+.+.|
T Consensus        45 a~l~~~e~serAL~lt~~aI~l--nP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n--pknyqaW~~R~~~l~~l~  120 (320)
T PLN02789         45 AVYASDERSPRALDLTADVIRL--NPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN--PKNYQIWHHRRWLAEKLG  120 (320)
T ss_pred             HHHHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC--CcchHHhHHHHHHHHHcC
Confidence            3455567888888888887741  2334557777777777777 6899999999999876  456678887776677777


Q ss_pred             Ch--HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc---C
Q 041804           82 LV--NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM---S  156 (403)
Q Consensus        82 ~~--~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~  156 (403)
                      ..  ++++.+++++.+.++.+..+|+....++...|+++++++.+.++.+       ..+.|..+|+.......+.   |
T Consensus       121 ~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~-------~d~~N~sAW~~R~~vl~~~~~l~  193 (320)
T PLN02789        121 PDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLE-------EDVRNNSAWNQRYFVITRSPLLG  193 (320)
T ss_pred             chhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHH-------HCCCchhHHHHHHHHHHhccccc
Confidence            63  6789999999999988999999999999999999999999999887       4466777888777666554   2


Q ss_pred             Ch----hHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc----CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh
Q 041804          157 WW----GKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS----GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV  224 (403)
Q Consensus       157 ~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  224 (403)
                      ..    ++..++..++....+. |...|+-+...+...    ++..+|...+.+....+ +.+......|+..|+.
T Consensus       194 ~~~~~~e~el~y~~~aI~~~P~-N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~-~~s~~al~~l~d~~~~  267 (320)
T PLN02789        194 GLEAMRDSELKYTIDAILANPR-NESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKD-SNHVFALSDLLDLLCE  267 (320)
T ss_pred             cccccHHHHHHHHHHHHHhCCC-CcCHHHHHHHHHhcCCcccccchhHHHHHHHhhccc-CCcHHHHHHHHHHHHh
Confidence            22    4677777788877766 888999888888773    34466888888776653 3356677777777764

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.96  E-value=9.7e-07  Score=70.36  Aligned_cols=287  Identities=9%  Similarity=0.014  Sum_probs=194.8

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHH-HH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYN-MI  148 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~l  148 (403)
                      +...+..+.+..+++.|++++..-.+..+.+....+.|..+|....++..|-..++++-..        .|...-|. .-
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--------~P~~~qYrlY~   84 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--------HPELEQYRLYQ   84 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--------ChHHHHHHHHH
Confidence            4566777788899999999999999988889999999999999999999999999888663        34333333 23


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHH--HHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcC
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI--MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSE  226 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  226 (403)
                      ...+.+.+.+.+|+++...|.+.   |+...-..-+.+  ....+++..+..++++....|   +..+.+.......+.|
T Consensus        85 AQSLY~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykeg  158 (459)
T KOG4340|consen   85 AQSLYKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEG  158 (459)
T ss_pred             HHHHHHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccc
Confidence            46677889999999999998764   232222222222  234678888888887766433   3444444444556899


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC-------------Chh--------hH
Q 041804          227 GVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP-------------DVI--------TY  285 (403)
Q Consensus       227 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p-------------~~~--------~~  285 (403)
                      +.+.|.+-|+...+.+---....||..+. ..+.|+...|.+...++.++|++-             |..        .-
T Consensus       159 qyEaAvqkFqaAlqvsGyqpllAYniALa-Hy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~  237 (459)
T KOG4340|consen  159 QYEAAVQKFQAALQVSGYQPLLAYNLALA-HYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQ  237 (459)
T ss_pred             cHHHHHHHHHHHHhhcCCCchhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHH
Confidence            99999999999988744445667776554 457789999999999998876542             211        11


Q ss_pred             HHHHHhh----------CCHHHHHHHHHHHH-HcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHH
Q 041804          286 HCFFRCL----------EKPREILGLFDRMI-ESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNA  354 (403)
Q Consensus       286 ~~l~~~~----------~~~~~a~~~~~~~~-~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  354 (403)
                      +.++.++          ++.+.|.+-+..|. +.....|+.|...+.-.= ..+++.....-+.-+.... +-...||..
T Consensus       238 Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~n-PfP~ETFAN  315 (459)
T KOG4340|consen  238 SALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQN-PFPPETFAN  315 (459)
T ss_pred             HHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcC-CCChHHHHH
Confidence            2333333          34455555555554 122334666655443221 2345555555555555543 345789999


Q ss_pred             HHHHHHhcCCHHHHHHHHH
Q 041804          355 LVDALIDKGMLDMARKYDE  373 (403)
Q Consensus       355 l~~~~~~~g~~~~a~~~~~  373 (403)
                      ++-.|++..-++-|-.++-
T Consensus       316 lLllyCKNeyf~lAADvLA  334 (459)
T KOG4340|consen  316 LLLLYCKNEYFDLAADVLA  334 (459)
T ss_pred             HHHHHhhhHHHhHHHHHHh
Confidence            9999999998888877664

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

Probab=98.95  E-value=1.2e-06  Score=83.55  Aligned_cols=227  Identities=14%  Similarity=0.104  Sum_probs=135.3

Q ss_pred             CcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC-CCCC---cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhh
Q 041804          139 MNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR-GVVK---DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVA  214 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  214 (403)
                      |.+...|-..|......++.++|.+++++.+.. ++.-   -...|.++++.-..-|.-+...++|+++.+.  .-...+
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy--cd~~~V 1532 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY--CDAYTV 1532 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh--cchHHH
Confidence            444555666666666666666666666555432 1110   1124555555555555555666666666654  112345


Q ss_pred             HHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC------hhhHHHH
Q 041804          215 YNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD------VITYHCF  288 (403)
Q Consensus       215 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~------~~~~~~l  288 (403)
                      |..|...|.+.+.+++|.++++.|.+. ..-....|...+..+.+..+-+.|..++.+..+.  .|-      ..-+..|
T Consensus      1533 ~~~L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAqL 1609 (1710)
T KOG1070|consen 1533 HLKLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQL 1609 (1710)
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHH
Confidence            566666666666666666666666654 2235556666666666666666666666665543  222      1112223


Q ss_pred             HHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCC--HHHHHHHHHHHHhcCCHH
Q 041804          289 FRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPD--EFAYNALVDALIDKGMLD  366 (403)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~  366 (403)
                      .-.+|+.+.+..+|+......++ -...|+.+++.-.++|+.+.++.+|++....++.|-  ...|...+..=-+.|+-+
T Consensus      1610 EFk~GDaeRGRtlfEgll~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~ 1688 (1710)
T KOG1070|consen 1610 EFKYGDAERGRTLFEGLLSAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEK 1688 (1710)
T ss_pred             HhhcCCchhhHHHHHHHHhhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchh
Confidence            33456666666677766665333 456788889888899999999999999988877664  356677777666677765


Q ss_pred             HHHHH
Q 041804          367 MARKY  371 (403)
Q Consensus       367 ~a~~~  371 (403)
                      .+..+
T Consensus      1689 ~vE~V 1693 (1710)
T KOG1070|consen 1689 NVEYV 1693 (1710)
T ss_pred             hHHHH
Confidence            44443

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.94  E-value=8.8e-06  Score=66.37  Aligned_cols=286  Identities=8%  Similarity=-0.037  Sum_probs=194.2

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHH-HHHHHHHHHhcCChH
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHAT-FRIMFKRYVTAHLVN   84 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~   84 (403)
                      ..+|++..|+.-|+...  .+.+.+-.++..-...|...|+...|+.=+.+..+.   +||... .-.-...+.+.|.++
T Consensus        49 la~~Q~sDALt~yHaAv--e~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel---KpDF~~ARiQRg~vllK~Gele  123 (504)
T KOG0624|consen   49 LARGQLSDALTHYHAAV--EGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL---KPDFMAARIQRGVVLLKQGELE  123 (504)
T ss_pred             HHhhhHHHHHHHHHHHH--cCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc---CccHHHHHHHhchhhhhcccHH
Confidence            34688999999998887  344445556666778899999999999999999984   588754 334456788999999


Q ss_pred             HHHHHHHHHhhcCCC---cHHH------------HHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           85 EAMGTFNKLDEFGLK---DEVS------------YCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~---~~~~------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      +|..=|+.+....+.   ....            ....+..+...|+...|......+.+       ..+-+...+..-.
T Consensus       124 ~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llE-------i~~Wda~l~~~Ra  196 (504)
T KOG0624|consen  124 QAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLE-------IQPWDASLRQARA  196 (504)
T ss_pred             HHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHh-------cCcchhHHHHHHH
Confidence            999999999988763   2222            22334556678899999999888887       4466888889999


Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHH-----------
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTV-----------  218 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-----------  218 (403)
                      .+|...|++..|+.=++...+..-. ++.++--+-..+...|+.+.++...++.++.  .||...+-..           
T Consensus       197 kc~i~~~e~k~AI~Dlk~askLs~D-nTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK~Cf~~YKklkKv~K~l  273 (504)
T KOG0624|consen  197 KCYIAEGEPKKAIHDLKQASKLSQD-NTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHKLCFPFYKKLKKVVKSL  273 (504)
T ss_pred             HHHHhcCcHHHHHHHHHHHHhcccc-chHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--CcchhhHHHHHHHHHHHHHHH
Confidence            9999999999999888777766555 6777777888889999999999999888875  5665432211           


Q ss_pred             --HHHHhhcCCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC-hhhHHHHHHhh
Q 041804          219 --IRAVGVSEGVDFAMRVYREMREMGCQPSV---VTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD-VITYHCFFRCL  292 (403)
Q Consensus       219 --l~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~  292 (403)
                        +......+++..+..-.+...+.......   ..+..+-.++...+++.+|+....+..+.  .|| ..++.--..++
T Consensus       274 es~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~--d~~dv~~l~dRAeA~  351 (504)
T KOG0624|consen  274 ESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDI--DPDDVQVLCDRAEAY  351 (504)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhc--CchHHHHHHHHHHHH
Confidence              11223345555666666655554332122   22334445556666777777776666653  333 33332222222


Q ss_pred             ---CCHHHHHHHHHHHHHc
Q 041804          293 ---EKPREILGLFDRMIES  308 (403)
Q Consensus       293 ---~~~~~a~~~~~~~~~~  308 (403)
                         ..++.|+.-|+...+.
T Consensus       352 l~dE~YD~AI~dye~A~e~  370 (504)
T KOG0624|consen  352 LGDEMYDDAIHDYEKALEL  370 (504)
T ss_pred             hhhHHHHHHHHHHHHHHhc
Confidence               2345555555555543

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

Probab=98.94  E-value=2.9e-05  Score=70.12  Aligned_cols=212  Identities=12%  Similarity=0.003  Sum_probs=155.8

Q ss_pred             CCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcC--CCcHH
Q 041804           25 CHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFG--LKDEV  102 (403)
Q Consensus        25 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~  102 (403)
                      ..+..++..|..+.-++..+|+++.+.+.|++...-.  ......|+.+...|...|....|..+++.-....  +.++.
T Consensus       317 ~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~--~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s  394 (799)
T KOG4162|consen  317 KKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFS--FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDIS  394 (799)
T ss_pred             hhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh--hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcch
Confidence            4456688999999999999999999999999877642  3567789999999999999999999999877766  44677


Q ss_pred             HHHHHHHHHHh-cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc-----------CChhHHHHHHHHHHh
Q 041804          103 SYCNLVDALCE-YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM-----------SWWGKCREFWEEMDK  170 (403)
Q Consensus       103 ~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------~~~~~a~~~~~~~~~  170 (403)
                      .+-..-+.|.+ .+..++++....++....+..  ........|..+.-+|...           ....++.+.+++..+
T Consensus       395 ~~Lmasklc~e~l~~~eegldYA~kai~~~~~~--~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~  472 (799)
T KOG4162|consen  395 VLLMASKLCIERLKLVEEGLDYAQKAISLLGGQ--RSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQ  472 (799)
T ss_pred             HHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhh--hhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHh
Confidence            66666666664 666777777666655522111  1122333445555444322           124567788888877


Q ss_pred             CCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          171 RGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       171 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      .+.. |....-.+.--|+..++.+.|.+..++..+.+-.-+...|..+.-.+...+++..|+.+.+...+.
T Consensus       473 ~d~~-dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E  542 (799)
T KOG4162|consen  473 FDPT-DPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEE  542 (799)
T ss_pred             cCCC-CchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence            7654 333333344457788899999999999999866778899999999999999999999999877654

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.94  E-value=1.2e-07  Score=81.96  Aligned_cols=255  Identities=10%  Similarity=-0.016  Sum_probs=192.3

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+.+.|+..+|.-.|+...++  .+-+..+|-.|...-...++-..|+..+++..+..  +.|..+.-.|.-.|...|.
T Consensus       293 ~~lm~nG~L~~A~LafEAAVkq--dP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld--P~NleaLmaLAVSytNeg~  368 (579)
T KOG1125|consen  293 CNLMKNGDLSEAALAFEAAVKQ--DPQHAEAWQKLGITQAENENEQNAISALRRCLELD--PTNLEALMALAVSYTNEGL  368 (579)
T ss_pred             HHHHhcCCchHHHHHHHHHHhh--ChHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC--CccHHHHHHHHHHHhhhhh
Confidence            3466789999999999998853  35568899999999999999999999999999976  4567889999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHH-------HHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCN-------LVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~-------l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      -..|+.+++......++-...-..       .-........+....++|-++....     +..++..+...|.-.|.-.
T Consensus       369 q~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~-----~~~~DpdvQ~~LGVLy~ls  443 (579)
T KOG1125|consen  369 QNQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQL-----PTKIDPDVQSGLGVLYNLS  443 (579)
T ss_pred             HHHHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhC-----CCCCChhHHhhhHHHHhcc
Confidence            999999999887655431100000       0012222334455566666555432     4457888899999999999


Q ss_pred             CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh-hhHHHHHHHHhhcCCHHHHHHH
Q 041804          156 SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV-VAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      |++++|.+.|+..+...+. |...||-|.-.++...+..+|+..|.+.++.  +|+- .+.-.|.-+|...|.+.+|.+.
T Consensus       444 ~efdraiDcf~~AL~v~Pn-d~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~h  520 (579)
T KOG1125|consen  444 GEFDRAVDCFEAALQVKPN-DYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKH  520 (579)
T ss_pred             hHHHHHHHHHHHHHhcCCc-hHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHH
Confidence            9999999999999998777 8899999999999999999999999999986  5553 3555677788899999999998


Q ss_pred             HHHHHHcC---------CCCCHHHHHHHHHHHHhcCcHHHHHHH
Q 041804          235 YREMREMG---------CQPSVVTCNTVIKLLCENGRVREAYAV  269 (403)
Q Consensus       235 ~~~~~~~~---------~~~~~~~~~~li~~~~~~g~~~~a~~~  269 (403)
                      |-..+...         ..++...|.+|=.++.-.++.+.+...
T Consensus       521 lL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a  564 (579)
T KOG1125|consen  521 LLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEA  564 (579)
T ss_pred             HHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHh
Confidence            87765321         112334666666666666666544443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.92  E-value=2.8e-07  Score=75.27  Aligned_cols=188  Identities=10%  Similarity=-0.061  Sum_probs=130.1

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHH---HH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEV---SY  104 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~  104 (403)
                      .....+..+...+...|++++|...|+++....+..|. ..++..+..++...|++++|+..++++.+..+.+..   ++
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~  110 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAY  110 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHH
Confidence            45677888889999999999999999999886511121 246788899999999999999999999988876443   56


Q ss_pred             HHHHHHHHhc--------CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCc
Q 041804          105 CNLVDALCEY--------KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKD  176 (403)
Q Consensus       105 ~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  176 (403)
                      ..+..++...        |+.++|.+.++++...       .+.+...+..+...              ..+...    -
T Consensus       111 ~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~-------~p~~~~~~~a~~~~--------------~~~~~~----~  165 (235)
T TIGR03302       111 YLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR-------YPNSEYAPDAKKRM--------------DYLRNR----L  165 (235)
T ss_pred             HHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH-------CCCChhHHHHHHHH--------------HHHHHH----H
Confidence            6666666654        7788899988887763       22222222222111              000000    0


Q ss_pred             HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC--CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          177 LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI--KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       177 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ......+...|.+.|++++|...++...+...  +.....+..+..++.+.|+.++|..+++.+...
T Consensus       166 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       166 AGKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            01122455678888888888888888877621  223467778888888888988888888887765

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).

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.92  E-value=4.6e-07  Score=70.98  Aligned_cols=158  Identities=9%  Similarity=-0.038  Sum_probs=93.9

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      ..+-..+...|+-+....+........+.+.......+....+.|++..|...+++...       ..++|..+|+.+.-
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~-------l~p~d~~~~~~lga  142 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAAR-------LAPTDWEAWNLLGA  142 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhc-------cCCCChhhhhHHHH
Confidence            44455555566666666655555544444555666666666666666666666666655       44666666666666


Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHH
Q 041804          151 GWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDF  230 (403)
Q Consensus       151 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~  230 (403)
                      +|.+.|+++.|..-|.+..+..+. +...++.+.-.|.-.|+.+.|..++......+ .-|..+-..+.......|+++.
T Consensus       143 aldq~Gr~~~Ar~ay~qAl~L~~~-~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~-~ad~~v~~NLAl~~~~~g~~~~  220 (257)
T COG5010         143 ALDQLGRFDEARRAYRQALELAPN-EPSIANNLGMSLLLRGDLEDAETLLLPAYLSP-AADSRVRQNLALVVGLQGDFRE  220 (257)
T ss_pred             HHHHccChhHHHHHHHHHHHhccC-CchhhhhHHHHHHHcCCHHHHHHHHHHHHhCC-CCchHHHHHHHHHHhhcCChHH
Confidence            666666666666666666555444 44455666666666666666666666665553 2245555556666666666666


Q ss_pred             HHHHHHH
Q 041804          231 AMRVYRE  237 (403)
Q Consensus       231 a~~~~~~  237 (403)
                      |..+...
T Consensus       221 A~~i~~~  227 (257)
T COG5010         221 AEDIAVQ  227 (257)
T ss_pred             HHhhccc
Confidence            6655443

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.91  E-value=1.8e-07  Score=83.28  Aligned_cols=222  Identities=13%  Similarity=0.019  Sum_probs=181.6

Q ss_pred             CcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHH
Q 041804           27 FTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN  106 (403)
Q Consensus        27 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  106 (403)
                      .+|--..--.+...+.+.|-..+|..+|+++.          .|.-++.+|...|+..+|..+..+..+ ..+++..|..
T Consensus       394 lpp~Wq~q~~laell~slGitksAl~I~Erle----------mw~~vi~CY~~lg~~~kaeei~~q~le-k~~d~~lyc~  462 (777)
T KOG1128|consen  394 LPPIWQLQRLLAELLLSLGITKSALVIFERLE----------MWDPVILCYLLLGQHGKAEEINRQELE-KDPDPRLYCL  462 (777)
T ss_pred             CCCcchHHHHHHHHHHHcchHHHHHHHHHhHH----------HHHHHHHHHHHhcccchHHHHHHHHhc-CCCcchhHHH
Confidence            44545555677888999999999999998875          467789999999999999999998888 5569999999


Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHH
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI  186 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  186 (403)
                      +.+.....--+++|.++.+....             .+-..+.......++++++.+.|+.-.+.++- ...+|-.+..+
T Consensus       463 LGDv~~d~s~yEkawElsn~~sa-------------rA~r~~~~~~~~~~~fs~~~~hle~sl~~npl-q~~~wf~~G~~  528 (777)
T KOG1128|consen  463 LGDVLHDPSLYEKAWELSNYISA-------------RAQRSLALLILSNKDFSEADKHLERSLEINPL-QLGTWFGLGCA  528 (777)
T ss_pred             hhhhccChHHHHHHHHHhhhhhH-------------HHHHhhccccccchhHHHHHHHHHHHhhcCcc-chhHHHhccHH
Confidence            99999888889999998765433             22233333344578999999999988776544 56788889999


Q ss_pred             HHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHH
Q 041804          187 MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREA  266 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  266 (403)
                      ..+.++++.|.+.|....... +-+...|+.+-.+|.+.++-.+|...+.+..+.+ .-+...|...+......|.+++|
T Consensus       529 ALqlek~q~av~aF~rcvtL~-Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda  606 (777)
T KOG1128|consen  529 ALQLEKEQAAVKAFHRCVTLE-PDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDA  606 (777)
T ss_pred             HHHHhhhHHHHHHHHHHhhcC-CCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHH
Confidence            999999999999999888762 3345689999999999999999999999999987 44667777777788899999999


Q ss_pred             HHHHHhchh
Q 041804          267 YAVLAEMPK  275 (403)
Q Consensus       267 ~~~~~~~~~  275 (403)
                      ++.+.++..
T Consensus       607 ~~A~~rll~  615 (777)
T KOG1128|consen  607 IKAYHRLLD  615 (777)
T ss_pred             HHHHHHHHH
Confidence            999998764

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.90  E-value=1.2e-05  Score=69.39  Aligned_cols=328  Identities=12%  Similarity=0.059  Sum_probs=209.9

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV  117 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (403)
                      -.+.+..|+++.|+..|-+.....  ++|...|..-..+|...|++++|++=-.+-.+..+.=+..|+....++.-.|++
T Consensus         9 gnaa~s~~d~~~ai~~~t~ai~l~--p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~p~w~kgy~r~Gaa~~~lg~~   86 (539)
T KOG0548|consen    9 GNAAFSSGDFETAIRLFTEAIMLS--PTNHVLYSNRSAAYASLGSYEKALKDATKTRRLNPDWAKGYSRKGAALFGLGDY   86 (539)
T ss_pred             HHhhcccccHHHHHHHHHHHHccC--CCccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCchhhHHHHhHHHHHhcccH
Confidence            345678899999999999988876  578899999999999999999999988888888877788999999999999999


Q ss_pred             HHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHH---HHHHHHHHhCC---CCCcHHHHHHHHHHHHHc-
Q 041804          118 IEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC---REFWEEMDKRG---VVKDLHSYSIYMDIMCKS-  190 (403)
Q Consensus       118 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a---~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~-  190 (403)
                      ++|...|.+-..       ..+.|...++-+..++.........   -.++..+...-   .......|..++..+-+. 
T Consensus        87 ~eA~~ay~~GL~-------~d~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p  159 (539)
T KOG0548|consen   87 EEAILAYSEGLE-------KDPSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNP  159 (539)
T ss_pred             HHHHHHHHHHhh-------cCCchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCc
Confidence            999999998777       3466777777777777211000000   01111111100   000112233333322111 


Q ss_pred             ------CChhHHHHHHHHHH--------HcC-------CCC----------------------ChhhHHHHHHHHhhcCC
Q 041804          191 ------GKPWKAVKLYKEMK--------KKG-------IKM----------------------DVVAYNTVIRAVGVSEG  227 (403)
Q Consensus       191 ------~~~~~a~~~~~~~~--------~~~-------~~~----------------------~~~~~~~ll~~~~~~~~  227 (403)
                            .+.+...+..-.+.        ..+       ..|                      -..-...+.++..+..+
T Consensus       160 ~~l~~~l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~  239 (539)
T KOG0548|consen  160 TSLKLYLNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKD  239 (539)
T ss_pred             HhhhcccccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhh
Confidence                  01111111111110        001       111                      11234567788888999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh----------CCHHH
Q 041804          228 VDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL----------EKPRE  297 (403)
Q Consensus       228 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~----------~~~~~  297 (403)
                      ++.+.+-+....+..  -+..-++....+|...|........-....+.|-. ....|+.+-.++          ++.+.
T Consensus       240 f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre-~rad~klIak~~~r~g~a~~k~~~~~~  316 (539)
T KOG0548|consen  240 FETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRE-LRADYKLIAKALARLGNAYTKREDYEG  316 (539)
T ss_pred             HHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHH-HHHHHHHHHHHHHHhhhhhhhHHhHHH
Confidence            999999999988864  46666677778888888877777666655544321 122233222222          22344


Q ss_pred             HHHHHHHHHHcCCCCchhh-------------------------HHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHH
Q 041804          298 ILGLFDRMIESGIRPKMDT-------------------------YVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAY  352 (403)
Q Consensus       298 a~~~~~~~~~~~~~~~~~~-------------------------~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  352 (403)
                      ++..|.+.....-.|+..+                         .-.-...+.+.|++..|+..+.++++.. +-|...|
T Consensus       317 ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~-P~Da~lY  395 (539)
T KOG0548|consen  317 AIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRD-PEDARLY  395 (539)
T ss_pred             HHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CchhHHH
Confidence            5555555444333332211                         1112345788999999999999999876 6688999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          353 NALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       353 ~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      ..-.-+|.+.|.+..|+.=.+..++.
T Consensus       396 sNRAac~~kL~~~~~aL~Da~~~ieL  421 (539)
T KOG0548|consen  396 SNRAACYLKLGEYPEALKDAKKCIEL  421 (539)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            99999999999999998877766654

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.89  E-value=4.5e-06  Score=78.59  Aligned_cols=260  Identities=8%  Similarity=0.049  Sum_probs=171.6

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           64 IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      +.+...|..|+..+...+++++|.++.+...+..+.....|-.+...+.+.++..++..+                    
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv--------------------   87 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLL--------------------   87 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhh--------------------
Confidence            445677888888888888888888888877777766666666655566676665554433                    


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHh
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVG  223 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  223 (403)
                         .++.......++..+.-+...|.+.+  -+..++-.+..+|-+.|+.+++..+|+++.+.. +-|..+.|.+...|+
T Consensus        88 ---~~l~~~~~~~~~~~ve~~~~~i~~~~--~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~a  161 (906)
T PRK14720         88 ---NLIDSFSQNLKWAIVEHICDKILLYG--ENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYE  161 (906)
T ss_pred             ---hhhhhcccccchhHHHHHHHHHHhhh--hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHH
Confidence               22333333344444444444555432  234477788888888899999999999988886 557778888888888


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHH
Q 041804          224 VSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFD  303 (403)
Q Consensus       224 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~  303 (403)
                      .. ++++|..++.++...               |...+++..+.++|.++...  .|+.            .+.-..+.+
T Consensus       162 e~-dL~KA~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~--~~~d------------~d~f~~i~~  211 (906)
T PRK14720        162 EE-DKEKAITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHY--NSDD------------FDFFLRIER  211 (906)
T ss_pred             Hh-hHHHHHHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhc--Cccc------------chHHHHHHH
Confidence            88 888888888877764               56677888888888888875  2332            222333334


Q ss_pred             HHHHc-CCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-cCCC
Q 041804          304 RMIES-GIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA-KGLS  381 (403)
Q Consensus       304 ~~~~~-~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~~~~  381 (403)
                      .+... |..--..++-.+-..|-..++++++..+++.+.+.. +-|.....-++.+|.  +.+.. ...|++.++ .|+.
T Consensus       212 ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~-~~n~~a~~~l~~~y~--~kY~~-~~~~ee~l~~s~l~  287 (906)
T PRK14720        212 KVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHD-NKNNKAREELIRFYK--EKYKD-HSLLEDYLKMSDIG  287 (906)
T ss_pred             HHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcC-CcchhhHHHHHHHHH--HHccC-cchHHHHHHHhccc
Confidence            44432 333345566677778888888999999999998875 446667777777776  33333 333444333 3554


Q ss_pred             CC
Q 041804          382 AK  383 (403)
Q Consensus       382 p~  383 (403)
                      -.
T Consensus       288 ~~  289 (906)
T PRK14720        288 NN  289 (906)
T ss_pred             cC
Confidence            44

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.89  E-value=5.6e-07  Score=73.56  Aligned_cols=189  Identities=11%  Similarity=-0.098  Sum_probs=135.9

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcH---HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           64 IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE---VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                      ......+..+...+...|+++.|...|+++....+.++   .++..+..++...|++++|...++++....     +..+
T Consensus        30 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~-----p~~~  104 (235)
T TIGR03302        30 EWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLH-----PNHP  104 (235)
T ss_pred             cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC-----cCCC
Confidence            35667788888999999999999999999998876643   577888999999999999999999987642     1111


Q ss_pred             c-hHHHHHHHHHHHhc--------CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC
Q 041804          141 K-TKIYNMILRGWFKM--------SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD  211 (403)
Q Consensus       141 ~-~~~~~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  211 (403)
                      . ..++..+..++...        |++++|.+.|+.+.+..+. +...+..+.....    ...      ...       
T Consensus       105 ~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~a~~~~~~----~~~------~~~-------  166 (235)
T TIGR03302       105 DADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPN-SEYAPDAKKRMDY----LRN------RLA-------  166 (235)
T ss_pred             chHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCC-ChhHHHHHHHHHH----HHH------HHH-------
Confidence            1 12455555566554        7788999999998877544 3333322221111    000      000       


Q ss_pred             hhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          212 VVAYNTVIRAVGVSEGVDFAMRVYREMREMGC--QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       212 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                       .....+...+.+.|+++.|...++...+...  +.....+..+..++...|++++|..+++.+...
T Consensus       167 -~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       167 -GKELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             -HHHHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence             0112455678899999999999999988732  123578889999999999999999999988765

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).

>PF12854 PPR_1: PPR repeat

Probab=98.88  E-value=3.2e-09  Score=56.19  Aligned_cols=32  Identities=41%  Similarity=0.717  Sum_probs=21.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 041804          344 GCSPDEFAYNALVDALIDKGMLDMARKYDEEM  375 (403)
Q Consensus       344 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  375 (403)
                      |+.||..+|+++|.+|++.|+.++|.++|++|
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            56666666666666666666666666666665

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.87  E-value=3.9e-07  Score=71.46  Aligned_cols=156  Identities=7%  Similarity=0.037  Sum_probs=117.1

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV  117 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (403)
                      +-.|...|+++.+....+.+..     |.        ..+...++.++++..++...+..+.+...|..+...|...|++
T Consensus        23 ~~~Y~~~g~~~~v~~~~~~~~~-----~~--------~~~~~~~~~~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~~~g~~   89 (198)
T PRK10370         23 VGSYLLSPKWQAVRAEYQRLAD-----PL--------HQFASQQTPEAQLQALQDKIRANPQNSEQWALLGEYYLWRNDY   89 (198)
T ss_pred             HHHHHHcchHHHHHHHHHHHhC-----cc--------ccccCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCH
Confidence            3457788888877555533322     11        0122366678888888888888888889999999999999999


Q ss_pred             HHHHHHHhcccccccccccccCcchHHHHHHHHH-HHhcCC--hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChh
Q 041804          118 IEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG-WFKMSW--WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPW  194 (403)
Q Consensus       118 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  194 (403)
                      ++|...+++...       ..+.+..++..+..+ +...|+  .++|.+++++..+.++. +..++..+...+...|+++
T Consensus        90 ~~A~~a~~~Al~-------l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~  161 (198)
T PRK10370         90 DNALLAYRQALQ-------LRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDAN-EVTALMLLASDAFMQADYA  161 (198)
T ss_pred             HHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHH
Confidence            999999888877       445677777777776 466676  58899999999888777 7788888888888999999


Q ss_pred             HHHHHHHHHHHcCCCCChhhH
Q 041804          195 KAVKLYKEMKKKGIKMDVVAY  215 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~  215 (403)
                      +|...|+.+.+.. +|+..-+
T Consensus       162 ~Ai~~~~~aL~l~-~~~~~r~  181 (198)
T PRK10370        162 QAIELWQKVLDLN-SPRVNRT  181 (198)
T ss_pred             HHHHHHHHHHhhC-CCCccHH
Confidence            9999999988773 4444433

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.86  E-value=1.3e-07  Score=74.00  Aligned_cols=166  Identities=11%  Similarity=-0.040  Sum_probs=137.8

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      |..+ ..+-..+...|+-+....+........  +.|....+..+....+.|++..|+..|++.....++|..+|+.+.-
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~--~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~lga  142 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIAY--PKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLGA  142 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhccC--cccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhHHHH
Confidence            4445 666778888888888888887765543  3566677778999999999999999999999988889999999999


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                      +|.+.|+++.|...|.+..+       -.+.+....|.+.-.|.-.|+.+.|..++......+.. |...-..+.-....
T Consensus       143 aldq~Gr~~~Ar~ay~qAl~-------L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~a-d~~v~~NLAl~~~~  214 (257)
T COG5010         143 ALDQLGRFDEARRAYRQALE-------LAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAA-DSRVRQNLALVVGL  214 (257)
T ss_pred             HHHHccChhHHHHHHHHHHH-------hccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCC-chHHHHHHHHHHhh
Confidence            99999999999999988877       44666777888998999999999999999998887665 77777788888899


Q ss_pred             cCChhHHHHHHHHHHHc
Q 041804          190 SGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~  206 (403)
                      .|+++.|.++...-...
T Consensus       215 ~g~~~~A~~i~~~e~~~  231 (257)
T COG5010         215 QGDFREAEDIAVQELLS  231 (257)
T ss_pred             cCChHHHHhhccccccc
Confidence            99999999887665543

>PF12854 PPR_1: PPR repeat

Probab=98.86  E-value=5.5e-09  Score=55.29  Aligned_cols=32  Identities=53%  Similarity=0.980  Sum_probs=22.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      |+.||..+|++||.+|++.|++++|.++|++|
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            56667777777777777777777777776666

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.82  E-value=3.4e-05  Score=76.44  Aligned_cols=334  Identities=9%  Similarity=-0.079  Sum_probs=206.1

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCC-----CCCH--HHHHHHHHHHHhc
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSS-----IPNH--ATFRIMFKRYVTA   80 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~--~~~~~l~~~~~~~   80 (403)
                      .|++..+.+.++.+.. .....++.........+...|+++++..+++.....-..     .+..  .....+...+...
T Consensus       387 ~g~~~~l~~~l~~lp~-~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  465 (903)
T PRK04841        387 QGELSLLEECLNALPW-EVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAIND  465 (903)
T ss_pred             cCChHHHHHHHHhCCH-HHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhC
Confidence            4566666666655431 111122333344556667889999999999877543100     1111  1222334556689


Q ss_pred             CChHHHHHHHHHHhhcCCC-cH----HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           81 HLVNEAMGTFNKLDEFGLK-DE----VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~-~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      |+++.|...++........ +.    ...+.+...+...|++++|...+.+........+ .......+...+...+...
T Consensus       466 g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g-~~~~~~~~~~~la~~~~~~  544 (903)
T PRK04841        466 GDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHD-VYHYALWSLLQQSEILFAQ  544 (903)
T ss_pred             CCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhc-chHHHHHHHHHHHHHHHHC
Confidence            9999999999998764222 22    3456667777889999999999887664321000 1111234556677788899


Q ss_pred             CChhHHHHHHHHHHhC----CCC--C-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHc--CCCCC--hhhHHHHHHHHhh
Q 041804          156 SWWGKCREFWEEMDKR----GVV--K-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK--GIKMD--VVAYNTVIRAVGV  224 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~--~~~~~~ll~~~~~  224 (403)
                      |+++.|...+++....    +..  + ....+..+...+...|++++|...+.+....  ...+.  ...+..+...+..
T Consensus       545 G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~  624 (903)
T PRK04841        545 GFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLA  624 (903)
T ss_pred             CCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHH
Confidence            9999999998876542    211  1 2234455666778889999999999887653  11122  2344445667778


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCC-HHHH-----HHHHHHHHhcCcHHHHHHHHHhchhcCCCCChh------hHHHHHHhh
Q 041804          225 SEGVDFAMRVYREMREMGCQPS-VVTC-----NTVIKLLCENGRVREAYAVLAEMPKKGCVPDVI------TYHCFFRCL  292 (403)
Q Consensus       225 ~~~~~~a~~~~~~~~~~~~~~~-~~~~-----~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~------~~~~l~~~~  292 (403)
                      .|+.+.|...+........... ...+     ...+..+...|+.+.|...+.............      ....+....
T Consensus       625 ~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~  704 (903)
T PRK04841        625 RGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILL  704 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHc
Confidence            9999999999988865311111 1111     112244556899999999987765422111111      111223344


Q ss_pred             CCHHHHHHHHHHHHHc----CCCCc-hhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          293 EKPREILGLFDRMIES----GIRPK-MDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       293 ~~~~~a~~~~~~~~~~----~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      ++.++|...++.....    |..++ ..+...+..++...|+.++|...+.+..+.
T Consensus       705 g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~l  760 (903)
T PRK04841        705 GQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKL  760 (903)
T ss_pred             CCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7888998888887753    32222 245666777888999999999999998765

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

Probab=98.79  E-value=2.9e-06  Score=81.01  Aligned_cols=249  Identities=10%  Similarity=0.017  Sum_probs=192.3

Q ss_pred             cHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC---CHHHHHHHHHHHHhcCChHHH
Q 041804           10 DWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP---NHATFRIMFKRYVTAHLVNEA   86 (403)
Q Consensus        10 ~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a   86 (403)
                      .++.|.++-+.+..   .+.+...|-..|......+++++|++++++....-...-   -...|-++++.-..-|.-+..
T Consensus      1440 ~pesaeDferlvrs---sPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl 1516 (1710)
T KOG1070|consen 1440 APESAEDFERLVRS---SPNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESL 1516 (1710)
T ss_pred             CCcCHHHHHHHHhc---CCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHH
Confidence            44556666666654   244567899999999999999999999999887521111   134677888877778888999


Q ss_pred             HHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHH
Q 041804           87 MGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWE  166 (403)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  166 (403)
                      .++|+++.+.. ..-..|..|...|.+.+..++|-++++.|.+.       ......+|...+..+.+.++-+.|..++.
T Consensus      1517 ~kVFeRAcqyc-d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KK-------F~q~~~vW~~y~~fLl~~ne~~aa~~lL~ 1588 (1710)
T KOG1070|consen 1517 KKVFERACQYC-DAYTVHLKLLGIYEKSEKNDEADELLRLMLKK-------FGQTRKVWIMYADFLLRQNEAEAARELLK 1588 (1710)
T ss_pred             HHHHHHHHHhc-chHHHHHHHHHHHHHhhcchhHHHHHHHHHHH-------hcchhhHHHHHHHHHhcccHHHHHHHHHH
Confidence            99999988732 24456888999999999999999999999985       34677889999999999999999999999


Q ss_pred             HHHhCCCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC
Q 041804          167 EMDKRGVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQP  245 (403)
Q Consensus       167 ~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  245 (403)
                      +..+.=++ -......-.+..-.+.|+.+.+..+|+...... +--...|+..+..-.+.++.+.++.+|+++...++.|
T Consensus      1589 rAL~~lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1589 RALKSLPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             HHHhhcchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            88775322 122334444555678999999999999998873 3356789999999999999999999999999988766


Q ss_pred             CH--HHHHHHHHHHHhcCcHHHHHHHH
Q 041804          246 SV--VTCNTVIKLLCENGRVREAYAVL  270 (403)
Q Consensus       246 ~~--~~~~~li~~~~~~g~~~~a~~~~  270 (403)
                      ..  ..|...+..--+.|+-+.+..+=
T Consensus      1668 kkmKfffKkwLeyEk~~Gde~~vE~VK 1694 (1710)
T KOG1070|consen 1668 KKMKFFFKKWLEYEKSHGDEKNVEYVK 1694 (1710)
T ss_pred             hHhHHHHHHHHHHHHhcCchhhHHHHH
Confidence            53  56777777666677755544443

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.78  E-value=5e-05  Score=69.23  Aligned_cols=325  Identities=12%  Similarity=0.082  Sum_probs=192.1

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCC--------CCCHHHHHHHHH
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSS--------IPNHATFRIMFK   75 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~--------~~~~~~~~~l~~   75 (403)
                      ++..-|+.+.|.+-.+.+.       +..+|..+.+.|.+.++++-|.-.+-.|....+.        .|+ ..=.....
T Consensus       737 fyvtiG~MD~AfksI~~Ik-------S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAv  808 (1416)
T KOG3617|consen  737 FYVTIGSMDAAFKSIQFIK-------SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAV  808 (1416)
T ss_pred             EEEEeccHHHHHHHHHHHh-------hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHH
Confidence            3455688999988888776       3568999999999999888887766666542110        121 11112233


Q ss_pred             HHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           76 RYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        76 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      .....|..++|+.+|++.+.        |..|-+.|-..|.+++|.++-+.--.         ..-..+|......+-..
T Consensus       809 LAieLgMlEeA~~lYr~ckR--------~DLlNKlyQs~g~w~eA~eiAE~~DR---------iHLr~Tyy~yA~~Lear  871 (1416)
T KOG3617|consen  809 LAIELGMLEEALILYRQCKR--------YDLLNKLYQSQGMWSEAFEIAETKDR---------IHLRNTYYNYAKYLEAR  871 (1416)
T ss_pred             HHHHHhhHHHHHHHHHHHHH--------HHHHHHHHHhcccHHHHHHHHhhccc---------eehhhhHHHHHHHHHhh
Confidence            34567889999999988877        55666778889999999988543221         11223456666666677


Q ss_pred             CChhHHHHHHHHHH----------hCCC---------CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHH
Q 041804          156 SWWGKCREFWEEMD----------KRGV---------VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYN  216 (403)
Q Consensus       156 ~~~~~a~~~~~~~~----------~~~~---------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  216 (403)
                      ++.+.|++.|++..          ...+         ..|...|.-....+-..|+.+.|+.+|...+.         |-
T Consensus       872 ~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~f  942 (1416)
T KOG3617|consen  872 RDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YF  942 (1416)
T ss_pred             ccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hh
Confidence            88888888777532          1111         11333344444444455666666666655443         33


Q ss_pred             HHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcC--------CCCChhhHHHH
Q 041804          217 TVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKG--------CVPDVITYHCF  288 (403)
Q Consensus       217 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~--------~~p~~~~~~~l  288 (403)
                      .+++..|-.|+.++|.++-++-      -|......+.+.|-..|++.+|...|.+.....        ...+...+|..
T Consensus       943 s~VrI~C~qGk~~kAa~iA~es------gd~AAcYhlaR~YEn~g~v~~Av~FfTrAqafsnAIRlcKEnd~~d~L~nla 1016 (1416)
T KOG3617|consen  943 SMVRIKCIQGKTDKAARIAEES------GDKAACYHLARMYENDGDVVKAVKFFTRAQAFSNAIRLCKENDMKDRLANLA 1016 (1416)
T ss_pred             hheeeEeeccCchHHHHHHHhc------ccHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            4555556677777777664432      255666678888999999999998887754210        00111222211


Q ss_pred             HH-hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHH--------HHh--cCCCCCHHHHHHHHH
Q 041804          289 FR-CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKK--------MEE--LGCSPDEFAYNALVD  357 (403)
Q Consensus       289 ~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~--------~~~--~~~~~~~~~~~~l~~  357 (403)
                      +. .-.+.-.|-.+|++   .|..     +...+..|-+.|.+.+|+++--+        +..  ..-..|+...+...+
T Consensus      1017 l~s~~~d~v~aArYyEe---~g~~-----~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~Rcad 1088 (1416)
T KOG3617|consen 1017 LMSGGSDLVSAARYYEE---LGGY-----AHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCAD 1088 (1416)
T ss_pred             hhcCchhHHHHHHHHHH---cchh-----hhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHH
Confidence            11 11112223333332   2221     22334556777877777765321        111  222357777777778


Q ss_pred             HHHhcCCHHHHHHHHHHHH
Q 041804          358 ALIDKGMLDMARKYDEEMF  376 (403)
Q Consensus       358 ~~~~~g~~~~a~~~~~~m~  376 (403)
                      .++...++++|..++-...
T Consensus      1089 FF~~~~qyekAV~lL~~ar 1107 (1416)
T KOG3617|consen 1089 FFENNQQYEKAVNLLCLAR 1107 (1416)
T ss_pred             HHHhHHHHHHHHHHHHHHH
Confidence            8888888888877665433

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.75  E-value=4.7e-05  Score=60.03  Aligned_cols=88  Identities=13%  Similarity=0.053  Sum_probs=40.8

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS  225 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  225 (403)
                      ..+.+..+++-|.+.+++|.+..   +..|.+.|..++.+    .+.+.+|.-+|++|-+. .+|+..+.+-...++...
T Consensus       145 qI~lk~~r~d~A~~~lk~mq~id---ed~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~  220 (299)
T KOG3081|consen  145 QILLKMHRFDLAEKELKKMQQID---EDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQL  220 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHccc---hHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHh
Confidence            33344444555555555554431   33344444444332    23344555555555443 344444444445555555


Q ss_pred             CCHHHHHHHHHHHHHc
Q 041804          226 EGVDFAMRVYREMREM  241 (403)
Q Consensus       226 ~~~~~a~~~~~~~~~~  241 (403)
                      +++++|..+++.....
T Consensus       221 ~~~eeAe~lL~eaL~k  236 (299)
T KOG3081|consen  221 GRYEEAESLLEEALDK  236 (299)
T ss_pred             cCHHHHHHHHHHHHhc
Confidence            5555555555555444

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.74  E-value=0.00019  Score=66.17  Aligned_cols=181  Identities=12%  Similarity=0.095  Sum_probs=112.8

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      .++++.|+.....+.+.++..+...++.++  .+.+.|+.++|..+++.....+  ..|..|...+-.+|-..++.++|.
T Consensus        22 ~~qfkkal~~~~kllkk~Pn~~~a~vLkaL--sl~r~gk~~ea~~~Le~~~~~~--~~D~~tLq~l~~~y~d~~~~d~~~   97 (932)
T KOG2053|consen   22 SSQFKKALAKLGKLLKKHPNALYAKVLKAL--SLFRLGKGDEALKLLEALYGLK--GTDDLTLQFLQNVYRDLGKLDEAV   97 (932)
T ss_pred             hHHHHHHHHHHHHHHHHCCCcHHHHHHHHH--HHHHhcCchhHHHHHhhhccCC--CCchHHHHHHHHHHHHHhhhhHHH
Confidence            478889999888887655444433344333  3458899999999998887765  247888999999999999999999


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC----------
Q 041804           88 GTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW----------  157 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------  157 (403)
                      .+|++.....+. ......+..+|.+.+.+.+-.++--++.+       ..+.+...+-++++.+...-.          
T Consensus        98 ~~Ye~~~~~~P~-eell~~lFmayvR~~~yk~qQkaa~~LyK-------~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~  169 (932)
T KOG2053|consen   98 HLYERANQKYPS-EELLYHLFMAYVREKSYKKQQKAALQLYK-------NFPKRAYYFWSVISLILQSIFSENELLDPIL  169 (932)
T ss_pred             HHHHHHHhhCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------hCCcccchHHHHHHHHHHhccCCcccccchh
Confidence            999999887766 77777788888888877665554444433       223344444444444433211          


Q ss_pred             hhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHHcCChhHHHHHH
Q 041804          158 WGKCREFWEEMDKRG-VVKDLHSYSIYMDIMCKSGKPWKAVKLY  200 (403)
Q Consensus       158 ~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~  200 (403)
                      ..-|.+.++.+.+.+ ..-+..-.......+...|++++|++++
T Consensus       170 l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l  213 (932)
T KOG2053|consen  170 LALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFL  213 (932)
T ss_pred             HHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHH
Confidence            123444455544433 1111111222223334556666666665

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.74  E-value=9.2e-07  Score=65.61  Aligned_cols=92  Identities=5%  Similarity=-0.188  Sum_probs=46.1

Q ss_pred             HHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC
Q 041804           36 SVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK  115 (403)
Q Consensus        36 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  115 (403)
                      .+...+...|++++|...|+......  +.+..+|..+..++...|++++|+..|+.....++.+...+..+..++...|
T Consensus        29 ~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~~g  106 (144)
T PRK15359         29 ASGYASWQEGDYSRAVIDFSWLVMAQ--PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKMMG  106 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcC
Confidence            34444455555555555555554443  2344445555555555555555555555555544445555555555555555


Q ss_pred             CHHHHHHHHhcccc
Q 041804          116 HVIEAQELCFGENK  129 (403)
Q Consensus       116 ~~~~a~~~~~~~~~  129 (403)
                      +.++|...|+....
T Consensus       107 ~~~eAi~~~~~Al~  120 (144)
T PRK15359        107 EPGLAREAFQTAIK  120 (144)
T ss_pred             CHHHHHHHHHHHHH
Confidence            55555555544433

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.73  E-value=6.8e-07  Score=70.12  Aligned_cols=127  Identities=9%  Similarity=0.107  Sum_probs=108.0

Q ss_pred             cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH-HhcCC--HHHH
Q 041804           44 FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL-CEYKH--VIEA  120 (403)
Q Consensus        44 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~--~~~a  120 (403)
                      .++.+++...++...+..  +.+...|..+...|...|+++.|+..|++..+..+.+...+..+..++ ...|+  .++|
T Consensus        52 ~~~~~~~i~~l~~~L~~~--P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         52 QQTPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            567788888888877765  578889999999999999999999999999999988999999998874 67676  5999


Q ss_pred             HHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHH
Q 041804          121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY  180 (403)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  180 (403)
                      ..++++...       ..+.+..++..+...+.+.|++++|...|+++.+...+ +..-+
T Consensus       130 ~~~l~~al~-------~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~~~-~~~r~  181 (198)
T PRK10370        130 REMIDKALA-------LDANEVTALMLLASDAFMQADYAQAIELWQKVLDLNSP-RVNRT  181 (198)
T ss_pred             HHHHHHHHH-------hCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CccHH
Confidence            999999888       44667888999999999999999999999999887544 44333

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.72  E-value=1.2e-05  Score=62.74  Aligned_cols=85  Identities=16%  Similarity=0.024  Sum_probs=39.0

Q ss_pred             hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCCh
Q 041804           79 TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWW  158 (403)
Q Consensus        79 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  158 (403)
                      ..|++++|+++|+.+.+.++.|..++..-+...-..|+.-+|++-+....+       .+..|...|.-+...|...|++
T Consensus        98 a~~~~~~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~-------~F~~D~EAW~eLaeiY~~~~~f  170 (289)
T KOG3060|consen   98 ATGNYKEAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLD-------KFMNDQEAWHELAEIYLSEGDF  170 (289)
T ss_pred             HhhchhhHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHH-------HhcCcHHHHHHHHHHHHhHhHH
Confidence            344445555555555544444444444444444444444444444444443       3344444444444444444444


Q ss_pred             hHHHHHHHHHHh
Q 041804          159 GKCREFWEEMDK  170 (403)
Q Consensus       159 ~~a~~~~~~~~~  170 (403)
                      ++|.=.++++.-
T Consensus       171 ~kA~fClEE~ll  182 (289)
T KOG3060|consen  171 EKAAFCLEELLL  182 (289)
T ss_pred             HHHHHHHHHHHH
Confidence            444444444443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.71  E-value=4.5e-06  Score=77.67  Aligned_cols=135  Identities=7%  Similarity=0.072  Sum_probs=106.4

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           64 IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      +.+...+..|.....+.|..++|+.+++...+..+.+...+..+..++.+.+++++|...+++...       ..+.+..
T Consensus        83 ~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~-------~~p~~~~  155 (694)
T PRK15179         83 PHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFS-------GGSSSAR  155 (694)
T ss_pred             cccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhh-------cCCCCHH
Confidence            345677777888888888888888888888888877888888888888888888888888887777       4466677


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ....+..++.+.|++++|..+|+++...+.. +..++..+..++...|+.++|...|+...+.
T Consensus       156 ~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p~-~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        156 EILLEAKSWDEIGQSEQADACFERLSRQHPE-FENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            7777888888888888888888888875444 5677888888888888888888888887765

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.71  E-value=7.8e-07  Score=79.31  Aligned_cols=226  Identities=10%  Similarity=-0.006  Sum_probs=174.8

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVN   84 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   84 (403)
                      +..-|-.+.|+.+|+.+.          .|..+|.+|...|+..+|..+..+-.++   +|+...|..+.+.....--++
T Consensus       408 l~slGitksAl~I~Erle----------mw~~vi~CY~~lg~~~kaeei~~q~lek---~~d~~lyc~LGDv~~d~s~yE  474 (777)
T KOG1128|consen  408 LLSLGITKSALVIFERLE----------MWDPVILCYLLLGQHGKAEEINRQELEK---DPDPRLYCLLGDVLHDPSLYE  474 (777)
T ss_pred             HHHcchHHHHHHHHHhHH----------HHHHHHHHHHHhcccchHHHHHHHHhcC---CCcchhHHHhhhhccChHHHH
Confidence            344566777888887654          5888899999999999999999888884   489999988888887777788


Q ss_pred             HHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHH
Q 041804           85 EAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREF  164 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  164 (403)
                      +|.++++.....      +-..+.....+.+++.++.+.++....       -.+....+|..+..++.+.++++.|.+.
T Consensus       475 kawElsn~~sar------A~r~~~~~~~~~~~fs~~~~hle~sl~-------~nplq~~~wf~~G~~ALqlek~q~av~a  541 (777)
T KOG1128|consen  475 KAWELSNYISAR------AQRSLALLILSNKDFSEADKHLERSLE-------INPLQLGTWFGLGCAALQLEKEQAAVKA  541 (777)
T ss_pred             HHHHHhhhhhHH------HHHhhccccccchhHHHHHHHHHHHhh-------cCccchhHHHhccHHHHHHhhhHHHHHH
Confidence            888888765442      223333333457899999998887665       3456677889999999999999999999


Q ss_pred             HHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC-
Q 041804          165 WEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC-  243 (403)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-  243 (403)
                      |..-....+. +...||.+-.+|.+.++-.+|...+.+..+.+ .-+...|...+....+.|.+++|.+.+.++.+... 
T Consensus       542 F~rcvtL~Pd-~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~~~~~  619 (777)
T KOG1128|consen  542 FHRCVTLEPD-NAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDLRKK  619 (777)
T ss_pred             HHHHhhcCCC-chhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHHhhhh
Confidence            9998887665 77899999999999999999999999999887 55667788888888899999999999998875421 


Q ss_pred             CCCHHHHHHHHHHHH
Q 041804          244 QPSVVTCNTVIKLLC  258 (403)
Q Consensus       244 ~~~~~~~~~li~~~~  258 (403)
                      ..+..+...++....
T Consensus       620 ~~d~~vl~~iv~~~~  634 (777)
T KOG1128|consen  620 YKDDEVLLIIVRTVL  634 (777)
T ss_pred             cccchhhHHHHHHHH
Confidence            124444444444433

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.67  E-value=0.00014  Score=62.57  Aligned_cols=113  Identities=11%  Similarity=-0.052  Sum_probs=58.7

Q ss_pred             HhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcC
Q 041804          112 CEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSG  191 (403)
Q Consensus       112 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  191 (403)
                      ...|+.++|+..++.+..       ..|.|...+......+.+.++.++|.+.++++....+. ....+..+..+|.+.|
T Consensus       317 ~~~~~~d~A~~~l~~L~~-------~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~-~~~l~~~~a~all~~g  388 (484)
T COG4783         317 YLAGQYDEALKLLQPLIA-------AQPDNPYYLELAGDILLEANKAKEAIERLKKALALDPN-SPLLQLNLAQALLKGG  388 (484)
T ss_pred             HHhcccchHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCC-ccHHHHHHHHHHHhcC
Confidence            344555555555555544       23444444555555555555555555555555554322 1344444555555555


Q ss_pred             ChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHH
Q 041804          192 KPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMR  233 (403)
Q Consensus       192 ~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  233 (403)
                      ++++|+.+++...... +-|...|..|.++|...|+..++..
T Consensus       389 ~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~  429 (484)
T COG4783         389 KPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALL  429 (484)
T ss_pred             ChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHH
Confidence            5555555555555442 3355555555555555555544443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.67  E-value=1.1e-06  Score=65.16  Aligned_cols=106  Identities=11%  Similarity=-0.040  Sum_probs=91.1

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.+..  -.+.+...|..+..++.+.|++++|...|++.....  +.+..++..+..++...|+
T Consensus        32 ~~~~~~g~~~~A~~~~~~al~--~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~--p~~~~a~~~lg~~l~~~g~  107 (144)
T PRK15359         32 YASWQEGDYSRAVIDFSWLVM--AQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD--ASHPEPVYQTGVCLKMMGE  107 (144)
T ss_pred             HHHHHcCCHHHHHHHHHHHHH--cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--CCCcHHHHHHHHHHHHcCC
Confidence            345678999999999999884  235578899999999999999999999999999876  4678899999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      +++|+..|+...+..+.+...+.....++.
T Consensus       108 ~~eAi~~~~~Al~~~p~~~~~~~~~~~~~~  137 (144)
T PRK15359        108 PGLAREAFQTAIKMSYADASWSEIRQNAQI  137 (144)
T ss_pred             HHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            999999999999998888888766655544

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

Probab=98.66  E-value=0.00023  Score=62.64  Aligned_cols=197  Identities=10%  Similarity=0.094  Sum_probs=132.6

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      .-+=++.+.+.|++++|.+...++...+  +.+..++..-+-+.++.+.+++|+.+.+.-.... .+...+..-..+..+
T Consensus        15 l~t~ln~~~~~~e~e~a~k~~~Kil~~~--pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~-~~~~~~fEKAYc~Yr   91 (652)
T KOG2376|consen   15 LLTDLNRHGKNGEYEEAVKTANKILSIV--PDDEDAIRCKVVALIQLDKYEDALKLIKKNGALL-VINSFFFEKAYCEYR   91 (652)
T ss_pred             HHHHHHHhccchHHHHHHHHHHHHHhcC--CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhh-hcchhhHHHHHHHHH
Confidence            3344677889999999999999999875  4556778888888999999999996554332211 111222223344457


Q ss_pred             cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-------------------
Q 041804          114 YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV-------------------  174 (403)
Q Consensus       114 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-------------------  174 (403)
                      .+..++|...+....          +.+..+...-...+.+.|++++|.++|+.+.+.+..                   
T Consensus        92 lnk~Dealk~~~~~~----------~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~  161 (652)
T KOG2376|consen   92 LNKLDEALKTLKGLD----------RLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQV  161 (652)
T ss_pred             cccHHHHHHHHhccc----------ccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhH
Confidence            999999999887322          233446666778899999999999999998655431                   


Q ss_pred             --------CcHHHHHHHHH---HHHHcCChhHHHHHHHHHHHcC-------CCCCh-------hhHHHHHHHHhhcCCHH
Q 041804          175 --------KDLHSYSIYMD---IMCKSGKPWKAVKLYKEMKKKG-------IKMDV-------VAYNTVIRAVGVSEGVD  229 (403)
Q Consensus       175 --------~~~~~~~~l~~---~~~~~~~~~~a~~~~~~~~~~~-------~~~~~-------~~~~~ll~~~~~~~~~~  229 (403)
                              ....+|..+.+   .+...|++.+|+++++...+.+       -.-+.       .+-..+.-.+-..|+.+
T Consensus       162 ~~~q~v~~v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~  241 (652)
T KOG2376|consen  162 QLLQSVPEVPEDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTA  241 (652)
T ss_pred             HHHHhccCCCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchH
Confidence                    11224544443   4556899999999999883221       11011       11223444566789999


Q ss_pred             HHHHHHHHHHHcCC
Q 041804          230 FAMRVYREMREMGC  243 (403)
Q Consensus       230 ~a~~~~~~~~~~~~  243 (403)
                      +|..++....+...
T Consensus       242 ea~~iy~~~i~~~~  255 (652)
T KOG2376|consen  242 EASSIYVDIIKRNP  255 (652)
T ss_pred             HHHHHHHHHHHhcC
Confidence            99999998887643

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.66  E-value=1.4e-05  Score=74.10  Aligned_cols=154  Identities=12%  Similarity=-0.007  Sum_probs=72.8

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      +-..+...|.+.|+....  -...+..........|+...+++.|..+.-...+......-...|....-.|...++...
T Consensus       503 rd~~Dm~RA~kCf~KAFe--LDatdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yyLea~n~h~  580 (1238)
T KOG1127|consen  503 RDSDDMKRAKKCFDKAFE--LDATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYYLEAHNLHG  580 (1238)
T ss_pred             HHHHHHHHHHHHHHHHhc--CCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccccCccchhh
Confidence            333344455555544432  012234444555555555555555555533322221000111122233334445555666


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      |+..|+...+.+|.|...|..++.+|.+.|.+..|.++|.+...-       .|.+...-.-....-+..|.+.+|...+
T Consensus       581 aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~L-------rP~s~y~~fk~A~~ecd~GkYkeald~l  653 (1238)
T KOG1127|consen  581 AVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLL-------RPLSKYGRFKEAVMECDNGKYKEALDAL  653 (1238)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhc-------CcHhHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            666666666655556666666666666666666666666555431       1222222222333344556666665555


Q ss_pred             HHH
Q 041804          166 EEM  168 (403)
Q Consensus       166 ~~~  168 (403)
                      ...
T Consensus       654 ~~i  656 (1238)
T KOG1127|consen  654 GLI  656 (1238)
T ss_pred             HHH
Confidence            544

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.66  E-value=2.8e-05  Score=72.57  Aligned_cols=200  Identities=11%  Similarity=-0.001  Sum_probs=152.1

Q ss_pred             CHHhHHHHHHHHHccCChhHHH-HHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSW-NLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      ++.....+=.+.+.-|..++|- +++.+..+             ++....+.....+++.-........+.+...+..|.
T Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~La   93 (694)
T PRK15179         27 GPTILDLLEAALAEPGESEEAGRELLQQARQ-------------VLERHAAVHKPAAALPELLDYVRRYPHTELFQVLVA   93 (694)
T ss_pred             CcHHHhHHHHHhcCcccchhHHHHHHHHHHH-------------HHHHhhhhcchHhhHHHHHHHHHhccccHHHHHHHH
Confidence            3444555555666677766663 34443332             223333333444444444444444455899999999


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      .+..+.|..++|..+++...+       -.|.+......+...+.+.+++++|....++.....+. +......+..++.
T Consensus        94 ~i~~~~g~~~ea~~~l~~~~~-------~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~-~~~~~~~~a~~l~  165 (694)
T PRK15179         94 RALEAAHRSDEGLAVWRGIHQ-------RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSS-SAREILLEAKSWD  165 (694)
T ss_pred             HHHHHcCCcHHHHHHHHHHHh-------hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCC-CHHHHHHHHHHHH
Confidence            999999999999999999887       55777888999999999999999999999999998877 7888899999999


Q ss_pred             HcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 041804          189 KSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNT  252 (403)
Q Consensus       189 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  252 (403)
                      +.|++++|..+|+++...+ +-+..++..+..++...|+.++|...|+...+.. .+...-|+.
T Consensus       166 ~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~-~~~~~~~~~  227 (694)
T PRK15179        166 EIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGLDAI-GDGARKLTR  227 (694)
T ss_pred             HhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhh-CcchHHHHH
Confidence            9999999999999999853 3457889999999999999999999999998762 233444443

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.66  E-value=4.9e-05  Score=59.97  Aligned_cols=233  Identities=11%  Similarity=0.080  Sum_probs=99.3

Q ss_pred             HHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh
Q 041804           75 KRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK  154 (403)
Q Consensus        75 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  154 (403)
                      +-+.-.|++..++..-....... .+...-.-+-++|...|.......   +...       +..|.......+......
T Consensus        16 Rn~fY~Gnyq~~ine~~~~~~~~-~~~e~d~y~~raylAlg~~~~~~~---eI~~-------~~~~~lqAvr~~a~~~~~   84 (299)
T KOG3081|consen   16 RNYFYLGNYQQCINEAEKFSSSK-TDVELDVYMYRAYLALGQYQIVIS---EIKE-------GKATPLQAVRLLAEYLEL   84 (299)
T ss_pred             HHHHHhhHHHHHHHHHHhhcccc-chhHHHHHHHHHHHHccccccccc---cccc-------ccCChHHHHHHHHHHhhC
Confidence            33444555655555444433322 234444445555665565433221   1111       112222222322222222


Q ss_pred             cCChhHH-HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHH
Q 041804          155 MSWWGKC-REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMR  233 (403)
Q Consensus       155 ~~~~~~a-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  233 (403)
                      -++.+.- .++.+.+.......+......-...|+..+++++|++......      +......=...+.+..+++.|.+
T Consensus        85 e~~~~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~~  158 (299)
T KOG3081|consen   85 ESNKKSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAEK  158 (299)
T ss_pred             cchhHHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHHH
Confidence            2222222 2333344433333233333333445666666666666655411      22222222334445666666666


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHH
Q 041804          234 VYREMREMGCQPSVVTCNTVIKLLCE----NGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMI  306 (403)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~  306 (403)
                      .+++|.+.   .+..+.+.|..++.+    .+.+..|.-+|++|.++ ..|+..+.+....++   +++++|..+++...
T Consensus       159 ~lk~mq~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL  234 (299)
T KOG3081|consen  159 ELKKMQQI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEAL  234 (299)
T ss_pred             HHHHHHcc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHH
Confidence            66666653   244444444444433    33455566666665543 233333333222211   34444444444444


Q ss_pred             HcCCCCchhhHHHHHHHHHhcCC
Q 041804          307 ESGIRPKMDTYVMLLRKFGRWGF  329 (403)
Q Consensus       307 ~~~~~~~~~~~~~li~~~~~~g~  329 (403)
                      ..... ++.+...++.+-...|.
T Consensus       235 ~kd~~-dpetL~Nliv~a~~~Gk  256 (299)
T KOG3081|consen  235 DKDAK-DPETLANLIVLALHLGK  256 (299)
T ss_pred             hccCC-CHHHHHHHHHHHHHhCC
Confidence            43322 34444444444334443

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.61  E-value=2.4e-06  Score=63.01  Aligned_cols=94  Identities=10%  Similarity=-0.000  Sum_probs=40.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      ...+...+...|++++|.+.|+.+...++.+...+..+..++...|++++|...+++...       ..+.+...+..+.
T Consensus        20 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-------~~p~~~~~~~~la   92 (135)
T TIGR02552        20 IYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAA-------LDPDDPRPYFHAA   92 (135)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------cCCCChHHHHHHH
Confidence            333444444444444444444444444433444444444444444444444444444333       1122333333344


Q ss_pred             HHHHhcCChhHHHHHHHHHHh
Q 041804          150 RGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      ..+...|++++|.+.|+...+
T Consensus        93 ~~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        93 ECLLALGEPESALKALDLAIE  113 (135)
T ss_pred             HHHHHcCCHHHHHHHHHHHHH
Confidence            444444444444444444433

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.60  E-value=7.6e-05  Score=64.10  Aligned_cols=146  Identities=12%  Similarity=-0.044  Sum_probs=123.8

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      +--....+...|+++.|+..++.+.+..+.|+..+......+.+.++.++|.+.++++...       .+......-.+.
T Consensus       309 ~YG~A~~~~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l-------~P~~~~l~~~~a  381 (484)
T COG4783         309 QYGRALQTYLAGQYDEALKLLQPLIAAQPDNPYYLELAGDILLEANKAKEAIERLKKALAL-------DPNSPLLQLNLA  381 (484)
T ss_pred             HHHHHHHHHHhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc-------CCCccHHHHHHH
Confidence            3334445667899999999999999988889999999999999999999999999998874       344467788889


Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHH
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVD  229 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~  229 (403)
                      .++.+.|++.+|.++++........ |+..|..|..+|...|+..++..-..+                  .+...|+++
T Consensus       382 ~all~~g~~~eai~~L~~~~~~~p~-dp~~w~~LAqay~~~g~~~~a~~A~AE------------------~~~~~G~~~  442 (484)
T COG4783         382 QALLKGGKPQEAIRILNRYLFNDPE-DPNGWDLLAQAYAELGNRAEALLARAE------------------GYALAGRLE  442 (484)
T ss_pred             HHHHhcCChHHHHHHHHHHhhcCCC-CchHHHHHHHHHHHhCchHHHHHHHHH------------------HHHhCCCHH
Confidence            9999999999999999999988777 899999999999999999888765544                  345578888


Q ss_pred             HHHHHHHHHHHc
Q 041804          230 FAMRVYREMREM  241 (403)
Q Consensus       230 ~a~~~~~~~~~~  241 (403)
                      .|...+....+.
T Consensus       443 ~A~~~l~~A~~~  454 (484)
T COG4783         443 QAIIFLMRASQQ  454 (484)
T ss_pred             HHHHHHHHHHHh
Confidence            888888888776

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.57  E-value=5.6e-05  Score=71.52  Aligned_cols=218  Identities=11%  Similarity=0.026  Sum_probs=124.8

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH-HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH-ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN  106 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  106 (403)
                      +.+...+..|+..+...+++++|.++.+...+..   |+. ..|-.+...+.+.++.+.+.-+  .+...          
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~---P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~----------   92 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKEH---KKSISALYISGILSLSRRPLNDSNLL--NLIDS----------   92 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC---CcceehHHHHHHHHHhhcchhhhhhh--hhhhh----------
Confidence            3457899999999999999999999999888765   443 3344444466677776665554  22222          


Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHH
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI  186 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  186 (403)
                          .....++.-...+...+..        ...+..++..+..+|-+.|+.++|..+|+++.+.++. |+.+.|.+...
T Consensus        93 ----~~~~~~~~~ve~~~~~i~~--------~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~-n~~aLNn~AY~  159 (906)
T PRK14720         93 ----FSQNLKWAIVEHICDKILL--------YGENKLALRTLAEAYAKLNENKKLKGVWERLVKADRD-NPEIVKKLATS  159 (906)
T ss_pred             ----cccccchhHHHHHHHHHHh--------hhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcc-cHHHHHHHHHH
Confidence                1222222111111111111        1223335666667777777777777777777776654 66677777777


Q ss_pred             HHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHH-----hhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhc
Q 041804          187 MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV-----GVSEGVDFAMRVYREMREM-GCQPSVVTCNTVIKLLCEN  260 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~-----~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~li~~~~~~  260 (403)
                      |... +.++|.+++.+....-+  +..-|+.+...+     ....+++.-.++.+.+... |..--..++-.+-..|-..
T Consensus       160 ~ae~-dL~KA~~m~~KAV~~~i--~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~  236 (906)
T PRK14720        160 YEEE-DKEKAITYLKKAIYRFI--KKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKAL  236 (906)
T ss_pred             HHHh-hHHHHHHHHHHHHHHHH--hhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhh
Confidence            7666 77777777666655411  111122222111     1223344444444444443 3333344555566677777


Q ss_pred             CcHHHHHHHHHhchhc
Q 041804          261 GRVREAYAVLAEMPKK  276 (403)
Q Consensus       261 g~~~~a~~~~~~~~~~  276 (403)
                      .+|+++..+++.+.+.
T Consensus       237 ~~~~~~i~iLK~iL~~  252 (906)
T PRK14720        237 EDWDEVIYILKKILEH  252 (906)
T ss_pred             hhhhHHHHHHHHHHhc
Confidence            7788888888877765

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.56  E-value=4.7e-06  Score=61.48  Aligned_cols=97  Identities=10%  Similarity=-0.011  Sum_probs=58.0

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ......+...+...|++++|...|+.+...+  +.+...|..+..++...|++++|...++...+.++.+...+..+..+
T Consensus        17 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~   94 (135)
T TIGR02552        17 LEQIYALAYNLYQQGRYDEALKLFQLLAAYD--PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAEC   94 (135)
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHH
Confidence            3444555555666666666666666665543  23455566666666666666666666666666555566666666666


Q ss_pred             HHhcCCHHHHHHHHhcccc
Q 041804          111 LCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~  129 (403)
                      +...|++++|...++....
T Consensus        95 ~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        95 LLALGEPESALKALDLAIE  113 (135)
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            6666666666666655544

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.54  E-value=0.00033  Score=65.60  Aligned_cols=125  Identities=11%  Similarity=0.147  Sum_probs=88.5

Q ss_pred             HHHHHHHHHhcCcHHHHHHHHHhchhc---CCCCChhhHHHHHHhhC--CHHHHHHHHHHHHHcCCCCchhhHHHHHHHH
Q 041804          250 CNTVIKLLCENGRVREAYAVLAEMPKK---GCVPDVITYHCFFRCLE--KPREILGLFDRMIESGIRPKMDTYVMLLRKF  324 (403)
Q Consensus       250 ~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~p~~~~~~~l~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  324 (403)
                      +-.+.+.|.++|-...|++.+.++.+-   -+..+...-..+..-++  ..+++.+.++.|...+++-|..+...+..-|
T Consensus       609 ra~IAqLCEKAGL~qraLehytDl~DIKR~vVhth~L~pEwLv~yFg~lsve~s~eclkaml~~NirqNlQi~VQvatky  688 (1666)
T KOG0985|consen  609 RAEIAQLCEKAGLLQRALEHYTDLYDIKRVVVHTHLLNPEWLVNYFGSLSVEDSLECLKAMLSANIRQNLQIVVQVATKY  688 (1666)
T ss_pred             HHHHHHHHHhcchHHHHHHhcccHHHHHHHHHHhccCCHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            566778899999999999888776431   11111111123333343  4788999999999988888877777777777


Q ss_pred             HhcCCcchHHHHHHHHHhc-----------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 041804          325 GRWGFLRPVFVVWKKMEEL-----------GCSPDEFAYNALVDALIDKGMLDMARKYDEE  374 (403)
Q Consensus       325 ~~~g~~~~a~~~~~~~~~~-----------~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  374 (403)
                      ...=-.+..+++|+..+..           ++.-|+...-..|.+.++.|++.+..++.++
T Consensus       689 ~eqlg~~~li~lFE~fks~eGL~yfLgSivn~seDpevh~KYIqAA~kt~QikEvERicre  749 (1666)
T KOG0985|consen  689 HEQLGAQALIELFESFKSYEGLYYFLGSIVNFSEDPEVHFKYIQAACKTGQIKEVERICRE  749 (1666)
T ss_pred             HHHhCHHHHHHHHHhhccchhHHHHHHHHhccccCchHHHHHHHHHHhhccHHHHHHHHhc
Confidence            7666667777777776532           3567788888889999999999998887653

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.54  E-value=0.00048  Score=60.09  Aligned_cols=129  Identities=8%  Similarity=0.085  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC-ChhhHHHHHHhhC--CHHHHHHHHHHHHHcCCCCchhhHHHHHHHH
Q 041804          248 VTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP-DVITYHCFFRCLE--KPREILGLFDRMIESGIRPKMDTYVMLLRKF  324 (403)
Q Consensus       248 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  324 (403)
                      .+|..+++.-.+..-++.|..+|.+..+.+..+ +...+++++..++  +..-|.++|+.=...-. -++.-....+..+
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cskD~~~AfrIFeLGLkkf~-d~p~yv~~YldfL  445 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSKDKETAFRIFELGLKKFG-DSPEYVLKYLDFL  445 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC-CChHHHHHHHHHH
Confidence            456666777777777888888888888777766 6777777877663  45567777776554321 1333445666777


Q ss_pred             HhcCCcchHHHHHHHHHhcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          325 GRWGFLRPVFVVWKKMEELGCSPD--EFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       325 ~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      ...++-..|..+|++....++.|+  ...|..+++.=..-|+...+.++-+++..
T Consensus       446 ~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  446 SHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            788888888888888887755554  46788888888888888888887777665

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.52  E-value=0.00057  Score=64.14  Aligned_cols=219  Identities=15%  Similarity=0.116  Sum_probs=109.3

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCC-CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSI-PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      .|++..+..+.++...+-..+.+++++++.-.+..- .+...-|.|+-... .-+..++.+..+++...+.++.      
T Consensus       982 ~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAi-kad~trVm~YI~rLdnyDa~~i------ 1054 (1666)
T KOG0985|consen  982 QDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAI-KADRTRVMEYINRLDNYDAPDI------ 1054 (1666)
T ss_pred             CChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHh-hcChHHHHHHHHHhccCCchhH------
Confidence            356666677788888888888888888887543221 22223333333333 3344566666666655544322      


Q ss_pred             HHHHHhcCCHHHHHHHHhcccccc-----------------cccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 041804          108 VDALCEYKHVIEAQELCFGENKNV-----------------GFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      ...+...+-+++|..+|++.....                 ++.  .......+|..+..+-.+.|...+|.+-|-+.. 
T Consensus      1055 a~iai~~~LyEEAF~ifkkf~~n~~A~~VLie~i~~ldRA~efA--e~~n~p~vWsqlakAQL~~~~v~dAieSyikad- 1131 (1666)
T KOG0985|consen 1055 AEIAIENQLYEEAFAIFKKFDMNVSAIQVLIENIGSLDRAYEFA--ERCNEPAVWSQLAKAQLQGGLVKDAIESYIKAD- 1131 (1666)
T ss_pred             HHHHhhhhHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHHHHHH--HhhCChHHHHHHHHHHHhcCchHHHHHHHHhcC-
Confidence            122333444555555554432210                 000  001122345555555555555555555443332 


Q ss_pred             CCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 041804          171 RGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTC  250 (403)
Q Consensus       171 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  250 (403)
                           |+..|...+....+.|.+++-.+.+...++..-.|...  +.|+-+|++.++..+.+.++       .-|+....
T Consensus      1132 -----Dps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi-------~gpN~A~i 1197 (1666)
T KOG0985|consen 1132 -----DPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFI-------AGPNVANI 1197 (1666)
T ss_pred             -----CcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHh-------cCCCchhH
Confidence                 44556666666666666666666555555544333333  34555666666554433332       12344444


Q ss_pred             HHHHHHHHhcCcHHHHHHHHH
Q 041804          251 NTVIKLLCENGRVREAYAVLA  271 (403)
Q Consensus       251 ~~li~~~~~~g~~~~a~~~~~  271 (403)
                      ..+.+-|...|.++.|.-+|.
T Consensus      1198 ~~vGdrcf~~~~y~aAkl~y~ 1218 (1666)
T KOG0985|consen 1198 QQVGDRCFEEKMYEAAKLLYS 1218 (1666)
T ss_pred             HHHhHHHhhhhhhHHHHHHHH
Confidence            444444444444444444443

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.52  E-value=9.2e-05  Score=68.95  Aligned_cols=182  Identities=12%  Similarity=0.045  Sum_probs=127.5

Q ss_pred             ChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHH
Q 041804           46 EFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELC  124 (403)
Q Consensus        46 ~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  124 (403)
                      +...|...|-+....+   |+ ...|..|...|....+...|.+.|++..+.+..+........+.|++..+++.|..+.
T Consensus       473 ~~~~al~ali~alrld---~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~  549 (1238)
T KOG1127|consen  473 NSALALHALIRALRLD---VSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEIC  549 (1238)
T ss_pred             hHHHHHHHHHHHHhcc---cchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHH
Confidence            3555555555555433   33 4578888888888889999999999999988889999999999999999999999885


Q ss_pred             hcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 041804          125 FGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMK  204 (403)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  204 (403)
                      -...+..     ....-...|-...-.|.+.++...|..-|+...+..++ |...|..++.+|...|++..|+++|.+..
T Consensus       550 l~~~qka-----~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPk-D~n~W~gLGeAY~~sGry~~AlKvF~kAs  623 (1238)
T KOG1127|consen  550 LRAAQKA-----PAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPK-DYNLWLGLGEAYPESGRYSHALKVFTKAS  623 (1238)
T ss_pred             HHHhhhc-----hHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCch-hHHHHHHHHHHHHhcCceehHHHhhhhhH
Confidence            4433321     11111222333445567788888999889888888777 88889999999999999999999998876


Q ss_pred             HcCCCCChhhHHHHH--HHHhhcCCHHHHHHHHHHHH
Q 041804          205 KKGIKMDVVAYNTVI--RAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       205 ~~~~~~~~~~~~~ll--~~~~~~~~~~~a~~~~~~~~  239 (403)
                      ..  .|+. +|...-  -.-+..|.+.++...+....
T Consensus       624 ~L--rP~s-~y~~fk~A~~ecd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  624 LL--RPLS-KYGRFKEAVMECDNGKYKEALDALGLII  657 (1238)
T ss_pred             hc--CcHh-HHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            64  3332 222221  22345666666666666554

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.49  E-value=0.00077  Score=61.91  Aligned_cols=191  Identities=14%  Similarity=0.065  Sum_probs=110.9

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      .|+.+.|+.+|+...          -|-+++++.+-+|+.++|-.+-++-       -|..+.-.+.+.|-..|++.+|.
T Consensus       925 ~GemdaAl~~Y~~A~----------D~fs~VrI~C~qGk~~kAa~iA~es-------gd~AAcYhlaR~YEn~g~v~~Av  987 (1416)
T KOG3617|consen  925 VGEMDAALSFYSSAK----------DYFSMVRIKCIQGKTDKAARIAEES-------GDKAACYHLARMYENDGDVVKAV  987 (1416)
T ss_pred             ccchHHHHHHHHHhh----------hhhhheeeEeeccCchHHHHHHHhc-------ccHHHHHHHHHHhhhhHHHHHHH
Confidence            355555555555443          2555666666667777776655442       46667788999999999999999


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHH---------------HHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           88 GTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEA---------------QELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      ..|.+...        +.+.|+.|-.++--++.               -..|++.-.              -+...+-.|
T Consensus       988 ~FfTrAqa--------fsnAIRlcKEnd~~d~L~nlal~s~~~d~v~aArYyEe~g~--------------~~~~AVmLY 1045 (1416)
T KOG3617|consen  988 KFFTRAQA--------FSNAIRLCKENDMKDRLANLALMSGGSDLVSAARYYEELGG--------------YAHKAVMLY 1045 (1416)
T ss_pred             HHHHHHHH--------HHHHHHHHHhcCHHHHHHHHHhhcCchhHHHHHHHHHHcch--------------hhhHHHHHH
Confidence            99987654        55556655544433332               223322211              123344567


Q ss_pred             HhcCChhHHHHHHHH--------HHh--CCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH----------cCC----
Q 041804          153 FKMSWWGKCREFWEE--------MDK--RGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK----------KGI----  208 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~--------~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----------~~~----  208 (403)
                      .+.|.+.+|+++--+        +..  .....|+...+--...++...++++|..++-..++          .|+    
T Consensus      1046 HkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~ar~~~~AlqlC~~~nv~vte 1125 (1416)
T KOG3617|consen 1046 HKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLAREFSGALQLCKNRNVRVTE 1125 (1416)
T ss_pred             HhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhH
Confidence            778888887764211        122  22334555566666666677777777766543322          111    


Q ss_pred             ------------CCCh----hhHHHHHHHHhhcCCHHHHHHHHHH
Q 041804          209 ------------KMDV----VAYNTVIRAVGVSEGVDFAMRVYRE  237 (403)
Q Consensus       209 ------------~~~~----~~~~~ll~~~~~~~~~~~a~~~~~~  237 (403)
                                  .|+.    .....+...|.+.|.+..|.+-|.+
T Consensus      1126 e~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~AtKKfTQ 1170 (1416)
T KOG3617|consen 1126 EFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHAATKKFTQ 1170 (1416)
T ss_pred             HHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHHHHHHHhh
Confidence                        2222    2345566677788877766655543

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.49  E-value=0.0002  Score=56.19  Aligned_cols=188  Identities=12%  Similarity=-0.043  Sum_probs=109.4

Q ss_pred             CChhHHHHHHHHhhhCCC---CCCCHH-HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHH
Q 041804           45 FEFDLSWNLIHRMKDNPS---SIPNHA-TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEA  120 (403)
Q Consensus        45 ~~~~~a~~~~~~~~~~~~---~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  120 (403)
                      .+.++..+++..+.....   ..++.. .|..++-+....|+.+.|..+++.+...-+.+..+-..-.-.+-..|++++|
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~~~~~A  105 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEATGNYKEA  105 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhchhhH
Confidence            455555666555543211   123332 3555666666777777777777777666544444444444444556777777


Q ss_pred             HHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHH
Q 041804          121 QELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLY  200 (403)
Q Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  200 (403)
                      .++++.+..       ..|.|..++---+...-..|+.-+|++-+....+.=+. |...|.-+...|...|++++|.-.+
T Consensus       106 ~e~y~~lL~-------ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~-D~EAW~eLaeiY~~~~~f~kA~fCl  177 (289)
T KOG3060|consen  106 IEYYESLLE-------DDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMN-DQEAWHELAEIYLSEGDFEKAAFCL  177 (289)
T ss_pred             HHHHHHHhc-------cCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC-cHHHHHHHHHHHHhHhHHHHHHHHH
Confidence            777777666       33556666666666666666666666666665554333 6777777777777777777777777


Q ss_pred             HHHHHcCCCCChhhHHHHHHHHhh---cCCHHHHHHHHHHHHHc
Q 041804          201 KEMKKKGIKMDVVAYNTVIRAVGV---SEGVDFAMRVYREMREM  241 (403)
Q Consensus       201 ~~~~~~~~~~~~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~~  241 (403)
                      +++.-.. |.+...+..+...+.-   ..+.+.+.++|....+.
T Consensus       178 EE~ll~~-P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl  220 (289)
T KOG3060|consen  178 EELLLIQ-PFNPLYFQRLAEVLYTQGGAENLELARKYYERALKL  220 (289)
T ss_pred             HHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence            7766542 2233333333333322   33455666666666664

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.48  E-value=0.00071  Score=59.08  Aligned_cols=172  Identities=17%  Similarity=0.219  Sum_probs=125.2

Q ss_pred             hhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHHHHHHHHH
Q 041804          193 PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQP-SVVTCNTVIKLLCENGRVREAYAVLA  271 (403)
Q Consensus       193 ~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~  271 (403)
                      .+....++++++..-..--..+|..+|+...+..-+..|+.+|.++.+.+..+ ++.++++++.-|| .++.+-|.++|+
T Consensus       347 ~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFe  425 (656)
T KOG1914|consen  347 EKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFE  425 (656)
T ss_pred             hhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHH
Confidence            45566666666655322234577888888889999999999999999988777 7788888888776 478889999999


Q ss_pred             hch-hcCCCCC-hhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCch--hhHHHHHHHHHhcCCcchHHHHHHHHHhc---C
Q 041804          272 EMP-KKGCVPD-VITYHCFFRCLEKPREILGLFDRMIESGIRPKM--DTYVMLLRKFGRWGFLRPVFVVWKKMEEL---G  344 (403)
Q Consensus       272 ~~~-~~~~~p~-~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~  344 (403)
                      --. ..|-.|- ...|-..+..+++-..+..+|++....++.|+.  ..|..++..=+.-|+...+.++-+++...   .
T Consensus       426 LGLkkf~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~  505 (656)
T KOG1914|consen  426 LGLKKFGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPAD  505 (656)
T ss_pred             HHHHhcCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchh
Confidence            754 4333332 334556677788889999999999988666554  78999999999999999999998887543   1


Q ss_pred             CCCCHHHHHHHHHHHHhcCCH
Q 041804          345 CSPDEFAYNALVDALIDKGML  365 (403)
Q Consensus       345 ~~~~~~~~~~l~~~~~~~g~~  365 (403)
                      ..+....-..+++-|.-.+..
T Consensus       506 qe~~~~~~~~~v~RY~~~d~~  526 (656)
T KOG1914|consen  506 QEYEGNETALFVDRYGILDLY  526 (656)
T ss_pred             hcCCCChHHHHHHHHhhcccc
Confidence            122223344556666555544

>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=98.47  E-value=7.6e-06  Score=70.52  Aligned_cols=126  Identities=11%  Similarity=0.113  Sum_probs=101.4

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      ....|+..+...++++.|+.+|+++.+..   |+..  ..+++.+...++-.+|++++++..+..+.+...+..-.+.+.
T Consensus       171 Lv~~Ll~~l~~t~~~~~ai~lle~L~~~~---pev~--~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl  245 (395)
T PF09295_consen  171 LVDTLLKYLSLTQRYDEAIELLEKLRERD---PEVA--VLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLL  245 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcC---CcHH--HHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            34556666777888999999999998865   6543  457788888888889999999988877778888888888888


Q ss_pred             hcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 041804          113 EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      +.++.+.|+.+.+++..       -.|.+..+|..|..+|.+.|+++.|+-.++.+.-
T Consensus       246 ~k~~~~lAL~iAk~av~-------lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm  296 (395)
T PF09295_consen  246 SKKKYELALEIAKKAVE-------LSPSEFETWYQLAECYIQLGDFENALLALNSCPM  296 (395)
T ss_pred             hcCCHHHHHHHHHHHHH-------hCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcC
Confidence            99999999999888877       4456667889999999999999999888887653

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.46  E-value=0.0004  Score=62.88  Aligned_cols=79  Identities=11%  Similarity=0.196  Sum_probs=45.7

Q ss_pred             HHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHH
Q 041804          185 DIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVR  264 (403)
Q Consensus       185 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  264 (403)
                      .+......|.+|+.+++.+.....  -..-|..+...|+..|+++.|.++|-+.-         .++-.|.+|.+.|+|+
T Consensus       740 eaai~akew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw~  808 (1636)
T KOG3616|consen  740 EAAIGAKEWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKWE  808 (1636)
T ss_pred             HHHhhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccHH
Confidence            344455566666666666655532  22335556666777777777776664332         2344566667777777


Q ss_pred             HHHHHHHhch
Q 041804          265 EAYAVLAEMP  274 (403)
Q Consensus       265 ~a~~~~~~~~  274 (403)
                      .|.++-.+..
T Consensus       809 da~kla~e~~  818 (1636)
T KOG3616|consen  809 DAFKLAEECH  818 (1636)
T ss_pred             HHHHHHHHhc
Confidence            7766665544

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.43  E-value=2.9e-05  Score=57.88  Aligned_cols=126  Identities=10%  Similarity=0.020  Sum_probs=95.9

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH----ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVS  103 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~  103 (403)
                      ...|..++..+ ..++...+...++.+....   |+.    .+.-.+...+...|++++|...|+++....+.   ....
T Consensus        12 ~~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~---~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a   87 (145)
T PF09976_consen   12 SALYEQALQAL-QAGDPAKAEAAAEQLAKDY---PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLA   87 (145)
T ss_pred             HHHHHHHHHHH-HCCCHHHHHHHHHHHHHHC---CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHH
Confidence            34566666666 4888899999999998875   333    34445668888999999999999999987743   2345


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHH
Q 041804          104 YCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEM  168 (403)
Q Consensus       104 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  168 (403)
                      ...+..++...|++++|+..++.....        ......+......|.+.|++++|...|+..
T Consensus        88 ~l~LA~~~~~~~~~d~Al~~L~~~~~~--------~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   88 RLRLARILLQQGQYDEALATLQQIPDE--------AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHhccCc--------chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            666788899999999999999764332        345556778888999999999999888764

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.42  E-value=5.9e-07  Score=48.39  Aligned_cols=33  Identities=30%  Similarity=0.572  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 041804          351 AYNALVDALIDKGMLDMARKYDEEMFAKGLSAK  383 (403)
Q Consensus       351 ~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~  383 (403)
                      +|++++.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            567777777777777777777777777777765

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.39  E-value=7.6e-07  Score=47.53  Aligned_cols=33  Identities=33%  Similarity=0.408  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 041804          350 FAYNALVDALIDKGMLDMARKYDEEMFAKGLSA  382 (403)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p  382 (403)
                      .+|+.++.+|.+.|+++.|.++|++|.+.|++|
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            367777777777777777777777777777665

>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=98.34  E-value=2.2e-05  Score=67.75  Aligned_cols=127  Identities=12%  Similarity=0.008  Sum_probs=87.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHH
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHS  179 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  179 (403)
                      +......++..+...++++.|..+++++...        .|+  +...+++.+...++..+|.+++++.....+. +...
T Consensus       168 ~NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~--------~pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~-d~~L  236 (395)
T PF09295_consen  168 NNYLVDTLLKYLSLTQRYDEAIELLEKLRER--------DPE--VAVLLARVYLLMNEEVEAIRLLNEALKENPQ-DSEL  236 (395)
T ss_pred             chHHHHHHHHHHhhcccHHHHHHHHHHHHhc--------CCc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCC-CHHH
Confidence            4455556666666677777777777777654        233  3345667777777777777777777765444 5566


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC-hhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD-VVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       180 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      ...-...+.+.++++.|+.+.+++.+.  .|+ -.+|..|..+|.+.|+++.|+..++.+.
T Consensus       237 L~~Qa~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  237 LNLQAEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            666666777777788888887777776  344 4477778888888888888877777665

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.33  E-value=0.0002  Score=64.74  Aligned_cols=75  Identities=15%  Similarity=0.186  Sum_probs=33.1

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHH
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVD  229 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~  229 (403)
                      .+.....+|.+|+.+++.+......  ..-|..+..-|...|+++.|.++|-+.-         .++-.|..|.+.|+++
T Consensus       740 eaai~akew~kai~ildniqdqk~~--s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw~  808 (1636)
T KOG3616|consen  740 EAAIGAKEWKKAISILDNIQDQKTA--SGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKWE  808 (1636)
T ss_pred             HHHhhhhhhhhhHhHHHHhhhhccc--cccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccHH
Confidence            3344444555555555544443221  1234444445555555555555443221         1233344455555555


Q ss_pred             HHHHHH
Q 041804          230 FAMRVY  235 (403)
Q Consensus       230 ~a~~~~  235 (403)
                      .|.++-
T Consensus       809 da~kla  814 (1636)
T KOG3616|consen  809 DAFKLA  814 (1636)
T ss_pred             HHHHHH
Confidence            554443

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.30  E-value=1.4e-06  Score=46.90  Aligned_cols=33  Identities=39%  Similarity=0.776  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD  211 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  211 (403)
                      +|+.+|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            455555555555555555555555555555554

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.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.30  E-value=1.2e-06  Score=46.71  Aligned_cols=33  Identities=24%  Similarity=0.433  Sum_probs=19.1

Q ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC
Q 041804          248 VTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP  280 (403)
Q Consensus       248 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p  280 (403)
                      .+|+.++.+|++.|+++.|.++|++|.+.|+.|
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            355555666666666666666666655555554

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.24  E-value=0.00014  Score=54.24  Aligned_cols=128  Identities=12%  Similarity=0.047  Sum_probs=93.8

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC--cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh--hhHHHH
Q 041804          143 KIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK--DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV--VAYNTV  218 (403)
Q Consensus       143 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l  218 (403)
                      ..|..++..+ ..++...+...++.+.+....-  .....-.+...+...|++++|...|+........|+.  .....+
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            3455666665 4788899999999998875441  1233444567888999999999999999987533322  234456


Q ss_pred             HHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          219 IRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       219 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      ...+...|++++|+..++.....  ......+......|.+.|++++|...|+..
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~--~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDE--AFKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCc--chHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            77888999999999999774433  234556777889999999999999998763

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=98.18  E-value=5.5e-05  Score=51.35  Aligned_cols=77  Identities=22%  Similarity=0.319  Sum_probs=43.9

Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHcCC-CCChhhHHHHHHHHhhcC--------CHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 041804          183 YMDIMCKSGKPWKAVKLYKEMKKKGI-KMDVVAYNTVIRAVGVSE--------GVDFAMRVYREMREMGCQPSVVTCNTV  253 (403)
Q Consensus       183 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~~~l  253 (403)
                      .|..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        ++-..+.+|+.|...+++|+..+|+.+
T Consensus        31 ~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYniv  110 (120)
T PF08579_consen   31 NINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIV  110 (120)
T ss_pred             HHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHH
Confidence            34444444666666666666666666 566666666666554322        233455566666666666666666666


Q ss_pred             HHHHHh
Q 041804          254 IKLLCE  259 (403)
Q Consensus       254 i~~~~~  259 (403)
                      +..+.+
T Consensus       111 l~~Llk  116 (120)
T PF08579_consen  111 LGSLLK  116 (120)
T ss_pred             HHHHHH
Confidence            655543

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 [, , ].

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.18  E-value=7.2e-05  Score=64.95  Aligned_cols=122  Identities=12%  Similarity=0.089  Sum_probs=79.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHH
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHS  179 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  179 (403)
                      +......++..+....+.+.+..++.+......    ....-..+..++++.|.+.|..+.+..++..=...|+-||..+
T Consensus        65 S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~----~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s  140 (429)
T PF10037_consen   65 SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPN----CSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFS  140 (429)
T ss_pred             cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcc----cccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhh
Confidence            555666666776667777777777666655321    1111222335777777777777777777777777777777777


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc
Q 041804          180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS  225 (403)
Q Consensus       180 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  225 (403)
                      +|.||..+.+.|++..|.++...|...+...+..|+...+.+|.+.
T Consensus       141 ~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  141 FNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            7777777777777777777777776666555666665555555444

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 [].

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=98.17  E-value=0.00015  Score=55.79  Aligned_cols=93  Identities=10%  Similarity=-0.063  Sum_probs=67.6

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      ....+..+...+...|++++|...|++.......+++ ...+..+..++.+.|++++|+..+++..+..+.+...+..+.
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg  113 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIA  113 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHH
Confidence            3456777777888888888888888888764411222 356777888888888888888888888887766777777777


Q ss_pred             HHHHhcCCHHHHHH
Q 041804          109 DALCEYKHVIEAQE  122 (403)
Q Consensus       109 ~~~~~~~~~~~a~~  122 (403)
                      .++...|+...+..
T Consensus       114 ~~~~~~g~~~~a~~  127 (172)
T PRK02603        114 VIYHKRGEKAEEAG  127 (172)
T ss_pred             HHHHHcCChHhHhh
Confidence            77777776655443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=98.15  E-value=0.0018  Score=52.75  Aligned_cols=66  Identities=5%  Similarity=-0.026  Sum_probs=40.8

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHH-H---HHHHHHHHHhcCChHHHHHHHHHHhhcCCC
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHA-T---FRIMFKRYVTAHLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~   99 (403)
                      +..+-.....+...|++++|.+.|+.+....   |+.. +   .-.+..++.+.+++++|...|++..+..|.
T Consensus        32 ~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~y---P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~  101 (243)
T PRK10866         32 PSEIYATAQQKLQDGNWKQAITQLEALDNRY---PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT  101 (243)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC---CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcC
Confidence            3333344555566777777777777777654   3222 1   234556667777777777777777776665

>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=98.15  E-value=7e-05  Score=57.58  Aligned_cols=43  Identities=21%  Similarity=0.342  Sum_probs=23.6

Q ss_pred             HHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHH
Q 041804          263 VREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRM  305 (403)
Q Consensus       263 ~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~  305 (403)
                      -+-|++++++|...|+.||..++..++..+|+...+..-+.+|
T Consensus       119 q~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~p~~K~~rm  161 (228)
T PF06239_consen  119 QECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSHPMKKYRRM  161 (228)
T ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccHHHHHHHHH
Confidence            3445556666666666666666666666665555444444433

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=98.14  E-value=5.2e-05  Score=51.45  Aligned_cols=79  Identities=13%  Similarity=0.261  Sum_probs=67.9

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCC-CCcHHHHHHHHHHHHHcC--------ChhHHHHHHHHHHHcCCCCChhhHH
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKRGV-VKDLHSYSIYMDIMCKSG--------KPWKAVKLYKEMKKKGIKMDVVAYN  216 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~~  216 (403)
                      ...+..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        +.-..+.+|++|...+++|+..+|+
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            4455666677999999999999999999 999999999999988754        2346788999999999999999999


Q ss_pred             HHHHHHhh
Q 041804          217 TVIRAVGV  224 (403)
Q Consensus       217 ~ll~~~~~  224 (403)
                      .++..+.+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            99988754

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 [, , ].

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.13  E-value=6.5e-05  Score=65.22  Aligned_cols=121  Identities=12%  Similarity=0.018  Sum_probs=99.1

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           64 IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                      +.+......+++.+....+++.+..++.+.....-.   -+.+..++++.|.+.|..+.+..++..-...      |+-|
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~y------GiF~  136 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQY------GIFP  136 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhc------ccCC
Confidence            456667777888888888889999998888776432   5667789999999999999999998877776      8999


Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      |..++|.||..+.+.|++..|.++...|...+.-.+..|+..-+.+|.+-
T Consensus       137 D~~s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  137 DNFSFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             ChhhHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            99999999999999999999999998887777666777777766666655

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 [].

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=98.13  E-value=5e-05  Score=51.75  Aligned_cols=92  Identities=16%  Similarity=0.122  Sum_probs=47.6

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      +..+...+...|++++|..+++...+..  +.+...+..+..++...+++++|.+.|+......+.+..++..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD--PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHH
Confidence            3344455555555555555555555433  12234455555555555555555555555555544444455555555555


Q ss_pred             cCCHHHHHHHHhcc
Q 041804          114 YKHVIEAQELCFGE  127 (403)
Q Consensus       114 ~~~~~~a~~~~~~~  127 (403)
                      .|+.+.|...+...
T Consensus        81 ~~~~~~a~~~~~~~   94 (100)
T cd00189          81 LGKYEEALEAYEKA   94 (100)
T ss_pred             HHhHHHHHHHHHHH
Confidence            55555555554443

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.12  E-value=8.7e-05  Score=53.19  Aligned_cols=98  Identities=11%  Similarity=-0.027  Sum_probs=65.9

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHH
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP-NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNL  107 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l  107 (403)
                      .++..+...+.+.|++++|.+.|+.+.+..+..+ ....+..+..++...|+++.|...|+.+....+.   ...++..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            3455666777777788888887777766431111 1345666777777778888888888777765443   24566677


Q ss_pred             HHHHHhcCCHHHHHHHHhcccc
Q 041804          108 VDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      ..++...|+.++|...++++..
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~~~  104 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQVIK  104 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHHHH
Confidence            7777777777777777777665

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.

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=98.11  E-value=5.2e-05  Score=51.67  Aligned_cols=92  Identities=15%  Similarity=0.149  Sum_probs=75.4

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.+.+.  .+.+...+..+..++...+++++|.+.++......  +.+..++..+...+...|+
T Consensus         8 ~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~   83 (100)
T cd00189           8 NLYYKLGDYDEALEYYEKALEL--DPDNADAYYNLAAAYYKLGKYEEALEDYEKALELD--PDNAKAYYNLGLAYYKLGK   83 (100)
T ss_pred             HHHHHHhcHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC--CcchhHHHHHHHHHHHHHh
Confidence            3456689999999999998752  23445778888999999999999999999988865  3455688889999999999


Q ss_pred             hHHHHHHHHHHhhcCC
Q 041804           83 VNEAMGTFNKLDEFGL   98 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~   98 (403)
                      .+.|...+....+..+
T Consensus        84 ~~~a~~~~~~~~~~~~   99 (100)
T cd00189          84 YEEALEAYEKALELDP   99 (100)
T ss_pred             HHHHHHHHHHHHccCC
Confidence            9999999998876543

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=98.11  E-value=4.3e-06  Score=43.42  Aligned_cols=30  Identities=27%  Similarity=0.479  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 041804          351 AYNALVDALIDKGMLDMARKYDEEMFAKGL  380 (403)
Q Consensus       351 ~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~  380 (403)
                      +|+.++++|++.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            566666666666666666666666666553

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.

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.10  E-value=0.0086  Score=55.84  Aligned_cols=224  Identities=13%  Similarity=0.078  Sum_probs=156.9

Q ss_pred             HHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHH--HHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH
Q 041804           41 LGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFK--RYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI  118 (403)
Q Consensus        41 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  118 (403)
                      ....+++..|..-...+....   |+.... .++.  .+.+.|+.++|..+++.....+..|..+...+-.+|.+.++.+
T Consensus        19 ~ld~~qfkkal~~~~kllkk~---Pn~~~a-~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d   94 (932)
T KOG2053|consen   19 LLDSSQFKKALAKLGKLLKKH---PNALYA-KVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLD   94 (932)
T ss_pred             HhhhHHHHHHHHHHHHHHHHC---CCcHHH-HHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhh
Confidence            346688999999999988865   665432 3333  3468899999999999988877779999999999999999999


Q ss_pred             HHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc-CCh----
Q 041804          119 EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS-GKP----  193 (403)
Q Consensus       119 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~----  193 (403)
                      +|..++++....        -|+......+..+|.+.+++.+-.++--++-+.-++ +...+=.+++.+... ...    
T Consensus        95 ~~~~~Ye~~~~~--------~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~pk-~~yyfWsV~Slilqs~~~~~~~~  165 (932)
T KOG2053|consen   95 EAVHLYERANQK--------YPSEELLYHLFMAYVREKSYKKQQKAALQLYKNFPK-RAYYFWSVISLILQSIFSENELL  165 (932)
T ss_pred             HHHHHHHHHHhh--------CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCc-ccchHHHHHHHHHHhccCCcccc
Confidence            999999998864        456777888889999998887776666666554333 444444444444432 122    


Q ss_pred             -----hHHHHHHHHHHHcC-CCCChhhHHHHHHHHhhcCCHHHHHHHHH-HHHHcCCCCCHHHHHHHHHHHHhcCcHHHH
Q 041804          194 -----WKAVKLYKEMKKKG-IKMDVVAYNTVIRAVGVSEGVDFAMRVYR-EMREMGCQPSVVTCNTVIKLLCENGRVREA  266 (403)
Q Consensus       194 -----~~a~~~~~~~~~~~-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~-~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  266 (403)
                           .-|.+.++.+.+.+ ---+..-.......+...+++++|..++. ...+.-..-+...-+.-+..+...++|.+.
T Consensus       166 ~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l  245 (932)
T KOG2053|consen  166 DPILLALAEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQEL  245 (932)
T ss_pred             cchhHHHHHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHH
Confidence                 23455566666553 11122222333444557888999999994 444443344555556677888889999999


Q ss_pred             HHHHHhchhcC
Q 041804          267 YAVLAEMPKKG  277 (403)
Q Consensus       267 ~~~~~~~~~~~  277 (403)
                      .++-.++...|
T Consensus       246 ~~l~~~Ll~k~  256 (932)
T KOG2053|consen  246 FELSSRLLEKG  256 (932)
T ss_pred             HHHHHHHHHhC
Confidence            99999888774

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=98.10  E-value=9.3e-05  Score=61.75  Aligned_cols=133  Identities=9%  Similarity=0.013  Sum_probs=99.3

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh-cCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT-AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      .+|..++...-+.+..+.|..+|.+..+.+..  +...|-.....-.+ .++.+.|.++|+...+.-+.+...|...++.
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 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRC--TYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS---THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            46888889999999999999999999876522  33444444444233 5677779999999998876788999999999


Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCc-chHHHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMN-KTKIYNMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      +...++.+.|..+|++.....     .... ....|...+..=.+.|+.+.+.++.+++.+.
T Consensus        80 l~~~~d~~~aR~lfer~i~~l-----~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSL-----PKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTS-----SCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHhc-----CchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999988752     2222 3457888888888888888888888887765

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.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=98.08  E-value=6.2e-06  Score=54.87  Aligned_cols=80  Identities=6%  Similarity=0.085  Sum_probs=32.4

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMG   88 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~   88 (403)
                      |+++.|+.+|+.+.......++...+..+..++.+.|++++|..+++. ...+  +.+....-.+..++...|++++|++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~--~~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLD--PSNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHH--HCHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCC--CCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            445555555555443211111223333345555555555555555544 1111  1122222233444555555555555


Q ss_pred             HHH
Q 041804           89 TFN   91 (403)
Q Consensus        89 ~~~   91 (403)
                      .|+
T Consensus        80 ~l~   82 (84)
T PF12895_consen   80 ALE   82 (84)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            444

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.08  E-value=0.00017  Score=52.90  Aligned_cols=99  Identities=9%  Similarity=-0.048  Sum_probs=87.2

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      +......+...+...|++++|.++|+.+..-+  +-+..-|-.|..++-..|++.+|+..|......++.++..+..+..
T Consensus        34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~D--p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~  111 (157)
T PRK15363         34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIYD--AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAE  111 (157)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHH
Confidence            34456667778889999999999999999876  3567788899999999999999999999999999889999999999


Q ss_pred             HHHhcCCHHHHHHHHhccccc
Q 041804          110 ALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      ++...|+.+.|.+.|+.....
T Consensus       112 c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        112 CYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999998876654

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.06  E-value=0.0002  Score=51.32  Aligned_cols=58  Identities=12%  Similarity=-0.071  Sum_probs=27.1

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCc---HHHHHHHHHHHHhcCCHHHHHHHHhccc
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKD---EVSYCNLVDALCEYKHVIEAQELCFGEN  128 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~  128 (403)
                      ..+...+.+.|++++|.+.|..+....+.+   ...+..+..++.+.|+++.|...++.+.
T Consensus         6 ~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~   66 (119)
T TIGR02795         6 YDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVV   66 (119)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence            344444455555555555555554433321   2334444444445555555555444443

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.

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=98.04  E-value=0.00051  Score=52.71  Aligned_cols=102  Identities=6%  Similarity=-0.201  Sum_probs=55.9

Q ss_pred             HHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC-CHHHHHHHHHHHHhcCChHHHHHH
Q 041804           11 WKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP-NHATFRIMFKRYVTAHLVNEAMGT   89 (403)
Q Consensus        11 ~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~   89 (403)
                      +..+.+.+..+.+..+.......|..+...+...|++++|+..|++.......++ ...+|..+..++...|++++|+..
T Consensus        15 ~~~~~~~l~~~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~   94 (168)
T CHL00033         15 FTIVADILLRILPTTSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEY   94 (168)
T ss_pred             cccchhhhhHhccCCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHH
Confidence            3334444444432222222344556666666667777777777776655431111 123566666677777777777777


Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHH
Q 041804           90 FNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        90 ~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      +++.....+....++..+...+.
T Consensus        95 ~~~Al~~~~~~~~~~~~la~i~~  117 (168)
T CHL00033         95 YFQALERNPFLPQALNNMAVICH  117 (168)
T ss_pred             HHHHHHhCcCcHHHHHHHHHHHH
Confidence            77766655445555555555555

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.00  E-value=0.00055  Score=55.32  Aligned_cols=101  Identities=16%  Similarity=0.238  Sum_probs=79.6

Q ss_pred             HHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh
Q 041804           75 KRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK  154 (403)
Q Consensus        75 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  154 (403)
                      .-+.+.+++.+|+..|.+.++..+.|...|..-..+|++.|.++.|.+-.+....       -.+....+|..|-.+|..
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~-------iDp~yskay~RLG~A~~~  161 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALS-------IDPHYSKAYGRLGLAYLA  161 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHh-------cChHHHHHHHHHHHHHHc
Confidence            4456778899999999999998888999999999999999999988888777666       335566788888888888


Q ss_pred             cCChhHHHHHHHHHHhCCCCCcHHHHHHHH
Q 041804          155 MSWWGKCREFWEEMDKRGVVKDLHSYSIYM  184 (403)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  184 (403)
                      .|++++|.+.|++.++.  .|+..+|-.=+
T Consensus       162 ~gk~~~A~~aykKaLel--dP~Ne~~K~nL  189 (304)
T KOG0553|consen  162 LGKYEEAIEAYKKALEL--DPDNESYKSNL  189 (304)
T ss_pred             cCcHHHHHHHHHhhhcc--CCCcHHHHHHH
Confidence            88888888888888775  45554544433

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.99  E-value=1.4e-05  Score=53.20  Aligned_cols=82  Identities=13%  Similarity=0.060  Sum_probs=65.2

Q ss_pred             cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHH
Q 041804           44 FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQEL  123 (403)
Q Consensus        44 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  123 (403)
                      .|+++.|+.+++++.+..+..++...+..+..+|.+.|++++|+.+++. .+.++.+......+..++.+.|++++|++.
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPSNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHCHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            6899999999999999762112455666789999999999999999999 555555656666779999999999999999


Q ss_pred             Hhc
Q 041804          124 CFG  126 (403)
Q Consensus       124 ~~~  126 (403)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            875

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.99  E-value=8.1e-06  Score=42.35  Aligned_cols=29  Identities=38%  Similarity=0.650  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHhcCcHHHHHHHHHhchhcC
Q 041804          249 TCNTVIKLLCENGRVREAYAVLAEMPKKG  277 (403)
Q Consensus       249 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~  277 (403)
                      +|+.++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45666666666666666666666666554

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.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.97  E-value=0.0089  Score=51.44  Aligned_cols=384  Identities=10%  Similarity=0.068  Sum_probs=201.6

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCC---HH-hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHH--HH
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHT---TD-TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFK--RY   77 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~---~~-~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~--~~   77 (403)
                      +++.++++.+|.++|..+-.+....|.   .+ .-+.++++|. .++++.....+....+..   |. ..|-.+..  .+
T Consensus        15 ~Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAff-l~nld~Me~~l~~l~~~~---~~-s~~l~LF~~L~~   89 (549)
T PF07079_consen   15 ILQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFF-LNNLDLMEKQLMELRQQF---GK-SAYLPLFKALVA   89 (549)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHH-HhhHHHHHHHHHHHHHhc---CC-chHHHHHHHHHH
Confidence            466789999999999888753222222   12 2345556655 456777777777777754   32 23333333  33


Q ss_pred             HhcCChHHHHHHHHHHhhc--C--CC--cHHH---------HHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcch
Q 041804           78 VTAHLVNEAMGTFNKLDEF--G--LK--DEVS---------YCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKT  142 (403)
Q Consensus        78 ~~~~~~~~a~~~~~~~~~~--~--~~--~~~~---------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  142 (403)
                      -+.+++++|++.+......  +  ++  +...         =+..+.++...|.+.++..+++++....-..  ...-+.
T Consensus        90 Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkr--E~~w~~  167 (549)
T PF07079_consen   90 YKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKR--ECEWNS  167 (549)
T ss_pred             HHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhh--hhcccH
Confidence            5788999999988776654  2  11  2222         2345677788999999999998887642100  223577


Q ss_pred             HHHHHHHHHHHhcC--------C-------hhHHHHHHHHHHhC------CCCCcHHHHHHHHHHHHHc--CChhHHHHH
Q 041804          143 KIYNMILRGWFKMS--------W-------WGKCREFWEEMDKR------GVVKDLHSYSIYMDIMCKS--GKPWKAVKL  199 (403)
Q Consensus       143 ~~~~~l~~~~~~~~--------~-------~~~a~~~~~~~~~~------~~~~~~~~~~~l~~~~~~~--~~~~~a~~~  199 (403)
                      .+|+.++-.++++=        .       ++.+.-+..+|...      .+.|-......++....-.  .+..--.++
T Consensus       168 d~yd~~vlmlsrSYfLEl~e~~s~dl~pdyYemilfY~kki~~~d~~~Y~k~~peeeL~s~imqhlfi~p~e~l~~~mq~  247 (549)
T PF07079_consen  168 DMYDRAVLMLSRSYFLELKESMSSDLYPDYYEMILFYLKKIHAFDQRPYEKFIPEEELFSTIMQHLFIVPKERLPPLMQI  247 (549)
T ss_pred             HHHHHHHHHHhHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHhhchHHhhCcHHHHHHHHHHHHHhCCHhhccHHHHH
Confidence            88888665554431        1       22222222333221      2334444444444433322  122333444


Q ss_pred             HHHHHHcCCCCChh-hHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          200 YKEMKKKGIKMDVV-AYNTVIRAVGVSEGVDFAMRVYREMREMGCQP----SVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       200 ~~~~~~~~~~~~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      ++.....-+.|+.. +...+...+.+  +.+++..+-+.+....+.+    -..+|..++....+.++...|...+.-+.
T Consensus       248 l~~We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~lL~  325 (549)
T PF07079_consen  248 LENWENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYLALLK  325 (549)
T ss_pred             HHHHHhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            44444444555533 33334444433  4445544444443332111    13355556666666666666655554433


Q ss_pred             hcCCCC---------------------ChhhHHHH------------------------HHhh------CC-HHHHHHHH
Q 041804          275 KKGCVP---------------------DVITYHCF------------------------FRCL------EK-PREILGLF  302 (403)
Q Consensus       275 ~~~~~p---------------------~~~~~~~l------------------------~~~~------~~-~~~a~~~~  302 (403)
                      -.  .|                     |...++.+                        +...      |. -++|++++
T Consensus       326 ~l--dp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~DiDrqQLvh~L~~~Ak~lW~~g~~dekalnLL  403 (549)
T PF07079_consen  326 IL--DPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDIDRQQLVHYLVFGAKHLWEIGQCDEKALNLL  403 (549)
T ss_pred             hc--CCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHhcCCccHHHHHHH
Confidence            21  11                     11111100                        0000      11 12232222


Q ss_pred             HHH-----------------------------------------HHcCCCCch----hhHHHHHH--HHHhcCCcchHHH
Q 041804          303 DRM-----------------------------------------IESGIRPKM----DTYVMLLR--KFGRWGFLRPVFV  335 (403)
Q Consensus       303 ~~~-----------------------------------------~~~~~~~~~----~~~~~li~--~~~~~g~~~~a~~  335 (403)
                      +.+                                         .+.|+.|-.    ..-|.|..  .+...|++.++.-
T Consensus       404 k~il~ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEyLysqgey~kc~~  483 (549)
T PF07079_consen  404 KLILQFTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLADAEYLYSQGEYHKCYL  483 (549)
T ss_pred             HHHHHhccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHhcccHHHHHH
Confidence            222                                         233444322    22223332  2456677777776


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhhHHHHHHHhCCCCCC
Q 041804          336 VWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREELGTKLVQGGLDGE  400 (403)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~~~~~~~~~~~~  400 (403)
                      .-..+.+  +.|++.+|..+.-++....++++|..++..+.-..---|..+.-+..+++.-+..+
T Consensus       484 ys~WL~~--iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~LP~n~~~~dskvqKAl~lCqKh~~kd  546 (549)
T PF07079_consen  484 YSSWLTK--IAPSPQAYRLLGLCLMENKRYQEAWEYLQKLPPNERMRDSKVQKALALCQKHLPKD  546 (549)
T ss_pred             HHHHHHH--hCCcHHHHHHHHHHHHHHhhHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHhhhhh
Confidence            6555555  57999999999999999999999999998775533333444455555555544433

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.96  E-value=0.00032  Score=60.83  Aligned_cols=89  Identities=15%  Similarity=-0.024  Sum_probs=49.6

Q ss_pred             HHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH
Q 041804           39 DILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI  118 (403)
Q Consensus        39 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  118 (403)
                      ..+...|++++|+..|++..+..  +.+...|..+..+|...|++++|+..++++....+.+...|..+..+|...|+++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~--P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD--PNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCHH
Confidence            34445556666666666555543  2334455555555555666666666666655555555555555555555555555


Q ss_pred             HHHHHHhcccc
Q 041804          119 EAQELCFGENK  129 (403)
Q Consensus       119 ~a~~~~~~~~~  129 (403)
                      +|...|++...
T Consensus        88 eA~~~~~~al~   98 (356)
T PLN03088         88 TAKAALEKGAS   98 (356)
T ss_pred             HHHHHHHHHHH
Confidence            55555555443

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.96  E-value=0.00049  Score=57.49  Aligned_cols=131  Identities=11%  Similarity=0.030  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh-cCCHHHHHHHHhcccccccccccccCcchHHHH
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE-YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYN  146 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (403)
                      .+|-.+++..-+.+..+.|..+|.+..+.+..+..+|......-.. .++.+.|.++|+...+       ..+.+...|.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk-------~f~~~~~~~~   74 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCNKDPKRARKIFERGLK-------KFPSDPDFWL   74 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHH-------HHTT-HHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-------HCCCCHHHHH
Confidence            3566667777777777777777777765444355555544444223 4555557777777666       4456666677


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCc---HHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKRGVVKD---LHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..+..+.+.++.+.|..+|++.... +.++   ...|...+..-.+.|+.+.+.++.+++.+.
T Consensus        75 ~Y~~~l~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~  136 (280)
T PF05843_consen   75 EYLDFLIKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL  136 (280)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            7777777777777777777777654 2212   136677777666777777777777666664

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.

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.94  E-value=0.00079  Score=61.08  Aligned_cols=137  Identities=7%  Similarity=-0.077  Sum_probs=85.0

Q ss_pred             CCCCHHHHHHHHHHHHhcC-----ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC--------CHHHHHHHHhcccc
Q 041804           63 SIPNHATFRIMFKRYVTAH-----LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK--------HVIEAQELCFGENK  129 (403)
Q Consensus        63 ~~~~~~~~~~l~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--------~~~~a~~~~~~~~~  129 (403)
                      .+.+..+|...+++.....     +...|..+|++..+.++.....+..+..++....        +...+.+...+...
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            3567788888888765432     3679999999999999888777777655554321        12222222222111


Q ss_pred             cccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          130 NVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..     ..+.+..+|..+.-.+...|++++|...+++....+  |+...|..+...+...|++++|.+.|++....
T Consensus       413 l~-----~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L  482 (517)
T PRK10153        413 LP-----ELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL  482 (517)
T ss_pred             cc-----cCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            10     123334556666555555677777777777776664  45666777777777777777777777666654

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.92  E-value=0.0002  Score=62.09  Aligned_cols=102  Identities=8%  Similarity=-0.024  Sum_probs=85.9

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVN   84 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   84 (403)
                      +...|++++|++.|+.+...  .+.+...|..+..+|.+.|++++|+..+++.....  +.+...|..+..+|...|+++
T Consensus        12 a~~~~~~~~Ai~~~~~Al~~--~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~--P~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         12 AFVDDDFALAVDLYTQAIDL--DPNNAELYADRAQANIKLGNFTEAVADANKAIELD--PSLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHhCCHH
Confidence            34578999999999999852  34567889999999999999999999999999976  346778999999999999999


Q ss_pred             HHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           85 EAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      +|+..|++..+.++.+......+-.+
T Consensus        88 eA~~~~~~al~l~P~~~~~~~~l~~~  113 (356)
T PLN03088         88 TAKAALEKGASLAPGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            99999999999887776665555444

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.91  E-value=0.0061  Score=49.66  Aligned_cols=177  Identities=10%  Similarity=0.016  Sum_probs=97.3

Q ss_pred             HHHHHHcCChhHHHHHHHHHHHcCCCCChhhH---HHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh-
Q 041804          184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAY---NTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCE-  259 (403)
Q Consensus       184 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~-  259 (403)
                      ...+...|++++|.+.|+.+...-.. +....   -.+..++.+.++++.|...+++..+..+.....-+...+.+.+. 
T Consensus        39 A~~~~~~g~y~~Ai~~f~~l~~~yP~-s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~  117 (243)
T PRK10866         39 AQQKLQDGNWKQAITQLEALDNRYPF-GPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNM  117 (243)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhh
Confidence            33445566666666666666654211 11111   23445556666666676666666665333222233333333221 


Q ss_pred             -c---------------Cc---HHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHH
Q 041804          260 -N---------------GR---VREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVML  320 (403)
Q Consensus       260 -~---------------g~---~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (403)
                       .               .+   ..+|+..|+++.+.  -|+..-          ..+|...+..+...   .- ..--.+
T Consensus       118 ~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~--yP~S~y----------a~~A~~rl~~l~~~---la-~~e~~i  181 (243)
T PRK10866        118 ALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRG--YPNSQY----------TTDATKRLVFLKDR---LA-KYELSV  181 (243)
T ss_pred             hcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHH--CcCChh----------HHHHHHHHHHHHHH---HH-HHHHHH
Confidence             1               11   23444555555543  233211          22333322222211   00 111245


Q ss_pred             HHHHHhcCCcchHHHHHHHHHhc--CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          321 LRKFGRWGFLRPVFVVWKKMEEL--GCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       321 i~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      .+.|.+.|.+..|..-++.+.+.  +.+........++.+|.+.|..++|..+...+..
T Consensus       182 a~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~~  240 (243)
T PRK10866        182 AEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIAA  240 (243)
T ss_pred             HHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHhc
Confidence            67789999999999999999875  3344566777888999999999999988776643

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.88  E-value=0.00034  Score=51.35  Aligned_cols=97  Identities=9%  Similarity=-0.055  Sum_probs=75.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHH
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNM  147 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (403)
                      ...-.+...+...|++++|.++|+-+...++.+..-|-.|.-++-..|++++|...|.....       -.+.+...+..
T Consensus        36 ~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~-------L~~ddp~~~~~  108 (157)
T PRK15363         36 NTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQ-------IKIDAPQAPWA  108 (157)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-------cCCCCchHHHH
Confidence            34445566667788888888888888888877888888888888888888888888877766       33566777778


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhC
Q 041804          148 ILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       148 l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      +..++...|+.+.|.+.|+.....
T Consensus       109 ag~c~L~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        109 AAECYLACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            888888888888888888776654

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.84  E-value=0.005  Score=48.93  Aligned_cols=220  Identities=10%  Similarity=0.053  Sum_probs=111.8

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcH----------------HHHH-HHHHH--HHhcCCHHHHHHHHhccc
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE----------------VSYC-NLVDA--LCEYKHVIEAQELCFGEN  128 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----------------~~~~-~l~~~--~~~~~~~~~a~~~~~~~~  128 (403)
                      ..|..-+.++.+.+.+++|..-++...+.+.++-                ..|. .++.+  ....|...+.+.-+..+.
T Consensus        70 q~wT~r~~~l~kLR~~~~a~~EL~~f~~lD~pdl~Yey~p~iyp~rrGSmVPFsmR~lhAe~~~~lgnpqesLdRl~~L~  149 (366)
T KOG2796|consen   70 QLWTVRLALLVKLRLFQNAEMELEPFGNLDQPDLYYEYYPHVYPGRRGSMVPFSMRILHAELQQYLGNPQESLDRLHKLK  149 (366)
T ss_pred             HHHHHHHHHHHHHhhhHHHHhhhhhhccCCCcceeeeeccccCCCCcCccccHHHHHHHHHHHHhcCCcHHHHHHHHHHH
Confidence            3566667778888888888877776655443211                0011 11111  112444444333332222


Q ss_pred             ccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC
Q 041804          129 KNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI  208 (403)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  208 (403)
                      ..              ..-.++.+-.....+...+.|++-...       ..+.++.++.-.+.+.-...++.+.++...
T Consensus       150 ~~--------------V~~ii~~~e~~~~~ESsv~lW~KRl~~-------Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~  208 (366)
T KOG2796|consen  150 TV--------------VSKILANLEQGLAEESSIRLWRKRLGR-------VMYSMANCLLGMKEYVLSVDAYHSVIKYYP  208 (366)
T ss_pred             HH--------------HHHHHHHHHhccchhhHHHHHHHHHHH-------HHHHHHHHHhcchhhhhhHHHHHHHHHhCC
Confidence            11              111222222222234445555554332       445556666666666666777777766655


Q ss_pred             CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCC-----HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCC-CCCh
Q 041804          209 KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS-----VVTCNTVIKLLCENGRVREAYAVLAEMPKKGC-VPDV  282 (403)
Q Consensus       209 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~-~p~~  282 (403)
                      +.++.....|.+.-.+.||.+.|...|+...+..-..+     ..+.......|.-++++..|...+.++..... .|-.
T Consensus       209 e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a  288 (366)
T KOG2796|consen  209 EQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDPRNAVA  288 (366)
T ss_pred             cccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccCCCchhh
Confidence            55666666666666677777777777776554422222     22233333445556666677777766654321 1111


Q ss_pred             hhHHHHHHhh-CCHHHHHHHHHHHHHc
Q 041804          283 ITYHCFFRCL-EKPREILGLFDRMIES  308 (403)
Q Consensus       283 ~~~~~l~~~~-~~~~~a~~~~~~~~~~  308 (403)
                      ..-.+++..| ++..+|++.++.|...
T Consensus       289 ~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  289 NNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             hchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            1112333333 6667777777777664

>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=97.81  E-value=0.00052  Score=52.94  Aligned_cols=104  Identities=19%  Similarity=0.370  Sum_probs=68.3

Q ss_pred             CCChhhHHHHHHHHhh-----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChh
Q 041804          209 KMDVVAYNTVIRAVGV-----SEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVI  283 (403)
Q Consensus       209 ~~~~~~~~~ll~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~  283 (403)
                      .-|..+|..++..|.+     .|.++-....++.|.+.|+.-|..+|+.|++.+=+ |.+-               |.. 
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv---------------p~n-  106 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV---------------PRN-  106 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc---------------ccc-
Confidence            3466777777777653     35666677777777777777777777777766543 3221               111 


Q ss_pred             hHHHHHHhh-CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCC
Q 041804          284 TYHCFFRCL-EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGF  329 (403)
Q Consensus       284 ~~~~l~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  329 (403)
                      .+-++...+ .+.+-|++++++|...|+-||..++..+++.|++.+.
T Consensus       107 ~fQ~~F~hyp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  107 FFQAEFMHYPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHhccCcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            111122222 2345688999999999999999999999998887664

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.81  E-value=0.0047  Score=48.93  Aligned_cols=188  Identities=10%  Similarity=0.071  Sum_probs=93.9

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP-NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLV  108 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~  108 (403)
                      ...+-.....+...|++.+|...|+.+....+..| ...+.-.++.++.+.|+++.|...+++..+..|. ....+...+
T Consensus         5 ~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~   84 (203)
T PF13525_consen    5 AEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYM   84 (203)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHH
Confidence            34444556777788999999999998887642222 2345667788888889999999999998887766 222333333


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      .+.+.........    ......    .....-...+..++.-|=.+.-..+|...+..+.+.    =...--.+...|.
T Consensus        85 ~g~~~~~~~~~~~----~~~~D~----~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~----la~~e~~ia~~Y~  152 (203)
T PF13525_consen   85 LGLSYYKQIPGIL----RSDRDQ----TSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNR----LAEHELYIARFYY  152 (203)
T ss_dssp             HHHHHHHHHHHHH-----TT-------HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHH----HHHHHHHHHHHHH
T ss_pred             HHHHHHHhCccch----hcccCh----HHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            3332211111110    000000    000011122444444444455555555544444322    0111122455667


Q ss_pred             HcCChhHHHHHHHHHHHc--CCCCChhhHHHHHHHHhhcCCHHH
Q 041804          189 KSGKPWKAVKLYKEMKKK--GIKMDVVAYNTVIRAVGVSEGVDF  230 (403)
Q Consensus       189 ~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~ll~~~~~~~~~~~  230 (403)
                      +.|.+..|..-++.+++.  +.+........++.+|.+.|..+.
T Consensus       153 ~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~  196 (203)
T PF13525_consen  153 KRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQA  196 (203)
T ss_dssp             CTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHH
T ss_pred             HcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHH
Confidence            777777777777776665  111112244555566666666553

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.81  E-value=0.0016  Score=53.04  Aligned_cols=101  Identities=7%  Similarity=-0.000  Sum_probs=43.8

Q ss_pred             CcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcC---ChhHHHHHHHHHHHcCCCCChhhH
Q 041804          139 MNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSG---KPWKAVKLYKEMKKKGIKMDVVAY  215 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~  215 (403)
                      +.|...|-.|...|...|+.+.|..-|....+...+ +...+..+..++....   ...++.++|+++...+ +-|..+.
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 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGD-NPEILLGLAEALYYQAGQQMTAKARALLRQALALD-PANIRAL  230 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcC-CccHHHH
Confidence            334444444444444445544444444444443322 3333444433333222   1234444444444442 2233344


Q ss_pred             HHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          216 NTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       216 ~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ..|...+...|++.+|...++.|.+.
T Consensus       231 ~lLA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         231 SLLAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhc
Confidence            44444444455555555555554443

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.80  E-value=0.0069  Score=50.87  Aligned_cols=94  Identities=13%  Similarity=0.135  Sum_probs=41.4

Q ss_pred             HHHHHHHhc-CChhHHHHHHHHHHh----CCCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCC-----Chh-h
Q 041804          147 MILRGWFKM-SWWGKCREFWEEMDK----RGVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKM-----DVV-A  214 (403)
Q Consensus       147 ~l~~~~~~~-~~~~~a~~~~~~~~~----~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~-~  214 (403)
                      .+...|-.. |+++.|.+.|++..+    .+.. --...+..+...+.+.|++++|.++|++....-...     +.. .
T Consensus       119 ~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~  198 (282)
T PF14938_consen  119 ELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEY  198 (282)
T ss_dssp             HHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHH
Confidence            344444444 556666665555432    1100 012334455556666666666666666655432111     111 1


Q ss_pred             HHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          215 YNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       215 ~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      +-..+-++...||+..|.+.++....
T Consensus       199 ~l~a~l~~L~~~D~v~A~~~~~~~~~  224 (282)
T PF14938_consen  199 FLKAILCHLAMGDYVAARKALERYCS  224 (282)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHGT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            11222233445666666666665554

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.77  E-value=0.0077  Score=50.59  Aligned_cols=169  Identities=14%  Similarity=0.108  Sum_probs=96.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCC----C--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGL----K--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      |......|...|++++|.+.|.+..+...    +  -...|.....+|.+. ++++|...                    
T Consensus        38 y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~--------------------   96 (282)
T PF14938_consen   38 YEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIEC--------------------   96 (282)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHH--------------------
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHH--------------------
Confidence            34445566677777777777766543211    1  112233333333222 55555444                    


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc-CChhHHHHHHHHHHHc----CCCCC--hhhHH
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS-GKPWKAVKLYKEMKKK----GIKMD--VVAYN  216 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~----~~~~~--~~~~~  216 (403)
                       |...+..|...|++..|-+.+..+-               ..|... |++++|++.|++..+.    + .+.  ..++.
T Consensus        97 -~~~A~~~y~~~G~~~~aA~~~~~lA---------------~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~  159 (282)
T PF14938_consen   97 -YEKAIEIYREAGRFSQAAKCLKELA---------------EIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLL  159 (282)
T ss_dssp             -HHHHHHHHHHCT-HHHHHHHHHHHH---------------HHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred             -HHHHHHHHHhcCcHHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHH
Confidence             4445566777777777766655543               445555 7888888888886553    2 111  23556


Q ss_pred             HHHHHHhhcCCHHHHHHHHHHHHHcCCCC-----CHH-HHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          217 TVIRAVGVSEGVDFAMRVYREMREMGCQP-----SVV-TCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       217 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~-~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      .+...+.+.|++++|..+|+++.......     +.. .+-..+-++...||...|.+.|++....
T Consensus       160 ~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~  225 (282)
T PF14938_consen  160 KAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQ  225 (282)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTT
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            67778889999999999999887653221     221 2333444666788999999999887643

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.74  E-value=0.004  Score=47.93  Aligned_cols=90  Identities=13%  Similarity=-0.047  Sum_probs=64.8

Q ss_pred             cchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCc--HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHH
Q 041804          140 NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKD--LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNT  217 (403)
Q Consensus       140 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  217 (403)
                      .....+..+...+...|++++|...|++..+....++  ...+..+..++.+.|++++|...+++..+.. +-+...+..
T Consensus        33 ~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~  111 (172)
T PRK02603         33 KEAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELN-PKQPSALNN  111 (172)
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHH
Confidence            3455677788888888999999999988876544332  3577888888888999999999888888763 224555666


Q ss_pred             HHHHHhhcCCHHH
Q 041804          218 VIRAVGVSEGVDF  230 (403)
Q Consensus       218 ll~~~~~~~~~~~  230 (403)
                      +..++...|+...
T Consensus       112 lg~~~~~~g~~~~  124 (172)
T PRK02603        112 IAVIYHKRGEKAE  124 (172)
T ss_pred             HHHHHHHcCChHh
Confidence            6666666666433

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.74  E-value=0.0015  Score=50.15  Aligned_cols=82  Identities=11%  Similarity=-0.059  Sum_probs=49.1

Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC--cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHH
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK--DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTV  218 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  218 (403)
                      ....+..+...+...|++++|...|++.......|  ...++..+..++...|++++|++.++...... +....++..+
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~l  112 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNM  112 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHH
Confidence            34556666666777777777777777776543222  22466667777777777777777777766542 2223344444


Q ss_pred             HHHHh
Q 041804          219 IRAVG  223 (403)
Q Consensus       219 l~~~~  223 (403)
                      ...+.
T Consensus       113 a~i~~  117 (168)
T CHL00033        113 AVICH  117 (168)
T ss_pred             HHHHH
Confidence            44444

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.74  E-value=0.00024  Score=44.95  Aligned_cols=51  Identities=18%  Similarity=-0.000  Sum_probs=32.3

Q ss_pred             hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           79 TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        79 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      ..|++++|+++|+++....+.+..++..+..+|.+.|++++|..+++++..
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~   53 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLK   53 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred             hccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            456666666666666666655666666666666666666666666666655

...

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.73  E-value=0.003  Score=51.26  Aligned_cols=88  Identities=13%  Similarity=-0.048  Sum_probs=79.6

Q ss_pred             HHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHH
Q 041804           40 ILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIE  119 (403)
Q Consensus        40 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  119 (403)
                      -+.+.+++++|+..|.+..+..  +.|.+.|..-..+|.+.|.++.|++-.+.....++....+|..|..+|...|++++
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 KLMKNKDYQEAVDKYTEAIELD--PTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHH
Confidence            4567889999999999999975  46778888899999999999999999999999988899999999999999999999


Q ss_pred             HHHHHhcccc
Q 041804          120 AQELCFGENK  129 (403)
Q Consensus       120 a~~~~~~~~~  129 (403)
                      |...|++...
T Consensus       168 A~~aykKaLe  177 (304)
T KOG0553|consen  168 AIEAYKKALE  177 (304)
T ss_pred             HHHHHHhhhc
Confidence            9999988775

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.73  E-value=0.00023  Score=44.50  Aligned_cols=59  Identities=10%  Similarity=0.075  Sum_probs=34.4

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL   98 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   98 (403)
                      ...+.+.|++++|...|+.+.+..  +-+...+..+..++...|++++|...|+++.+..+
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P   62 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD--PDNPEAWYLLGRILYQQGRYDEALAYYERALELDP   62 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS--TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence            445556666666666666666654  22445566666666666666666666666655444

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.70  E-value=0.00019  Score=45.43  Aligned_cols=53  Identities=13%  Similarity=0.132  Sum_probs=30.6

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCC
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP   61 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~   61 (403)
                      .+|++++|++.|+.+...  .+.+..++..+..+|.+.|++++|..+++++....
T Consensus         3 ~~~~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~   55 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQD   55 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGG
T ss_pred             hccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            356666666666665532  23355555566666666666666666666666643

...

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.66  E-value=0.00042  Score=43.32  Aligned_cols=58  Identities=12%  Similarity=0.201  Sum_probs=43.1

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          148 ILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       148 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      +...+.+.|++++|.+.|+++.+..+. +...+..+..++...|++++|...|+++.+.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPD-NPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTT-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            345677778888888888888777655 7777777777888888888888888877665

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.64  E-value=0.0052  Score=46.12  Aligned_cols=157  Identities=11%  Similarity=0.008  Sum_probs=101.2

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcC
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYK  115 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~  115 (403)
                      +.....+.=+++...+-..+-...   -|+....-.|..+....|+..+|...|.+...--.. |......+.++....+
T Consensus        62 ~~~a~~q~ldP~R~~Rea~~~~~~---ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~  138 (251)
T COG4700          62 LLMALQQKLDPERHLREATEELAI---APTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQ  138 (251)
T ss_pred             HHHHHHHhcChhHHHHHHHHHHhh---chhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhc
Confidence            344444444444443333333332   366666677888888888888888888887764444 8888888888888888


Q ss_pred             CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhH
Q 041804          116 HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWK  195 (403)
Q Consensus       116 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  195 (403)
                      ++..+...++++.+...   .+..|+  ..-.+.+.+...|.+.+|+..|+.....-..|....|  ....+.+.|+.++
T Consensus       139 ~~A~a~~tLe~l~e~~p---a~r~pd--~~Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~ar~~--Y~e~La~qgr~~e  211 (251)
T COG4700         139 EFAAAQQTLEDLMEYNP---AFRSPD--GHLLFARTLAAQGKYADAESAFEVAISYYPGPQARIY--YAEMLAKQGRLRE  211 (251)
T ss_pred             cHHHHHHHHHHHhhcCC---ccCCCC--chHHHHHHHHhcCCchhHHHHHHHHHHhCCCHHHHHH--HHHHHHHhcchhH
Confidence            88888888887765431   122333  3455667788888888888888888887444433333  3344566776665


Q ss_pred             HHHHHHHH
Q 041804          196 AVKLYKEM  203 (403)
Q Consensus       196 a~~~~~~~  203 (403)
                      +..-+..+
T Consensus       212 a~aq~~~v  219 (251)
T COG4700         212 ANAQYVAV  219 (251)
T ss_pred             HHHHHHHH
Confidence            55444443

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.62  E-value=0.0087  Score=47.65  Aligned_cols=134  Identities=9%  Similarity=-0.024  Sum_probs=76.6

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      +.++.++.-.|.+.-...+++++.+..++ ++.....|++.-.+.|+.+.|...|++..+..+.-+ +..-+..+.....
T Consensus       181 y~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~-~~q~~~~V~~n~a  259 (366)
T KOG2796|consen  181 YSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLD-GLQGKIMVLMNSA  259 (366)
T ss_pred             HHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhh-ccchhHHHHhhhh
Confidence            34555555566666677777777776655 777777777777777777777777665443210000 1122222223333


Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..|.-.+++..|...+.++...+.. |+...|.-.-+..-.|+..+|++.++.|...
T Consensus       260 ~i~lg~nn~a~a~r~~~~i~~~D~~-~~~a~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  260 FLHLGQNNFAEAHRFFTEILRMDPR-NAVANNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             hheecccchHHHHHHHhhccccCCC-chhhhchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4445556666666666666665544 5555555444555566666676666666665

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.60  E-value=0.036  Score=50.56  Aligned_cols=59  Identities=12%  Similarity=0.065  Sum_probs=32.5

Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhc-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 041804          317 YVMLLRKFGRWGFLRPVFVVWKKMEEL-GCSPDEFAYNALVDALIDKGMLDMARKYDEEM  375 (403)
Q Consensus       317 ~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  375 (403)
                      |-+|.+--...|.++.|.+.--.+.+. .+-|....|..+.-+-+....+.-.-+.|-++
T Consensus      1024 FmilAQrql~eg~v~~Al~Tal~L~DYEd~lpP~eiySllALaaca~raFGtCSKAfmkL 1083 (1189)
T KOG2041|consen 1024 FMILAQRQLFEGRVKDALQTALILSDYEDFLPPAEIYSLLALAACAVRAFGTCSKAFMKL 1083 (1189)
T ss_pred             HHHHHHHHHHhchHHHHHHHHhhhccHhhcCCHHHHHHHHHHHHhhhhhhhhhHHHHHHH
Confidence            344444455667777777765555432 45577777877665544444444333333333

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.59  E-value=0.00035  Score=44.29  Aligned_cols=64  Identities=11%  Similarity=0.114  Sum_probs=36.1

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC-ChHHHHHHHHHHhhc
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH-LVNEAMGTFNKLDEF   96 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~   96 (403)
                      +.+|..+...+...|++++|+..|++..+..  +.+...|..+..++...| ++++|++.+++..+.
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~--p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD--PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS--TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            4455555566666666666666666655543  234445555556666665 466666666555543

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.58  E-value=0.021  Score=48.66  Aligned_cols=50  Identities=12%  Similarity=0.091  Sum_probs=32.2

Q ss_pred             HHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHH
Q 041804           75 KRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELC  124 (403)
Q Consensus        75 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  124 (403)
                      ..+.+..++..|+..+....+..+.+..-|..-...+...++++++..-.
T Consensus        57 n~~yk~k~Y~nal~~yt~Ai~~~pd~a~yy~nRAa~~m~~~~~~~a~~da  106 (486)
T KOG0550|consen   57 NAFYKQKTYGNALKNYTFAIDMCPDNASYYSNRAATLMMLGRFEEALGDA  106 (486)
T ss_pred             chHHHHhhHHHHHHHHHHHHHhCccchhhhchhHHHHHHHHhHhhcccch
Confidence            44555666777777777777777666666666666666666666655443

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.58  E-value=0.0078  Score=54.81  Aligned_cols=136  Identities=10%  Similarity=-0.064  Sum_probs=80.3

Q ss_pred             cCcchHHHHHHHHHHHhc-----CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCC--------hhHHHHHHHHHH
Q 041804          138 EMNKTKIYNMILRGWFKM-----SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK--------PWKAVKLYKEMK  204 (403)
Q Consensus       138 ~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------~~~a~~~~~~~~  204 (403)
                      .+.+...|...+++....     ++...|..+|++..+..+. ....|..+..++.....        ...+.+......
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~-~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~  411 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPD-FTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIV  411 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhh
Confidence            355667777777665432     2256777778877776544 44555554444433211        122222233222


Q ss_pred             Hc-CCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          205 KK-GIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       205 ~~-~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      .. ....+...+..+.-.....|++++|...++++.+.+  |+...|..+...+...|+.++|.+.+++....
T Consensus       412 al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L  482 (517)
T PRK10153        412 ALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL  482 (517)
T ss_pred             hcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            21 123344556655555556677888888888777753  56677777777777788888888777776654

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.57  E-value=0.012  Score=41.77  Aligned_cols=106  Identities=9%  Similarity=-0.023  Sum_probs=63.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCc--HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC----hhhHHHHHH
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKRGVVKD--LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD----VVAYNTVIR  220 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~ll~  220 (403)
                      .+..++-..|+.++|+.+|++....|...+  ...+-.+.+.+...|++++|..++++....-  |+    ......+..
T Consensus         6 ~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al   83 (120)
T PF12688_consen    6 ELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLAL   83 (120)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHH
Confidence            344556667777778877777777765533  3455566667777777777777777776551  22    122222334


Q ss_pred             HHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 041804          221 AVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLC  258 (403)
Q Consensus       221 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  258 (403)
                      ++...|+.++|...+-.....    +...|.--|..|.
T Consensus        84 ~L~~~gr~~eAl~~~l~~la~----~~~~y~ra~~~ya  117 (120)
T PF12688_consen   84 ALYNLGRPKEALEWLLEALAE----TLPRYRRAIRFYA  117 (120)
T ss_pred             HHHHCCCHHHHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence            555677777777776554432    3334554444443

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.57  E-value=0.0049  Score=50.26  Aligned_cols=126  Identities=9%  Similarity=0.007  Sum_probs=95.1

Q ss_pred             HHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC---ChhHH
Q 041804           85 EAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS---WWGKC  161 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a  161 (403)
                      ....-++.-...++.|...|-.|...|...|+...|...|.+..+       -.++|...+..+..++....   ...++
T Consensus       140 ~l~a~Le~~L~~nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~r-------L~g~n~~~~~g~aeaL~~~a~~~~ta~a  212 (287)
T COG4235         140 ALIARLETHLQQNPGDAEGWDLLGRAYMALGRASDALLAYRNALR-------LAGDNPEILLGLAEALYYQAGQQMTAKA  212 (287)
T ss_pred             HHHHHHHHHHHhCCCCchhHHHHHHHHHHhcchhHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhcCCcccHHH
Confidence            333444555666767999999999999999999999999988877       44666777777776665543   46788


Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHH
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIR  220 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  220 (403)
                      ..+|+++...+.. |+.+...|...+...|++.+|...|+.|.+.. + ....+..++.
T Consensus       213 ~~ll~~al~~D~~-~iral~lLA~~afe~g~~~~A~~~Wq~lL~~l-p-~~~~rr~~ie  268 (287)
T COG4235         213 RALLRQALALDPA-NIRALSLLAFAAFEQGDYAEAAAAWQMLLDLL-P-ADDPRRSLIE  268 (287)
T ss_pred             HHHHHHHHhcCCc-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC-C-CCCchHHHHH
Confidence            8999999988777 88888888888999999999999999999873 3 3334444444

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.57  E-value=0.007  Score=42.86  Aligned_cols=55  Identities=16%  Similarity=0.033  Sum_probs=27.9

Q ss_pred             HHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           75 KRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        75 ~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      .++-..|+.++|+.+|++....|+.   ....+..+...+...|++++|..++++...
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~   66 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALE   66 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3444455555555555555555544   123444445555555555555555554443

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.55  E-value=0.04  Score=46.70  Aligned_cols=300  Identities=14%  Similarity=0.099  Sum_probs=192.3

Q ss_pred             HHHHHHHHHHh--cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH--HhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           69 TFRIMFKRYVT--AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL--CEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        69 ~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      -|..|-.++..  .|+-..|.++-.+..+.=..|...+..++.+-  .-.|+.+.|.+-|+.|....       +....-
T Consensus        84 gyqALStGliAagAGda~lARkmt~~~~~llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~dP-------EtRllG  156 (531)
T COG3898          84 GYQALSTGLIAAGAGDASLARKMTARASKLLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDDP-------ETRLLG  156 (531)
T ss_pred             HHHHHhhhhhhhccCchHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcCh-------HHHHHh
Confidence            35566655554  46777777766655433223666666665543  45899999999999987641       111112


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC-CCCChh--hHHHHHHH
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG-IKMDVV--AYNTVIRA  221 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~--~~~~ll~~  221 (403)
                      ...|.-..-+.|+.+.|..+-+..-..-.. -...+...+...+..|+++.|+++++.-+... +.++..  .-..|+.+
T Consensus       157 LRgLyleAqr~GareaAr~yAe~Aa~~Ap~-l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtA  235 (531)
T COG3898         157 LRGLYLEAQRLGAREAARHYAERAAEKAPQ-LPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTA  235 (531)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHhhccC-CchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHH
Confidence            333444445778899999888887776555 45678889999999999999999998876552 333432  22233332


Q ss_pred             Hh---hcCCHHHHHHHHHHHHHcCCCCCHHHH-HHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHH
Q 041804          222 VG---VSEGVDFAMRVYREMREMGCQPSVVTC-NTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPRE  297 (403)
Q Consensus       222 ~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~  297 (403)
                      -.   -..+...|...-.+..+  +.|+..-- -.-..++.+.|+..++-.+++.+-+....|+  .+.....+-. .+.
T Consensus       236 kA~s~ldadp~~Ar~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~--ia~lY~~ar~-gdt  310 (531)
T COG3898         236 KAMSLLDADPASARDDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPD--IALLYVRARS-GDT  310 (531)
T ss_pred             HHHHHhcCChHHHHHHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChH--HHHHHHHhcC-CCc
Confidence            21   12345566665555554  35554332 2335788999999999999999988744444  4443333321 122


Q ss_pred             HHHHHHHHHH-cCCCC-chhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHH-hcCCHHHHHHHHHH
Q 041804          298 ILGLFDRMIE-SGIRP-KMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALI-DKGMLDMARKYDEE  374 (403)
Q Consensus       298 a~~~~~~~~~-~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~a~~~~~~  374 (403)
                      +..-+++... ..++| +..+...+..+-...|++..|..--+...+.  .|....|-.|.+.-. ..|+-.++..++-+
T Consensus       311 a~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~--~pres~~lLlAdIeeAetGDqg~vR~wlAq  388 (531)
T COG3898         311 ALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAARE--APRESAYLLLADIEEAETGDQGKVRQWLAQ  388 (531)
T ss_pred             HHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhhh--CchhhHHHHHHHHHhhccCchHHHHHHHHH
Confidence            2222222221 12334 4466677788888999999998877777664  688889988887654 45999999999998


Q ss_pred             HHHcCCCCC
Q 041804          375 MFAKGLSAK  383 (403)
Q Consensus       375 m~~~~~~p~  383 (403)
                      .++.--.|.
T Consensus       389 av~APrdPa  397 (531)
T COG3898         389 AVKAPRDPA  397 (531)
T ss_pred             HhcCCCCCc
Confidence            887655554

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.52  E-value=0.00045  Score=43.82  Aligned_cols=64  Identities=23%  Similarity=0.122  Sum_probs=58.6

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC-CHHHHHHHHhcccc
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK-HVIEAQELCFGENK  129 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~  129 (403)
                      +..+|..+...+...|++++|+..|++..+.++.+...|..+..++...| ++++|.+.+++..+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999889999999999999999 79999999887654

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.44  E-value=0.061  Score=45.98  Aligned_cols=265  Identities=11%  Similarity=-0.003  Sum_probs=163.2

Q ss_pred             HHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC
Q 041804           36 SVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK  115 (403)
Q Consensus        36 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  115 (403)
                      .....+.+..++..|++.+....+..  +.+...|..-...+...+++++|+--.+.-.+.....+......-+++...+
T Consensus        54 ~~gn~~yk~k~Y~nal~~yt~Ai~~~--pd~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd~~~k~~~r~~~c~~a~~  131 (486)
T KOG0550|consen   54 EEGNAFYKQKTYGNALKNYTFAIDMC--PDNASYYSNRAATLMMLGRFEEALGDARQSVRLKDGFSKGQLREGQCHLALS  131 (486)
T ss_pred             hhcchHHHHhhHHHHHHHHHHHHHhC--ccchhhhchhHHHHHHHHhHhhcccchhhheecCCCccccccchhhhhhhhH
Confidence            34445666778888888888888765  3455667777777778888888877776666655444555555555555555


Q ss_pred             CHHHHHHHHhccc---------cccccc-ccccCcchHHHHHHH-HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHH
Q 041804          116 HVIEAQELCFGEN---------KNVGFS-GLVEMNKTKIYNMIL-RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYM  184 (403)
Q Consensus       116 ~~~~a~~~~~~~~---------~~~~~~-~~~~~~~~~~~~~l~-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  184 (403)
                      +..+|...++.-.         ...... ....+|....+..+- .++...|++++|..+--...+.+.. +......-.
T Consensus       132 ~~i~A~~~~~~~~~~~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld~~-n~~al~vrg  210 (486)
T KOG0550|consen  132 DLIEAEEKLKSKQAYKAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLDAT-NAEALYVRG  210 (486)
T ss_pred             HHHHHHHHhhhhhhhHHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhcccc-hhHHHHhcc
Confidence            5555554443211         000000 001223334443332 4556678899998887777766433 333333333


Q ss_pred             HHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHH-------------HHHHhhcCCHHHHHHHHHHHHHc---CCCCCHH
Q 041804          185 DIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTV-------------IRAVGVSEGVDFAMRVYREMREM---GCQPSVV  248 (403)
Q Consensus       185 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-------------l~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~  248 (403)
                      .++....+.+.+...|++.+..  .|+...-..+             -.-..+.|++..|.+.|.+.+..   +..|+..
T Consensus       211 ~~~yy~~~~~ka~~hf~qal~l--dpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~nak  288 (486)
T KOG0550|consen  211 LCLYYNDNADKAINHFQQALRL--DPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAK  288 (486)
T ss_pred             cccccccchHHHHHHHhhhhcc--ChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHH
Confidence            4555677888898888888765  3444322221             12234688899999999888765   3445666


Q ss_pred             HHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH------hhCCHHHHHHHHHHHHHcC
Q 041804          249 TCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR------CLEKPREILGLFDRMIESG  309 (403)
Q Consensus       249 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~------~~~~~~~a~~~~~~~~~~~  309 (403)
                      .|........+.|+.++|+.--++..+-    |..-.-.++.      .++++++|.+-++...+..
T Consensus       289 lY~nra~v~~rLgrl~eaisdc~~Al~i----D~syikall~ra~c~l~le~~e~AV~d~~~a~q~~  351 (486)
T KOG0550|consen  289 LYGNRALVNIRLGRLREAISDCNEALKI----DSSYIKALLRRANCHLALEKWEEAVEDYEKAMQLE  351 (486)
T ss_pred             HHHHhHhhhcccCCchhhhhhhhhhhhc----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            6777777788889999998887776653    4444444433      2366788888877776543

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.41  E-value=0.032  Score=42.12  Aligned_cols=158  Identities=9%  Similarity=0.001  Sum_probs=109.7

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           73 MFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        73 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      +..+..+.=+++...+-..+-.+.- ++......|..+..+.|+..+|...|.+....      ....|....-.+.++.
T Consensus        62 ~~~a~~q~ldP~R~~Rea~~~~~~A-pTvqnr~rLa~al~elGr~~EA~~hy~qalsG------~fA~d~a~lLglA~Aq  134 (251)
T COG4700          62 LLMALQQKLDPERHLREATEELAIA-PTVQNRYRLANALAELGRYHEAVPHYQQALSG------IFAHDAAMLLGLAQAQ  134 (251)
T ss_pred             HHHHHHHhcChhHHHHHHHHHHhhc-hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhcc------ccCCCHHHHHHHHHHH
Confidence            3334444444444443333222221 24555667888899999999999999998875      5677888888899999


Q ss_pred             HhcCChhHHHHHHHHHHhCCCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHH
Q 041804          153 FKMSWWGKCREFWEEMDKRGVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFA  231 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a  231 (403)
                      ...+++..|...++.+-+.++. -++.+...+.+.+...|++.+|..-|+.....  -|+..........+.+.|+.+++
T Consensus       135 fa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea  212 (251)
T COG4700         135 FAIQEFAAAQQTLEDLMEYNPAFRSPDGHLLFARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREA  212 (251)
T ss_pred             HhhccHHHHHHHHHHHhhcCCccCCCCchHHHHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHH
Confidence            9999999999999998876421 12335567788999999999999999999887  45555444445556677776665


Q ss_pred             HHHHHHHH
Q 041804          232 MRVYREMR  239 (403)
Q Consensus       232 ~~~~~~~~  239 (403)
                      ..-+..+.
T Consensus       213 ~aq~~~v~  220 (251)
T COG4700         213 NAQYVAVV  220 (251)
T ss_pred             HHHHHHHH
Confidence            54444443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.40  E-value=0.043  Score=43.50  Aligned_cols=182  Identities=13%  Similarity=-0.035  Sum_probs=88.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYN  146 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (403)
                      +-.....+...|++.+|.+.|+.+....+.   ...+...++.++.+.|+++.|...+++.....     +..|.. .+.
T Consensus         8 lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~y-----P~~~~~-~~A   81 (203)
T PF13525_consen    8 LYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLY-----PNSPKA-DYA   81 (203)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH------TT-TTH-HHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-----CCCcch-hhH
Confidence            334455667788888888888888876554   45566677788888888888888888776643     111111 122


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCC---cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHh
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKRGVVK---DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVG  223 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  223 (403)
                      ..+.+.+.........     ....+...   -...+..++.-|=.+.-..+|...+..+...   .-. .--.+...|.
T Consensus        82 ~Y~~g~~~~~~~~~~~-----~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~---la~-~e~~ia~~Y~  152 (203)
T PF13525_consen   82 LYMLGLSYYKQIPGIL-----RSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNR---LAE-HELYIARFYY  152 (203)
T ss_dssp             HHHHHHHHHHHHHHHH------TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHH---HHH-HHHHHHHHHH
T ss_pred             HHHHHHHHHHhCccch-----hcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHH---HHH-HHHHHHHHHH
Confidence            2222221111111000     00000000   0112333333333334444454444444332   000 1122456677


Q ss_pred             hcCCHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHHhcCcHHHH
Q 041804          224 VSEGVDFAMRVYREMREMGCQ--PSVVTCNTVIKLLCENGRVREA  266 (403)
Q Consensus       224 ~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a  266 (403)
                      +.|.+..|..-++.+.+.-..  ......-.++.+|.+.|..+.+
T Consensus       153 ~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a  197 (203)
T PF13525_consen  153 KRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAA  197 (203)
T ss_dssp             CTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred             HcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHH
Confidence            788888888888877776211  1123445566777777776644

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.40  E-value=0.0032  Score=51.76  Aligned_cols=96  Identities=10%  Similarity=-0.006  Sum_probs=79.6

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHH
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH----ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSY  104 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~  104 (403)
                      ..|...+..+.+.|++++|...|+.+....   |+.    .++-.+..+|...|++++|...|+.+.+..+.   ...++
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~y---P~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl  220 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKKY---PDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAM  220 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHC---cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHH
Confidence            356666666677899999999999999865   543    57888999999999999999999999977655   56666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHhccccc
Q 041804          105 CNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus       105 ~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      ..+..++...|+.++|...++.+...
T Consensus       221 ~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        221 FKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            67778888999999999999988764

>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=97.35  E-value=0.0016  Score=48.54  Aligned_cols=72  Identities=21%  Similarity=0.186  Sum_probs=56.0

Q ss_pred             hHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCCChhhHH
Q 041804          316 TYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA-----KGLSAKPREEL  388 (403)
Q Consensus       316 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~~~~p~~~~~~  388 (403)
                      +...++..+...|++++|..+.+.+.... +-+...|..+|.+|...|+..+|.++|+++..     .|+.|++.+.-
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            56677788889999999999999998875 66889999999999999999999999998765     39999887654

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.29  E-value=0.0022  Score=54.31  Aligned_cols=268  Identities=10%  Similarity=0.072  Sum_probs=161.2

Q ss_pred             ccccccHHHHHHhhhhhcccCCC---cCCHHhHHHHHHHHHccCChhHHHHHHHHhhh----CCCCCCCHHHHHHHHHHH
Q 041804            5 SCYANDWKRALEFFNWVETDCHF---THTTDTYNSVIDILGKFFEFDLSWNLIHRMKD----NPSSIPNHATFRIMFKRY   77 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~~~~~~l~~~~   77 (403)
                      +++.|+...-+.+|+...+ -|.   +.-..+|..|..+|.-.+++++|+++...=..    .+...-...+...|.+.+
T Consensus        27 Lck~gdcraGv~ff~aA~q-vGTeDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLGNtl  105 (639)
T KOG1130|consen   27 LCKMGDCRAGVDFFKAALQ-VGTEDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLGNTL  105 (639)
T ss_pred             HHhccchhhhHHHHHHHHH-hcchHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccccccccchh
Confidence            4667899999999998885 332   22245677888888888899999887542110    010011222334555666


Q ss_pred             HhcCChHHHHHHHHHH----hhcCCC--cHHHHHHHHHHHHhcCC--------------------HHHHHHHHhcccccc
Q 041804           78 VTAHLVNEAMGTFNKL----DEFGLK--DEVSYCNLVDALCEYKH--------------------VIEAQELCFGENKNV  131 (403)
Q Consensus        78 ~~~~~~~~a~~~~~~~----~~~~~~--~~~~~~~l~~~~~~~~~--------------------~~~a~~~~~~~~~~~  131 (403)
                      --.|.+++|+-+-.+-    .+.|-.  ...++-.+...|...|.                    ++.|.+.|.+-.+..
T Consensus       106 Kv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~fy~eNL~l~  185 (639)
T KOG1130|consen  106 KVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVKFYMENLELS  185 (639)
T ss_pred             hhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHHHHHHHHHHH
Confidence            6677888876654432    333333  45566677777765543                    222333332211100


Q ss_pred             cccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHH----HhCCC-CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          132 GFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEM----DKRGV-VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       132 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ...+ .......+|..|.+.|.-.|+++.|+..-+.-    .+.|- ..-..++..+.+++.-.|+++.|.+.|+.....
T Consensus       186 ~~lg-Dr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~L  264 (639)
T KOG1130|consen  186 EKLG-DRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNL  264 (639)
T ss_pred             HHhh-hHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHH
Confidence            0000 00111233555666666678899987765432    22221 123457788889999999999999998875432


Q ss_pred             ----CC-CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc-----CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          207 ----GI-KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM-----GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       207 ----~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                          |- ......+-+|...|.-..+++.|+.++..-...     ...-....+.+|..+|...|..++|+.+...-.
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                21 223345567788888888899998887754321     122356788889999999999999988776543

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.28  E-value=0.0067  Score=49.86  Aligned_cols=99  Identities=8%  Similarity=-0.082  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc---HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD---EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      .|......+.+.|++++|+..|+.+.+..+.+   +.++..+..+|...|++++|...|..+....+    ..+....++
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP----~s~~~~dAl  220 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYP----KSPKAADAM  220 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC----CCcchhHHH
Confidence            34444444445566666666666666655542   34555566666666666666666665554211    112223333


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      ..+...+...|+.++|.++|+.+.+.
T Consensus       221 ~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        221 FKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34444555555555555555555544

>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=97.27  E-value=0.0026  Score=47.49  Aligned_cols=57  Identities=11%  Similarity=0.231  Sum_probs=29.9

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEM  203 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  203 (403)
                      ..++..+...|+++.|.++.+.+....+- |...|..+|.+|...|+...|.+.|+.+
T Consensus        66 ~~l~~~~~~~~~~~~a~~~~~~~l~~dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~  122 (146)
T PF03704_consen   66 ERLAEALLEAGDYEEALRLLQRALALDPY-DEEAYRLLMRALAAQGRRAEALRVYERY  122 (146)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHhccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            34444455555555555555555555444 5555555555555555555555555554

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.21  E-value=0.0029  Score=40.57  Aligned_cols=58  Identities=9%  Similarity=0.058  Sum_probs=30.8

Q ss_pred             HHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC
Q 041804           40 ILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        40 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~   99 (403)
                      +|.+.+++++|.++++.+...+  +.+...|.....++...|++++|.+.|+...+.++.
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~   61 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELD--PDDPELWLQRARCLFQLGRYEEALEDLERALELSPD   61 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC--cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCC
Confidence            4455555555555555555543  233444555555555555555555555555555443

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.14  E-value=0.0046  Score=39.58  Aligned_cols=56  Identities=9%  Similarity=-0.005  Sum_probs=38.4

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..|.+.+++++|.++++.+...++. +...|.....++...|++++|.+.|+...+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~   58 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPD-DPELWLQRARCLFQLGRYEEALEDLERALEL   58 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            4566667777777777777766555 6666666667777777777777777776655

>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=97.01  E-value=0.16  Score=42.56  Aligned_cols=16  Identities=13%  Similarity=-0.076  Sum_probs=11.1

Q ss_pred             HHhcCcHHHHHHHHHh
Q 041804          257 LCENGRVREAYAVLAE  272 (403)
Q Consensus       257 ~~~~g~~~~a~~~~~~  272 (403)
                      +.+.++++.|.+.|+-
T Consensus       256 ~~~~k~y~~A~~w~~~  271 (278)
T PF08631_consen  256 HYKAKNYDEAIEWYEL  271 (278)
T ss_pred             HHhhcCHHHHHHHHHH
Confidence            4467778888777764

It is also involved in sporulation [].

>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=96.99  E-value=0.015  Score=41.67  Aligned_cols=46  Identities=4%  Similarity=-0.025  Sum_probs=20.8

Q ss_pred             CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHH
Q 041804          209 KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM-GCQPSVVTCNTVI  254 (403)
Q Consensus       209 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~li  254 (403)
                      .|+..+..+++.+|+..+++..|.++++...+. +++.+..+|..|+
T Consensus        49 ~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll   95 (126)
T PF12921_consen   49 YPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLL   95 (126)
T ss_pred             CCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            344444444444444444444444444444332 3333344444444

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=96.97  E-value=0.03  Score=47.70  Aligned_cols=60  Identities=13%  Similarity=-0.001  Sum_probs=37.5

Q ss_pred             hHHHHHHHHhhcCCHHHHHHHHHHHH----HcCCC-CCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          214 AYNTVIRAVGVSEGVDFAMRVYREMR----EMGCQ-PSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       214 ~~~~ll~~~~~~~~~~~a~~~~~~~~----~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      .|..|-..|.-.|+++.|....+.-.    +.|-. ..-..+..+..++.-.|+++.|.+.|+.-
T Consensus       197 a~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~t  261 (639)
T KOG1130|consen  197 AYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLT  261 (639)
T ss_pred             hhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHH
Confidence            45555556666778888877665432    22211 12345666777777788888888877653

>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=96.96  E-value=0.019  Score=41.13  Aligned_cols=86  Identities=9%  Similarity=0.062  Sum_probs=70.8

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhh--------------hCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMK--------------DNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDE   95 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~--------------~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   95 (403)
                      |..++..+|.++++.|+++....+++..-              ...+..|+..+..+++.+|+..|++..|+++.+...+
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSR   80 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            46788999999999999999999988642              2234578999999999999999999999999998866


Q ss_pred             c-CCC-cHHHHHHHHHHHHhcC
Q 041804           96 F-GLK-DEVSYCNLVDALCEYK  115 (403)
Q Consensus        96 ~-~~~-~~~~~~~l~~~~~~~~  115 (403)
                      . +++ +..+|..|+.-+...-
T Consensus        81 ~Y~I~i~~~~W~~Ll~W~~v~s  102 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLEWAYVLS  102 (126)
T ss_pred             HcCCCCCHHHHHHHHHHHHHhc
Confidence            4 455 8899999988765443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.95  E-value=0.0023  Score=41.71  Aligned_cols=68  Identities=13%  Similarity=0.126  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc-chHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 041804          102 VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN-KTKIYNMILRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       102 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      .+++.+..+|...|++++|+..+++........+ ...| ...+++.+...|...|++++|++.+++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~-~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLG-DDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4566666666667777766666655543211111 1122 255677788888888888888888877653

...

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=96.94  E-value=0.05  Score=38.49  Aligned_cols=139  Identities=12%  Similarity=0.094  Sum_probs=84.0

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHH
Q 041804          224 VSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFD  303 (403)
Q Consensus       224 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~  303 (403)
                      ..|.+++..++..+....   .+..-+|.+|--....-+-+-..++++.+-.-   -|       +..|++.......+-
T Consensus        14 ldG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGki---FD-------is~C~NlKrVi~C~~   80 (161)
T PF09205_consen   14 LDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGKI---FD-------ISKCGNLKRVIECYA   80 (161)
T ss_dssp             HTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGG---S--------GGG-S-THHHHHHHH
T ss_pred             HhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhhh---cC-------chhhcchHHHHHHHH
Confidence            457777777777777764   35556666665555444444444554443321   12       122344444333332


Q ss_pred             HHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 041804          304 RMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLS  381 (403)
Q Consensus       304 ~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~  381 (403)
                      .+     ..+...+...+......|+-+.-.+++..+.+.+ .+++...-.+..||.+.|+..++.+++.+.-++|++
T Consensus        81 ~~-----n~~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   81 KR-----NKLSEYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HT-----T---HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             Hh-----cchHHHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            22     2355667788888999999999999999987644 788999999999999999999999999999999874

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.89  E-value=0.004  Score=40.54  Aligned_cols=65  Identities=15%  Similarity=0.232  Sum_probs=41.6

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhC----CCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDN----PSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDE   95 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   95 (403)
                      ..+++.+..+|...|++++|++.|++..+.    +...|+ ..+++.+..++...|++++|++.+++..+
T Consensus         5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            346777777788888888888777766532    111122 34566777777777777777777776543

...

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.89  E-value=0.032  Score=49.70  Aligned_cols=158  Identities=13%  Similarity=0.074  Sum_probs=98.2

Q ss_pred             HHHHccCChhHHHHHHH--HhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC
Q 041804           39 DILGKFFEFDLSWNLIH--RMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH  116 (403)
Q Consensus        39 ~~~~~~~~~~~a~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  116 (403)
                      ....-.++++++.++.+  ++...   .| ....+.++..+-+.|..+.|+++..+        +.   .-.....+.|+
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~~---i~-~~~~~~i~~fL~~~G~~e~AL~~~~D--------~~---~rFeLAl~lg~  333 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLPN---IP-KDQGQSIARFLEKKGYPELALQFVTD--------PD---HRFELALQLGN  333 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGGG------HHHHHHHHHHHHHTT-HHHHHHHSS---------HH---HHHHHHHHCT-
T ss_pred             HHHHHcCChhhhhhhhhhhhhccc---CC-hhHHHHHHHHHHHCCCHHHHHhhcCC--------hH---HHhHHHHhcCC
Confidence            44455688888766665  22221   12 44577788888888888888876533        22   23344567788


Q ss_pred             HHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHH
Q 041804          117 VIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKA  196 (403)
Q Consensus       117 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  196 (403)
                      ++.|.++.++.            ++...|..|.....+.|+++-|++.|.+..         -|..|+-.|.-.|+.+.-
T Consensus       334 L~~A~~~a~~~------------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~---------d~~~L~lLy~~~g~~~~L  392 (443)
T PF04053_consen  334 LDIALEIAKEL------------DDPEKWKQLGDEALRQGNIELAEECYQKAK---------DFSGLLLLYSSTGDREKL  392 (443)
T ss_dssp             HHHHHHHCCCC------------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHH
T ss_pred             HHHHHHHHHhc------------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhc---------CccccHHHHHHhCCHHHH
Confidence            88888775432            355678888888888888888888888765         355666677778888877


Q ss_pred             HHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHH
Q 041804          197 VKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREM  238 (403)
Q Consensus       197 ~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  238 (403)
                      .++.+.....|-      ++....++...|+.++..+++...
T Consensus       393 ~kl~~~a~~~~~------~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  393 SKLAKIAEERGD------INIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             HHHHHHHHHTT-------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             HHHHHHHHHccC------HHHHHHHHHHcCCHHHHHHHHHHc
Confidence            777777776651      345555666678888877777654

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.

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.88  E-value=0.15  Score=46.34  Aligned_cols=263  Identities=15%  Similarity=0.130  Sum_probs=136.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .+.+-+..|...|.+++|.++-    -.|+ ...-|.-|.......=+++-|.+.+.+....                  
T Consensus       558 p~~~~m~q~Ieag~f~ea~~ia----clgV-v~~DW~~LA~~ALeAL~f~~ARkAY~rVRdl------------------  614 (1081)
T KOG1538|consen  558 PQSAPMYQYIERGLFKEAYQIA----CLGV-TDTDWRELAMEALEALDFETARKAYIRVRDL------------------  614 (1081)
T ss_pred             cccccchhhhhccchhhhhccc----ccce-ecchHHHHHHHHHhhhhhHHHHHHHHHHhcc------------------
Confidence            3444556677777777775431    1111 3333444444433444444444444333221                  


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC----CCChhhHHHHHHHHhh
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI----KMDVVAYNTVIRAVGV  224 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~ll~~~~~  224 (403)
                              .+-+...-++++.++|-.|+...   +...++-.|++.+|-++|.+--..+-    -.|...| -+.+-+..
T Consensus       615 --------~~L~li~EL~~~k~rge~P~~iL---lA~~~Ay~gKF~EAAklFk~~G~enRAlEmyTDlRMF-D~aQE~~~  682 (1081)
T KOG1538|consen  615 --------RYLELISELEERKKRGETPNDLL---LADVFAYQGKFHEAAKLFKRSGHENRALEMYTDLRMF-DYAQEFLG  682 (1081)
T ss_pred             --------HHHHHHHHHHHHHhcCCCchHHH---HHHHHHhhhhHHHHHHHHHHcCchhhHHHHHHHHHHH-HHHHHHhh
Confidence                    12233444567778887777643   34456667777777777754221100    0011111 12333444


Q ss_pred             cCCHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHh------chhcCCCCC---hhhHHHH---HH
Q 041804          225 SEGVDFAMRVYREMREM--GCQPSVVTCNTVIKLLCENGRVREAYAVLAE------MPKKGCVPD---VITYHCF---FR  290 (403)
Q Consensus       225 ~~~~~~a~~~~~~~~~~--~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~------~~~~~~~p~---~~~~~~l---~~  290 (403)
                      .|+.++-..+.++-.+.  .++-.    .+....+..+|+..+|..+..+      +.+-+.+.|   ..+...+   +.
T Consensus       683 ~g~~~eKKmL~RKRA~WAr~~keP----kaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk  758 (1081)
T KOG1538|consen  683 SGDPKEKKMLIRKRADWARNIKEP----KAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLK  758 (1081)
T ss_pred             cCChHHHHHHHHHHHHHhhhcCCc----HHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHh
Confidence            45544444444332222  11111    1233445567777777765432      111111222   2222222   22


Q ss_pred             hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHH-----------HHHHHHHHH
Q 041804          291 CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEF-----------AYNALVDAL  359 (403)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-----------~~~~l~~~~  359 (403)
                      ....+.-|-++|.+|-+         ...++......+++++|..+-++..+.  .||..           -|.-.-.+|
T Consensus       759 ~l~~~gLAaeIF~k~gD---------~ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwLAE~DrFeEAqkAf  827 (1081)
T KOG1538|consen  759 KLDSPGLAAEIFLKMGD---------LKSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWLAENDRFEEAQKAF  827 (1081)
T ss_pred             hccccchHHHHHHHhcc---------HHHHhhheeecccchHhHhhhhhCccc--cccccchHHHHhhhhhhHHHHHHHH
Confidence            22334556677776643         235677888899999999988877653  33322           344556789


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCC
Q 041804          360 IDKGMLDMARKYDEEMFAKGLS  381 (403)
Q Consensus       360 ~~~g~~~~a~~~~~~m~~~~~~  381 (403)
                      .++|+..+|.++++++....+.
T Consensus       828 hkAGr~~EA~~vLeQLtnnav~  849 (1081)
T KOG1538|consen  828 HKAGRQREAVQVLEQLTNNAVA  849 (1081)
T ss_pred             HHhcchHHHHHHHHHhhhhhhh
Confidence            9999999999999998876543

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.82  E-value=0.4  Score=44.20  Aligned_cols=206  Identities=10%  Similarity=0.034  Sum_probs=107.0

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHH----------HHHHhcCChHHHHHHHHHHhhcC
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMF----------KRYVTAHLVNEAMGTFNKLDEFG   97 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~----------~~~~~~~~~~~a~~~~~~~~~~~   97 (403)
                      .|.+..|..+.......-.++.|...|-+...-    |.......|-          ..-+--|.+++|+++|-++.+++
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY----~Gik~vkrl~~i~s~~~q~aei~~~~g~feeaek~yld~drrD  764 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDY----AGIKLVKRLRTIHSKEQQRAEISAFYGEFEEAEKLYLDADRRD  764 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccc----cchhHHHHhhhhhhHHHHhHhHhhhhcchhHhhhhhhccchhh
Confidence            466677777766666666666666666554432    2221111111          11122367777777776665533


Q ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH
Q 041804           98 LKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL  177 (403)
Q Consensus        98 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  177 (403)
                              ..+..+.+.|++-...++++.--...     ....-..+|+.+...+.....|++|.+.+..-..      .
T Consensus       765 --------LAielr~klgDwfrV~qL~r~g~~d~-----dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~------~  825 (1189)
T KOG2041|consen  765 --------LAIELRKKLGDWFRVYQLIRNGGSDD-----DDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD------T  825 (1189)
T ss_pred             --------hhHHHHHhhhhHHHHHHHHHccCCCc-----chHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc------h
Confidence                    23444555666666666554322111     2222344566666666666666666666654321      1


Q ss_pred             HHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 041804          178 HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLL  257 (403)
Q Consensus       178 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  257 (403)
                         ...+.++.+..++++-..+-+.     ++-+....-.+..++.+.|.-++|.+.|-+...    |     -+.+.+|
T Consensus       826 ---e~~~ecly~le~f~~LE~la~~-----Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~----p-----kaAv~tC  888 (1189)
T KOG2041|consen  826 ---ENQIECLYRLELFGELEVLART-----LPEDSELLPVMADMFTSVGMCDQAVEAYLRRSL----P-----KAAVHTC  888 (1189)
T ss_pred             ---HhHHHHHHHHHhhhhHHHHHHh-----cCcccchHHHHHHHHHhhchHHHHHHHHHhccC----c-----HHHHHHH
Confidence               1234455555444444333332     233444555666677777777766665533211    1     1345566


Q ss_pred             HhcCcHHHHHHHHHhc
Q 041804          258 CENGRVREAYAVLAEM  273 (403)
Q Consensus       258 ~~~g~~~~a~~~~~~~  273 (403)
                      ...++|.+|.++-++.
T Consensus       889 v~LnQW~~avelaq~~  904 (1189)
T KOG2041|consen  889 VELNQWGEAVELAQRF  904 (1189)
T ss_pred             HHHHHHHHHHHHHHhc
Confidence            6666777776666554

>PRK15331 chaperone protein SicA; Provisional

Probab=96.80  E-value=0.021  Score=42.45  Aligned_cols=95  Identities=6%  Similarity=-0.186  Sum_probs=81.1

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      ......-+-..|++++|..+|.-+.-.+  +-+..-|..|..++-..+++++|+..|...-..+..|+..+-....++..
T Consensus        40 iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d--~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~  117 (165)
T PRK15331         40 LYAHAYEFYNQGRLDEAETFFRFLCIYD--FYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLL  117 (165)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHH
Confidence            3344556678999999999999988866  35666788888899999999999999999988887788889999999999


Q ss_pred             cCCHHHHHHHHhccccc
Q 041804          114 YKHVIEAQELCFGENKN  130 (403)
Q Consensus       114 ~~~~~~a~~~~~~~~~~  130 (403)
                      .|+.+.|...|......
T Consensus       118 l~~~~~A~~~f~~a~~~  134 (165)
T PRK15331        118 MRKAAKARQCFELVNER  134 (165)
T ss_pred             hCCHHHHHHHHHHHHhC
Confidence            99999999998877663

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=96.74  E-value=0.32  Score=41.97  Aligned_cols=80  Identities=9%  Similarity=-0.073  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcC---CCCChhhHHHHHHHHhh---cCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKG---IKMDVVAYNTVIRAVGV---SEGVDFAMRVYREMREMGCQPSVVTCNT  252 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~  252 (403)
                      +...++-+|....+++..+++++.+....   +.-...+-....-++.+   .|+.+.|++++..+....-.+++.+|..
T Consensus       143 iv~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL  222 (374)
T PF13281_consen  143 IVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGL  222 (374)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHH
Confidence            33345556777778888888888877651   11122222334445556   7788888888887666556667777777


Q ss_pred             HHHHHH
Q 041804          253 VIKLLC  258 (403)
Q Consensus       253 li~~~~  258 (403)
                      +.+.|-
T Consensus       223 ~GRIyK  228 (374)
T PF13281_consen  223 LGRIYK  228 (374)
T ss_pred             HHHHHH
Confidence            666653

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.69  E-value=0.33  Score=41.44  Aligned_cols=284  Identities=12%  Similarity=0.071  Sum_probs=166.7

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHH--HHccCChhHHHHHHHHhhhCCCCCCCHHH--HHHHHHHHHh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDI--LGKFFEFDLSWNLIHRMKDNPSSIPNHAT--FRIMFKRYVT   79 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~   79 (403)
                      |..-.|+-..|.+.-....+  -+.-|..-.-.++.+  -.-.|+++.|.+-|+.|...    |....  ...|.-.--+
T Consensus        93 iAagAGda~lARkmt~~~~~--llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d----PEtRllGLRgLyleAqr  166 (531)
T COG3898          93 IAAGAGDASLARKMTARASK--LLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD----PETRLLGLRGLYLEAQR  166 (531)
T ss_pred             hhhccCchHHHHHHHHHHHh--hhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC----hHHHHHhHHHHHHHHHh
Confidence            34445777777776655442  123333334444433  34579999999999999874    44332  2334444457


Q ss_pred             cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH--HHHHHHHHHh---
Q 041804           80 AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI--YNMILRGWFK---  154 (403)
Q Consensus        80 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~---  154 (403)
                      .|..+.|.+.-+..-..-+.-...+..++...+..|+++.|+++++.-....     .+.++..-  -..|+.+-..   
T Consensus       167 ~GareaAr~yAe~Aa~~Ap~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~-----vie~~~aeR~rAvLLtAkA~s~l  241 (531)
T COG3898         167 LGAREAARHYAERAAEKAPQLPWAARATLEARCAAGDWDGALKLVDAQRAAK-----VIEKDVAERSRAVLLTAKAMSLL  241 (531)
T ss_pred             cccHHHHHHHHHHHHhhccCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHH-----hhchhhHHHHHHHHHHHHHHHHh
Confidence            8999999999998888777788899999999999999999999988755432     22333221  1222222111   


Q ss_pred             cCChhHHHHHHHHHHhCCCCCcHH-HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHH
Q 041804          155 MSWWGKCREFWEEMDKRGVVKDLH-SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMR  233 (403)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  233 (403)
                      ..+...|...-.+..+.  .||.. .-..-..++.+.|+..++-.+++.+-+....|+.  +  .+-.+.+.|+.  +..
T Consensus       242 dadp~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~i--a--~lY~~ar~gdt--a~d  313 (531)
T COG3898         242 DADPASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPDI--A--LLYVRARSGDT--ALD  313 (531)
T ss_pred             cCChHHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChHH--H--HHHHHhcCCCc--HHH
Confidence            12344444444444332  33332 2334456788888898888888888887544443  2  22223345543  333


Q ss_pred             HHHHHHHc-CCCC-CHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHh----hCCHHHHHHHHHHHHH
Q 041804          234 VYREMREM-GCQP-SVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRC----LEKPREILGLFDRMIE  307 (403)
Q Consensus       234 ~~~~~~~~-~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~----~~~~~~a~~~~~~~~~  307 (403)
                      -++...+. ..+| +..+.-.+..+-...|++..|..--+...+.  .|....|..|-..    -|+.+++..++-+...
T Consensus       314 RlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~--~pres~~lLlAdIeeAetGDqg~vR~wlAqav~  391 (531)
T COG3898         314 RLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAARE--APRESAYLLLADIEEAETGDQGKVRQWLAQAVK  391 (531)
T ss_pred             HHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhhh--CchhhHHHHHHHHHhhccCchHHHHHHHHHHhc
Confidence            33333221 1233 3455556667777788887777665555443  4555445444321    1556667666666665


Q ss_pred             c
Q 041804          308 S  308 (403)
Q Consensus       308 ~  308 (403)
                      .
T Consensus       392 A  392 (531)
T COG3898         392 A  392 (531)
T ss_pred             C
Confidence            4

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=96.65  E-value=0.38  Score=41.58  Aligned_cols=172  Identities=10%  Similarity=-0.054  Sum_probs=112.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh---cCChhHHHHHHHHHHhCCCCCc
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK---MSWWGKCREFWEEMDKRGVVKD  176 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~  176 (403)
                      +..+...++-+|....+++...++++.+......   .......+-....-++.+   .|+.++|.+++..+......++
T Consensus       140 s~div~~lllSyRdiqdydamI~Lve~l~~~p~~---~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~  216 (374)
T PF13281_consen  140 SPDIVINLLLSYRDIQDYDAMIKLVETLEALPTC---DVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPD  216 (374)
T ss_pred             ChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCcc---chhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCC
Confidence            6667778888899999999999999988764211   122233444455566666   8999999999999777667778


Q ss_pred             HHHHHHHHHHHHHc---------CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCC-H---HHHHHHH---HH-HH
Q 041804          177 LHSYSIYMDIMCKS---------GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG-V---DFAMRVY---RE-MR  239 (403)
Q Consensus       177 ~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~-~---~~a~~~~---~~-~~  239 (403)
                      ..+|..+...|-..         ...++|+..|.+.-+.  .||.++=-.++..+...|. .   .+..++-   .. +.
T Consensus       217 ~d~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~--~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg  294 (374)
T PF13281_consen  217 PDTLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGFEI--EPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLG  294 (374)
T ss_pred             hHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHHcC--CccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHH
Confidence            88999988877431         2366788888776654  3555432222222222232 1   1222222   11 12


Q ss_pred             HcCC---CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          240 EMGC---QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       240 ~~~~---~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      +.|.   ..+-..+.+++.++.-.|+.++|.+..+.|...
T Consensus       295 ~kg~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  295 RKGSLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             hhccccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            2332   235556677888888899999999999998866

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.64  E-value=0.1  Score=44.39  Aligned_cols=107  Identities=11%  Similarity=0.093  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      +.+..+.-+...|+...|.++-.+.   .+++...|-..+.+++..++|++-.++...            ..++.-|...
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~F---kv~dkrfw~lki~aLa~~~~w~eL~~fa~s------------kKsPIGyepF  243 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEF---KVPDKRFWWLKIKALAENKDWDELEKFAKS------------KKSPIGYEPF  243 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHc---CCcHHHHHHHHHHHHHhcCCHHHHHHHHhC------------CCCCCChHHH
Confidence            4556677778889988888876544   557889999999999999999988876432            1223557888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHH
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLY  200 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  200 (403)
                      +..|.+.|+..+|..+...+          .+..-+..|.+.|++.+|.+.-
T Consensus       244 v~~~~~~~~~~eA~~yI~k~----------~~~~rv~~y~~~~~~~~A~~~A  285 (319)
T PF04840_consen  244 VEACLKYGNKKEASKYIPKI----------PDEERVEMYLKCGDYKEAAQEA  285 (319)
T ss_pred             HHHHHHCCCHHHHHHHHHhC----------ChHHHHHHHHHCCCHHHHHHHH
Confidence            89999999999999888772          2245677888899998887653

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

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.64  E-value=0.071  Score=46.64  Aligned_cols=64  Identities=11%  Similarity=0.022  Sum_probs=45.5

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcH---HHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE---VSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      +...|+.+..+|...|++++|+..|++..+..+.+.   .+|..+..+|...|+.++|...+++...
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455677777777777777777777777777766644   3477777777777777777777766654

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.64  E-value=0.032  Score=47.56  Aligned_cols=126  Identities=17%  Similarity=0.038  Sum_probs=82.3

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCC----CCCC---------CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNP----SSIP---------NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSY  104 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~----~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  104 (403)
                      ...+.+.|++..|...|++....-    ...+         -..+++.+..+|.+.+++..|++.-++.+..++.+....
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KAL  294 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKAL  294 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHH
Confidence            446778888888888887754321    0111         122566777778888888888888888888887788777


Q ss_pred             HHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChh-HHHHHHHHHHh
Q 041804          105 CNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWG-KCREFWEEMDK  170 (403)
Q Consensus       105 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~a~~~~~~~~~  170 (403)
                      -.-..++...|+++.|...|+++.+       ..|.|..+-+.++..-.+..... ...++|..|..
T Consensus       295 yRrG~A~l~~~e~~~A~~df~ka~k-------~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~mF~  354 (397)
T KOG0543|consen  295 YRRGQALLALGEYDLARDDFQKALK-------LEPSNKAARAELIKLKQKIREYEEKEKKMYANMFA  354 (397)
T ss_pred             HHHHHHHHhhccHHHHHHHHHHHHH-------hCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            7778888888888888888877776       33445455555555444443333 23555655543

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.63  E-value=0.31  Score=44.28  Aligned_cols=164  Identities=12%  Similarity=-0.079  Sum_probs=97.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHH------HHHHHHHHHHh----cCCHHHHHHHHhccccccccccccc
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEV------SYCNLVDALCE----YKHVIEAQELCFGENKNVGFSGLVE  138 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~------~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  138 (403)
                      +..++...+=.||-+.+++.+....+.+-- .+.      .|...+..++.    ....+.+.+++..+...       .
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~-------y  263 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR-------Y  263 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh-------C
Confidence            345666666677777777777776553321 222      23333333332    34667777777777763       2


Q ss_pred             CcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC---CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhH
Q 041804          139 MNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG---VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAY  215 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  215 (403)
                      |.+....-.-.+.+...|++++|.+.|+......   .+.....+--+.-++.-..+|++|.+.|..+.+.. ..+..+|
T Consensus       264 P~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y  342 (468)
T PF10300_consen  264 PNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFY  342 (468)
T ss_pred             CCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHH
Confidence            3333333444456666788888888888654321   12233345556667777888888888888888763 3344555


Q ss_pred             HHHHHHH-hhcCCH-------HHHHHHHHHHHHc
Q 041804          216 NTVIRAV-GVSEGV-------DFAMRVYREMREM  241 (403)
Q Consensus       216 ~~ll~~~-~~~~~~-------~~a~~~~~~~~~~  241 (403)
                      .-+..+| ...++.       ++|..+|.+....
T Consensus       343 ~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~l  376 (468)
T PF10300_consen  343 AYLAAACLLMLGREEEAKEHKKEAEELFRKVPKL  376 (468)
T ss_pred             HHHHHHHHHhhccchhhhhhHHHHHHHHHHHHHH
Confidence            5444433 345555       7888888877643

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.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.62  E-value=0.42  Score=41.68  Aligned_cols=145  Identities=14%  Similarity=0.167  Sum_probs=108.4

Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhH-HHHH
Q 041804          142 TKIYNMILRGWFKMSWWGKCREFWEEMDKRG-VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAY-NTVI  219 (403)
Q Consensus       142 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~ll  219 (403)
                      +.+|...++.-.+..-.+.|..+|-+..+.+ +.+++..++++|..++ .|++.-|..+|+--...  -||...| .-.+
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~--f~d~~~y~~kyl  473 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLK--FPDSTLYKEKYL  473 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHh--CCCchHHHHHHH
Confidence            4567788888888888999999999999988 6788889999998664 57888999999886655  3344433 4456


Q ss_pred             HHHhhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh
Q 041804          220 RAVGVSEGVDFAMRVYREMREMGCQPS--VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL  292 (403)
Q Consensus       220 ~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  292 (403)
                      ..+...++-+.|..+|+..... +..+  ...|..+|.--..-|+...+..+=++|.+.  .|...+...+...+
T Consensus       474 ~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry  545 (660)
T COG5107         474 LFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRY  545 (660)
T ss_pred             HHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHH
Confidence            6667889999999999966654 2223  567888998888999998888887777764  45554544444444

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.62  E-value=0.064  Score=42.44  Aligned_cols=227  Identities=12%  Similarity=0.059  Sum_probs=105.4

Q ss_pred             cHHHHHHhhhhhcccCCCcCC----HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804           10 DWKRALEFFNWVETDCHFTHT----TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus        10 ~~~~A~~~~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      +..++.+....-..  .++||    ...|..-..+|....++++|..-+.+..+--  ..+...| ....      .++.
T Consensus         8 ki~ea~e~~a~t~~--~wkad~dgaas~yekAAvafRnAk~feKakdcLlkA~~~y--Ennrslf-hAAK------ayEq   76 (308)
T KOG1585|consen    8 KISEADEMTALTLT--RWKADWDGAASLYEKAAVAFRNAKKFEKAKDCLLKASKGY--ENNRSLF-HAAK------AYEQ   76 (308)
T ss_pred             HHHHHHHHHHHHhh--ccCCCchhhHHHHHHHHHHHHhhccHHHHHHHHHHHHHHH--HhcccHH-HHHH------HHHH
Confidence            34555555544332  14555    4567777888888999999998777765311  1222212 1122      2233


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      |.-+.+++.+.. .-...+.-....|...|.++.|-..+++..+..                      +.-++++|++++
T Consensus        77 aamLake~~kls-Evvdl~eKAs~lY~E~GspdtAAmaleKAak~l----------------------env~Pd~AlqlY  133 (308)
T KOG1585|consen   77 AAMLAKELSKLS-EVVDLYEKASELYVECGSPDTAAMALEKAAKAL----------------------ENVKPDDALQLY  133 (308)
T ss_pred             HHHHHHHHHHhH-HHHHHHHHHHHHHHHhCCcchHHHHHHHHHHHh----------------------hcCCHHHHHHHH
Confidence            333333333211 022234444455666666655555444432210                      111223333333


Q ss_pred             HHHHh---CC--CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc----CCCCCh-hhHHHHHHHHhhcCCHHHHHHHH
Q 041804          166 EEMDK---RG--VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK----GIKMDV-VAYNTVIRAVGVSEGVDFAMRVY  235 (403)
Q Consensus       166 ~~~~~---~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~ll~~~~~~~~~~~a~~~~  235 (403)
                      ++...   .+  ...-...+...-..+.+..++++|-..+.+-...    .--++. ..|...|-.+.-..++..|.+.+
T Consensus       134 qralavve~~dr~~ma~el~gk~sr~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~  213 (308)
T KOG1585|consen  134 QRALAVVEEDDRDQMAFELYGKCSRVLVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCY  213 (308)
T ss_pred             HHHHHHHhccchHHHHHHHHHHhhhHhhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHh
Confidence            32210   00  0011123333344455555555554443332111    111222 23444555555666777777777


Q ss_pred             HHHHHcC---CCCCHHHHHHHHHHHHhcCcHHHHHHHHH
Q 041804          236 REMREMG---CQPSVVTCNTVIKLLCENGRVREAYAVLA  271 (403)
Q Consensus       236 ~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~a~~~~~  271 (403)
                      +.-.+.+   -.-+..+...|+.+| ..|+.+.+.+++.
T Consensus       214 r~~~qip~f~~sed~r~lenLL~ay-d~gD~E~~~kvl~  251 (308)
T KOG1585|consen  214 RDCSQIPAFLKSEDSRSLENLLTAY-DEGDIEEIKKVLS  251 (308)
T ss_pred             cchhcCccccChHHHHHHHHHHHHh-ccCCHHHHHHHHc
Confidence            7654432   122455666666666 4566666666554

>PRK15331 chaperone protein SicA; Provisional

Probab=96.61  E-value=0.017  Score=42.86  Aligned_cols=92  Identities=15%  Similarity=0.016  Sum_probs=69.1

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           73 MFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        73 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      ...-+-..|++++|..+|.-+.-.++.+..-|..|..++-..+++++|...|......       ...|...+.....+|
T Consensus        43 ~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l-------~~~dp~p~f~agqC~  115 (165)
T PRK15331         43 HAYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTL-------LKNDYRPVFFTGQCQ  115 (165)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-------ccCCCCccchHHHHH
Confidence            3444567899999999999888888778888888888888888999988887654432       123344456677788


Q ss_pred             HhcCChhHHHHHHHHHHhC
Q 041804          153 FKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~  171 (403)
                      ...|+.+.|...|+...+.
T Consensus       116 l~l~~~~~A~~~f~~a~~~  134 (165)
T PRK15331        116 LLMRKAAKARQCFELVNER  134 (165)
T ss_pred             HHhCCHHHHHHHHHHHHhC
Confidence            8888888888888877763

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.58  E-value=0.33  Score=39.90  Aligned_cols=143  Identities=10%  Similarity=-0.002  Sum_probs=72.0

Q ss_pred             HHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           76 RYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        76 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      .....|++.+|..+|.......+.+...-..+..+|...|+.+.|..++..+....      ..........-+..+.+.
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~------~~~~~~~l~a~i~ll~qa  216 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQA------QDKAAHGLQAQIELLEQA  216 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccc------hhhHHHHHHHHHHHHHHH
Confidence            34456666677777776666665566666666677777777777777666654431      111111112223333333


Q ss_pred             CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC-CCChhhHHHHHHHHhhcC
Q 041804          156 SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI-KMDVVAYNTVIRAVGVSE  226 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~  226 (403)
                      ....+...+-.+.-.. +. |...-..+...+...|+.+.|++.+-.+.+.+. --|...-..++..+.-.|
T Consensus       217 a~~~~~~~l~~~~aad-Pd-d~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g  286 (304)
T COG3118         217 AATPEIQDLQRRLAAD-PD-DVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFG  286 (304)
T ss_pred             hcCCCHHHHHHHHHhC-CC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcC
Confidence            3333333333333332 11 444555555666666666666665555544411 123334444444444444

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=96.50  E-value=0.056  Score=39.22  Aligned_cols=62  Identities=5%  Similarity=-0.039  Sum_probs=28.9

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIP-NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~   99 (403)
                      .....+.|++++|.+.|+.+..+-+..| ...+--.++.+|.+.++++.|...+++..+..|.
T Consensus        17 a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~   79 (142)
T PF13512_consen   17 AQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPT   79 (142)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC
Confidence            3444445555555555555554431111 1223334445555555555555555555555544

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.49  E-value=0.0084  Score=33.80  Aligned_cols=40  Identities=13%  Similarity=0.140  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      +|..+...|.+.|++++|+++|++..+..+.+...+..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La   42 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALA   42 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhh
Confidence            4555666666666666666666666666655665555443

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=96.43  E-value=0.46  Score=39.88  Aligned_cols=53  Identities=21%  Similarity=0.172  Sum_probs=25.7

Q ss_pred             HccCChhHHHHHHHHhhhCC-CCCCCHH------HHHHHHHHHHhcC-ChHHHHHHHHHHhh
Q 041804           42 GKFFEFDLSWNLIHRMKDNP-SSIPNHA------TFRIMFKRYVTAH-LVNEAMGTFNKLDE   95 (403)
Q Consensus        42 ~~~~~~~~a~~~~~~~~~~~-~~~~~~~------~~~~l~~~~~~~~-~~~~a~~~~~~~~~   95 (403)
                      .+.|+++.|..++.+..... ...|+..      .|+.-.. ....+ +++.|..++++..+
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~-l~~~~~~~~~a~~wL~~a~~   64 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKS-LLSKKDKYEEAVKWLQRAYD   64 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHH-HHHcCCChHHHHHHHHHHHH
Confidence            35666777777766665533 1223322      2222222 22333 66666666655443

It is also involved in sporulation [].

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.42  E-value=0.17  Score=44.38  Aligned_cols=69  Identities=7%  Similarity=-0.099  Sum_probs=60.4

Q ss_pred             ccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH---HHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          137 VEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL---HSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       137 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..+.+...++.+..+|.+.|++++|...|++..+.++. +.   .+|..+..+|...|+.++|++.+++..+.
T Consensus        70 ~dP~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd-~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         70 ADVKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPN-PDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-chHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            34567788999999999999999999999999887655 33   46999999999999999999999999885

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.41  E-value=0.19  Score=45.63  Aligned_cols=160  Identities=13%  Similarity=0.097  Sum_probs=80.1

Q ss_pred             HhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCcHHHHHHHH-HH
Q 041804          112 CEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK----MSWWGKCREFWEEMDKRGVVKDLHSYSIYM-DI  186 (403)
Q Consensus       112 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~-~~  186 (403)
                      .-.|+-+.+++.+.+..+..+..+.-...-...|...+..++.    ..+.+.|.++++.+.++  -|+...|...- +.
T Consensus       199 GF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~lfl~~~gR~  276 (468)
T PF10300_consen  199 GFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSALFLFFEGRL  276 (468)
T ss_pred             CcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHH
Confidence            3466777777777665553211111111111223444433333    33556677777777665  34444444332 34


Q ss_pred             HHHcCChhHHHHHHHHHHHcC---CCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-HHHHhcCc
Q 041804          187 MCKSGKPWKAVKLYKEMKKKG---IKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVI-KLLCENGR  262 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li-~~~~~~g~  262 (403)
                      +...|++++|++.|+......   .+.....+--+.-.+.-..++++|...|..+.+.. ..+..+|..+. .++...|+
T Consensus       277 ~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a~c~~~l~~  355 (468)
T PF10300_consen  277 ERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAAACLLMLGR  355 (468)
T ss_pred             HHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHHhhcc
Confidence            555677777777777654321   01122233334445556677777777777776642 12333333332 23334555


Q ss_pred             H-------HHHHHHHHhch
Q 041804          263 V-------REAYAVLAEMP  274 (403)
Q Consensus       263 ~-------~~a~~~~~~~~  274 (403)
                      .       ++|.++|.+..
T Consensus       356 ~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  356 EEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             chhhhhhHHHHHHHHHHHH
Confidence            5       56666666544

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.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=96.37  E-value=0.31  Score=41.06  Aligned_cols=47  Identities=21%  Similarity=0.415  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHcCCCCChhhHHHHHHHHhh--cC----CHHHHHHHHHHHHHc
Q 041804          195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGV--SE----GVDFAMRVYREMREM  241 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~--~~----~~~~a~~~~~~~~~~  241 (403)
                      +.+.+++.|.+.|+.-+..+|-+.......  ..    ....|..+|+.|++.
T Consensus        80 ~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~  132 (297)
T PF13170_consen   80 EVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKK  132 (297)
T ss_pred             HHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHh
Confidence            444556666666666665555443322222  11    234566666666655

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.37  E-value=0.18  Score=42.08  Aligned_cols=157  Identities=10%  Similarity=-0.090  Sum_probs=111.9

Q ss_pred             HhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC
Q 041804           78 VTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW  157 (403)
Q Consensus        78 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  157 (403)
                      .-.|++.+|-..++++.+..|.|..++...=.+|.-.|+.+.....++++......   +.|-...+-..+.-++..+|-
T Consensus       114 ~~~g~~h~a~~~wdklL~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~---dlp~~sYv~GmyaFgL~E~g~  190 (491)
T KOG2610|consen  114 WGRGKHHEAAIEWDKLLDDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNA---DLPCYSYVHGMYAFGLEECGI  190 (491)
T ss_pred             hccccccHHHHHHHHHHHhCchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCC---CCcHHHHHHHHHHhhHHHhcc
Confidence            34678888888899999888779999998889999999998888888887763210   222233344455556678899


Q ss_pred             hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC---hhhHHHHHHHHhhcCCHHHHHHH
Q 041804          158 WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD---VVAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      +++|++.-++..+.+.. |..+..+....+.-.+++.++.+...+-...--..+   ..-|-...-.+...+.++.|+.+
T Consensus       191 y~dAEk~A~ralqiN~~-D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleI  269 (491)
T KOG2610|consen  191 YDDAEKQADRALQINRF-DCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEI  269 (491)
T ss_pred             chhHHHHHHhhccCCCc-chHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHH
Confidence            99999999999888766 888888888888889999999887765443211101   11222233344566889999999


Q ss_pred             HHHH
Q 041804          235 YREM  238 (403)
Q Consensus       235 ~~~~  238 (403)
                      |+.-
T Consensus       270 yD~e  273 (491)
T KOG2610|consen  270 YDRE  273 (491)
T ss_pred             HHHH
Confidence            9753

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.35  E-value=0.051  Score=43.95  Aligned_cols=89  Identities=15%  Similarity=0.162  Sum_probs=68.4

Q ss_pred             CCcHHHHHHHHHHHHHc-----CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcC----------------CHHHHH
Q 041804          174 VKDLHSYSIYMDIMCKS-----GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSE----------------GVDFAM  232 (403)
Q Consensus       174 ~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~----------------~~~~a~  232 (403)
                      +-|..+|...+..+...     +..+-....++.|.+.|+.-|..+|+.|++.+-+..                +-+-+.
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            34777888888877653     456666677888899999999999999999886533                224477


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhcCc
Q 041804          233 RVYREMREMGCQPSVVTCNTVIKLLCENGR  262 (403)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  262 (403)
                      .++++|...|+.||..+-..++.++.+.+-
T Consensus       144 ~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  144 KVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            888888888888888888888888877664

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.29  E-value=0.63  Score=41.72  Aligned_cols=158  Identities=13%  Similarity=0.057  Sum_probs=81.9

Q ss_pred             HHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh
Q 041804           76 RYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK  154 (403)
Q Consensus        76 ~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  154 (403)
                      ...-.++++.+.++...-.-. +. +....+.++..+.+.|..+.|+.+...             |     ..-.....+
T Consensus       270 ~av~~~d~~~v~~~i~~~~ll-~~i~~~~~~~i~~fL~~~G~~e~AL~~~~D-------------~-----~~rFeLAl~  330 (443)
T PF04053_consen  270 TAVLRGDFEEVLRMIAASNLL-PNIPKDQGQSIARFLEKKGYPELALQFVTD-------------P-----DHRFELALQ  330 (443)
T ss_dssp             HHHHTT-HHH-----HHHHTG-GG--HHHHHHHHHHHHHTT-HHHHHHHSS--------------H-----HHHHHHHHH
T ss_pred             HHHHcCChhhhhhhhhhhhhc-ccCChhHHHHHHHHHHHCCCHHHHHhhcCC-------------h-----HHHhHHHHh
Confidence            334456666665555311100 11 344566666666777777777665221             1     223344556


Q ss_pred             cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHH
Q 041804          155 MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      .|+++.|.++.++..      +...|..|.......|+++-|.+.|.+...         +..|+-.|...|+.+...++
T Consensus       331 lg~L~~A~~~a~~~~------~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl  395 (443)
T PF04053_consen  331 LGNLDIALEIAKELD------DPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKL  395 (443)
T ss_dssp             CT-HHHHHHHCCCCS------THHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHH
T ss_pred             cCCHHHHHHHHHhcC------cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHH
Confidence            677777766544332      555777777777777777777776665432         34555556666777666666


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          235 YREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      .+.....|-      ++....++.-.|+.++..+++.+-
T Consensus       396 ~~~a~~~~~------~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  396 AKIAEERGD------INIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             HHHHHHTT-------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             HHHHHHccC------HHHHHHHHHHcCCHHHHHHHHHHc
Confidence            666665542      233344444556666666666543

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.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.18  E-value=0.58  Score=38.54  Aligned_cols=151  Identities=12%  Similarity=0.008  Sum_probs=102.8

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcC
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYK  115 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~  115 (403)
                      -.......|++.+|..+|.......  +.+...--.+..+|...|+.+.|..++..+...... .......-+..+.+..
T Consensus       140 ~~~~~~~~e~~~~a~~~~~~al~~~--~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa  217 (304)
T COG3118         140 EAKELIEAEDFGEAAPLLKQALQAA--PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAA  217 (304)
T ss_pred             HhhhhhhccchhhHHHHHHHHHHhC--cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHh
Confidence            3456678899999999999998875  345567778899999999999999999988765433 2222223334444433


Q ss_pred             CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC--CCCCcHHHHHHHHHHHHHcCCh
Q 041804          116 HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR--GVVKDLHSYSIYMDIMCKSGKP  193 (403)
Q Consensus       116 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~  193 (403)
                      ...+...+-.+...        .+.|...-..+...+...|+.+.|.+.+-.+.+.  |.. |...-..++..+.--|.-
T Consensus       218 ~~~~~~~l~~~~aa--------dPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~-d~~~Rk~lle~f~~~g~~  288 (304)
T COG3118         218 ATPEIQDLQRRLAA--------DPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFE-DGEARKTLLELFEAFGPA  288 (304)
T ss_pred             cCCCHHHHHHHHHh--------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccc-CcHHHHHHHHHHHhcCCC
Confidence            33333333233322        2447777888899999999999998877766554  344 666777788877777754


Q ss_pred             hHHHH
Q 041804          194 WKAVK  198 (403)
Q Consensus       194 ~~a~~  198 (403)
                      +.+..
T Consensus       289 Dp~~~  293 (304)
T COG3118         289 DPLVL  293 (304)
T ss_pred             CHHHH
Confidence            44433

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.18  E-value=0.36  Score=36.19  Aligned_cols=134  Identities=10%  Similarity=0.056  Sum_probs=77.5

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      +...|...+. +.+.+..++|+.-|..+.+.|..  ...............|+...|...|.++-...      ..|-..
T Consensus        58 sgd~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt------~~P~~~  130 (221)
T COG4649          58 SGDAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADT------SIPQIG  130 (221)
T ss_pred             chHHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccC------CCcchh
Confidence            3444544444 45667778888888888777765  33333344455566777777777777766542      222211


Q ss_pred             -HHHHH--HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          144 -IYNMI--LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       144 -~~~~l--~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                       -...|  .-.+...|.+++.....+.+...+-+.....-..|.-+-.+.|++.+|...|..+...
T Consensus       131 rd~ARlraa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~D  196 (221)
T COG4649         131 RDLARLRAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAND  196 (221)
T ss_pred             hHHHHHHHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHcc
Confidence             11111  1223456667776666666655544444445555666666777777777777766554

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.15  E-value=0.1  Score=42.29  Aligned_cols=100  Identities=13%  Similarity=-0.003  Sum_probs=73.5

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCC-CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSS-IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCN  106 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~  106 (403)
                      ...|+.-+.. .+.|++..|...|....+..+- .-...++-.|..++...|+++.|..+|..+.+..+.   -+..+.-
T Consensus       142 ~~~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallK  220 (262)
T COG1729         142 TKLYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLK  220 (262)
T ss_pred             hHHHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHH
Confidence            3466665544 4566688888888888876410 112346667888888899999998888888876654   5567777


Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccc
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNV  131 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~  131 (403)
                      |..+..+.|+.++|...|+++.+..
T Consensus       221 lg~~~~~l~~~d~A~atl~qv~k~Y  245 (262)
T COG1729         221 LGVSLGRLGNTDEACATLQQVIKRY  245 (262)
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHC
Confidence            8888888888899988888877764

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.12  E-value=0.74  Score=39.28  Aligned_cols=48  Identities=23%  Similarity=0.087  Sum_probs=22.4

Q ss_pred             HHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHH
Q 041804          218 VIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAV  269 (403)
Q Consensus       218 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~  269 (403)
                      .+.-+...|+...|.++-.+.   + .|+...|...+.+++..++|++...+
T Consensus       183 Ti~~li~~~~~k~A~kl~k~F---k-v~dkrfw~lki~aLa~~~~w~eL~~f  230 (319)
T PF04840_consen  183 TIRKLIEMGQEKQAEKLKKEF---K-VPDKRFWWLKIKALAENKDWDELEKF  230 (319)
T ss_pred             HHHHHHHCCCHHHHHHHHHHc---C-CcHHHHHHHHHHHHHhcCCHHHHHHH
Confidence            334444445544444443322   1 24555555555555555555544443

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

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=96.12  E-value=0.13  Score=44.11  Aligned_cols=106  Identities=8%  Similarity=-0.086  Sum_probs=55.7

Q ss_pred             HHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHH
Q 041804           74 FKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWF  153 (403)
Q Consensus        74 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  153 (403)
                      .+.|.+.|++..|...|++....=.            |.+.-+.++.....              ..-..++..+.-+|.
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~------------~~~~~~~ee~~~~~--------------~~k~~~~lNlA~c~l  268 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLE------------YRRSFDEEEQKKAE--------------ALKLACHLNLAACYL  268 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhh------------ccccCCHHHHHHHH--------------HHHHHHhhHHHHHHH
Confidence            4578889999999999888654211            00111111111110              112233455555556


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          154 KMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      +.+++..|++.-++.+..+.. |.-..---..++...|+++.|...|+.+.+.
T Consensus       269 Kl~~~~~Ai~~c~kvLe~~~~-N~KALyRrG~A~l~~~e~~~A~~df~ka~k~  320 (397)
T KOG0543|consen  269 KLKEYKEAIESCNKVLELDPN-NVKALYRRGQALLALGEYDLARDDFQKALKL  320 (397)
T ss_pred             hhhhHHHHHHHHHHHHhcCCC-chhHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            666666666655555555433 4444444455556666666666666666554

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.12  E-value=0.14  Score=41.57  Aligned_cols=98  Identities=10%  Similarity=-0.029  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      .|+.-+. +.+.|++..|...|....+..+.   .+..+-.|..++...|++++|..+|..+.+..+    ..+.-...+
T Consensus       144 ~Y~~A~~-~~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P----~s~KApdal  218 (262)
T COG1729         144 LYNAALD-LYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYP----KSPKAPDAL  218 (262)
T ss_pred             HHHHHHH-HHHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCC----CCCCChHHH
Confidence            4666655 44566688888888888887765   666777888888888888888888877776542    112223556


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      .-|..+..+.|+.++|..+|+++.+.
T Consensus       219 lKlg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         219 LKLGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            66777777788888888888887765

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.03  E-value=0.4  Score=35.35  Aligned_cols=126  Identities=10%  Similarity=0.089  Sum_probs=69.4

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      ...++..+.+.+.......+++.+...+  ..+...++.++..|++.+ ..+.+..+..  .   .+......+++.|.+
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~--~~~~~~~~~li~ly~~~~-~~~ll~~l~~--~---~~~yd~~~~~~~c~~   81 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLN--SENPALQTKLIELYAKYD-PQKEIERLDN--K---SNHYDIEKVGKLCEK   81 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccC--ccchhHHHHHHHHHHHHC-HHHHHHHHHh--c---cccCCHHHHHHHHHH
Confidence            3456666666777777778777777665  256667777777777653 3333444432  1   122334445666666


Q ss_pred             cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc-CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          114 YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM-SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       114 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      .+-++++..++.++..               +...+..+... ++++.|.+++.+-      .+...|..++..+.
T Consensus        82 ~~l~~~~~~l~~k~~~---------------~~~Al~~~l~~~~d~~~a~~~~~~~------~~~~lw~~~~~~~l  136 (140)
T smart00299       82 AKLYEEAVELYKKDGN---------------FKDAIVTLIEHLGNYEKAIEYFVKQ------NNPELWAEVLKALL  136 (140)
T ss_pred             cCcHHHHHHHHHhhcC---------------HHHHHHHHHHcccCHHHHHHHHHhC------CCHHHHHHHHHHHH
Confidence            6666666666655432               22233333333 5566666655541      14445655555544

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=96.02  E-value=0.22  Score=35.34  Aligned_cols=93  Identities=13%  Similarity=-0.022  Sum_probs=64.3

Q ss_pred             HHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcc--hHHHHHHHHHH
Q 041804           75 KRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNK--TKIYNMILRGW  152 (403)
Q Consensus        75 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--~~~~~~l~~~~  152 (403)
                      -+.+..|+.+.|++.|.+....-+.....||.-.+++.-.|+.++|+.-+++..+-.     +....  ...|---...|
T Consensus        51 valaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLa-----g~~trtacqa~vQRg~ly  125 (175)
T KOG4555|consen   51 IALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELA-----GDQTRTACQAFVQRGLLY  125 (175)
T ss_pred             HHHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhc-----CccchHHHHHHHHHHHHH
Confidence            456677888888888888888777788888888888888888888888777766542     21111  11233333456


Q ss_pred             HhcCChhHHHHHHHHHHhCC
Q 041804          153 FKMSWWGKCREFWEEMDKRG  172 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~  172 (403)
                      ...|+-+.|..=|+...+.|
T Consensus       126 Rl~g~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  126 RLLGNDDAARADFEAAAQLG  145 (175)
T ss_pred             HHhCchHHHHHhHHHHHHhC
Confidence            66777788877777766655

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.01  E-value=0.72  Score=42.23  Aligned_cols=217  Identities=13%  Similarity=0.096  Sum_probs=115.1

Q ss_pred             HHHHHHHHHccCChh--HHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--cHHHH-----
Q 041804           34 YNSVIDILGKFFEFD--LSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--DEVSY-----  104 (403)
Q Consensus        34 ~~~li~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~-----  104 (403)
                      ++..=.+|.+.++..  +.+.-++++.+++ ..|+...   +...++-.|++.+|-++|.+   .|..  -.+.|     
T Consensus       601 f~~ARkAY~rVRdl~~L~li~EL~~~k~rg-e~P~~iL---lA~~~Ay~gKF~EAAklFk~---~G~enRAlEmyTDlRM  673 (1081)
T KOG1538|consen  601 FETARKAYIRVRDLRYLELISELEERKKRG-ETPNDLL---LADVFAYQGKFHEAAKLFKR---SGHENRALEMYTDLRM  673 (1081)
T ss_pred             hHHHHHHHHHHhccHHHHHHHHHHHHHhcC-CCchHHH---HHHHHHhhhhHHHHHHHHHH---cCchhhHHHHHHHHHH
Confidence            344445666555543  4444566777777 4466542   34445556666666666643   2222  11111     


Q ss_pred             HHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHH------HHHhCCCCC---
Q 041804          105 CNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWE------EMDKRGVVK---  175 (403)
Q Consensus       105 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~------~~~~~~~~~---  175 (403)
                      .-..+-+...|..++-..+.++-..-   .....+|     .+....+...|+.++|..+.-      -+.+.+.+.   
T Consensus       674 FD~aQE~~~~g~~~eKKmL~RKRA~W---Ar~~keP-----kaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~  745 (1081)
T KOG1538|consen  674 FDYAQEFLGSGDPKEKKMLIRKRADW---ARNIKEP-----KAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKA  745 (1081)
T ss_pred             HHHHHHHhhcCChHHHHHHHHHHHHH---hhhcCCc-----HHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchh
Confidence            12334444555555444443322110   0001122     233444555666666654321      111111111   


Q ss_pred             cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHH-------
Q 041804          176 DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVV-------  248 (403)
Q Consensus       176 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------  248 (403)
                      +..+...+...+.+...+.-|-++|..|-..         ..+++.....+++++|..+-+...+.  .|++.       
T Consensus       746 ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwL  814 (1081)
T KOG1538|consen  746 EREPLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWL  814 (1081)
T ss_pred             hhhHHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCccc--cccccchHHHHh
Confidence            3445555555555666778888888877533         35677788889999998887766553  33332       


Q ss_pred             ----HHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          249 ----TCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       249 ----~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                          -|...-++|.++|+-.+|..+++++...
T Consensus       815 AE~DrFeEAqkAfhkAGr~~EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  815 AENDRFEEAQKAFHKAGRQREAVQVLEQLTNN  846 (1081)
T ss_pred             hhhhhHHHHHHHHHHhcchHHHHHHHHHhhhh
Confidence                2334456777888888888888877654

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.00  E-value=0.77  Score=43.36  Aligned_cols=182  Identities=11%  Similarity=0.073  Sum_probs=115.4

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      ....-+..+.+...++-|+.+-+.-...+..-........+-+.+.|++++|...|-+...       ...|     ..+
T Consensus       336 ~le~kL~iL~kK~ly~~Ai~LAk~~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~-------~le~-----s~V  403 (933)
T KOG2114|consen  336 DLETKLDILFKKNLYKVAINLAKSQHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIG-------FLEP-----SEV  403 (933)
T ss_pred             cHHHHHHHHHHhhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcc-------cCCh-----HHH
Confidence            3445677777788888888776443211101333344444555679999999998877665       2334     345


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCH
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGV  228 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  228 (403)
                      +.-|.+...+..-..+++.+.+.|.. +...-..|+.+|.+.++.++-.++.+.-. .|..  ..-....+..+.+.+-.
T Consensus       404 i~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~snyl  479 (933)
T KOG2114|consen  404 IKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNYL  479 (933)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhChH
Confidence            66677777788888899999999988 77788899999999999888776665443 2211  11133455556566666


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          229 DFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       229 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      +.|..+-.....     +......++   -..+++++|.+.+..+.
T Consensus       480 ~~a~~LA~k~~~-----he~vl~ill---e~~~ny~eAl~yi~slp  517 (933)
T KOG2114|consen  480 DEAELLATKFKK-----HEWVLDILL---EDLHNYEEALRYISSLP  517 (933)
T ss_pred             HHHHHHHHHhcc-----CHHHHHHHH---HHhcCHHHHHHHHhcCC
Confidence            666555433322     333333333   34577888888777765

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.98  E-value=0.094  Score=42.50  Aligned_cols=104  Identities=17%  Similarity=0.380  Sum_probs=67.0

Q ss_pred             CCChhhHHHHHHHHhh-----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChh
Q 041804          209 KMDVVAYNTVIRAVGV-----SEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVI  283 (403)
Q Consensus       209 ~~~~~~~~~ll~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~  283 (403)
                      .-|..+|-..+..+..     .+.++-....++.|.+.|+.-|..+|+.|+..+-+..                ..|.. 
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgk----------------fiP~n-  126 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGK----------------FIPQN-  126 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccc----------------cccHH-
Confidence            3455666666665543     3566777777788888888888888887777654321                12221 


Q ss_pred             hHHHHHHhhC-CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCC
Q 041804          284 TYHCFFRCLE-KPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGF  329 (403)
Q Consensus       284 ~~~~l~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  329 (403)
                      .+..++-.|- ..+-++++++.|...|+.||..+-..|++++.+.+-
T Consensus       127 vfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  127 VFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            1222222332 234467888888888888888888888888887765

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.95  E-value=0.89  Score=42.97  Aligned_cols=184  Identities=12%  Similarity=0.053  Sum_probs=121.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHH
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHS  179 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  179 (403)
                      .......-+..+.+...++-|..+.+....       +..--..........+.+.|++++|...+-+-... +.|    
T Consensus       333 ~ek~le~kL~iL~kK~ly~~Ai~LAk~~~~-------d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~----  400 (933)
T KOG2114|consen  333 IEKDLETKLDILFKKNLYKVAINLAKSQHL-------DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP----  400 (933)
T ss_pred             eeccHHHHHHHHHHhhhHHHHHHHHHhcCC-------CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh----
Confidence            334455667777788888888887654322       11112223444455667889999998887766543 222    


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 041804          180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCE  259 (403)
Q Consensus       180 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  259 (403)
                       ..+|.-|........-..+++.+.+.|+. +...-+.|+.+|.+.++.+...++.+... .|..  ..-....+..+.+
T Consensus       401 -s~Vi~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~  475 (933)
T KOG2114|consen  401 -SEVIKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRK  475 (933)
T ss_pred             -HHHHHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHH
Confidence             23456666666777777888899988866 55566789999999999998888776554 2211  1123455666677


Q ss_pred             cCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHH
Q 041804          260 NGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRM  305 (403)
Q Consensus       260 ~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~  305 (403)
                      .+-.+.|..+-.....     .......++...+++++|++.+..+
T Consensus       476 snyl~~a~~LA~k~~~-----he~vl~ille~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  476 SNYLDEAELLATKFKK-----HEWVLDILLEDLHNYEEALRYISSL  516 (933)
T ss_pred             hChHHHHHHHHHHhcc-----CHHHHHHHHHHhcCHHHHHHHHhcC
Confidence            7777777766555432     4566777888888899988877665

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.93  E-value=0.49  Score=35.54  Aligned_cols=138  Identities=6%  Similarity=-0.035  Sum_probs=95.2

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC-C-cH--HHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL-K-DE--VSYCN  106 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~-~~--~~~~~  106 (403)
                      ...|..-+. +.+.+..++|+.-|..+...|...--....-.+.......|+...|...|+++-.... | -.  ..-..
T Consensus        59 gd~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlr  137 (221)
T COG4649          59 GDAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLR  137 (221)
T ss_pred             hHHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHH
Confidence            444544333 4577889999999999998773222222333445566788999999999999865432 2 11  11222


Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK  175 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  175 (403)
                      -...+...|.++......+-+...      +.+.....-..|.-+-.+.|++.+|.+.|.++......|
T Consensus       138 aa~lLvD~gsy~dV~srvepLa~d------~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da~ap  200 (221)
T COG4649         138 AAYLLVDNGSYDDVSSRVEPLAGD------GNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAP  200 (221)
T ss_pred             HHHHHhccccHHHHHHHhhhccCC------CChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccccCc
Confidence            233456789999888877766654      666677778888888999999999999999998754444

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.84  E-value=1.6  Score=40.80  Aligned_cols=116  Identities=13%  Similarity=0.081  Sum_probs=82.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHH
Q 041804          242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLL  321 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  321 (403)
                      |......+.+--+..+...|+..+|.++-.+.+    .||...|-.=+.++...++-.++++-..+..   .+.-|.-++
T Consensus       679 ~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskk---sPIGy~PFV  751 (829)
T KOG2280|consen  679 GGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKK---SPIGYLPFV  751 (829)
T ss_pred             ccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC---CCCCchhHH
Confidence            333344455666777788999999999888876    5788888777777766555555555554432   255688889


Q ss_pred             HHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 041804          322 RKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDE  373 (403)
Q Consensus       322 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  373 (403)
                      .+|.+.|+.++|.+.+.+....     .    -.+.+|.+.|++.+|.++--
T Consensus       752 e~c~~~~n~~EA~KYiprv~~l-----~----ekv~ay~~~~~~~eAad~A~  794 (829)
T KOG2280|consen  752 EACLKQGNKDEAKKYIPRVGGL-----Q----EKVKAYLRVGDVKEAADLAA  794 (829)
T ss_pred             HHHHhcccHHHHhhhhhccCCh-----H----HHHHHHHHhccHHHHHHHHH
Confidence            9999999999999987765421     1    45678888898888876543

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.83  E-value=0.42  Score=33.97  Aligned_cols=93  Identities=9%  Similarity=-0.050  Sum_probs=69.4

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHH---HHHHhhc
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTV---IRAVGVS  225 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l---l~~~~~~  225 (403)
                      .-+....|+.+.|++.|.+....-++ ....||.-..++.-.|+.++|++=+++..+..-.-+...+.+.   ...|...
T Consensus        50 ~valaE~g~Ld~AlE~F~qal~l~P~-raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~  128 (175)
T KOG4555|consen   50 AIALAEAGDLDGALELFGQALCLAPE-RASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLL  128 (175)
T ss_pred             HHHHHhccchHHHHHHHHHHHHhccc-chHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHh
Confidence            34567789999999999998877655 7788999999999999999999888888776222233333322   3356677


Q ss_pred             CCHHHHHHHHHHHHHcC
Q 041804          226 EGVDFAMRVYREMREMG  242 (403)
Q Consensus       226 ~~~~~a~~~~~~~~~~~  242 (403)
                      |+-+.|..-|+..-+.|
T Consensus       129 g~dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  129 GNDDAARADFEAAAQLG  145 (175)
T ss_pred             CchHHHHHhHHHHHHhC
Confidence            88888888888887766

>PRK11906 transcriptional regulator; Provisional

Probab=95.83  E-value=0.86  Score=40.27  Aligned_cols=118  Identities=11%  Similarity=0.015  Sum_probs=73.9

Q ss_pred             cHHHHHHhhhhhcccCCCcCC-HHhHHHHHHHHHc---------cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh
Q 041804           10 DWKRALEFFNWVETDCHFTHT-TDTYNSVIDILGK---------FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT   79 (403)
Q Consensus        10 ~~~~A~~~~~~~~~~~~~~~~-~~~~~~li~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~   79 (403)
                      +.+.|+.+|..........|+ ...|..+..++..         .....+|.++.++..+.+  +-|..+...+..+...
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld--~~Da~a~~~~g~~~~~  350 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT--TVDGKILAIMGLITGL  350 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHh
Confidence            345677777776633334444 3344443333221         223456666666776665  4566666666666677


Q ss_pred             cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           80 AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        80 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      .++++.|..+|++....++....+|......+.-.|+.++|...+++..+
T Consensus       351 ~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alr  400 (458)
T PRK11906        351 SGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEKIEEARICIDKSLQ  400 (458)
T ss_pred             hcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            77788888888888777777666666666666667778888777777444

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=95.80  E-value=0.79  Score=36.99  Aligned_cols=183  Identities=8%  Similarity=-0.007  Sum_probs=94.7

Q ss_pred             HHHHHHHccCChhHHHHHHHHhhhCCCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHh
Q 041804           36 SVIDILGKFFEFDLSWNLIHRMKDNPSSIP-NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCE  113 (403)
Q Consensus        36 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~  113 (403)
                      .-+..-.+.|++++|.+.|+.+..+.+..| ...+.-.++-++-+.++++.|+..+++.....+. ....|..-|.+.+.
T Consensus        39 ~~g~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs~  118 (254)
T COG4105          39 NEGLTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKGLSY  118 (254)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHHHHH
Confidence            334555677888888888888887652222 2334555666777788888888888888887776 55556666666552


Q ss_pred             cC-------CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHH
Q 041804          114 YK-------HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI  186 (403)
Q Consensus       114 ~~-------~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  186 (403)
                      .-       +...+...+..                  +..++.-|=.+.-...|......+...    =...=..+.+.
T Consensus       119 ~~~i~~~~rDq~~~~~A~~~------------------f~~~i~ryPnS~Ya~dA~~~i~~~~d~----LA~~Em~Iary  176 (254)
T COG4105         119 FFQIDDVTRDQSAARAAFAA------------------FKELVQRYPNSRYAPDAKARIVKLNDA----LAGHEMAIARY  176 (254)
T ss_pred             hccCCccccCHHHHHHHHHH------------------HHHHHHHCCCCcchhhHHHHHHHHHHH----HHHHHHHHHHH
Confidence            11       11111111111                  111111111111112222222111110    00001234456


Q ss_pred             HHHcCChhHHHHHHHHHHHcCCCCC---hhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          187 MCKSGKPWKAVKLYKEMKKKGIKMD---VVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      |.+.|.+-.|..-++.|.+. .+-+   ...+-.+..+|...|-.++|.+.-+-+...
T Consensus       177 Y~kr~~~~AA~nR~~~v~e~-y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         177 YLKRGAYVAAINRFEEVLEN-YPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             HHHhcChHHHHHHHHHHHhc-cccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhc
Confidence            77777777777777777766 2222   223445556666777777766665555443

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=95.80  E-value=0.17  Score=41.71  Aligned_cols=77  Identities=16%  Similarity=0.257  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHH-----cCCCCCHHHHHHH
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE-----MGCQPSVVTCNTV  253 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~~l  253 (403)
                      ++..++..+...|+.+.+...++++.... +-+...|..+|.+|.+.|+...|+..|+.+.+     .|+.|...+....
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            44455555555555555555555555542 33455555555555555555555555555443     3555555555444


Q ss_pred             HHH
Q 041804          254 IKL  256 (403)
Q Consensus       254 i~~  256 (403)
                      ...
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            444

>PRK11906 transcriptional regulator; Provisional

Probab=95.80  E-value=1  Score=39.81  Aligned_cols=162  Identities=7%  Similarity=0.027  Sum_probs=94.4

Q ss_pred             HhH--HHHHHHHHcc-----CChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHh---------cCChHHHHHHHHHHh
Q 041804           32 DTY--NSVIDILGKF-----FEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVT---------AHLVNEAMGTFNKLD   94 (403)
Q Consensus        32 ~~~--~~li~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~   94 (403)
                      ..|  ...+.+....     ...+.|..+|.+........|+ ...|..+..++..         .....+|.++-++..
T Consensus       252 ~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAv  331 (458)
T PRK11906        252 NHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVS  331 (458)
T ss_pred             cchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHH
Confidence            455  5555554442     2456788888888833223354 3344444433332         234556777777788


Q ss_pred             hcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC
Q 041804           95 EFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV  174 (403)
Q Consensus        95 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  174 (403)
                      +.+..|+.+...+..+..-.++.+.|..+|++....       .|....+|........-.|+.++|.+.+++..+.++.
T Consensus       332 eld~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L-------~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~  404 (458)
T PRK11906        332 DITTVDGKILAIMGLITGLSGQAKVSHILFEQAKIH-------STDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPR  404 (458)
T ss_pred             hcCCCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhc-------CCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCch
Confidence            887778888888887777777788888888777652       2444455555555556677788888887776655322


Q ss_pred             Cc-HHHHHHHHHHHHHcCChhHHHHHHH
Q 041804          175 KD-LHSYSIYMDIMCKSGKPWKAVKLYK  201 (403)
Q Consensus       175 ~~-~~~~~~l~~~~~~~~~~~~a~~~~~  201 (403)
                      -- .......+..|+.. ..+.|+++|-
T Consensus       405 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~  431 (458)
T PRK11906        405 RRKAVVIKECVDMYVPN-PLKNNIKLYY  431 (458)
T ss_pred             hhHHHHHHHHHHHHcCC-chhhhHHHHh
Confidence            11 11222223344433 3555555553

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.69  E-value=0.42  Score=39.95  Aligned_cols=153  Identities=8%  Similarity=-0.084  Sum_probs=88.0

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHH--HH--HHHHHHHhcCCh
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHAT--FR--IMFKRYVTAHLV   83 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~--~l~~~~~~~~~~   83 (403)
                      +|++.+|-..++.+.  ...|.|..++...=.++.-.|+.......++++...-  .|+...  |.  ...-++...|-+
T Consensus       116 ~g~~h~a~~~wdklL--~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~w--n~dlp~~sYv~GmyaFgL~E~g~y  191 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLL--DDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKW--NADLPCYSYVHGMYAFGLEECGIY  191 (491)
T ss_pred             cccccHHHHHHHHHH--HhCchhhhhhhhhhhHHHhccchhhhhhHHHHhcccc--CCCCcHHHHHHHHHHhhHHHhccc
Confidence            455666666666666  3345566666666667777777777777777666541  133322  22  122233456777


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHH
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCRE  163 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  163 (403)
                      ++|++.-++..+.+..|..+...+...+--.+++.++.+...+-.....-   +...-...|-...-.+...+.++.|++
T Consensus       192 ~dAEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~---s~mlasHNyWH~Al~~iE~aeye~ale  268 (491)
T KOG2610|consen  192 DDAEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQ---SWMLASHNYWHTALFHIEGAEYEKALE  268 (491)
T ss_pred             hhHHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhh---hhHHHhhhhHHHHHhhhcccchhHHHH
Confidence            77777777777766667777777777777777777777765554332210   111112224444455566677777777


Q ss_pred             HHHH
Q 041804          164 FWEE  167 (403)
Q Consensus       164 ~~~~  167 (403)
                      +|+.
T Consensus       269 IyD~  272 (491)
T KOG2610|consen  269 IYDR  272 (491)
T ss_pred             HHHH
Confidence            7754

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.58  E-value=0.049  Score=30.62  Aligned_cols=36  Identities=6%  Similarity=0.066  Sum_probs=19.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHH
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYS  181 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  181 (403)
                      +..+...|...|++++|.++|++..+..+. |...+.
T Consensus         4 ~~~la~~~~~~G~~~~A~~~~~~~l~~~P~-~~~a~~   39 (44)
T PF13428_consen    4 WLALARAYRRLGQPDEAERLLRRALALDPD-DPEAWR   39 (44)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-CHHHHH
Confidence            445555555555555555555555555443 444333

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=95.50  E-value=1.6  Score=38.34  Aligned_cols=127  Identities=13%  Similarity=0.129  Sum_probs=83.2

Q ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHhchhcC-CCCChhhHHHHHHhh--CCHHHHHHHHHHHHHcCCCCchhhH-HHHHHH
Q 041804          248 VTCNTVIKLLCENGRVREAYAVLAEMPKKG-CVPDVITYHCFFRCL--EKPREILGLFDRMIESGIRPKMDTY-VMLLRK  323 (403)
Q Consensus       248 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~p~~~~~~~l~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~-~~li~~  323 (403)
                      .+|...+..-.+..-++.|..+|-++.+.+ +.++...+++++..+  ++..-|..+|+.=...-  ||...| .-.+..
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~d~~ta~~ifelGl~~f--~d~~~y~~kyl~f  475 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATGDRATAYNIFELGLLKF--PDSTLYKEKYLLF  475 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcCCcchHHHHHHHHHHhC--CCchHHHHHHHHH
Confidence            445666666667777888888888888777 667788888888766  44556677776544432  333332 344555


Q ss_pred             HHhcCCcchHHHHHHHHHhcCCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          324 FGRWGFLRPVFVVWKKMEELGCSPD--EFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       324 ~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      +...++-..|..+|+..... +..+  ...|..+|+.-..-|+...|..+-++|..
T Consensus       476 Li~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         476 LIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            66778888888888855432 1122  45777788777777877776666666654

>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=95.46  E-value=0.6  Score=35.97  Aligned_cols=100  Identities=13%  Similarity=0.015  Sum_probs=71.6

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC--HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--cHHHHH-
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN--HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--DEVSYC-  105 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~-  105 (403)
                      ...+..+...|.+.|+.+.|.+.|.++.+.. ..+.  ...+-.+++...-.+++..+.....+.......  |...-+ 
T Consensus        36 r~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~-~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nr  114 (177)
T PF10602_consen   36 RMALEDLADHYCKIGDLEEALKAYSRARDYC-TSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNR  114 (177)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhhhc-CCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHH
Confidence            3468899999999999999999999998864 2233  346778889999999999999988887654332  222211 


Q ss_pred             -HHH--HHHHhcCCHHHHHHHHhcccccc
Q 041804          106 -NLV--DALCEYKHVIEAQELCFGENKNV  131 (403)
Q Consensus       106 -~l~--~~~~~~~~~~~a~~~~~~~~~~~  131 (403)
                       ...  -.+...+++..|-+.|-......
T Consensus       115 lk~~~gL~~l~~r~f~~AA~~fl~~~~t~  143 (177)
T PF10602_consen  115 LKVYEGLANLAQRDFKEAAELFLDSLSTF  143 (177)
T ss_pred             HHHHHHHHHHHhchHHHHHHHHHccCcCC
Confidence             111  12335789999999887776543

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.

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=95.31  E-value=0.44  Score=40.31  Aligned_cols=231  Identities=10%  Similarity=-0.022  Sum_probs=118.9

Q ss_pred             ccccHHHHHHhhhhhcccCCCc-CCHHhHHHHHHHHHccCChhHHHHHHH----HhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            7 YANDWKRALEFFNWVETDCHFT-HTTDTYNSVIDILGKFFEFDLSWNLIH----RMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~----~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      ++++.++|+..+.....+.... .-..+|..+..+.++.|.+++++..--    ...+.....---.+|..+.+++-+..
T Consensus        18 ~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l~   97 (518)
T KOG1941|consen   18 QSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKLC   97 (518)
T ss_pred             cCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456677776665554311111 123467777778888888877665322    11111100011235666666666666


Q ss_pred             ChHHHHHHHHHHhhcCCCc-----HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC
Q 041804           82 LVNEAMGTFNKLDEFGLKD-----EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS  156 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  156 (403)
                      ++.+++.+-..-......+     -....++..++...+.++++++.|+....-....+ .......++-.|-..|....
T Consensus        98 ~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~-D~~LElqvcv~Lgslf~~l~  176 (518)
T KOG1941|consen   98 EFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNND-DAMLELQVCVSLGSLFAQLK  176 (518)
T ss_pred             HhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccC-CceeeeehhhhHHHHHHHHH
Confidence            7777776666554433221     23444566666667777777777665543210000 11223445677777777777


Q ss_pred             ChhHHHHHHHHHHh----CCCCCcHHH-H-----HHHHHHHHHcCChhHHHHHHHHHHH----cCCCCC-hhhHHHHHHH
Q 041804          157 WWGKCREFWEEMDK----RGVVKDLHS-Y-----SIYMDIMCKSGKPWKAVKLYKEMKK----KGIKMD-VVAYNTVIRA  221 (403)
Q Consensus       157 ~~~~a~~~~~~~~~----~~~~~~~~~-~-----~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~-~~~~~~ll~~  221 (403)
                      |+++|.-+..+..+    .++. |... |     ..|.-++-..|...+|.+.-++..+    .|-.+. ......+...
T Consensus       177 D~~Kal~f~~kA~~lv~s~~l~-d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDI  255 (518)
T KOG1941|consen  177 DYEKALFFPCKAAELVNSYGLK-DWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADI  255 (518)
T ss_pred             hhhHHhhhhHhHHHHHHhcCcC-chhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            77777655544322    2222 2211 1     2233345556666666665555432    232221 1233345556


Q ss_pred             HhhcCCHHHHHHHHHHHH
Q 041804          222 VGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       222 ~~~~~~~~~a~~~~~~~~  239 (403)
                      |...|+.+.|+.-|+...
T Consensus       256 yR~~gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  256 YRSRGDLERAFRRYEQAM  273 (518)
T ss_pred             HHhcccHhHHHHHHHHHH
Confidence            666777777666665543

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=95.26  E-value=0.72  Score=32.92  Aligned_cols=59  Identities=25%  Similarity=0.290  Sum_probs=22.1

Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          183 YMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       183 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      .+..+..+|+-++-.+++..+.+.+ .+++...-.+..+|.+.|+..++.+++.++-+.|
T Consensus        92 ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG  150 (161)
T PF09205_consen   92 ALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKG  150 (161)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhc
Confidence            3334444444444444444443321 3333344444444444444444444444444443

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.18  E-value=0.88  Score=33.49  Aligned_cols=85  Identities=8%  Similarity=0.081  Sum_probs=48.5

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      ..++..+...+........++.+...+..++..++.++..|++.+ ..+....+..-            .+......+++
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~~-~~~ll~~l~~~------------~~~yd~~~~~~   77 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKYD-PQKEIERLDNK------------SNHYDIEKVGK   77 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHHC-HHHHHHHHHhc------------cccCCHHHHHH
Confidence            345666666677777777777777766457777777777777653 23333333310            11111233555


Q ss_pred             HHHhcCChhHHHHHHHHH
Q 041804          151 GWFKMSWWGKCREFWEEM  168 (403)
Q Consensus       151 ~~~~~~~~~~a~~~~~~~  168 (403)
                      .|.+.+-++++.-++.++
T Consensus        78 ~c~~~~l~~~~~~l~~k~   95 (140)
T smart00299       78 LCEKAKLYEEAVELYKKD   95 (140)
T ss_pred             HHHHcCcHHHHHHHHHhh
Confidence            555555555555555554

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=95.17  E-value=0.37  Score=39.76  Aligned_cols=76  Identities=20%  Similarity=0.181  Sum_probs=55.8

Q ss_pred             hhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCCChhhHHH
Q 041804          315 DTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA-----KGLSAKPREELG  389 (403)
Q Consensus       315 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~~~~p~~~~~~~  389 (403)
                      .++..++..+...|+++.+...++++.... +-+...|..++.+|.+.|+...|+..|+.+.+     .|+.|.+.....
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            356677777778888888888888887764 45777888888888888888888888877665     377766655444


Q ss_pred             HH
Q 041804          390 TK  391 (403)
Q Consensus       390 ~~  391 (403)
                      ..
T Consensus       233 y~  234 (280)
T COG3629         233 YE  234 (280)
T ss_pred             HH
Confidence            43

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=94.90  E-value=2.5  Score=37.24  Aligned_cols=44  Identities=7%  Similarity=0.148  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHcCC----CCChhhHHHHHHHHh
Q 041804          180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGI----KMDVVAYNTVIRAVG  223 (403)
Q Consensus       180 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~ll~~~~  223 (403)
                      =++.+.++...|.+.++..+++++...=+    ..+..+|+.++-.++
T Consensus       131 ~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vlmls  178 (549)
T PF07079_consen  131 DEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVLMLS  178 (549)
T ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHHHHh
Confidence            34556677778888888777777665422    356667776555553

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=94.86  E-value=0.036  Score=29.05  Aligned_cols=32  Identities=22%  Similarity=0.233  Sum_probs=20.3

Q ss_pred             HHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHH
Q 041804           90 FNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ  121 (403)
Q Consensus        90 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  121 (403)
                      |++.++..|.+..+|..+..++...|++++|+
T Consensus         2 y~kAie~~P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    2 YKKAIELNPNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             hHHHHHHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence            44555555556666777777777667666664

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.83  E-value=1.7  Score=34.88  Aligned_cols=194  Identities=12%  Similarity=0.014  Sum_probs=106.4

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHH
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNM  147 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (403)
                      ..|.....+|-...++++|...+.+..+..-.+...|. ..      ...+.|.-+.+++..-        +.-+..|+-
T Consensus        32 s~yekAAvafRnAk~feKakdcLlkA~~~yEnnrslfh-AA------KayEqaamLake~~kl--------sEvvdl~eK   96 (308)
T KOG1585|consen   32 SLYEKAAVAFRNAKKFEKAKDCLLKASKGYENNRSLFH-AA------KAYEQAAMLAKELSKL--------SEVVDLYEK   96 (308)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHHHHhcccHHH-HH------HHHHHHHHHHHHHHHh--------HHHHHHHHH
Confidence            35666677788888888888877776642211222221 11      2233333333333321        222334666


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc---C--CCCChhhHHHHHHHH
Q 041804          148 ILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK---G--IKMDVVAYNTVIRAV  222 (403)
Q Consensus       148 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~--~~~~~~~~~~ll~~~  222 (403)
                      ....|..+|..+.|-..+++.-+.                ..+-++++|+++|.+...-   +  ...-...+..+-+.+
T Consensus        97 As~lY~E~GspdtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~l  160 (308)
T KOG1585|consen   97 ASELYVECGSPDTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVL  160 (308)
T ss_pred             HHHHHHHhCCcchHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHh
Confidence            667788888887777776665431                2344566666666664432   1  011112344445566


Q ss_pred             hhcCCHHHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHHhcCcHHHHHHHHHhchh---cCCCCChhhHHHHHHhh
Q 041804          223 GVSEGVDFAMRVYREMREM----GCQPSV-VTCNTVIKLLCENGRVREAYAVLAEMPK---KGCVPDVITYHCFFRCL  292 (403)
Q Consensus       223 ~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~p~~~~~~~l~~~~  292 (403)
                      .+...+++|-..+.+-...    .-.++. ..|-..|-.|....++..|..+++.-..   ..-.-+..+...++.+|
T Consensus       161 Vrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay  238 (308)
T KOG1585|consen  161 VRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY  238 (308)
T ss_pred             hhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh
Confidence            6777777766555433211    111222 3355566667777899999999988432   22223566677777777

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=94.78  E-value=1.2  Score=33.16  Aligned_cols=51  Identities=12%  Similarity=0.073  Sum_probs=22.3

Q ss_pred             ccCChhHHHHHHHHhhhCCCCCCCHHHHHH-HHHHHHhcCChHHHHHHHHHHhhc
Q 041804           43 KFFEFDLSWNLIHRMKDNPSSIPNHATFRI-MFKRYVTAHLVNEAMGTFNKLDEF   96 (403)
Q Consensus        43 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~   96 (403)
                      +.++.+++..++..+.-..   |....... -...+...|++.+|+++|+.+.+.
T Consensus        22 ~~~~~~D~e~lL~ALrvLR---P~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   22 RLGDPDDAEALLDALRVLR---PEFPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             ccCChHHHHHHHHHHHHhC---CCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            4455555555555554432   32222111 122334455555555555554443

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=94.70  E-value=2.8  Score=39.24  Aligned_cols=180  Identities=13%  Similarity=0.018  Sum_probs=90.1

Q ss_pred             hhHHHHHHHHhhhCCCCCCCHHHHHHHHH----H-HHhcCChHHHHHHHHHHhh-------cCCCcHHHHHHHHHHHHhc
Q 041804           47 FDLSWNLIHRMKDNPSSIPNHATFRIMFK----R-YVTAHLVNEAMGTFNKLDE-------FGLKDEVSYCNLVDALCEY  114 (403)
Q Consensus        47 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~----~-~~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~  114 (403)
                      ...|.++++.....+    +......+..    + +....+.+.|+.+|....+       .+  .+.....+..+|.+.
T Consensus       228 ~~~a~~~~~~~a~~g----~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~--~~~a~~~lg~~Y~~g  301 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG----HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG--LPPAQYGLGRLYLQG  301 (552)
T ss_pred             hhHHHHHHHHHHhhc----chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc--CCccccHHHHHHhcC
Confidence            467888888888876    2222222222    2 4456788999999988866       22  444555666666653


Q ss_pred             C-----CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh-cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          115 K-----HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK-MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       115 ~-----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      .     +.+.|..++.+....      + .|+....-..+..... ..+...|.++|......|.. +..-+..++....
T Consensus       302 ~~~~~~d~~~A~~~~~~aA~~------g-~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~-~A~~~la~~y~~G  373 (552)
T KOG1550|consen  302 LGVEKIDYEKALKLYTKAAEL------G-NPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHI-LAIYRLALCYELG  373 (552)
T ss_pred             CCCccccHHHHHHHHHHHHhc------C-CchHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCCh-HHHHHHHHHHHhC
Confidence            2     455566666655543      1 2222222111111111 23456677777776666544 2222222221111


Q ss_pred             --HcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          189 --KSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       189 --~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                        ...+...|..++.+.-+.| .|...--...+..+.. ++++.+...+..+.+.|
T Consensus       374 ~gv~r~~~~A~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g  427 (552)
T KOG1550|consen  374 LGVERNLELAFAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAELG  427 (552)
T ss_pred             CCcCCCHHHHHHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhh
Confidence              2235566666666666665 2222222222233333 55555555555555443

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=94.58  E-value=1.9  Score=34.53  Aligned_cols=224  Identities=14%  Similarity=0.030  Sum_probs=154.2

Q ss_pred             cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhh--cCCCcHHHHHHHHHHHHhcCCHHHHH
Q 041804           44 FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDE--FGLKDEVSYCNLVDALCEYKHVIEAQ  121 (403)
Q Consensus        44 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~  121 (403)
                      .+....+...+...............+......+...+.+..+...+.....  ........+......+...+....+.
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (291)
T COG0457          36 LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEAL  115 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHH
Confidence            5667777777777776541111356777788888888888888888888776  33347777777777888888888888


Q ss_pred             HHHhcccccccccccccCcchHHHHHHHH-HHHhcCChhHHHHHHHHHHhCCC--CCcHHHHHHHHHHHHHcCChhHHHH
Q 041804          122 ELCFGENKNVGFSGLVEMNKTKIYNMILR-GWFKMSWWGKCREFWEEMDKRGV--VKDLHSYSIYMDIMCKSGKPWKAVK  198 (403)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~  198 (403)
                      ..+.......       ..+......... .+...|+++.+...+.+......  ......+......+...++.+.+..
T Consensus       116 ~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  188 (291)
T COG0457         116 ELLEKALALD-------PDPDLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALE  188 (291)
T ss_pred             HHHHHHHcCC-------CCcchHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHH
Confidence            8887776531       111222333333 78888999999999988865332  1234445555555777889999999


Q ss_pred             HHHHHHHcCCCC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          199 LYKEMKKKGIKM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       199 ~~~~~~~~~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      .+....... .. ....+..+...+...++.+.+...+......... ....+..+...+...+..+.+...+......
T Consensus       189 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         189 LLEKALKLN-PDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPD-NAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHHHHHhhC-cccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcc-cHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            998888763 33 3567777888888888899999999888876322 2344444444444677788998888887765

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=94.56  E-value=2  Score=34.73  Aligned_cols=59  Identities=19%  Similarity=0.162  Sum_probs=44.8

Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhcCCCCCH---HHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          319 MLLRKFGRWGFLRPVFVVWKKMEELGCSPDE---FAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       319 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .+.+.|.+.|.+-.|..-+++|.+. .+-+.   ..+-.+..+|...|..++|.+.-+-+..+
T Consensus       172 ~IaryY~kr~~~~AA~nR~~~v~e~-y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         172 AIARYYLKRGAYVAAINRFEEVLEN-YPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             HHHHHHHHhcChHHHHHHHHHHHhc-cccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhc
Confidence            4567789999999999999999886 33333   34556678999999999998876666553

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=94.42  E-value=0.12  Score=27.40  Aligned_cols=27  Identities=30%  Similarity=0.317  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          351 AYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       351 ~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      +|..|...|.+.|++++|++++++...
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~   27 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALA   27 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            467788889999999999999988553

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=94.29  E-value=3.8  Score=36.65  Aligned_cols=95  Identities=11%  Similarity=0.072  Sum_probs=68.5

Q ss_pred             HHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHH
Q 041804           13 RALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNK   92 (403)
Q Consensus        13 ~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~   92 (403)
                      ....+|+...  ..++.|+..|...+..+-+.+.+.+...+|..|....+..|+...+.+. .-|..+.+++.|..+|.+
T Consensus        89 rIv~lyr~at--~rf~~D~~lW~~yi~f~kk~~~~~~v~ki~~~~l~~Hp~~~dLWI~aA~-wefe~n~ni~saRalflr  165 (568)
T KOG2396|consen   89 RIVFLYRRAT--NRFNGDVKLWLSYIAFCKKKKTYGEVKKIFAAMLAKHPNNPDLWIYAAK-WEFEINLNIESARALFLR  165 (568)
T ss_pred             HHHHHHHHHH--HhcCCCHHHHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCchhHHhhhh-hHHhhccchHHHHHHHHH
Confidence            3455666665  3466799999999999999999999999999999976444444443222 233444559999999999


Q ss_pred             HhhcCCCcHHHHHHHHHH
Q 041804           93 LDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        93 ~~~~~~~~~~~~~~l~~~  110 (403)
                      -....+.++..|....+.
T Consensus       166 gLR~npdsp~Lw~eyfrm  183 (568)
T KOG2396|consen  166 GLRFNPDSPKLWKEYFRM  183 (568)
T ss_pred             HhhcCCCChHHHHHHHHH
Confidence            999888777766554443

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=94.27  E-value=1.8  Score=32.79  Aligned_cols=136  Identities=12%  Similarity=0.094  Sum_probs=90.1

Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhC-CHHHHHHHHHHHHHcCC
Q 041804          232 MRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLE-KPREILGLFDRMIESGI  310 (403)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~-~~~~a~~~~~~~~~~~~  310 (403)
                      .++++.+.+.+++|+...+..++..+.+.|++.....    +...++-+|.......+-.++ ....+.++--+|...- 
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~q----llq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL-   88 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQ----LLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRL-   88 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHH----HHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHh-
Confidence            4556667778889999999999999999988655444    445566677766666555543 3334444444444320 


Q ss_pred             CCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          311 RPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       311 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                         ...+..++..+...|++-+|..+.+...... .+   ....++++..+.++...-..+++-...++
T Consensus        89 ---~~~~~~iievLL~~g~vl~ALr~ar~~~~~~-~~---~~~~fLeAA~~~~D~~lf~~V~~ff~~~n  150 (167)
T PF07035_consen   89 ---GTAYEEIIEVLLSKGQVLEALRYARQYHKVD-SV---PARKFLEAAANSNDDQLFYAVFRFFEERN  150 (167)
T ss_pred             ---hhhHHHHHHHHHhCCCHHHHHHHHHHcCCcc-cC---CHHHHHHHHHHcCCHHHHHHHHHHHHHhh
Confidence               1145667788889999999999987754322 22   23456788888888877666776666643

>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=94.23  E-value=1.8  Score=33.32  Aligned_cols=94  Identities=13%  Similarity=0.061  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh--hhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC---C----HHH
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV--VAYNTVIRAVGVSEGVDFAMRVYREMREMGCQP---S----VVT  249 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~----~~~  249 (403)
                      .+..+...|++.|+.+.|++.|.++.+....+..  ..+-.+++...-.+++..+...+.++...--.+   +    ...
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~  117 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKV  117 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence            4455555666666666666666665554322222  234445555555566666555555544321111   1    112


Q ss_pred             HHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          250 CNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       250 ~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      |..+  .+...+++..|-..|-...
T Consensus       118 ~~gL--~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  118 YEGL--ANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHH--HHHHhchHHHHHHHHHccC
Confidence            2222  2334678888887777654

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.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.19  E-value=3  Score=35.22  Aligned_cols=86  Identities=19%  Similarity=0.322  Sum_probs=45.9

Q ss_pred             hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH--cC----ChhHHHHHHHHHHHcC---CCCChhhHHHHHHHHhhcCC-
Q 041804          158 WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK--SG----KPWKAVKLYKEMKKKG---IKMDVVAYNTVIRAVGVSEG-  227 (403)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~----~~~~a~~~~~~~~~~~---~~~~~~~~~~ll~~~~~~~~-  227 (403)
                      +++...+++.|.+.|+.-+..+|.+..-....  ..    ....+..+|+.|++.-   ..++..++..++..  ..++ 
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            34445667777777777666666553333322  12    2346777777777762   13344555555433  2333 


Q ss_pred             ---HHHHHHHHHHHHHcCCCC
Q 041804          228 ---VDFAMRVYREMREMGCQP  245 (403)
Q Consensus       228 ---~~~a~~~~~~~~~~~~~~  245 (403)
                         .+.++.+|+.+.+.|...
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~k  176 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKK  176 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCC
Confidence               234555555665555443

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=93.88  E-value=2.6  Score=33.22  Aligned_cols=187  Identities=12%  Similarity=-0.011  Sum_probs=106.5

Q ss_pred             HHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH
Q 041804           40 ILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI  118 (403)
Q Consensus        40 ~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  118 (403)
                      .|-..|-..-|.-=|.+.....   |+ +.+||.+.-.+...|+++.|.+.|+...+.++....+...-.-++.-.|++.
T Consensus        74 lYDSlGL~~LAR~DftQaLai~---P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi~~YY~gR~~  150 (297)
T COG4785          74 LYDSLGLRALARNDFSQALAIR---PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRYK  150 (297)
T ss_pred             hhhhhhHHHHHhhhhhhhhhcC---CCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhccceeeeecCchH
Confidence            3444565566666666655533   44 5678888888889999999999999999988874444444443444567887


Q ss_pred             HHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH-HHHHhCCCCCcHHHHHHHHHHHHHcCChhHHH
Q 041804          119 EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW-EEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAV  197 (403)
Q Consensus       119 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  197 (403)
                      -|.+-+...-+..     ...|-...|--+..   ..-++.+|..-+ ++....    |..-|..-|-.|.- |++. ..
T Consensus       151 LAq~d~~~fYQ~D-----~~DPfR~LWLYl~E---~k~dP~~A~tnL~qR~~~~----d~e~WG~~iV~~yL-gkiS-~e  216 (297)
T COG4785         151 LAQDDLLAFYQDD-----PNDPFRSLWLYLNE---QKLDPKQAKTNLKQRAEKS----DKEQWGWNIVEFYL-GKIS-EE  216 (297)
T ss_pred             hhHHHHHHHHhcC-----CCChHHHHHHHHHH---hhCCHHHHHHHHHHHHHhc----cHhhhhHHHHHHHH-hhcc-HH
Confidence            7777666555432     22332222222221   233455665433 333332    43344433332221 2211 11


Q ss_pred             HHHHHHHHcCC------CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          198 KLYKEMKKKGI------KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       198 ~~~~~~~~~~~------~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      .+++++....-      ..=..||--+.+.+...|+.++|..+|+-....++
T Consensus       217 ~l~~~~~a~a~~n~~~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLaiannV  268 (297)
T COG4785         217 TLMERLKADATDNTSLAEHLTETYFYLGKYYLSLGDLDEATALFKLAVANNV  268 (297)
T ss_pred             HHHHHHHhhccchHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhH
Confidence            22333322210      11246788888999999999999999998877643

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=93.62  E-value=2.1  Score=31.33  Aligned_cols=54  Identities=9%  Similarity=0.089  Sum_probs=25.2

Q ss_pred             cccHHHHHHhhhhhcccCCCcC-CHHhHHHHHHHHHccCChhHHHHHHHHhhhCC
Q 041804            8 ANDWKRALEFFNWVETDCHFTH-TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP   61 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~   61 (403)
                      .|++++|++.|+.+..+....+ ...+--.++.+|.+.+++++|...+++..+..
T Consensus        23 ~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLh   77 (142)
T PF13512_consen   23 KGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLH   77 (142)
T ss_pred             hCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC
Confidence            4455555555555543322222 22334444555555555555555555555543

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=93.56  E-value=3.2  Score=33.25  Aligned_cols=221  Identities=13%  Similarity=-0.001  Sum_probs=138.5

Q ss_pred             cCChHHHHHHHHHHhhcCCC--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC
Q 041804           80 AHLVNEAMGTFNKLDEFGLK--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW  157 (403)
Q Consensus        80 ~~~~~~a~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  157 (403)
                      .+....+...+.........  ....+......+...+....+...+.......     ........+......+...++
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~  110 (291)
T COG0457          36 LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELE-----LLPNLAEALLNLGLLLEALGK  110 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhh-----hccchHHHHHHHHHHHHHHhh
Confidence            45566666666666655544  35667777777777888887777776655310     224555666777777777788


Q ss_pred             hhHHHHHHHHHHhCCCCCcHHHHHHHHH-HHHHcCChhHHHHHHHHHHHcCC--CCChhhHHHHHHHHhhcCCHHHHHHH
Q 041804          158 WGKCREFWEEMDKRGVVKDLHSYSIYMD-IMCKSGKPWKAVKLYKEMKKKGI--KMDVVAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      +..+.+.+.........+ ......... .+...|+++.+...+........  ......+......+...++.+.+...
T Consensus       111 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  189 (291)
T COG0457         111 YEEALELLEKALALDPDP-DLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALEL  189 (291)
T ss_pred             HHHHHHHHHHHHcCCCCc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHH
Confidence            888888888887765443 222233333 67788888888888888755321  11233344444446677888888888


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC----hhhHHHHHHhhCCHHHHHHHHHHHHHc
Q 041804          235 YREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD----VITYHCFFRCLEKPREILGLFDRMIES  308 (403)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~~~a~~~~~~~~~~  308 (403)
                      +....+.........+..+...+...++++.+...+......  .|+    ...........+...++...+......
T Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         190 LEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALEL--DPDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHHHHhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhh--CcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            888877532213566777777788888888888888877764  232    111222222334567777777776654

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=93.55  E-value=0.2  Score=26.60  Aligned_cols=24  Identities=8%  Similarity=0.101  Sum_probs=14.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKL   93 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~   93 (403)
                      |+.|...|.+.|++++|+++|++.
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            555666666666666666666663

>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=93.45  E-value=0.0041  Score=46.20  Aligned_cols=84  Identities=8%  Similarity=-0.002  Sum_probs=43.8

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH  116 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  116 (403)
                      ++..+.+.+.++....+++.+...+ ...+....+.++..|++.+..++..++++....      .-...+++.|.+.|.
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~------yd~~~~~~~c~~~~l   85 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKEN-KENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN------YDLDKALRLCEKHGL   85 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTS-TC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS------S-CTHHHHHHHTTTS
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcc-cccCHHHHHHHHHHHHhcCCchHHHHHcccccc------cCHHHHHHHHHhcch
Confidence            4555555666666666666666544 234456666666666666665666655541111      222344444555555


Q ss_pred             HHHHHHHHhcc
Q 041804          117 VIEAQELCFGE  127 (403)
Q Consensus       117 ~~~a~~~~~~~  127 (403)
                      ++++.-++.++
T Consensus        86 ~~~a~~Ly~~~   96 (143)
T PF00637_consen   86 YEEAVYLYSKL   96 (143)
T ss_dssp             HHHHHHHHHCC
T ss_pred             HHHHHHHHHHc
Confidence            55555544443

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.

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.30  E-value=7.4  Score=36.74  Aligned_cols=286  Identities=12%  Similarity=0.095  Sum_probs=141.1

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC---HHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           72 IMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH---VIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        72 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .+++-+...+.+..|+++-..+...-.....+|.....-+.+..+   .+.+.++-+++..       . .-....|..+
T Consensus       442 ~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~-------~-~~~~iSy~~i  513 (829)
T KOG2280|consen  442 VVIDRLVDRHLYSVAIQVAKLLNLPESQGDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSA-------K-LTPGISYAAI  513 (829)
T ss_pred             hhhHHHHhcchhHHHHHHHHHhCCccccccHHHHHHHHHHHhccCccchHHHHHHHHHhcc-------c-CCCceeHHHH
Confidence            456677778888888888777654322245666666666665532   2222222222222       1 1334567888


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCC----CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC-----------CCCChh
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVV----KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG-----------IKMDVV  213 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----------~~~~~~  213 (403)
                      .+....+|+.+-|..+++.=...+..    .+..-+...+.-+...|+.+-...++-.+...-           .+....
T Consensus       514 A~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~~~l~~~p~a~~  593 (829)
T KOG2280|consen  514 ARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLFMTLRNQPLALS  593 (829)
T ss_pred             HHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHhchhhhH
Confidence            88888889999888877643222211    122244555666677777777777666655431           111111


Q ss_pred             hHHHHHH---------HHhhcCCHHHHHHH-HHHHHHc-CCCCCHHHHHHHHHHHHhcCcHHH----------HHHHHHh
Q 041804          214 AYNTVIR---------AVGVSEGVDFAMRV-YREMREM-GCQPSVVTCNTVIKLLCENGRVRE----------AYAVLAE  272 (403)
Q Consensus       214 ~~~~ll~---------~~~~~~~~~~a~~~-~~~~~~~-~~~~~~~~~~~li~~~~~~g~~~~----------a~~~~~~  272 (403)
                      .|.-+++         .|-...+...+-.+ ++..... -+.+-..........+.+......          -+.+.+.
T Consensus       594 lY~~~~r~~~~~~l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~~s~e~ka~ed~~kLl~lQ~~  673 (829)
T KOG2280|consen  594 LYRQFMRHQDRATLYDFYNQDDNHQALASFHLQASYAAETIEGRIPALKTAANAFAKSKEKSFEAKALEDQMKLLKLQRT  673 (829)
T ss_pred             HHHHHHHhhchhhhhhhhhcccchhhhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            2221111         01111111111111 1110000 011111122223333433332111          1122222


Q ss_pred             chh-cCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCC
Q 041804          273 MPK-KGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPD  348 (403)
Q Consensus       273 ~~~-~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  348 (403)
                      +.. .|..-...+.+--+..+   |+..+|.++-.+.    --||-..|..-+.+++..+++++-+++-+..+      .
T Consensus       674 Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~F----kipdKr~~wLk~~aLa~~~kweeLekfAkskk------s  743 (829)
T KOG2280|consen  674 LEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDF----KIPDKRLWWLKLTALADIKKWEELEKFAKSKK------S  743 (829)
T ss_pred             HHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhc----CCcchhhHHHHHHHHHhhhhHHHHHHHHhccC------C
Confidence            221 12111222222222211   4455555554443    23677788888888888888877666544332      2


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 041804          349 EFAYNALVDALIDKGMLDMARKYDEEM  375 (403)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~a~~~~~~m  375 (403)
                      +.-|..++.+|.+.|+.++|.+++-+.
T Consensus       744 PIGy~PFVe~c~~~~n~~EA~KYiprv  770 (829)
T KOG2280|consen  744 PIGYLPFVEACLKQGNKDEAKKYIPRV  770 (829)
T ss_pred             CCCchhHHHHHHhcccHHHHhhhhhcc
Confidence            456777888899999999988887654

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=93.27  E-value=2.6  Score=37.64  Aligned_cols=59  Identities=20%  Similarity=0.080  Sum_probs=49.7

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCC--cHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLK--DEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      ..+..++-+.|+.++|++.|++|.+..+.  ...+...|+.++...+.+.++..++.+..+
T Consensus       263 rRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdD  323 (539)
T PF04184_consen  263 RRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDD  323 (539)
T ss_pred             HHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcc
Confidence            34666677889999999999999876554  566889999999999999999999988754

The molecular function of this protein is uncertain.

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.18  E-value=2.6  Score=38.48  Aligned_cols=150  Identities=11%  Similarity=0.027  Sum_probs=102.6

Q ss_pred             hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCCh
Q 041804           79 TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWW  158 (403)
Q Consensus        79 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  158 (403)
                      -.|+++.|..++-.+.      ....+.+...+.++|..++|+.+-             ..|+.     -.....+.|++
T Consensus       598 mrrd~~~a~~vLp~I~------k~~rt~va~Fle~~g~~e~AL~~s-------------~D~d~-----rFelal~lgrl  653 (794)
T KOG0276|consen  598 LRRDLEVADGVLPTIP------KEIRTKVAHFLESQGMKEQALELS-------------TDPDQ-----RFELALKLGRL  653 (794)
T ss_pred             hhccccccccccccCc------hhhhhhHHhHhhhccchHhhhhcC-------------CChhh-----hhhhhhhcCcH
Confidence            3456655555443222      345566777778888888887662             22221     22345567888


Q ss_pred             hHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHH
Q 041804          159 GKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREM  238 (403)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  238 (403)
                      +.|.++..+..      +..-|..|.++....+++..|.+.|.....         |..|+-.+...|+.+....+-...
T Consensus       654 ~iA~~la~e~~------s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~~la~~~  718 (794)
T KOG0276|consen  654 DIAFDLAVEAN------SEVKWRQLGDAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLAVLASLA  718 (794)
T ss_pred             HHHHHHHHhhc------chHHHHHHHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHHHHHHHH
Confidence            88888766653      666899999999999999999988877654         456777778888887777776666


Q ss_pred             HHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          239 REMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       239 ~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      .+.|..      |....+|...|+++++.+++.+-
T Consensus       719 ~~~g~~------N~AF~~~~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  719 KKQGKN------NLAFLAYFLSGDYEECLELLIST  747 (794)
T ss_pred             Hhhccc------chHHHHHHHcCCHHHHHHHHHhc
Confidence            666543      33345667789999998888654

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=93.05  E-value=1.1  Score=29.92  Aligned_cols=45  Identities=9%  Similarity=0.146  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      ++.+-++.+...++.|+..+..+.+++|.+.+|+..|.++|+-++
T Consensus        25 e~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          25 ELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            344444444444555555555556666666666666666555554

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.

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=93.04  E-value=1.9  Score=29.20  Aligned_cols=47  Identities=9%  Similarity=0.137  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      +..+-++.+...++.|+..+..+.+++|.+.+++..|.++|+.++..
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34444455555556666666666666666666666666666665543

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 ....

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=93.01  E-value=5.7  Score=34.63  Aligned_cols=67  Identities=12%  Similarity=0.096  Sum_probs=52.9

Q ss_pred             CchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          312 PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSP---DEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       312 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      ....+|..+...+-+.|.++.|...+.++...+..+   ++...-..++.+...|+..+|+..++.....
T Consensus       144 ~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~  213 (352)
T PF02259_consen  144 ELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKC  213 (352)
T ss_pred             HHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            345678889999999999999999999988743211   3455555677788899999999999988883

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=92.97  E-value=0.14  Score=26.77  Aligned_cols=31  Identities=10%  Similarity=0.128  Sum_probs=16.5

Q ss_pred             HHHHhCCCCCcHHHHHHHHHHHHHcCChhHHH
Q 041804          166 EEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAV  197 (403)
Q Consensus       166 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  197 (403)
                      ++.++..+. +..+|+.+...|...|++++|+
T Consensus         3 ~kAie~~P~-n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    3 KKAIELNPN-NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHHCCC-CHHHHHHHHHHHHHCcCHHhhc
Confidence            334444444 5555666666666666665553

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.64  E-value=1.4  Score=36.74  Aligned_cols=103  Identities=10%  Similarity=0.023  Sum_probs=74.2

Q ss_pred             ccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC---CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChh
Q 041804          137 VEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG---VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVV  213 (403)
Q Consensus       137 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  213 (403)
                      +.+.+..+...++..-....++++++..+-++...-   ..|+.. -.+.++.+ -.-++++++.++..=+..|+-||.+
T Consensus        59 g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~-~~~~irll-lky~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWT-IHTWIRLL-LKYDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             CCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhcccc-HHHHHHHH-HccChHHHHHHHhCcchhccccchh
Confidence            344455555666666666778888888888876542   122222 22233333 3347889999999989999999999


Q ss_pred             hHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          214 AYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       214 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      +++.+|..+.+.+++..|.++.-.|...
T Consensus       137 ~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            9999999999999999999988877755

>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=92.37  E-value=3.6  Score=30.77  Aligned_cols=56  Identities=11%  Similarity=0.099  Sum_probs=34.4

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      +..-.+.++.+++..++..+.-..+. |...++.  ...+...|++.+|..+|+++...
T Consensus        17 ~~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~--~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   17 LSVALRLGDPDDAEALLDALRVLRPEFPELDLFD--GWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HHHHHccCChHHHHHHHHHHHHhCCCchHHHHHH--HHHHHHhCCHHHHHHHHHHHhcc
Confidence            34445667778888888777654332 1222222  23456778888888888887665

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=92.23  E-value=8.4  Score=34.66  Aligned_cols=59  Identities=12%  Similarity=0.080  Sum_probs=32.9

Q ss_pred             HHHHHHHHHcCChhHHHHHHHHHHHcCCC-CChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          181 SIYMDIMCKSGKPWKAVKLYKEMKKKGIK-MDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       181 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      .-+..++-+.|+.++|.+.+++|.+.... -...+...|+.++...+.+.++..++.+-.
T Consensus       263 rRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYd  322 (539)
T PF04184_consen  263 RRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYD  322 (539)
T ss_pred             HHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhc
Confidence            33445555666666666666666544211 122345556666666666666666666543

The molecular function of this protein is uncertain.

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.11  E-value=0.51  Score=24.43  Aligned_cols=28  Identities=25%  Similarity=0.285  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          350 FAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      .+|..+..+|...|++++|+..|++.++
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            3556666666667777777766666655

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 ....

>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=91.91  E-value=4.4  Score=30.72  Aligned_cols=57  Identities=19%  Similarity=0.334  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       180 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      +..+++.+...|++-+|+++.+.....    +......++.+..+.+|...-..+++-..+
T Consensus        92 ~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   92 YEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            445555566666666666665543221    111223345555555555555555544444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.87  E-value=2.1  Score=35.73  Aligned_cols=101  Identities=17%  Similarity=0.225  Sum_probs=58.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc---CCCCChhhHHHHHHhh--CCHHHHHHHHHHHHHcCCCCchhh
Q 041804          242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK---GCVPDVITYHCFFRCL--EKPREILGLFDRMIESGIRPKMDT  316 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~~~p~~~~~~~l~~~~--~~~~~a~~~~~~~~~~~~~~~~~~  316 (403)
                      |......+...++..-....+++.+...+-.++..   -..|+.. ...+++-+  -++++++.++..=+..|+-||..+
T Consensus        59 g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~-~~~~irlllky~pq~~i~~l~npIqYGiF~dqf~  137 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWT-IHTWIRLLLKYDPQKAIYTLVNPIQYGIFPDQFT  137 (418)
T ss_pred             CCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhcccc-HHHHHHHHHccChHHHHHHHhCcchhccccchhh
Confidence            33344445555555555556666666666665532   1112211 11222222  234566666666667777788888


Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          317 YVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       317 ~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      ++.+|+.+.+.+++.+|..+...|+..
T Consensus       138 ~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  138 FCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            888888888888877777776666543

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.60  E-value=0.64  Score=24.01  Aligned_cols=28  Identities=14%  Similarity=0.180  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhc
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEF   96 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~   96 (403)
                      +|..+..+|...|++++|+..|++..+.
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~~   30 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALEL   30 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHH
Confidence            3444445555555555555555554443

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 ....

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=91.28  E-value=8.8  Score=32.96  Aligned_cols=230  Identities=11%  Similarity=0.028  Sum_probs=136.8

Q ss_pred             HccCChhHHHHHHHHhhhCCC-CCCCHHHHHHHHHHHHhcCChHHHHHHHHHH----hhcCCC--cHHHHHHHHHHHHhc
Q 041804           42 GKFFEFDLSWNLIHRMKDNPS-SIPNHATFRIMFKRYVTAHLVNEAMGTFNKL----DEFGLK--DEVSYCNLVDALCEY  114 (403)
Q Consensus        42 ~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~----~~~~~~--~~~~~~~l~~~~~~~  114 (403)
                      ....+.++|+..+......-. ..--..++..+..+.++.|.+++++..--.-    .+..-.  --..|..+.+++-+.
T Consensus        17 y~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l   96 (518)
T KOG1941|consen   17 YQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKL   96 (518)
T ss_pred             hcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345666777766665554310 1112335566677777888777665432221    111111  334667777777777


Q ss_pred             CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC-----CCCcHHHHHHHHHHHHH
Q 041804          115 KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG-----VVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       115 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~  189 (403)
                      -++.+++.+-..-....+... + ..-....-++..++...+.++++++.|+...+..     .......+..|.+.|.+
T Consensus        97 ~~f~kt~~y~k~~l~lpgt~~-~-~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~  174 (518)
T KOG1941|consen   97 CEFHKTISYCKTCLGLPGTRA-G-QLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQ  174 (518)
T ss_pred             HHhhhHHHHHHHHhcCCCCCc-c-cccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHH
Confidence            777777776544433321111 1 1112334457778888889999999998875532     22234678999999999


Q ss_pred             cCChhHHHHHHHHHHHc----CCCCChh-hHH-----HHHHHHhhcCCHHHHHHHHHHHHH----cCCCCC-HHHHHHHH
Q 041804          190 SGKPWKAVKLYKEMKKK----GIKMDVV-AYN-----TVIRAVGVSEGVDFAMRVYREMRE----MGCQPS-VVTCNTVI  254 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~----~~~~~~~-~~~-----~ll~~~~~~~~~~~a~~~~~~~~~----~~~~~~-~~~~~~li  254 (403)
                      ..|+++|.-+.....+.    ++. |.. -|.     .+.-++...|....|.+.-++..+    .|-.+. ......+.
T Consensus       175 l~D~~Kal~f~~kA~~lv~s~~l~-d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~a  253 (518)
T KOG1941|consen  175 LKDYEKALFFPCKAAELVNSYGLK-DWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFA  253 (518)
T ss_pred             HHhhhHHhhhhHhHHHHHHhcCcC-chhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHH
Confidence            99999998776665432    222 221 122     233455667777777777766554    342222 23455677


Q ss_pred             HHHHhcCcHHHHHHHHHhch
Q 041804          255 KLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       255 ~~~~~~g~~~~a~~~~~~~~  274 (403)
                      +.|...|+.+.|+.-|+...
T Consensus       254 DIyR~~gd~e~af~rYe~Am  273 (518)
T KOG1941|consen  254 DIYRSRGDLERAFRRYEQAM  273 (518)
T ss_pred             HHHHhcccHhHHHHHHHHHH
Confidence            88889999999988887643

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.24  E-value=0.7  Score=23.76  Aligned_cols=27  Identities=26%  Similarity=0.257  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          351 AYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       351 ~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      .|..+...+.+.|++++|++.+++.++
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            455566666777777777777776655

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 ....

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.23  E-value=0.75  Score=23.64  Aligned_cols=26  Identities=23%  Similarity=0.204  Sum_probs=11.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhh
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDE   95 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~   95 (403)
                      |..+..++...|++++|++.|++..+
T Consensus         4 ~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    4 WYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            33444444444444444444444443

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 ....

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=91.18  E-value=2.9  Score=32.61  Aligned_cols=72  Identities=6%  Similarity=-0.006  Sum_probs=31.3

Q ss_pred             hHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc---CCCCChhhHHHHHHHHhhcCCHHHH
Q 041804          159 GKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK---GIKMDVVAYNTVIRAVGVSEGVDFA  231 (403)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~ll~~~~~~~~~~~a  231 (403)
                      +.|.+.|-++...+.--++.....|...|. ..+.+++..++....+.   +-.+|+..+.+|+..+.+.++.+.|
T Consensus       123 ~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  123 QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            344444444444443323333333333332 34455555555444433   1234444555555555555544444

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=91.17  E-value=4.7  Score=29.67  Aligned_cols=49  Identities=10%  Similarity=-0.208  Sum_probs=18.7

Q ss_pred             cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhccc
Q 041804           80 AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGEN  128 (403)
Q Consensus        80 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  128 (403)
                      .++++++..++..|.-..|.....-..-...+...|++++|..+|+++.
T Consensus        23 ~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~   71 (153)
T TIGR02561        23 SADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILRELL   71 (153)
T ss_pred             cCCHHHHHHHHHHHHHhCCCccccchhHHHHHHHcCCHHHHHHHHHhhh
Confidence            3344444444444443333322222222233334444444444444433

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=91.15  E-value=0.73  Score=25.10  Aligned_cols=29  Identities=28%  Similarity=0.256  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          349 EFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      ..+++.+...|...|++++|..++++...
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            35778888889999999999999888765

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=90.97  E-value=8.2  Score=32.08  Aligned_cols=118  Identities=6%  Similarity=0.030  Sum_probs=86.1

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHc-c-CChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGK-F-FEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEA   86 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~-~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a   86 (403)
                      .-..+|+++|+....+..+-.|..+...+++.... . .....--++.+-+...-+..++..+.-.++..++..+++.+-
T Consensus       142 ~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl  221 (292)
T PF13929_consen  142 KIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKL  221 (292)
T ss_pred             HHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHH
Confidence            34567788887544222345577777777777665 2 233334445555554422467888888999999999999999


Q ss_pred             HHHHHHHhhc-CCC-cHHHHHHHHHHHHhcCCHHHHHHHHhc
Q 041804           87 MGTFNKLDEF-GLK-DEVSYCNLVDALCEYKHVIEAQELCFG  126 (403)
Q Consensus        87 ~~~~~~~~~~-~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~  126 (403)
                      .++++..... ++. |...|..+++.....|+..-..++..+
T Consensus       222 ~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  222 FQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            9999988777 444 999999999999999999998888765

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=90.96  E-value=2.6  Score=28.21  Aligned_cols=62  Identities=11%  Similarity=0.047  Sum_probs=47.8

Q ss_pred             hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHH
Q 041804          158 WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIR  220 (403)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~  220 (403)
                      .=++.+-++.+...+..|++....+.+++|-+.+++..|.++|+-.+.. ...+...|..+++
T Consensus        23 ~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K-~~~~~~~y~~~lq   84 (103)
T cd00923          23 GWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK-CGAHKEIYPYILQ   84 (103)
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccCchhhHHHHHH
Confidence            3456777788888888999999999999999999999999999987754 1224445665554

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.

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.92  E-value=4.3  Score=37.22  Aligned_cols=151  Identities=9%  Similarity=0.014  Sum_probs=88.0

Q ss_pred             HccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHH
Q 041804           42 GKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ  121 (403)
Q Consensus        42 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  121 (403)
                      .-.|+++.|..++..+++        ...+.+...+.+.|-.++|+++-       ..+..-|.    ...+.|+++.|.
T Consensus       597 vmrrd~~~a~~vLp~I~k--------~~rt~va~Fle~~g~~e~AL~~s-------~D~d~rFe----lal~lgrl~iA~  657 (794)
T KOG0276|consen  597 VLRRDLEVADGVLPTIPK--------EIRTKVAHFLESQGMKEQALELS-------TDPDQRFE----LALKLGRLDIAF  657 (794)
T ss_pred             hhhccccccccccccCch--------hhhhhHHhHhhhccchHhhhhcC-------CChhhhhh----hhhhcCcHHHHH
Confidence            345777777666555432        23344555566667666666542       11112222    234567777777


Q ss_pred             HHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHH
Q 041804          122 ELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYK  201 (403)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  201 (403)
                      ++..+.            .+..-|..|.++....+++..|.+.|.....         |..|+-.+...|+-+....+-.
T Consensus       658 ~la~e~------------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d---------~~~LlLl~t~~g~~~~l~~la~  716 (794)
T KOG0276|consen  658 DLAVEA------------NSEVKWRQLGDAALSAGELPLASECFLRARD---------LGSLLLLYTSSGNAEGLAVLAS  716 (794)
T ss_pred             HHHHhh------------cchHHHHHHHHHHhhcccchhHHHHHHhhcc---------hhhhhhhhhhcCChhHHHHHHH
Confidence            765443            2334477788888888888888887776652         4456666666777665555555


Q ss_pred             HHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHH
Q 041804          202 EMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREM  238 (403)
Q Consensus       202 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  238 (403)
                      ...+.| +.|.     ..-+|...|+++++.+++..-
T Consensus       717 ~~~~~g-~~N~-----AF~~~~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  717 LAKKQG-KNNL-----AFLAYFLSGDYEECLELLIST  747 (794)
T ss_pred             HHHhhc-ccch-----HHHHHHHcCCHHHHHHHHHhc
Confidence            555555 2232     223455677887777776544

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=90.89  E-value=15  Score=34.99  Aligned_cols=89  Identities=15%  Similarity=0.154  Sum_probs=44.9

Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHh--
Q 041804          183 YMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG-CQPSVVTCNTVIKLLCE--  259 (403)
Q Consensus       183 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~li~~~~~--  259 (403)
                      ....+.-.|.++.|.+.+-.  ..+...+.+.+...+.-|.-.+-.+...   ..+.... -.|...-+..||..|.+  
T Consensus       264 Yf~~LlLtgqFE~AI~~L~~--~~~~~~dAVH~AIaL~~~gLL~~~~~~~---~~lls~~~~~~~~ln~arLI~~Y~~~F  338 (613)
T PF04097_consen  264 YFQVLLLTGQFEAAIEFLYR--NEFNRVDAVHFAIALAYYGLLRVSDSSS---APLLSVDPGDPPPLNFARLIGQYTRSF  338 (613)
T ss_dssp             HHHHHHHTT-HHHHHHHHHT----T-HHHHHHHHHHHHHTT---------------------------HHHHHHHHHHTT
T ss_pred             HHHHHHHHhhHHHHHHHHHh--hccCcccHHHHHHHHHHcCCCCCCCccc---cceeeecCCCCCCcCHHHHHHHHHHHH
Confidence            44556678999999988876  2234556777776666654433322222   2222211 11222567788888876  


Q ss_pred             -cCcHHHHHHHHHhchhc
Q 041804          260 -NGRVREAYAVLAEMPKK  276 (403)
Q Consensus       260 -~g~~~~a~~~~~~~~~~  276 (403)
                       ..+...|.++|--+...
T Consensus       339 ~~td~~~Al~Y~~li~~~  356 (613)
T PF04097_consen  339 EITDPREALQYLYLICLF  356 (613)
T ss_dssp             TTT-HHHHHHHHHGGGGS
T ss_pred             hccCHHHHHHHHHHHHHc
Confidence             45788888888877654

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=90.51  E-value=7.4  Score=30.79  Aligned_cols=182  Identities=11%  Similarity=-0.066  Sum_probs=106.9

Q ss_pred             hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCCh
Q 041804           79 TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWW  158 (403)
Q Consensus        79 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  158 (403)
                      ..|-..-|.-=|.......|.-+.+||-+.--+...|+++.|.+.|+...+-      ...-+-...|.-+ .+.--|++
T Consensus        77 SlGL~~LAR~DftQaLai~P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~EL------Dp~y~Ya~lNRgi-~~YY~gR~  149 (297)
T COG4785          77 SLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL------DPTYNYAHLNRGI-ALYYGGRY  149 (297)
T ss_pred             hhhHHHHHhhhhhhhhhcCCCcHHHHHHHHHHHHhcccchHHHHHhhhHhcc------CCcchHHHhccce-eeeecCch
Confidence            3444555555566666666668889999999999999999999999987764      1112222222222 23346889


Q ss_pred             hHHHHHHHHHHhCCCC-CcHHHHHHHHHHHHHcCChhHHHHHHH-HHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHH
Q 041804          159 GKCREFWEEMDKRGVV-KDLHSYSIYMDIMCKSGKPWKAVKLYK-EMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYR  236 (403)
Q Consensus       159 ~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~-~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  236 (403)
                      +-|.+-|.+.-..+.. |-...|.-+.   -..-++.+|..-+. +...    .|..-|...|-.|. .|++. ...+++
T Consensus       150 ~LAq~d~~~fYQ~D~~DPfR~LWLYl~---E~k~dP~~A~tnL~qR~~~----~d~e~WG~~iV~~y-LgkiS-~e~l~~  220 (297)
T COG4785         150 KLAQDDLLAFYQDDPNDPFRSLWLYLN---EQKLDPKQAKTNLKQRAEK----SDKEQWGWNIVEFY-LGKIS-EETLME  220 (297)
T ss_pred             HhhHHHHHHHHhcCCCChHHHHHHHHH---HhhCCHHHHHHHHHHHHHh----ccHhhhhHHHHHHH-Hhhcc-HHHHHH
Confidence            9998877777665443 2223333332   23446666665443 3332    25445544444332 12211 111222


Q ss_pred             HHHHcC------CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          237 EMREMG------CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       237 ~~~~~~------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      .+....      .+.-..||--+.+-+...|+.++|..+|+-....
T Consensus       221 ~~~a~a~~n~~~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLaian  266 (297)
T COG4785         221 RLKADATDNTSLAEHLTETYFYLGKYYLSLGDLDEATALFKLAVAN  266 (297)
T ss_pred             HHHhhccchHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence            222111      0123568888999999999999999999987765

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=90.21  E-value=4.3  Score=27.58  Aligned_cols=78  Identities=4%  Similarity=-0.031  Sum_probs=46.9

Q ss_pred             HhHHHHHHHHHccCC--hhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           32 DTYNSVIDILGKFFE--FDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        32 ~~~~~li~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      ..|..--..+....+  .-+..+-++.+...+ ..|++....+.+++|-+.+++..|.++|+-++..-......|..+++
T Consensus         9 eeF~ary~~~F~~~~iD~we~rrglN~l~~~D-lVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~lq   87 (108)
T PF02284_consen    9 EEFDARYEKYFNRPDIDGWELRRGLNNLFGYD-LVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHHHH-TT--HHHHHHHHHHHTTSS-B---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHHH
T ss_pred             HHHHHHHHHHhCCccccHHHHHHHHHHHhccc-cCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHHH
Confidence            334443344443333  335666777777766 67888888888888888888888888888877654333336665554


Q ss_pred             H
Q 041804          110 A  110 (403)
Q Consensus       110 ~  110 (403)
                      -
T Consensus        88 E   88 (108)
T PF02284_consen   88 E   88 (108)
T ss_dssp             H
T ss_pred             H
Confidence            3

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 ....

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=90.09  E-value=14  Score=33.40  Aligned_cols=166  Identities=13%  Similarity=0.079  Sum_probs=89.6

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      .|....-+++..++.+....-++.+..+|...| .+...+..++++|... ..+.-..+++++.+.        .-+..+
T Consensus        64 l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~-e~kmal~el~q~y~en-~n~~l~~lWer~ve~--------dfnDvv  133 (711)
T COG1747          64 LDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG-ESKMALLELLQCYKEN-GNEQLYSLWERLVEY--------DFNDVV  133 (711)
T ss_pred             ccchHHHHHHHHhccchHHHHHHHHHHHHHHhc-chHHHHHHHHHHHHhc-CchhhHHHHHHHHHh--------cchhHH
Confidence            455556666677777766777777777776654 3555666677777666 444555555555442        122222


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCC-----CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc-CCCCChhhHHHH
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVV-----KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-GIKMDVVAYNTV  218 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l  218 (403)
                      ...-+.-+...++.+.+..+|.++..+=++     .-...|.-+...  -..+.+..+.+..+.... |...-...+.-+
T Consensus       134 ~~ReLa~~yEkik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~--i~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv  211 (711)
T COG1747         134 IGRELADKYEKIKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPEL--IGDDKDFFLRLQKKIQTKLGEGRGSVLMQDV  211 (711)
T ss_pred             HHHHHHHHHHHhchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHh--ccccHHHHHHHHHHHHHhhccchHHHHHHHH
Confidence            233333333336666666666665443211     011233333321  123455555555555544 333344455555


Q ss_pred             HHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          219 IRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       219 l~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      -.-|....++++|.+++..+.+..
T Consensus       212 ~~~Ys~~eN~~eai~Ilk~il~~d  235 (711)
T COG1747         212 YKKYSENENWTEAIRILKHILEHD  235 (711)
T ss_pred             HHHhccccCHHHHHHHHHHHhhhc
Confidence            666777778888888887766653

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=89.95  E-value=2.6  Score=33.19  Aligned_cols=58  Identities=12%  Similarity=0.035  Sum_probs=26.7

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhc
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEF   96 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~   96 (403)
                      .++.+.+.+++++++...+.-.+..  +.|...-..++..++-.|++++|..-++-.-..
T Consensus         7 t~seLL~~~sL~dai~~a~~qVkak--Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l   64 (273)
T COG4455           7 TISELLDDNSLQDAIGLARDQVKAK--PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATL   64 (273)
T ss_pred             HHHHHHHhccHHHHHHHHHHHHhcC--CccccchhHHHHHHhhcchHHHHHHHHHHHhhc
Confidence            3444445555555555544443332  223334444455555555555555444444333

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=89.95  E-value=10  Score=31.55  Aligned_cols=117  Identities=16%  Similarity=0.167  Sum_probs=58.4

Q ss_pred             cCChHHHHHHHHHHhhc-CC-CcHHHHHHHHHHHHh-cCC-HHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           80 AHLVNEAMGTFNKLDEF-GL-KDEVSYCNLVDALCE-YKH-VIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        80 ~~~~~~a~~~~~~~~~~-~~-~~~~~~~~l~~~~~~-~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      +..+.+|+++|+..... .+ .|+.+...+++.... .+. ...--++.+-+....     +..++..+....+..+++.
T Consensus       141 N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~-----~~~l~~~vi~~Il~~L~~~  215 (292)
T PF13929_consen  141 NKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTF-----SKSLTRNVIISILEILAES  215 (292)
T ss_pred             hHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhcc-----ccCCChhHHHHHHHHHHhc
Confidence            33455677777643322 12 277777777776665 221 111111111111111     2344555555566666666


Q ss_pred             CChhHHHHHHHHHHhC-CCCCcHHHHHHHHHHHHHcCChhHHHHHHH
Q 041804          156 SWWGKCREFWEEMDKR-GVVKDLHSYSIYMDIMCKSGKPWKAVKLYK  201 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  201 (403)
                      ++|.+-.++++..... ++.-|...|..+|+.-...|+..-..++.+
T Consensus       216 ~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  216 RDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             ccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhh
Confidence            6666666666555444 444455566666666666666554444443

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=89.70  E-value=15  Score=32.98  Aligned_cols=132  Identities=8%  Similarity=-0.015  Sum_probs=84.5

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH  116 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  116 (403)
                      -|.-....|++-.|-+-+.....+-...|+...  .....+...|+++.+.+.+....+.-.....+...+++.....|+
T Consensus       295 si~k~~~~gd~~aas~~~~~~lr~~~~~p~~i~--l~~~i~~~lg~ye~~~~~~s~~~~~~~s~~~~~~~~~r~~~~l~r  372 (831)
T PRK15180        295 SITKQLADGDIIAASQQLFAALRNQQQDPVLIQ--LRSVIFSHLGYYEQAYQDISDVEKIIGTTDSTLRCRLRSLHGLAR  372 (831)
T ss_pred             HHHHHhhccCHHHHHHHHHHHHHhCCCCchhhH--HHHHHHHHhhhHHHHHHHhhchhhhhcCCchHHHHHHHhhhchhh
Confidence            344455667777665544444443223344433  334456778999999988877765444477788888999999999


Q ss_pred             HHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH
Q 041804          117 VIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL  177 (403)
Q Consensus       117 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  177 (403)
                      ++.|...-..+...       ...+..+........-..|-++++.-.|+++...+.+.+.
T Consensus       373 ~~~a~s~a~~~l~~-------eie~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~~~~~~  426 (831)
T PRK15180        373 WREALSTAEMMLSN-------EIEDEEVLTVAAGSADALQLFDKSYHYWKRVLLLNPETQS  426 (831)
T ss_pred             HHHHHHHHHHHhcc-------ccCChhheeeecccHHHHhHHHHHHHHHHHHhccCChhcc
Confidence            99999887777653       2223333333334444557788888888888776554333

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=89.69  E-value=9.2  Score=34.16  Aligned_cols=126  Identities=10%  Similarity=-0.055  Sum_probs=90.1

Q ss_pred             HHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHH
Q 041804           74 FKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWF  153 (403)
Q Consensus        74 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  153 (403)
                      |.--...|+.-.|-+-+.......+.++.............|+++.+...+.....       .......+...+++...
T Consensus       296 i~k~~~~gd~~aas~~~~~~lr~~~~~p~~i~l~~~i~~~lg~ye~~~~~~s~~~~-------~~~s~~~~~~~~~r~~~  368 (831)
T PRK15180        296 ITKQLADGDIIAASQQLFAALRNQQQDPVLIQLRSVIFSHLGYYEQAYQDISDVEK-------IIGTTDSTLRCRLRSLH  368 (831)
T ss_pred             HHHHhhccCHHHHHHHHHHHHHhCCCCchhhHHHHHHHHHhhhHHHHHHHhhchhh-------hhcCCchHHHHHHHhhh
Confidence            33344567777776666666665555555555555566788999999988776654       33445567788999999


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC
Q 041804          154 KMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG  207 (403)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  207 (403)
                      +.|+++.|...-+.|....++ +...........-..|-++++...|+++...+
T Consensus       369 ~l~r~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~  421 (831)
T PRK15180        369 GLARWREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLLN  421 (831)
T ss_pred             chhhHHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhccC
Confidence            999999999999999888777 55555555455556677888888888886653

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=89.42  E-value=5  Score=27.16  Aligned_cols=88  Identities=10%  Similarity=0.086  Sum_probs=62.4

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMG   88 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~   88 (403)
                      ..+++|.-+-+|+.. .+.. ...+--.-+..+...|++++|..+.+.+.     .||...|..|-.  .+.|..+.+..
T Consensus        19 HcHqEA~tIAdwL~~-~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~-----~pdlepw~ALce--~rlGl~s~l~~   89 (115)
T TIGR02508        19 HCHQEANTIADWLHL-KGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLC-----YPDLEPWLALCE--WRLGLGSALES   89 (115)
T ss_pred             hHHHHHHHHHHHHhc-CCch-HHHHHHHHHHHHHccchHHHHHHhcCCCC-----CchHHHHHHHHH--HhhccHHHHHH
Confidence            467899999999985 2111 22223334566788999999999887773     489988877654  67788888888


Q ss_pred             HHHHHhhcCCCcHHHHH
Q 041804           89 TFNKLDEFGLKDEVSYC  105 (403)
Q Consensus        89 ~~~~~~~~~~~~~~~~~  105 (403)
                      .+.+|...|.+....|.
T Consensus        90 rl~rla~sg~p~lq~Fa  106 (115)
T TIGR02508        90 RLNRLAASGDPRLQTFV  106 (115)
T ss_pred             HHHHHHhCCCHHHHHHH
Confidence            88888887776444443

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.

>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=89.12  E-value=7.4  Score=30.44  Aligned_cols=74  Identities=9%  Similarity=0.078  Sum_probs=54.9

Q ss_pred             ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC----cHHHHHHHHHHHHhcCCHHHHH
Q 041804           46 EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK----DEVSYCNLVDALCEYKHVIEAQ  121 (403)
Q Consensus        46 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~  121 (403)
                      .-+.|...|-.+...+ ..-++. ....+..|-...+.++++.++.+..+...+    |+..+.+|+..+.+.++.+.|-
T Consensus       121 ~d~~A~~~fL~~E~~~-~l~t~e-lq~aLAtyY~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  121 GDQEALRRFLQLEGTP-ELETAE-LQYALATYYTKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             CcHHHHHHHHHHcCCC-CCCCHH-HHHHHHHHHHccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            4567888888888776 223444 444444555578899999999988765432    8899999999999999998874

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=89.08  E-value=12  Score=31.14  Aligned_cols=59  Identities=12%  Similarity=0.126  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHH
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREM  238 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  238 (403)
                      +++...+.|..+|.+.+|.++-+...... +.+...+..++..+...||--.+.+.++.+
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltld-pL~e~~nk~lm~~la~~gD~is~~khyery  339 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLD-PLSEQDNKGLMASLATLGDEISAIKHYERY  339 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcC-hhhhHHHHHHHHHHHHhccchhhhhHHHHH
Confidence            34444556666666666666666665553 445556666666666666655555555444

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=89.06  E-value=11  Score=37.65  Aligned_cols=17  Identities=29%  Similarity=0.294  Sum_probs=12.9

Q ss_pred             ccccHHHHHHhhhhhcc
Q 041804            7 YANDWKRALEFFNWVET   23 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~   23 (403)
                      .+.|+++=+.+++.+.+
T Consensus       863 SqkDPkEyLP~L~el~~  879 (1265)
T KOG1920|consen  863 SQKDPKEYLPFLNELKK  879 (1265)
T ss_pred             hccChHHHHHHHHHHhh
Confidence            35688888888888764

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=88.89  E-value=1.3  Score=24.09  Aligned_cols=28  Identities=14%  Similarity=0.163  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDE   95 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~   95 (403)
                      .+++.+...|...|++++|+.++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            3556666666666666666666665543

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.78  E-value=23  Score=33.93  Aligned_cols=151  Identities=11%  Similarity=0.029  Sum_probs=89.9

Q ss_pred             ccccHHHHHHhhhhhcccCCCcC---CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            7 YANDWKRALEFFNWVETDCHFTH---TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      ..+.+++|++.-+....   ..|   -.......|..+.-.|++++|-...-.|..     .+...|..-...+...++.
T Consensus       368 ~~k~yeeAl~~~k~~~~---~~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~g-----n~~~eWe~~V~~f~e~~~l  439 (846)
T KOG2066|consen  368 EKKKYEEALDAAKASIG---NEERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLG-----NNAAEWELWVFKFAELDQL  439 (846)
T ss_pred             HhhHHHHHHHHHHhccC---CccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhc-----chHHHHHHHHHHhcccccc
Confidence            34677888887766542   333   345677778888888999998888888765     4566666666666666654


Q ss_pred             HHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccc----------cccccCcchHHHHHHHHHH
Q 041804           84 NEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGF----------SGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----------~~~~~~~~~~~~~~l~~~~  152 (403)
                      ...   +.-+....+. ++..|..++-.+.. .+...-.++..+...+.-.          .-.....+...-..|+..|
T Consensus       440 ~~I---a~~lPt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q~Se~~~L~e~La~LY  515 (846)
T KOG2066|consen  440 TDI---APYLPTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTIISATEPQIKQNSESTALLEVLAHLY  515 (846)
T ss_pred             chh---hccCCCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHHhhcchHHHhhccchhHHHHHHHHH
Confidence            432   2223333333 67778777777766 3333333333222211100          0001112223345688899


Q ss_pred             HhcCChhHHHHHHHHHH
Q 041804          153 FKMSWWGKCREFWEEMD  169 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~  169 (403)
                      ...+++..|.+++-...
T Consensus       516 l~d~~Y~~Al~~ylklk  532 (846)
T KOG2066|consen  516 LYDNKYEKALPIYLKLQ  532 (846)
T ss_pred             HHccChHHHHHHHHhcc
Confidence            99999999988876665

>PF09477 Type_III_YscG: Bacterial type II secretion system chaperone protein (type_III_yscG); InterPro: IPR013348 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)

Probab=88.62  E-value=6.1  Score=27.13  Aligned_cols=87  Identities=10%  Similarity=0.106  Sum_probs=54.5

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMG   88 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~   88 (403)
                      ..+++|-.+.+|+.... . ....+--..+..+...|++++|  +..-...   ..||...|..|-.  .+.|-.+++..
T Consensus        20 HcH~EA~tIa~wL~~~~-~-~~E~v~lIr~~sLmNrG~Yq~A--Ll~~~~~---~~pdL~p~~AL~a--~klGL~~~~e~   90 (116)
T PF09477_consen   20 HCHQEANTIADWLEQEG-E-MEEVVALIRLSSLMNRGDYQEA--LLLPQCH---CYPDLEPWAALCA--WKLGLASALES   90 (116)
T ss_dssp             T-HHHHHHHHHHHHHTT-T-THHHHHHHHHHHHHHTT-HHHH--HHHHTTS-----GGGHHHHHHHH--HHCT-HHHHHH
T ss_pred             HHHHHHHHHHHHHHhCC-c-HHHHHHHHHHHHHHhhHHHHHH--HHhcccC---CCccHHHHHHHHH--HhhccHHHHHH
Confidence            46889999999998622 1 1223333445667899999999  3222222   3588887766544  68899999999


Q ss_pred             HHHHHhhcCCCcHHHH
Q 041804           89 TFNKLDEFGLKDEVSY  104 (403)
Q Consensus        89 ~~~~~~~~~~~~~~~~  104 (403)
                      .+.++...|.+....|
T Consensus        91 ~l~rla~~g~~~~q~F  106 (116)
T PF09477_consen   91 RLTRLASSGSPELQAF  106 (116)
T ss_dssp             HHHHHCT-SSHHHHHH
T ss_pred             HHHHHHhCCCHHHHHH
Confidence            9988887776544333

The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia, and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens.; GO: 0009405 pathogenesis; PDB: 3PH0_D 2UWJ_G 2P58_C.

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=88.48  E-value=13  Score=30.60  Aligned_cols=179  Identities=13%  Similarity=0.077  Sum_probs=78.2

Q ss_pred             CCcCCHHhHHHHHHHH-HccCChhHHHHHHHHhhhCCCCCC--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhc---CCC
Q 041804           26 HFTHTTDTYNSVIDIL-GKFFEFDLSWNLIHRMKDNPSSIP--NHATFRIMFKRYVTAHLVNEAMGTFNKLDEF---GLK   99 (403)
Q Consensus        26 ~~~~~~~~~~~li~~~-~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~   99 (403)
                      +-.||+..-|..-..- .+..++++|+.-|+...+..+-+-  ...+...++..+.+.+++++....|.++...   .+.
T Consensus        21 ~sEpdVDlENQYYnsK~l~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVT  100 (440)
T KOG1464|consen   21 NSEPDVDLENQYYNSKGLKEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAVT  100 (440)
T ss_pred             CCCCCcchHhhhhccccccccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHh
Confidence            3345554443332221 233456666666666665431111  1234445666666666666666666655421   111


Q ss_pred             ---cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC----
Q 041804          100 ---DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG----  172 (403)
Q Consensus       100 ---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----  172 (403)
                         +....+++++..+...+.+-....++.-.....-.. ....=-.+-.-|...|...+++.+..+++.++...-    
T Consensus       101 rNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAK-NeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~ed  179 (440)
T KOG1464|consen  101 RNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAK-NERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTED  179 (440)
T ss_pred             ccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhh-cceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhcccc
Confidence               334445555544444443333332221111000000 000000112334455555666666666666654321    


Q ss_pred             -CC------CcHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          173 -VV------KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       173 -~~------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                       -.      .=...|..=|..|....+-.+-..+|++...
T Consensus       180 GedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalh  219 (440)
T KOG1464|consen  180 GEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALH  219 (440)
T ss_pred             CchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHH
Confidence             00      0123455555555556665555666665543

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=88.44  E-value=43  Score=36.75  Aligned_cols=62  Identities=15%  Similarity=-0.039  Sum_probs=49.1

Q ss_pred             hhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          314 MDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       314 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      ..+|....+..-+.|.++.|...+-...+.+ .  +..+--....+...|+...|+.++++....
T Consensus      1670 ge~wLqsAriaR~aG~~q~A~nall~A~e~r-~--~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~ 1731 (2382)
T KOG0890|consen 1670 GECWLQSARIARLAGHLQRAQNALLNAKESR-L--PEIVLERAKLLWQTGDELNALSVLQEILSK 1731 (2382)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHhhhhcc-c--chHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            3567788888888999999998877777664 2  345555667788999999999999998865

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=88.23  E-value=1.2  Score=25.00  Aligned_cols=26  Identities=38%  Similarity=0.512  Sum_probs=21.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          354 ALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       354 ~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                      .|..+|...|+.+.|.+++++....|
T Consensus         4 dLA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         4 DLARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHcC
Confidence            35788999999999999999988654

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>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=87.79  E-value=0.3  Score=36.17  Aligned_cols=84  Identities=7%  Similarity=0.103  Sum_probs=36.2

Q ss_pred             HHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 041804          184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRV  263 (403)
Q Consensus       184 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  263 (403)
                      +..+.+.+.+.....+++.+...+...+....+.++..|++.++.+...++++.       .+..-...++..|.+.|.+
T Consensus        14 i~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~-------~~~yd~~~~~~~c~~~~l~   86 (143)
T PF00637_consen   14 ISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKT-------SNNYDLDKALRLCEKHGLY   86 (143)
T ss_dssp             HHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTS-------SSSS-CTHHHHHHHTTTSH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHccc-------ccccCHHHHHHHHHhcchH
Confidence            333444444555555555555443333444445555555555444444444441       0111122334444445555


Q ss_pred             HHHHHHHHhch
Q 041804          264 REAYAVLAEMP  274 (403)
Q Consensus       264 ~~a~~~~~~~~  274 (403)
                      +.+.-++.++.
T Consensus        87 ~~a~~Ly~~~~   97 (143)
T PF00637_consen   87 EEAVYLYSKLG   97 (143)
T ss_dssp             HHHHHHHHCCT
T ss_pred             HHHHHHHHHcc
Confidence            55555555443

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.

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=87.75  E-value=7.6  Score=30.28  Aligned_cols=57  Identities=14%  Similarity=0.055  Sum_probs=23.7

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..++.+.+.++.|++--...++.++. ...+..--..+|.+..++++|+.=|+.+.+.
T Consensus       141 aaa~iKl~k~e~aI~dcsKaiel~pt-y~kAl~RRAeayek~ek~eealeDyKki~E~  197 (271)
T KOG4234|consen  141 AAALIKLRKWESAIEDCSKAIELNPT-YEKALERRAEAYEKMEKYEEALEDYKKILES  197 (271)
T ss_pred             HHHHHHhhhHHHHHHHHHhhHhcCch-hHHHHHHHHHHHHhhhhHHHHHHHHHHHHHh
Confidence            33444444444444444444443322 1111222223444445555555555555544

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=87.46  E-value=22  Score=32.27  Aligned_cols=164  Identities=16%  Similarity=0.148  Sum_probs=122.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHH
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHS  179 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  179 (403)
                      |.....+++..+..+..+.-.+.+..++..-        ..+...|-.++.+|... ..+.-..+|+++.+..+. |+..
T Consensus        65 ~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~--------~e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~  134 (711)
T COG1747          65 DDSCLVTLLTIFGDNHKNQIVEHLCTRVLEY--------GESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVI  134 (711)
T ss_pred             cchHHHHHHHHhccchHHHHHHHHHHHHHHh--------cchHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHH
Confidence            6677888888888888888888888877653        45677889999999988 678889999999998777 7766


Q ss_pred             HHHHHHHHHHcCChhHHHHHHHHHHHcCCC-----CChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc-CCCCCHHHHHHH
Q 041804          180 YSIYMDIMCKSGKPWKAVKLYKEMKKKGIK-----MDVVAYNTVIRAVGVSEGVDFAMRVYREMREM-GCQPSVVTCNTV  253 (403)
Q Consensus       180 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l  253 (403)
                      -..|...|-+ ++.+.+...|......=++     .-...|.-+....  ..+.+...++...+.+. |...-...+.-+
T Consensus       135 ~ReLa~~yEk-ik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~i--~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv  211 (711)
T COG1747         135 GRELADKYEK-IKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPELI--GDDKDFFLRLQKKIQTKLGEGRGSVLMQDV  211 (711)
T ss_pred             HHHHHHHHHH-hchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhc--cccHHHHHHHHHHHHHhhccchHHHHHHHH
Confidence            6777776666 8888899999888766222     1123455554322  56778888888777654 444445666667


Q ss_pred             HHHHHhcCcHHHHHHHHHhchhc
Q 041804          254 IKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       254 i~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      -.-|....++++|++++..+.+.
T Consensus       212 ~~~Ys~~eN~~eai~Ilk~il~~  234 (711)
T COG1747         212 YKKYSENENWTEAIRILKHILEH  234 (711)
T ss_pred             HHHhccccCHHHHHHHHHHHhhh
Confidence            78888999999999999987764

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=87.19  E-value=2.4  Score=21.70  Aligned_cols=28  Identities=25%  Similarity=0.195  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          350 FAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      .+|..+...|...|++++|...|++.++
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3566777888888888888888888765

...

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=87.19  E-value=1.6  Score=36.79  Aligned_cols=88  Identities=11%  Similarity=-0.022  Sum_probs=61.2

Q ss_pred             HHHHccCChhHHHHHHHHhhhCCCCCC-CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH
Q 041804           39 DILGKFFEFDLSWNLIHRMKDNPSSIP-NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV  117 (403)
Q Consensus        39 ~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (403)
                      .-|.++|.+++|++.|..-....   | |.+++..-..+|.+...+..|+.=.+.....+-.-..+|..-+.+-...|..
T Consensus       105 N~yFKQgKy~EAIDCYs~~ia~~---P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd~~Y~KAYSRR~~AR~~Lg~~  181 (536)
T KOG4648|consen  105 NTYFKQGKYEEAIDCYSTAIAVY---PHNPVYHINRALAYLKQKSFAQAEEDCEAAIALDKLYVKAYSRRMQARESLGNN  181 (536)
T ss_pred             hhhhhccchhHHHHHhhhhhccC---CCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHHHHhhH
Confidence            35778889999999998877754   5 7788888888888888888887766666654433445555555555566666


Q ss_pred             HHHHHHHhcccc
Q 041804          118 IEAQELCFGENK  129 (403)
Q Consensus       118 ~~a~~~~~~~~~  129 (403)
                      .+|.+-++....
T Consensus       182 ~EAKkD~E~vL~  193 (536)
T KOG4648|consen  182 MEAKKDCETVLA  193 (536)
T ss_pred             HHHHHhHHHHHh
Confidence            666665555443

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=86.96  E-value=3.7  Score=34.76  Aligned_cols=93  Identities=8%  Similarity=-0.094  Sum_probs=65.2

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVN   84 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~   84 (403)
                      +..+|++++|++.|.....  -.+.|+..+..-..+|.+..++..|..=.......+  ..-..+|..-+.+-...|...
T Consensus       107 yFKQgKy~EAIDCYs~~ia--~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd--~~Y~KAYSRR~~AR~~Lg~~~  182 (536)
T KOG4648|consen  107 YFKQGKYEEAIDCYSTAIA--VYPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALD--KLYVKAYSRRMQARESLGNNM  182 (536)
T ss_pred             hhhccchhHHHHHhhhhhc--cCCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhh--HHHHHHHHHHHHHHHHHhhHH
Confidence            5678999999999987763  234488999999999999999988877666665532  112334555555555566777


Q ss_pred             HHHHHHHHHhhcCCCcH
Q 041804           85 EAMGTFNKLDEFGLKDE  101 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~  101 (403)
                      +|.+=++..++..+.+.
T Consensus       183 EAKkD~E~vL~LEP~~~  199 (536)
T KOG4648|consen  183 EAKKDCETVLALEPKNI  199 (536)
T ss_pred             HHHHhHHHHHhhCcccH
Confidence            77777777777665533

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=86.67  E-value=20  Score=30.93  Aligned_cols=99  Identities=7%  Similarity=0.022  Sum_probs=71.9

Q ss_pred             cCCHHhHHHHHHHHHccCC------------hhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhh
Q 041804           28 THTTDTYNSVIDILGKFFE------------FDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDE   95 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~------------~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~   95 (403)
                      +.|+.+|-.++..--..-.            .+.-+.++++..+.+  +.+...+...|..+.+..+.+...+.++++..
T Consensus        16 P~di~~Wl~li~~Qd~~~~~~~~~~~~~~a~~E~klsilerAL~~n--p~~~~L~l~~l~~~~~~~~~~~l~~~we~~l~   93 (321)
T PF08424_consen   16 PHDIEAWLELIEFQDELFRLQSSSKAERRALAERKLSILERALKHN--PDSERLLLGYLEEGEKVWDSEKLAKKWEELLF   93 (321)
T ss_pred             cccHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            5578888888765443321            355677888887775  35677788889999999999999999999999


Q ss_pred             cCCCcHHHHHHHHHHHHh---cCCHHHHHHHHhccc
Q 041804           96 FGLKDEVSYCNLVDALCE---YKHVIEAQELCFGEN  128 (403)
Q Consensus        96 ~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~  128 (403)
                      ..+.+...|...+.....   .-.++....+|.+..
T Consensus        94 ~~~~~~~LW~~yL~~~q~~~~~f~v~~~~~~y~~~l  129 (321)
T PF08424_consen   94 KNPGSPELWREYLDFRQSNFASFTVSDVRDVYEKCL  129 (321)
T ss_pred             HCCCChHHHHHHHHHHHHHhccCcHHHHHHHHHHHH
Confidence            887788888888887665   224555555554443

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=86.30  E-value=11  Score=29.42  Aligned_cols=61  Identities=11%  Similarity=0.050  Sum_probs=27.4

Q ss_pred             HHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC
Q 041804           36 SVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL   98 (403)
Q Consensus        36 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   98 (403)
                      .-..++.+.+.++.|+.-.....+.+  +....+...-..+|.+...++.|+.=|.++.+..+
T Consensus       139 Nraaa~iKl~k~e~aI~dcsKaiel~--pty~kAl~RRAeayek~ek~eealeDyKki~E~dP  199 (271)
T KOG4234|consen  139 NRAAALIKLRKWESAIEDCSKAIELN--PTYEKALERRAEAYEKMEKYEEALEDYKKILESDP  199 (271)
T ss_pred             hhHHHHHHhhhHHHHHHHHHhhHhcC--chhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCc
Confidence            33344445555555555554444433  11122222223344555555555555555555444

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=86.04  E-value=33  Score=32.82  Aligned_cols=89  Identities=13%  Similarity=0.075  Sum_probs=37.6

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh---cC
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT---AH   81 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~   81 (403)
                      +...|+++.|++++...   .....+...+...+..|.-.+-.+...   ..+.......|...-+..||..|.+   ..
T Consensus       268 LlLtgqFE~AI~~L~~~---~~~~~dAVH~AIaL~~~gLL~~~~~~~---~~lls~~~~~~~~ln~arLI~~Y~~~F~~t  341 (613)
T PF04097_consen  268 LLLTGQFEAAIEFLYRN---EFNRVDAVHFAIALAYYGLLRVSDSSS---APLLSVDPGDPPPLNFARLIGQYTRSFEIT  341 (613)
T ss_dssp             HHHTT-HHHHHHHHHT-----T-HHHHHHHHHHHHHTT---------------------------HHHHHHHHHHTTTTT
T ss_pred             HHHHhhHHHHHHHHHhh---ccCcccHHHHHHHHHHcCCCCCCCccc---cceeeecCCCCCCcCHHHHHHHHHHHHhcc
Confidence            34457778888777652   223444555544444433222211111   2222221111222456778888876   35


Q ss_pred             ChHHHHHHHHHHhhcCCC
Q 041804           82 LVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~   99 (403)
                      ++..|.+.|--+....-+
T Consensus       342 d~~~Al~Y~~li~~~~~~  359 (613)
T PF04097_consen  342 DPREALQYLYLICLFKDP  359 (613)
T ss_dssp             -HHHHHHHHHGGGGS-SC
T ss_pred             CHHHHHHHHHHHHHcCCc
Confidence            778888888777665443

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=85.86  E-value=1.3  Score=21.32  Aligned_cols=21  Identities=33%  Similarity=0.311  Sum_probs=12.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHH
Q 041804          353 NALVDALIDKGMLDMARKYDE  373 (403)
Q Consensus       353 ~~l~~~~~~~g~~~~a~~~~~  373 (403)
                      ..+..++...|++++|..+++
T Consensus         5 ~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    5 LALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHcCCHHHHHHHHh
Confidence            345566666666666666554

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=85.73  E-value=1.7  Score=24.30  Aligned_cols=23  Identities=22%  Similarity=0.302  Sum_probs=12.8

Q ss_pred             HHHHHHhcCcHHHHHHHHHhchh
Q 041804          253 VIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       253 li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      +..+|...|+.+.|.++++++..
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~   27 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIE   27 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHH
Confidence            34555555555555555555554

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=85.70  E-value=30  Score=32.04  Aligned_cols=346  Identities=13%  Similarity=0.072  Sum_probs=185.9

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHH-ccCChhHHHHHHHHhhhCCCC-CCCHHHHHHHHHHHHhcCChHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILG-KFFEFDLSWNLIHRMKDNPSS-IPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~-~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      -|..+.+.++|+.-.  .+++.+...|......+. ..|+.+...+.|++....-+. --+...|...|.--..++++..
T Consensus        92 lg~~~~s~~Vfergv--~aip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~  169 (577)
T KOG1258|consen   92 LGNAENSVKVFERGV--QAIPLSVDLWLSYLAFLKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKR  169 (577)
T ss_pred             hhhHHHHHHHHHHHH--HhhhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHHH
Confidence            356677788888777  566777777766665544 456777777788777664321 2344567777777777888888


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhc------CCHHHHHHHHhccccc--cc------------ccccccCcc--hH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEY------KHVIEAQELCFGENKN--VG------------FSGLVEMNK--TK  143 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~------~~~~~a~~~~~~~~~~--~~------------~~~~~~~~~--~~  143 (403)
                      ...+|+++++.....-.-|-....-+...      -..+++.++-......  ..            ......+.+  ..
T Consensus       170 v~~iyeRileiP~~~~~~~f~~f~~~l~~~~~~~l~~~d~~~~l~~~~~~~~~~~~~~~~~e~~~~~v~~~~~~s~~l~~  249 (577)
T KOG1258|consen  170 VANIYERILEIPLHQLNRHFDRFKQLLNQNEEKILLSIDELIQLRSDVAERSKITHSQEPLEELEIGVKDSTDPSKSLTE  249 (577)
T ss_pred             HHHHHHHHHhhhhhHhHHHHHHHHHHHhcCChhhhcCHHHHHHHhhhHHhhhhcccccChhHHHHHHHhhccCccchhhH
Confidence            88888888775443211111111111111      1222222221111100  00            000000000  00


Q ss_pred             HHHHHHHH-------HHhcCChhHHHHHHHHHHhCC-------CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCC
Q 041804          144 IYNMILRG-------WFKMSWWGKCREFWEEMDKRG-------VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK  209 (403)
Q Consensus       144 ~~~~l~~~-------~~~~~~~~~a~~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  209 (403)
                      ..+.+...       +............|+.-.++-       ..++..+|...+..-...|+++.+.-+|+...-. +.
T Consensus       250 ~~~~l~~~~~~~~~~~~~s~~~~~kr~~fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~-cA  328 (577)
T KOG1258|consen  250 EKTILKRIVSIHEKVYQKSEEEEEKRWGFEEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIP-CA  328 (577)
T ss_pred             HHHHHHHHHHHHHHHHHhhHhHHHHHHhhhhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhH-Hh
Confidence            11111111       111111222222233322221       1235578888888889999999999998887532 11


Q ss_pred             CChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChh----
Q 041804          210 MDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ--PSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVI----  283 (403)
Q Consensus       210 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~----  283 (403)
                      .=...|--.+.-....|+.+.|..++....+-..+  |....+.+.+  .-..|++..|..+++.+.+.-  |+..    
T Consensus       329 ~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~i~L~~a~f--~e~~~n~~~A~~~lq~i~~e~--pg~v~~~l  404 (577)
T KOG1258|consen  329 LYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPIIHLLEARF--EESNGNFDDAKVILQRIESEY--PGLVEVVL  404 (577)
T ss_pred             hhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcHHHHHHHHH--HHhhccHHHHHHHHHHHHhhC--CchhhhHH
Confidence            11223333344344459999999888877765443  3333344333  334789999999999988752  5432    


Q ss_pred             hHHHHHHhhCCHHHHH---HHHHHHHHcCCCCchhhHHHHHHH-----HHhcCCcchHHHHHHHHHhcCCCCCHHHHHHH
Q 041804          284 TYHCFFRCLEKPREIL---GLFDRMIESGIRPKMDTYVMLLRK-----FGRWGFLRPVFVVWKKMEELGCSPDEFAYNAL  355 (403)
Q Consensus       284 ~~~~l~~~~~~~~~a~---~~~~~~~~~~~~~~~~~~~~li~~-----~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  355 (403)
                      -+..+....++.+.+.   +++........  +..+...+.--     +.-.++.+.|..++.++.+. .+++...|..+
T Consensus       405 ~~~~~e~r~~~~~~~~~~~~l~s~~~~~~~--~~~i~~~l~~~~~r~~~~i~~d~~~a~~~l~~~~~~-~~~~k~~~~~~  481 (577)
T KOG1258|consen  405 RKINWERRKGNLEDANYKNELYSSIYEGKE--NNGILEKLYVKFARLRYKIREDADLARIILLEANDI-LPDCKVLYLEL  481 (577)
T ss_pred             HHHhHHHHhcchhhhhHHHHHHHHhccccc--CcchhHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhc-CCccHHHHHHH
Confidence            2233344445555554   33333222111  22222222222     33457889999999999876 47778888888


Q ss_pred             HHHHHhcC
Q 041804          356 VDALIDKG  363 (403)
Q Consensus       356 ~~~~~~~g  363 (403)
                      ++.....+
T Consensus       482 ~~~~~~~~  489 (577)
T KOG1258|consen  482 IRFELIQP  489 (577)
T ss_pred             HHHHHhCC
Confidence            88766655

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=85.66  E-value=32  Score=32.39  Aligned_cols=185  Identities=9%  Similarity=0.023  Sum_probs=112.2

Q ss_pred             cHHHHHHhhhhhcccCCCcCCHHhHHHHHHH-----HHccCChhHHHHHHHHhhhC---CCCCCCHHHHHHHHHHHHhcC
Q 041804           10 DWKRALEFFNWVETDCHFTHTTDTYNSVIDI-----LGKFFEFDLSWNLIHRMKDN---PSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus        10 ~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~-----~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      +...|.+.++.... .   -+...-..+..+     +....+++.|..+|+...+.   ...+-...+..-+..+|.+..
T Consensus       227 ~~~~a~~~~~~~a~-~---g~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~~~~a~~~lg~~Y~~g~  302 (552)
T KOG1550|consen  227 ELSEAFKYYREAAK-L---GHSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKGLPPAQYGLGRLYLQGL  302 (552)
T ss_pred             hhhHHHHHHHHHHh-h---cchHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhcCCccccHHHHHHhcCC
Confidence            45678888887775 2   233332233222     34667999999999988761   001113335666777777643


Q ss_pred             -----ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh-cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHH--
Q 041804           82 -----LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE-YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWF--  153 (403)
Q Consensus        82 -----~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~--  153 (403)
                           +.+.|+.+|...-+.|.++...+...+..... ..+...|.++|......      +..+   .+-.+..+|.  
T Consensus       303 ~~~~~d~~~A~~~~~~aA~~g~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~------G~~~---A~~~la~~y~~G  373 (552)
T KOG1550|consen  303 GVEKIDYEKALKLYTKAAELGNPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKA------GHIL---AIYRLALCYELG  373 (552)
T ss_pred             CCccccHHHHHHHHHHHHhcCCchHHHHHHHHHHcCCccccHHHHHHHHHHHHHc------CChH---HHHHHHHHHHhC
Confidence                 66779999999998887766555444444333 34678999999888764      3222   2222222221  


Q ss_pred             --hcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCC
Q 041804          154 --KMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK  209 (403)
Q Consensus       154 --~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  209 (403)
                        -..+...|..++.+..+.|.. ...--...+..+.. ++++.+.-.+..+...|..
T Consensus       374 ~gv~r~~~~A~~~~k~aA~~g~~-~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g~~  429 (552)
T KOG1550|consen  374 LGVERNLELAFAYYKKAAEKGNP-SAAYLLGAFYEYGV-GRYDTALALYLYLAELGYE  429 (552)
T ss_pred             CCcCCCHHHHHHHHHHHHHccCh-hhHHHHHHHHHHcc-ccccHHHHHHHHHHHhhhh
Confidence              234678888999988888732 32222233334444 7777777777777766533

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=85.42  E-value=1.2  Score=22.67  Aligned_cols=23  Identities=13%  Similarity=0.199  Sum_probs=11.5

Q ss_pred             HHHHHHccCChhHHHHHHHHhhh
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKD   59 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~   59 (403)
                      +..++.+.|++++|.+.|+++..
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~   28 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIK   28 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHH
Confidence            34444445555555555555544

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=84.97  E-value=2  Score=21.70  Aligned_cols=29  Identities=17%  Similarity=0.096  Sum_probs=20.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCC
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGL   98 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   98 (403)
                      +-.+..++.+.|++++|.+.|+++.+..|
T Consensus         3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~P   31 (33)
T PF13174_consen    3 LYRLARCYYKLGDYDEAIEYFQRLIKRYP   31 (33)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHCc
Confidence            34456677777888888888888776544

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=84.95  E-value=32  Score=31.81  Aligned_cols=326  Identities=10%  Similarity=0.064  Sum_probs=181.9

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH-HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH-ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      +...++.+|.---...+.+.+..+++.+...-   |.. --|......=.+.|..+.+.++|++-...-+.....|....
T Consensus        44 ~f~~wt~li~~~~~~~~~~~~r~~y~~fL~ky---Pl~~gyW~kfA~~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~  120 (577)
T KOG1258|consen   44 DFDAWTTLIQENDSIEDVDALREVYDIFLSKY---PLCYGYWKKFADYEYKLGNAENSVKVFERGVQAIPLSVDLWLSYL  120 (577)
T ss_pred             cccchHHHHhccCchhHHHHHHHHHHHHHhhC---ccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            44556666665555556677788888888653   554 35777777777889999999999998864433777777776


Q ss_pred             HHHH-hcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHH
Q 041804          109 DALC-EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIM  187 (403)
Q Consensus       109 ~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  187 (403)
                      ..+. ..|+.+.....|+......+    ..-.+...|...+..-...+++.....+++++++.    ....|+.....|
T Consensus       121 ~f~~n~~~d~~~lr~~fe~A~~~vG----~dF~S~~lWdkyie~en~qks~k~v~~iyeRilei----P~~~~~~~f~~f  192 (577)
T KOG1258|consen  121 AFLKNNNGDPETLRDLFERAKSYVG----LDFLSDPLWDKYIEFENGQKSWKRVANIYERILEI----PLHQLNRHFDRF  192 (577)
T ss_pred             HHHhccCCCHHHHHHHHHHHHHhcc----cchhccHHHHHHHHHHhccccHHHHHHHHHHHHhh----hhhHhHHHHHHH
Confidence            6655 46777788888877766442    22345566888888888889999999999999875    233344333333


Q ss_pred             HH---c------CChhHHHHHHHHHHHc---C-CCCChhhHHHHH------------------HH-------HhhcCCHH
Q 041804          188 CK---S------GKPWKAVKLYKEMKKK---G-IKMDVVAYNTVI------------------RA-------VGVSEGVD  229 (403)
Q Consensus       188 ~~---~------~~~~~a~~~~~~~~~~---~-~~~~~~~~~~ll------------------~~-------~~~~~~~~  229 (403)
                      .+   .      ...+++.++-......   + ..+.......-+                  ..       +-......
T Consensus       193 ~~~l~~~~~~~l~~~d~~~~l~~~~~~~~~~~~~~~~~e~~~~~v~~~~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~  272 (577)
T KOG1258|consen  193 KQLLNQNEEKILLSIDELIQLRSDVAERSKITHSQEPLEELEIGVKDSTDPSKSLTEEKTILKRIVSIHEKVYQKSEEEE  272 (577)
T ss_pred             HHHHhcCChhhhcCHHHHHHHhhhHHhhhhcccccChhHHHHHHHhhccCccchhhHHHHHHHHHHHHHHHHHHhhHhHH
Confidence            22   1      1233333332222210   0 000111111111                  11       11111111


Q ss_pred             HHHHHHHHHHHc---CCC----CCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC-C--hhhHHHHHHhhCCHHHHH
Q 041804          230 FAMRVYREMREM---GCQ----PSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP-D--VITYHCFFRCLEKPREIL  299 (403)
Q Consensus       230 ~a~~~~~~~~~~---~~~----~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p-~--~~~~~~l~~~~~~~~~a~  299 (403)
                      .....|+.-.+.   .++    +...+|+..+..-...|+.+.+.-+|++..-. +.. +  -.-|...+...++.+-+.
T Consensus       273 ~kr~~fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~-cA~Y~efWiky~~~m~~~~~~~~~~  351 (577)
T KOG1258|consen  273 EKRWGFEEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIP-CALYDEFWIKYARWMESSGDVSLAN  351 (577)
T ss_pred             HHHHhhhhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhH-HhhhHHHHHHHHHHHHHcCchhHHH
Confidence            222222222211   111    23567888888888888888888888876531 000 1  112233344456666565


Q ss_pred             HHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHH-HHHHHHHHHHhcCCHHHHH
Q 041804          300 GLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEF-AYNALVDALIDKGMLDMAR  369 (403)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~a~  369 (403)
                      .++....+-..+-.+.+-..-...+-..|++..|..+++.+.+.-  |+.. .-..-+....+.|..+.+.
T Consensus       352 ~~~~~~~~i~~k~~~~i~L~~a~f~e~~~n~~~A~~~lq~i~~e~--pg~v~~~l~~~~~e~r~~~~~~~~  420 (577)
T KOG1258|consen  352 NVLARACKIHVKKTPIIHLLEARFEESNGNFDDAKVILQRIESEY--PGLVEVVLRKINWERRKGNLEDAN  420 (577)
T ss_pred             HHHHhhhhhcCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHhhC--CchhhhHHHHHhHHHHhcchhhhh
Confidence            555555443333222222222222345678999999999887753  4432 2223345566778887777

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=84.85  E-value=18  Score=28.79  Aligned_cols=93  Identities=13%  Similarity=0.053  Sum_probs=65.9

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      .+..++.+.+.+...+++...+.-.+..+.+...-..+++.++-.|++++|..-++-...-..    ...+....|..++
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p----~~t~~a~lyr~li   79 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSP----QDTVGASLYRHLI   79 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCc----ccchHHHHHHHHH
Confidence            445567788889999999999998888888888899999999999999999877665433211    3345566777777


Q ss_pred             HHHHhcCChhHHHHHHHHHHhCC
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRG  172 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~  172 (403)
                      .+-.-.      .++|.--...|
T Consensus        80 r~ea~R------~evfag~~~Pg   96 (273)
T COG4455          80 RCEAAR------NEVFAGGAVPG   96 (273)
T ss_pred             HHHHHH------HHHhccCCCCC
Confidence            654322      34555544444

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=84.61  E-value=9.1  Score=27.23  Aligned_cols=47  Identities=11%  Similarity=0.128  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      +..+-+..+...++.|+..+....+++|.+.+|+..|.++|+-++..
T Consensus        67 EvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K  113 (149)
T KOG4077|consen   67 EVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDK  113 (149)
T ss_pred             HHHHHHHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            34455556666677777777777777777777777777777776643

>PRK09687 putative lyase; Provisional

Probab=84.32  E-value=24  Score=29.74  Aligned_cols=60  Identities=17%  Similarity=0.088  Sum_probs=29.1

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh----HHHHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV----NEAMGTFNKL   93 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~   93 (403)
                      +|.......+..+...|..+ +...+..+...    +|...-...+.+++..|+.    .++...+..+
T Consensus        35 ~d~~vR~~A~~aL~~~~~~~-~~~~l~~ll~~----~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l   98 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGGQD-VFRLAIELCSS----KNPIERDIGADILSQLGMAKRCQDNVFNILNNL   98 (280)
T ss_pred             CCHHHHHHHHHHHHhcCcch-HHHHHHHHHhC----CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHH
Confidence            45555555555665555432 33333333321    4555555555666666553    3455555444

>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function

Probab=84.23  E-value=26  Score=30.19  Aligned_cols=64  Identities=16%  Similarity=0.065  Sum_probs=34.1

Q ss_pred             CcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH---cCChhHHHHHHHHH
Q 041804          139 MNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK---SGKPWKAVKLYKEM  203 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~  203 (403)
                      +.+....-.++..+.+..+.+...+-|+++....+. +...|...+.....   .-.++.+..+|.+.
T Consensus        62 p~~~~L~l~~l~~~~~~~~~~~l~~~we~~l~~~~~-~~~LW~~yL~~~q~~~~~f~v~~~~~~y~~~  128 (321)
T PF08424_consen   62 PDSERLLLGYLEEGEKVWDSEKLAKKWEELLFKNPG-SPELWREYLDFRQSNFASFTVSDVRDVYEKC  128 (321)
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHCCC-ChHHHHHHHHHHHHHhccCcHHHHHHHHHHH
Confidence            345555566666666666666666666666665433 45555555554433   12344444444443

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=84.12  E-value=18  Score=30.14  Aligned_cols=60  Identities=17%  Similarity=0.082  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhccc
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGEN  128 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  128 (403)
                      +++...+.|..+|.+.+|.++-++....++-+...+..++..+...|+--.+.+-++.+.
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltldpL~e~~nk~lm~~la~~gD~is~~khyerya  340 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLDPLSEQDNKGLMASLATLGDEISAIKHYERYA  340 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcChhhhHHHHHHHHHHHHhccchhhhhHHHHHH
Confidence            445566789999999999999999999987799999999999999999777766655543

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.08  E-value=18  Score=28.18  Aligned_cols=117  Identities=12%  Similarity=0.004  Sum_probs=67.2

Q ss_pred             HHHHHHHHHhhcCCCcHH-HH--HHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHH
Q 041804           85 EAMGTFNKLDEFGLKDEV-SY--CNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC  161 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~-~~--~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  161 (403)
                      +.....+++......+.+ ++  ..+...+...+++++|+..++.......    .......+--.|.+.....|.+++|
T Consensus        70 ~~~~~~ekf~~~n~~t~Ya~laaL~lAk~~ve~~~~d~A~aqL~~~l~~t~----De~lk~l~~lRLArvq~q~~k~D~A  145 (207)
T COG2976          70 KSIAAAEKFVQANGKTIYAVLAALELAKAEVEANNLDKAEAQLKQALAQTK----DENLKALAALRLARVQLQQKKADAA  145 (207)
T ss_pred             hhHHHHHHHHhhccccHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccch----hHHHHHHHHHHHHHHHHHhhhHHHH
Confidence            444555555554433222 22  2344556677788888777776553310    1111222333455666777888888


Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG  207 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  207 (403)
                      ...++.....+..+  .....-.+.+...|+-++|..-|+.....+
T Consensus       146 L~~L~t~~~~~w~~--~~~elrGDill~kg~k~~Ar~ay~kAl~~~  189 (207)
T COG2976         146 LKTLDTIKEESWAA--IVAELRGDILLAKGDKQEARAAYEKALESD  189 (207)
T ss_pred             HHHHhccccccHHH--HHHHHhhhHHHHcCchHHHHHHHHHHHHcc
Confidence            88877776653331  123334567778888888888888877764

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=83.84  E-value=23  Score=29.43  Aligned_cols=56  Identities=5%  Similarity=-0.051  Sum_probs=22.7

Q ss_pred             HHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       184 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      |.+++..+++.+++...-+..+..-+....+...-|-.|.+.+.+..+.++-..-.
T Consensus        90 IQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL  145 (309)
T PF07163_consen   90 IQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWL  145 (309)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            34444445555544443333322111122223333334445555554444444443

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=83.81  E-value=3.9  Score=20.89  Aligned_cols=27  Identities=15%  Similarity=0.170  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      +|..+...|...|++++|.+.|++..+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            344555555566666666666555544

...

>PRK10941 hypothetical protein; Provisional

Probab=83.40  E-value=16  Score=30.43  Aligned_cols=78  Identities=8%  Similarity=-0.071  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      ..+.+-.+|.+.++++.|+++.+.+....+.++.-+.--.-.|.+.|.+..|..=++......     ...|+.......
T Consensus       183 ml~nLK~~~~~~~~~~~AL~~~e~ll~l~P~dp~e~RDRGll~~qL~c~~~A~~DL~~fl~~~-----P~dp~a~~ik~q  257 (269)
T PRK10941        183 LLDTLKAALMEEKQMELALRASEALLQFDPEDPYEIRDRGLIYAQLDCEHVALSDLSYFVEQC-----PEDPISEMIRAQ  257 (269)
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHhC-----CCchhHHHHHHH
Confidence            456677788999999999999999999998899988888888999999999998877776643     344554444444


Q ss_pred             HHH
Q 041804          149 LRG  151 (403)
Q Consensus       149 ~~~  151 (403)
                      +..
T Consensus       258 l~~  260 (269)
T PRK10941        258 IHS  260 (269)
T ss_pred             HHH
Confidence            333

>PRK09687 putative lyase; Provisional

Probab=83.04  E-value=27  Score=29.41  Aligned_cols=217  Identities=13%  Similarity=0.004  Sum_probs=137.2

Q ss_pred             cchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCCh----hHHHHHHHHHHHcCCCCChhhH
Q 041804          140 NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKP----WKAVKLYKEMKKKGIKMDVVAY  215 (403)
Q Consensus       140 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~~  215 (403)
                      ++..+....+..+...|.. .+...+..+...   +|...-...+.++...|+.    .++...+..+...  .++..+-
T Consensus        35 ~d~~vR~~A~~aL~~~~~~-~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR  108 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGGQ-DVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVR  108 (280)
T ss_pred             CCHHHHHHHHHHHHhcCcc-hHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHH
Confidence            4555666666777766653 333444444433   4666667777788888764    4677777776444  4566666


Q ss_pred             HHHHHHHhhcCCH-----HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH
Q 041804          216 NTVIRAVGVSEGV-----DFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR  290 (403)
Q Consensus       216 ~~ll~~~~~~~~~-----~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  290 (403)
                      ...+.+++..+..     ..+...+.....   .++..+-...+.++.+.++ +.+...+-.+.+.   ++...-...+.
T Consensus       109 ~~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---D~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L~d---~~~~VR~~A~~  181 (280)
T PRK09687        109 ASAINATGHRCKKNPLYSPKIVEQSQITAF---DKSTNVRFAVAFALSVIND-EAAIPLLINLLKD---PNGDVRNWAAF  181 (280)
T ss_pred             HHHHHHHhcccccccccchHHHHHHHHHhh---CCCHHHHHHHHHHHhccCC-HHHHHHHHHHhcC---CCHHHHHHHHH
Confidence            6777777665421     223333333333   3466666777888888887 4666776666653   45555555666


Q ss_pred             hhCC----HHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHH
Q 041804          291 CLEK----PREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLD  366 (403)
Q Consensus       291 ~~~~----~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  366 (403)
                      ++|+    ..++...+..+..   .++..+-...+.++.+.|+. .|...+-...+.+   +  .....+.++...|.. 
T Consensus       182 aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~---~--~~~~a~~ALg~ig~~-  251 (280)
T PRK09687        182 ALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKG---T--VGDLIIEAAGELGDK-  251 (280)
T ss_pred             HHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCC---c--hHHHHHHHHHhcCCH-
Confidence            6664    3356665555553   45777788888999999884 5666655555543   2  245678899999985 


Q ss_pred             HHHHHHHHHHHcC
Q 041804          367 MARKYDEEMFAKG  379 (403)
Q Consensus       367 ~a~~~~~~m~~~~  379 (403)
                      +|...+..+.+..
T Consensus       252 ~a~p~L~~l~~~~  264 (280)
T PRK09687        252 TLLPVLDTLLYKF  264 (280)
T ss_pred             hHHHHHHHHHhhC
Confidence            7899999888744

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=82.92  E-value=45  Score=31.91  Aligned_cols=198  Identities=11%  Similarity=0.085  Sum_probs=89.8

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhh-cCCC---cHHHHHHHHHHHH-hcCCHHHHHHHHhcccccccccccccC
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDE-FGLK---DEVSYCNLVDALC-EYKHVIEAQELCFGENKNVGFSGLVEM  139 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~---~~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~~~  139 (403)
                      .+...|..||.         .|+++++.+.+ ..++   ...++..+...+. ...+++.|+..+.+........+ -..
T Consensus        28 ~~l~~Y~kLI~---------~ai~CL~~~~~~~~l~p~~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~-~~d   97 (608)
T PF10345_consen   28 EQLKQYYKLIA---------TAIKCLEAVLKQFKLSPRQEARVRLRLASILLEETENLDLAETYLEKAILLCERHR-LTD   97 (608)
T ss_pred             hhHHHHHHHHH---------HHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccc-hHH
Confidence            34445555554         45555555552 2222   3444555555555 45667777776665433210000 000


Q ss_pred             cchHHHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCCcHHHHHHH-HHHHHHcCChhHHHHHHHHHHHcC---CCCC
Q 041804          140 NKTKIYNMILRGWFKMSWWGKCREFWEEMDKR----GVVKDLHSYSIY-MDIMCKSGKPWKAVKLYKEMKKKG---IKMD  211 (403)
Q Consensus       140 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~---~~~~  211 (403)
                      ..-..-..++..+.+.+... |.+.+++..+.    +..+-...+..+ +..+...+++..|.+.++.+...-   ..|-
T Consensus        98 ~k~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~  176 (608)
T PF10345_consen   98 LKFRCQFLLARIYFKTNPKA-ALKNLDKAIEDSETYGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPA  176 (608)
T ss_pred             HHHHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHH
Confidence            01122234455555555544 66666654432    112222333333 222223367777777776665442   2233


Q ss_pred             hhhHHHHHHHHh--hcCCHHHHHHHHHHHHHcCC---------CCCHHHHHHHHHHHH--hcCcHHHHHHHHHhc
Q 041804          212 VVAYNTVIRAVG--VSEGVDFAMRVYREMREMGC---------QPSVVTCNTVIKLLC--ENGRVREAYAVLAEM  273 (403)
Q Consensus       212 ~~~~~~ll~~~~--~~~~~~~a~~~~~~~~~~~~---------~~~~~~~~~li~~~~--~~g~~~~a~~~~~~~  273 (403)
                      ..++..++.+..  +.+..+++.+.++.+.....         .|-..+|..+++.++  ..|+++.+...++++
T Consensus       177 ~~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~l  251 (608)
T PF10345_consen  177 VFVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQL  251 (608)
T ss_pred             HHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            334444444333  33445555555555532211         123445555554433  456655555554443

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=82.79  E-value=31  Score=29.99  Aligned_cols=28  Identities=21%  Similarity=0.176  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          248 VTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       248 ~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      .+|..+...+.+.|.++.|...+..+..
T Consensus       147 ~~~l~~a~~aRk~g~~~~A~~~l~~~~~  174 (352)
T PF02259_consen  147 ETWLKFAKLARKAGNFQLALSALNRLFQ  174 (352)
T ss_pred             HHHHHHHHHHHHCCCcHHHHHHHHHHhc
Confidence            3444555555555555555555555544

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=82.73  E-value=46  Score=31.86  Aligned_cols=200  Identities=7%  Similarity=-0.006  Sum_probs=117.4

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH--HHHHHHHHHHH-hcCChHHHHHHHHHHhhcCCC----c
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH--ATFRIMFKRYV-TAHLVNEAMGTFNKLDEFGLK----D  100 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~l~~~~~-~~~~~~~a~~~~~~~~~~~~~----~  100 (403)
                      +.+...|..||..         |++.++.+.+....+|..  .++-.+...+. ...+++.|+..+++.......    +
T Consensus        27 ~~~l~~Y~kLI~~---------ai~CL~~~~~~~~l~p~~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d   97 (608)
T PF10345_consen   27 EEQLKQYYKLIAT---------AIKCLEAVLKQFKLSPRQEARVRLRLASILLEETENLDLAETYLEKAILLCERHRLTD   97 (608)
T ss_pred             hhhHHHHHHHHHH---------HHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHH
Confidence            3456677777765         566666666543344433  34555666665 678899999999876443322    2


Q ss_pred             H--HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH-HHHHHhcCChhHHHHHHHHHHhCC---CC
Q 041804          101 E--VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI-LRGWFKMSWWGKCREFWEEMDKRG---VV  174 (403)
Q Consensus       101 ~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~~~~~~~~a~~~~~~~~~~~---~~  174 (403)
                      .  ..-..+++.+.+.+... |...+++.......  .+..+-...|..+ +..+...+++..|.+.++.+....   ..
T Consensus        98 ~k~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~--~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d  174 (608)
T PF10345_consen   98 LKFRCQFLLARIYFKTNPKA-ALKNLDKAIEDSET--YGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGD  174 (608)
T ss_pred             HHHHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhc--cCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCC
Confidence            1  22334566666666655 88888876654211  0222333344444 333334479999999998876543   33


Q ss_pred             CcHHHHHHHHHHHH--HcCChhHHHHHHHHHHHcCC---------CCChhhHHHHHHHHh--hcCCHHHHHHHHHHHH
Q 041804          175 KDLHSYSIYMDIMC--KSGKPWKAVKLYKEMKKKGI---------KMDVVAYNTVIRAVG--VSEGVDFAMRVYREMR  239 (403)
Q Consensus       175 ~~~~~~~~l~~~~~--~~~~~~~a~~~~~~~~~~~~---------~~~~~~~~~ll~~~~--~~~~~~~a~~~~~~~~  239 (403)
                      |-...+-.++.+..  +.+.++++.+.++.+.....         .|-..+|..++..++  ..|+++.+...++.+.
T Consensus       175 ~~~~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq  252 (608)
T PF10345_consen  175 PAVFVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQ  252 (608)
T ss_pred             HHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44455555555544  45667778888777744321         334556777766554  5667666666655554

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=82.18  E-value=18  Score=26.73  Aligned_cols=92  Identities=15%  Similarity=0.232  Sum_probs=68.4

Q ss_pred             CCCcCCHH--hHHHHHHHHHccCChhHHHHHHHHhhhCCC----CCCCHHHHHHHHHHHHhcCC-hHHHHHHHHHHhhcC
Q 041804           25 CHFTHTTD--TYNSVIDILGKFFEFDLSWNLIHRMKDNPS----SIPNHATFRIMFKRYVTAHL-VNEAMGTFNKLDEFG   97 (403)
Q Consensus        25 ~~~~~~~~--~~~~li~~~~~~~~~~~a~~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~   97 (403)
                      .+..++..  ..+.++.-....+++.-.+.+++.+.....    ...+...|+.++.+.++... --.+..+|+.+++.+
T Consensus        31 ~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~  110 (145)
T PF13762_consen   31 ENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKND  110 (145)
T ss_pred             cccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcC
Confidence            34555543  467888888888999999998888854320    02344578999999977766 456788899999877


Q ss_pred             CC-cHHHHHHHHHHHHhcCC
Q 041804           98 LK-DEVSYCNLVDALCEYKH  116 (403)
Q Consensus        98 ~~-~~~~~~~l~~~~~~~~~  116 (403)
                      .+ ++.-|..++.++.+...
T Consensus       111 ~~~t~~dy~~li~~~l~g~~  130 (145)
T PF13762_consen  111 IEFTPSDYSCLIKAALRGYF  130 (145)
T ss_pred             CCCCHHHHHHHHHHHHcCCC
Confidence            77 99999999999887533

>PF14669 Asp_Glu_race_2: Putative aspartate racemase

Probab=81.89  E-value=22  Score=27.59  Aligned_cols=25  Identities=16%  Similarity=0.013  Sum_probs=14.7

Q ss_pred             HHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          182 IYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       182 ~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ++|-.|-+.-++.+..++++.|.+.
T Consensus       137 S~m~~Yhk~~qW~KGrkvLd~l~el  161 (233)
T PF14669_consen  137 SLMYSYHKTLQWSKGRKVLDKLHEL  161 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555666666666666666554

>KOG2300 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.66  E-value=40  Score=30.47  Aligned_cols=131  Identities=12%  Similarity=-0.048  Sum_probs=75.2

Q ss_pred             HHccCChhHHHHHHHHhhhCCCCCCCHH-------HHHHHHH-HHHhcCChHHHHHHHHHHhhcCCC-cHHHH--HHHHH
Q 041804           41 LGKFFEFDLSWNLIHRMKDNPSSIPNHA-------TFRIMFK-RYVTAHLVNEAMGTFNKLDEFGLK-DEVSY--CNLVD  109 (403)
Q Consensus        41 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~--~~l~~  109 (403)
                      -.-.|++.+|++-...|.+--...|...       ....++. .+...|.++.|+.-|....+.--. |...+  ..+.-
T Consensus       333 ~lv~~~~~~al~~i~dm~~w~~r~p~~~Llr~~~~~ih~LlGlys~sv~~~enAe~hf~~a~k~t~~~dl~a~~nlnlAi  412 (629)
T KOG2300|consen  333 RLVRGDYVEALEEIVDMKNWCTRFPTPLLLRAHEAQIHMLLGLYSHSVNCYENAEFHFIEATKLTESIDLQAFCNLNLAI  412 (629)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhCCchHHHHHhHHHHHHHHhhHhhhcchHHHHHHHHHHHHHhhhHHHHHHHHHHhHHH
Confidence            3457999999998888876432234421       1222333 344678999999988877664433 44444  34566


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      .|.+.++.+.-.++++.+-........+......++..-.-.....+++.+|...+.+-.+.
T Consensus       413 ~YL~~~~~ed~y~~ld~i~p~nt~s~ssq~l~a~~~~v~glfaf~qn~lnEaK~~l~e~Lkm  474 (629)
T KOG2300|consen  413 SYLRIGDAEDLYKALDLIGPLNTNSLSSQRLEASILYVYGLFAFKQNDLNEAKRFLRETLKM  474 (629)
T ss_pred             HHHHhccHHHHHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhh
Confidence            78888888887777766543210000011111111222222234668888888888776654

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=81.65  E-value=19  Score=26.67  Aligned_cols=68  Identities=7%  Similarity=-0.030  Sum_probs=45.9

Q ss_pred             HhHHHHHHH---HHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcH
Q 041804           32 DTYNSVIDI---LGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE  101 (403)
Q Consensus        32 ~~~~~li~~---~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  101 (403)
                      .+.+.||..   -...++++++..+++.|.-..+..|...++.  ...+...|++.+|+++|+.+.+.+...+
T Consensus         8 ~iv~gLi~~~~~aL~~~d~~D~e~lLdALrvLrP~~~e~d~~d--g~l~i~rg~w~eA~rvlr~l~~~~~~~p   78 (153)
T TIGR02561         8 RLLGGLIEVLMYALRSADPYDAQAMLDALRVLRPNLKELDMFD--GWLLIARGNYDEAARILRELLSSAGAPP   78 (153)
T ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCccccchhH--HHHHHHcCCHHHHHHHHHhhhccCCCch
Confidence            344444443   3458899999999999887542223333443  3446789999999999999988664433

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF11663 Toxin_YhaV: Toxin with endonuclease activity YhaV; InterPro: IPR021679 YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF

Probab=81.61  E-value=2  Score=30.83  Aligned_cols=34  Identities=24%  Similarity=0.500  Sum_probs=23.0

Q ss_pred             HHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHH
Q 041804          289 FRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKF  324 (403)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  324 (403)
                      ++++|...+|..+|++|++.|-+||  .|+.|+..+
T Consensus       105 lR~ygsk~DaY~VF~kML~~G~pPd--dW~~Ll~~a  138 (140)
T PF11663_consen  105 LRAYGSKTDAYAVFRKMLERGNPPD--DWDALLKEA  138 (140)
T ss_pred             hhhhccCCcHHHHHHHHHhCCCCCc--cHHHHHHHh
Confidence            4556666777777777777777766  566666543

The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity [].

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=81.10  E-value=30  Score=28.76  Aligned_cols=87  Identities=11%  Similarity=0.069  Sum_probs=64.8

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHh--
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCE--  113 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~--  113 (403)
                      =|++++..+++.+++.+.-+--+.. -+--......-|-.|++.+.+..+.++-.......-. +...|..+...|..  
T Consensus        89 GIQALAEmnrWreVLsWvlqyYq~p-EklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~V  167 (309)
T PF07163_consen   89 GIQALAEMNRWREVLSWVLQYYQVP-EKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHV  167 (309)
T ss_pred             hHHHHHHHhhHHHHHHHHHHHhcCc-ccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHH
Confidence            3788999999999988766555432 1223445666777899999999999998887776544 55568877776654  


Q ss_pred             ---cCCHHHHHHHH
Q 041804          114 ---YKHVIEAQELC  124 (403)
Q Consensus       114 ---~~~~~~a~~~~  124 (403)
                         .|.+++|+++.
T Consensus       168 LlPLG~~~eAeelv  181 (309)
T PF07163_consen  168 LLPLGHFSEAEELV  181 (309)
T ss_pred             HhccccHHHHHHHH
Confidence               89999999886

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B

Probab=80.31  E-value=4.3  Score=24.82  Aligned_cols=45  Identities=13%  Similarity=0.170  Sum_probs=23.6

Q ss_pred             chHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          331 RPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       331 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      +...++++.++..  +-|-.-.-.+|.+|...|++++|.++++++.+
T Consensus         7 ~~~~~~~~~lR~~--RHD~~NhLqvI~gllqlg~~~~a~eYi~~~~~   51 (62)
T PF14689_consen    7 EELEELIDSLRAQ--RHDFLNHLQVIYGLLQLGKYEEAKEYIKELSK   51 (62)
T ss_dssp             HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--hHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3344444444332  23333444556677777777777777666654

---

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	403
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	8e-15
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	6e-13
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 75.6 bits (184), Expect = 8e-15
 Identities = 16/170 (9%), Positives = 49/170 (28%), Gaps = 7/170 (4%)

Query: 162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKL---YKEMKKKGIKMDVVAYNTV 218
           +    +  +  +         +      + +   A  L   +   ++K   + +  YN V
Sbjct: 112 QAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAV 171

Query: 219 IRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYA-VLAEMPKKG 277
           +            + V   +++ G  P +++    ++ +    +        L +M ++G
Sbjct: 172 MLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEG 231

Query: 278 CVPDVITYHCFFRCLEK---PREILGLFDRMIESGIRPKMDTYVMLLRKF 324
                +         ++    + +  +          P       LLR  
Sbjct: 232 LKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDV 281

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 69.8 bits (169), Expect = 6e-13
 Identities = 28/194 (14%), Positives = 65/194 (33%), Gaps = 4/194 (2%)

Query: 199 LYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLC 258
            + + +  G +  ++A+                + V+   R+     ++   N V+    
Sbjct: 117 QHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWA 176

Query: 259 ENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEK----PREILGLFDRMIESGIRPKM 314
             G  +E   VL  +   G  PD+++Y    +C+ +       I    ++M + G++ + 
Sbjct: 177 RQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQA 236

Query: 315 DTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEE 374
               +LL +  R   L+ V  V          P     + L+  +  K       K    
Sbjct: 237 LFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLP 296

Query: 375 MFAKGLSAKPREEL 388
           +       + +  +
Sbjct: 297 LKTLQCLFEKQLHM 310

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 61.8 bits (148), Expect = 2e-10
 Identities = 25/241 (10%), Positives = 74/241 (30%), Gaps = 6/241 (2%)

Query: 43  KFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DE 101
           +     ++  L    +  P S P       + +       ++       +  +  L   +
Sbjct: 69  RLLSKQMAGCLEDCTRQAPES-PWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQ 127

Query: 102 VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC 161
                          +  A  L    +       L+      +YN ++ GW +   + + 
Sbjct: 128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLT---LDMYNAVMLGWARQGAFKEL 184

Query: 162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAV-KLYKEMKKKGIKMDVVAYNTVIR 220
                 +   G+  DL SY+  +  M +  +    + +  ++M ++G+K+  +    ++ 
Sbjct: 185 VYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLS 244

Query: 221 AVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP 280
               +  +    +V          P  V  + +++ +           +   +    C+ 
Sbjct: 245 EEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLF 304

Query: 281 D 281
           +
Sbjct: 305 E 305

>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 = 53.3 bits (127), Expect = 1e-07
 Identities = 66/478 (13%), Positives = 138/478 (28%), Gaps = 152/478 (31%)

Query: 8   ANDWKRALEFFN---WVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSI 64
              +K   +      W+    +  +      +V+++L           L++++  N +S 
Sbjct: 171 CLSYKVQCKMDFKIFWL----NLKNCNSP-ETVLEML---------QKLLYQIDPNWTSR 216

Query: 65  PNHAT------------FRIMF--KRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA 110
            +H++             R +   K Y    LV         L        V      +A
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV---------L------LNVQNAKAWNA 261

Query: 111 L---CE------YKHVIEAQELCFGENKNVGFSGLVEMNK--TKIYNM-ILRGWFKMSWW 158
               C+      +K V +   L      ++    L   +   T      +L  +      
Sbjct: 262 FNLSCKILLTTRFKQVTDF--LSAATTTHI---SLDHHSMTLTPDEVKSLLLKYLDCR-- 314

Query: 159 GKCREFWEEMDKRGVVKDL-HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKM----DVV 213
                           +DL          +     P   + +  E  + G+        V
Sbjct: 315 ---------------PQDLPRE-------VLT-TNPR-RLSIIAESIRDGLATWDNWKHV 350

Query: 214 AYNTVIRAVGVS-EGVDFAMRVYREMREMGCQPSVVTCNTVI--KLLC---ENGRVREAY 267
             + +   +  S   ++ A     E R+M  + SV   +  I   LL     +    +  
Sbjct: 351 NCDKLTTIIESSLNVLEPA-----EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405

Query: 268 AVLAEMPKKGCV-----PDVITYH-CFFRCLEKPREILGLFDRMIES-----------GI 310
            V+ ++ K   V        I+    +     K      L   +++             I
Sbjct: 406 VVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI 465

Query: 311 RPKMDTYV--------MLLRKFGRWGFLRPVFV----VWKKMEELGCSPDEFAYNALVDA 358
            P +D Y           +    R    R VF+    + +K+     + +  A  ++++ 
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWN--ASGSILNT 523

Query: 359 LIDKGMLDMARKY---DEEMFAKGLSA------KPREEL----GTKLVQGGLDGEQSG 403
           L     L   + Y   ++  + + ++A      K  E L     T L++  L  E   
Sbjct: 524 LQQ---LKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALMAEDEA 578

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	403
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.97
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.95
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.94
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.92
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.92
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.91
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.9
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.89
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.88
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.87
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.87
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.86
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.85
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.85
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.85
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.83
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.83
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.82
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.82
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.82
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.82
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.82
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.81
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.8
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.78
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.77
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.77
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.76
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.74
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.74
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.73
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.73
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.73
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.73
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.72
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.72
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.72
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.71
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.71
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.71
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.71
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.7
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.69
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.69
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.68
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.67
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.66
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.64
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.63
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.63
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.62
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.62
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.62
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.62
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.62
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.62
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.61
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.6
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.6
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.6
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.58
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.57
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.56
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.55
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.52
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.5
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.5
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.49
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.49
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.48
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.46
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.46
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.45
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.45
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.44
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.42
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.42
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.4
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.4
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.34
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.3
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.29
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.28
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.27
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.27
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.26
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.23
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.23
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.23
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.23
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.22
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.2
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.2
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.2
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.2
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.2
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.2
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.2
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.19
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.19
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.16
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.15
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.14
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.1
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.1
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.07
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.03
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	99.02
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	99.01
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.95
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.95
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.95
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.94
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.94
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.93
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.92
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.92
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.91
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.91
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.9
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.9
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.9
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.9
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.89
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.89
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.88
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.88
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.87
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.86
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.85
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.85
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.85
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.85
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.85
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.84
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.83
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.83
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.82
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.82
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.81
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.81
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.75
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.75
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.74
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.73
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.73
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.71
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.69
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.69
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.68
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.66
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.65
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.64
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.63
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.62
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.62
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.61
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.61
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.58
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.57
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.56
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.55
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.53
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.52
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.51
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.51
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.51
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.5
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.5
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.45
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.43
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.39
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.38
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.37
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.37
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.37
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.35
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.34
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.34
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.33
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.33
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.32
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.31
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.25
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.21
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.18
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.14
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.12
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.09
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.09
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	98.07
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.04
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.98
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.97
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.9
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.88
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.86
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.84
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.81
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.76
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.74
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.71
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.47
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.33
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.24
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.15
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.04
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	97.03
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.02
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.99
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.95
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.94
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.9
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.89
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.86
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.83
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.75
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.67
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.66
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	96.65
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.51
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.46
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.45
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.36
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	96.1
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	95.81
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	95.45
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.43
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.23
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.83
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	94.73
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	94.29
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.97
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	93.44
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	93.17
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	93.1
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	92.82
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	92.75
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	92.62
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	92.1
2p58_C	116	Putative type III secretion protein YSCG; type III	91.94
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	90.79
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	90.67
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	89.58
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	89.47
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	89.41
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	87.99
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	87.91
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	87.68
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	87.22
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	86.69
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	85.8
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	85.17
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	84.87
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	83.17
4a1g_A	152	Mitotic checkpoint serine/threonine-protein kinas;	80.96
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	80.21

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.7e-34  Score=267.30  Aligned_cols=359  Identities=10%  Similarity=-0.006  Sum_probs=231.7

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCC--------------CCCCCHHHH
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP--------------SSIPNHATF   70 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~--------------~~~~~~~~~   70 (403)
                      +...|++++|+.+|+.+..   .++++.+++.++.+|.+.|++++|.++|+++....              +.+++..+|
T Consensus       127 ~~~~g~~~~A~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  203 (597)
T 2xpi_A          127 YCCTGDYARAKCLLTKEDL---YNRSSACRYLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMC  203 (597)
T ss_dssp             HHHTTCHHHHHHHHHHTCG---GGTCHHHHHHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHH
T ss_pred             HHHcCcHHHHHHHHHHHhc---cccchhHHHHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHH
Confidence            4445666666666665542   24556666666666666666666666666322211              012345566


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH--------------------------------------HHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL--------------------------------------VDALC  112 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l--------------------------------------~~~~~  112 (403)
                      +.++.+|.+.|++++|+++|+++.+.++.+...+..+                                      +..|.
T Consensus       204 ~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  283 (597)
T 2xpi_A          204 YLRGQVYTNLSNFDRAKECYKEALMVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTS  283 (597)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCchhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHc
Confidence            6666666666666666666666666555444433332                                      33344


Q ss_pred             hcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCC
Q 041804          113 EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK  192 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  192 (403)
                      +.|++++|.++|+++...        +++..+++.++..|.+.|++++|.++|+++.+.++. +..++..++.+|.+.|+
T Consensus       284 ~~g~~~~A~~~~~~~~~~--------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~  354 (597)
T 2xpi_A          284 HEDELRRAEDYLSSINGL--------EKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPY-NLDVYPLHLASLHESGE  354 (597)
T ss_dssp             THHHHHHHHHHHHTSTTG--------GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CCTTHHHHHHHHHHHTC
T ss_pred             CcchHHHHHHHHHHhhcC--------CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcc-cHHHHHHHHHHHHHhCC
Confidence            556666666666665542        578899999999999999999999999999877654 66677777777777777


Q ss_pred             hhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHh
Q 041804          193 PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAE  272 (403)
Q Consensus       193 ~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  272 (403)
                      +++|.++++++.+.. +.+..++..++..|.+.|++++|.++|+++.+... .+..+|+.++.+|.+.|++++|.++|++
T Consensus       355 ~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~  432 (597)
T 2xpi_A          355 KNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMDP-QFGPAWIGFAHSFAIEGEHDQAISAYTT  432 (597)
T ss_dssp             HHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            777777777776552 44566777777777777777777777777766532 2466777777777777777777777777


Q ss_pred             chhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc----CC
Q 041804          273 MPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL----GC  345 (403)
Q Consensus       273 ~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~  345 (403)
                      +.+.+ ..+..+|..+...+   ++.++|.++|+++.+.... +..+|+.++..|.+.|++++|.++|+++.+.    +.
T Consensus       433 ~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  510 (597)
T 2xpi_A          433 AARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQY-DPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQS  510 (597)
T ss_dssp             HHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhcccc
Confidence            66542 22455555554444   5666777777776665332 5566667777777777777777777766554    44


Q ss_pred             CCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          346 SPD--EFAYNALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       346 ~~~--~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                      .|+  ..+|..++.+|.+.|++++|.++++++.+.+
T Consensus       511 ~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  546 (597)
T 2xpi_A          511 NEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS  546 (597)
T ss_dssp             CSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             chhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            555  5666777777777777777777777666643

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=4e-34  Score=266.09  Aligned_cols=362  Identities=10%  Similarity=-0.001  Sum_probs=313.5

Q ss_pred             ccccccccHHHHHHhhhhhcccC--------------CCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHH
Q 041804            3 TLSCYANDWKRALEFFNWVETDC--------------HFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHA   68 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~--------------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~   68 (403)
                      ..+.+.|++++|+++|+.+....              +.+++..+|+.++.+|.+.|++++|+++|+++.+.+  +.+..
T Consensus       158 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--p~~~~  235 (597)
T 2xpi_A          158 FCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVD--AKCYE  235 (597)
T ss_dssp             HHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHH
T ss_pred             HHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--chhhH
Confidence            45677899999999999654322              334568899999999999999999999999999865  22334


Q ss_pred             HHHHH--------------------------------------HHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           69 TFRIM--------------------------------------FKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        69 ~~~~l--------------------------------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ++..+                                      +..|.+.|++++|.++|+++.+. +++..++..++.+
T Consensus       236 ~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~l~~~  314 (597)
T 2xpi_A          236 AFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL-EKSSDLLLCKADT  314 (597)
T ss_dssp             HHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG-GGCHHHHHHHHHH
T ss_pred             HHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC-CchHHHHHHHHHH
Confidence            43333                                      45566789999999999999887 3599999999999


Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      |.+.|++++|..+|+++...       .+.+..+++.++.++.+.|++++|.++++++.+.... +..+|+.++..|.+.
T Consensus       315 ~~~~g~~~~A~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~  386 (597)
T 2xpi_A          315 LFVRSRFIDVLAITTKILEI-------DPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPE-KAVTWLAVGIYYLCV  386 (597)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH-------CTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-SHHHHHHHHHHHHHT
T ss_pred             HHHhcCHHHHHHHHHHHHHc-------CcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHh
Confidence            99999999999999998863       3557788999999999999999999999999876544 788999999999999


Q ss_pred             CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHH
Q 041804          191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVL  270 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  270 (403)
                      |++++|.++|+++.+.. +.+..+|+.++.+|.+.|++++|.++|+++.+.+. .+..+|+.++.+|.+.|++++|.++|
T Consensus       387 g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~  464 (597)
T 2xpi_A          387 NKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQ-GTHLPYLFLGMQHMQLGNILLANEYL  464 (597)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTT-TCSHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-cchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999999999998863 44678999999999999999999999999998743 47889999999999999999999999


Q ss_pred             HhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHc----CCCCc--hhhHHHHHHHHHhcCCcchHHHHHHHHH
Q 041804          271 AEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIES----GIRPK--MDTYVMLLRKFGRWGFLRPVFVVWKKME  341 (403)
Q Consensus       271 ~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~----~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~~~  341 (403)
                      +++.+.. ..+..+|+.+...+   ++.++|.++|+++.+.    +..|+  ..+|..++.+|.+.|++++|.+.++++.
T Consensus       465 ~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  543 (597)
T 2xpi_A          465 QSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGL  543 (597)
T ss_dssp             HHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            9998763 23677788777665   8899999999999875    66787  7899999999999999999999999998


Q ss_pred             hcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          342 ELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       342 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                      +.+ +.+..+|..+..+|.+.|++++|.++++++.+..
T Consensus       544 ~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~  580 (597)
T 2xpi_A          544 LLS-TNDANVHTAIALVYLHKKIPGLAITHLHESLAIS  580 (597)
T ss_dssp             HHS-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC
Confidence            875 5689999999999999999999999999999853

>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=4.6e-33  Score=248.98  Aligned_cols=201  Identities=14%  Similarity=0.252  Sum_probs=127.8

Q ss_pred             HHHHHHHHhCCCCCcH-HHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCC---------HHHH
Q 041804          162 REFWEEMDKRGVVKDL-HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG---------VDFA  231 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~---------~~~a  231 (403)
                      ..+.+++.+.+..+.+ ..++.+|++|++.|++++|+++|++|.+.|+.||..||++||.+|++.+.         ++.|
T Consensus        10 e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A   89 (501)
T 4g26_A           10 ENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRG   89 (501)
T ss_dssp             --------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHH
T ss_pred             HHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHH
Confidence            3444455444443322 24555666666666666666666666666666666666666666655433         4566


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHc
Q 041804          232 MRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIES  308 (403)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~  308 (403)
                      .++|++|.+.|+.||..+|+++|.+|++.|++++|.++|++|.+.|+.||..+|+++|.+|   ++.++|.++|++|.+.
T Consensus        90 ~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~  169 (501)
T 4g26_A           90 FDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVES  169 (501)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            6666666666666666666666666666666666666666666666666666666666665   4566666666667777


Q ss_pred             CCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhc
Q 041804          309 GIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDK  362 (403)
Q Consensus       309 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  362 (403)
                      |+.||..||++||.+|++.|++++|.+++++|.+.|..|+..||+.++..|...
T Consensus       170 G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          170 EVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             TCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             CCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            777788888888888888888888888888888888888888888887777653

>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=6e-33  Score=248.22  Aligned_cols=202  Identities=16%  Similarity=0.126  Sum_probs=162.2

Q ss_pred             HHHHHHHhhcCCC--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC--------
Q 041804           87 MGTFNKLDEFGLK--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS--------  156 (403)
Q Consensus        87 ~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--------  156 (403)
                      ..+.+++.+.+..  +...++.+|++|++.|++++|.++|++|...      ++.||..+||.||.+|++.+        
T Consensus        10 e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~------Gv~pd~~tyn~Li~~c~~~~~~~~~~~~   83 (501)
T 4g26_A           10 ENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRN------GVQLSQYHYNVLLYVCSLAEAATESSPN   83 (501)
T ss_dssp             --------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHH------TCCCCHHHHHHHHHHHTTCCCCSSSSCC
T ss_pred             HHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc------CCCCCHhHHHHHHHHHHhCCchhhhhhc
Confidence            3334444444433  2234555555555555555555555555554      55556666666665555443        


Q ss_pred             -ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHH
Q 041804          157 -WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVY  235 (403)
Q Consensus       157 -~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~  235 (403)
                       .++.|.++|++|.+.|+.||..||++||.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|
T Consensus        84 ~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~  163 (501)
T 4g26_A           84 PGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVD  163 (501)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHH
Confidence             3688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCC
Q 041804          236 REMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEK  294 (403)
Q Consensus       236 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~  294 (403)
                      ++|.+.|+.||..+|++||.+|++.|++++|.++|++|.+.|..|+..||+.++..+..
T Consensus       164 ~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          164 AHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             HHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999987744

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=100.00  E-value=2.3e-29  Score=221.38  Aligned_cols=361  Identities=12%  Similarity=0.020  Sum_probs=313.8

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      .+.+.|++++|++.+..+.+.  .+.+...+..+...+...|++++|...++......  +.+..+|..+..++.+.|++
T Consensus         8 ~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~--p~~~~~~~~lg~~~~~~g~~   83 (388)
T 1w3b_A            8 REYQAGDFEAAERHCMQLWRQ--EPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN--PLLAEAYSNLGNVYKERGQL   83 (388)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHHCCCH
Confidence            356789999999999988752  24456778888899999999999999999988865  46788999999999999999


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHH
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCRE  163 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  163 (403)
                      ++|+..|+++.+..+.+..+|..+..++...|++++|...++++..       ..+.+..++..+...+...|++++|.+
T Consensus        84 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~~~~g~~~~A~~  156 (388)
T 1w3b_A           84 QEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQ-------YNPDLYCVRSDLGNLLKALGRLEEAKA  156 (388)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHH-------HCTTCTHHHHHHHHHHHTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCCCcHHHHHHHHHHHHHccCHHHHHH
Confidence            9999999999999888999999999999999999999999998876       335567788889999999999999999


Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          164 FWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      .|+++.+..+. +..+|..+...+...|++++|...|+++.+.+ +.+...+..+...+...|++++|...+++..+...
T Consensus       157 ~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p  234 (388)
T 1w3b_A          157 CYLKAIETQPN-FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP  234 (388)
T ss_dssp             HHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT
T ss_pred             HHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc
Confidence            99999987655 67899999999999999999999999999874 44567888999999999999999999999988743


Q ss_pred             CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC-ChhhHHHHHHh---hCCHHHHHHHHHHHHHcCCCCchhhHHH
Q 041804          244 QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP-DVITYHCFFRC---LEKPREILGLFDRMIESGIRPKMDTYVM  319 (403)
Q Consensus       244 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (403)
                       .+..++..+...|.+.|++++|...|+++.+.  .| +...+..+...   .++.++|.+.++++.+.. +.+..++..
T Consensus       235 -~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~  310 (388)
T 1w3b_A          235 -NHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNN  310 (388)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             -CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHH
Confidence             36788999999999999999999999999876  34 34455555444   388999999999999874 347789999


Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCh
Q 041804          320 LLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKP  384 (403)
Q Consensus       320 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~  384 (403)
                      +...+.+.|++++|.+.++++.+.. +.+..++..+..+|.+.|++++|...++++.+.  .|+.
T Consensus       311 l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--~p~~  372 (388)
T 1w3b_A          311 LANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTF  372 (388)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCC
Confidence            9999999999999999999998763 557889999999999999999999999999874  4543

>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=99.97  E-value=1.4e-27  Score=209.94  Aligned_cols=345  Identities=11%  Similarity=0.021  Sum_probs=298.1

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      .++...|++++|...++...+  ..+.+..+|..+..++.+.|++++|...|+++....  +.+..+|..+..++...|+
T Consensus        41 ~~~~~~~~~~~a~~~~~~a~~--~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~  116 (388)
T 1w3b_A           41 SIHFQCRRLDRSAHFSTLAIK--QNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLK--PDFIDGYINLAAALVAAGD  116 (388)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHSC
T ss_pred             HHHHHcCCHHHHHHHHHHHHh--cCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC--cchHHHHHHHHHHHHHcCC
Confidence            456678999999999998875  235678899999999999999999999999999865  3456789999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCR  162 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  162 (403)
                      +++|++.|+++.+..+.+...+..+...+...|++++|...|+++..       ..+.+..+|..+...+...|++++|.
T Consensus       117 ~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~~~~g~~~~A~  189 (388)
T 1w3b_A          117 MEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIE-------TQPNFAVAWSNLGCVFNAQGEIWLAI  189 (388)
T ss_dssp             SSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999888889999999999999999999999999887       34567789999999999999999999


Q ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          163 EFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      ..|+++.+.++. +...|..+...+...|++++|...|++..... +.+..++..+..++...|++++|...|+.+.+..
T Consensus       190 ~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  267 (388)
T 1w3b_A          190 HHFEKAVTLDPN-FLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ  267 (388)
T ss_dssp             HHHHHHHHHCTT-CHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHhcCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            999999998766 77889999999999999999999999998873 3457889999999999999999999999999874


Q ss_pred             CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHH
Q 041804          243 CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVM  319 (403)
Q Consensus       243 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (403)
                      . .+..++..+...+.+.|++++|...|+++.+.. +.+..++..+...+   ++.++|...++++.+... .+..++..
T Consensus       268 p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~  344 (388)
T 1w3b_A          268 P-HFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFP-EFAAAHSN  344 (388)
T ss_dssp             S-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCT-TCHHHHHH
T ss_pred             C-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CcHHHHHH
Confidence            3 257789999999999999999999999998762 33566666655544   789999999999987532 35778999


Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC
Q 041804          320 LLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGM  364 (403)
Q Consensus       320 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  364 (403)
                      +...+.+.|++++|...++++.+.. +.+...|..+...+.+.|+
T Consensus       345 l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~a~~~lg~~~~~~~~  388 (388)
T 1w3b_A          345 LASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHhHHHHHHHccC
Confidence            9999999999999999999998753 4467788888777766653

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.95  E-value=2.7e-24  Score=192.83  Aligned_cols=346  Identities=12%  Similarity=0.030  Sum_probs=274.5

Q ss_pred             HHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHH
Q 041804           12 KRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFN   91 (403)
Q Consensus        12 ~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~   91 (403)
                      ..+...+..+..  ..+.+...+..+...+.+.|++++|+.+|+++.+..  +.+..+|..+..++...|++++|+..|+
T Consensus         9 ~~~~~~~~~~~~--~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~   84 (450)
T 2y4t_A            9 SGVDLGTENLYF--QSMADVEKHLELGKKLLAAGQLADALSQFHAAVDGD--PDNYIAYYRRATVFLAMGKSKAALPDLT   84 (450)
T ss_dssp             ----------------CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cccccccccccc--ccHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            334444544442  234567889999999999999999999999998864  4678899999999999999999999999


Q ss_pred             HHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcch---HHHHHH------------HHHHHhcC
Q 041804           92 KLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKT---KIYNMI------------LRGWFKMS  156 (403)
Q Consensus        92 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~  156 (403)
                      ++.+.++.+..++..+..+|...|++++|...|+++...       .+.+.   .++..+            ...+...|
T Consensus        85 ~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  157 (450)
T 2y4t_A           85 KVIQLKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS-------NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSG  157 (450)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-------CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            999999889999999999999999999999999998763       24444   555555            44589999


Q ss_pred             ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHH
Q 041804          157 WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYR  236 (403)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  236 (403)
                      ++++|...|+++.+..+. +..++..+..+|...|++++|...|+++.+.. +.+..++..+...|...|++++|...|+
T Consensus       158 ~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  235 (450)
T 2y4t_A          158 DYTAAIAFLDKILEVCVW-DAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVR  235 (450)
T ss_dssp             CHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            999999999999987655 78899999999999999999999999998873 4577899999999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHH------------HHHHHhcCcHHHHHHHHHhchhcCCCCCh-----hhHHHHHH---hhCCHH
Q 041804          237 EMREMGCQPSVVTCNTV------------IKLLCENGRVREAYAVLAEMPKKGCVPDV-----ITYHCFFR---CLEKPR  296 (403)
Q Consensus       237 ~~~~~~~~~~~~~~~~l------------i~~~~~~g~~~~a~~~~~~~~~~~~~p~~-----~~~~~l~~---~~~~~~  296 (403)
                      .+.+.... +...+..+            ...+...|++++|...|+++.+.  .|+.     ..+..+..   ..++.+
T Consensus       236 ~~~~~~p~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~  312 (450)
T 2y4t_A          236 ECLKLDQD-HKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPV  312 (450)
T ss_dssp             HHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHH
T ss_pred             HHHHhCCC-hHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHH
Confidence            99976432 44445444            78899999999999999999875  3442     23433333   337899


Q ss_pred             HHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHH------------HHhcC-
Q 041804          297 EILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDA------------LIDKG-  363 (403)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~------------~~~~g-  363 (403)
                      +|...++.+.+... .+..+|..+..+|...|++++|...++++.+.. +.+...+..+..+            |...| 
T Consensus       313 ~A~~~~~~a~~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~  390 (450)
T 2y4t_A          313 EAIRVCSEVLQMEP-DNVNALKDRAEAYLIEEMYDEAIQDYETAQEHN-ENDQQIREGLEKAQRLLKQSQKRDYYKILGV  390 (450)
T ss_dssp             HHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHHHHHHSCCSGGGSCS
T ss_pred             HHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-cchHHHHHHHHHHHHHhhcccchhHHHHhCC
Confidence            99999999987643 267899999999999999999999999998853 3456677766633            44444 


Q ss_pred             ----CHHHHHHHHHHH
Q 041804          364 ----MLDMARKYDEEM  375 (403)
Q Consensus       364 ----~~~~a~~~~~~m  375 (403)
                          +.+++.+.++++
T Consensus       391 ~~~~~~~~~~~~y~~~  406 (450)
T 2y4t_A          391 KRNAKKQEIIKAYRKL  406 (450)
T ss_dssp             STTCCTTHHHHHHHHH
T ss_pred             CccCCHHHHHHHHHHH
Confidence                556778888763

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.95  E-value=1.2e-24  Score=198.39  Aligned_cols=371  Identities=11%  Similarity=-0.032  Sum_probs=301.8

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.+...   .|++.++..+..++.+.|++++|...++++.+..  +.+..+|..+..++...|+
T Consensus        14 ~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~   88 (514)
T 2gw1_A           14 NQFFRNKKYDDAIKYYNWALEL---KEDPVFYSNLSACYVSVGDLKKVVEMSTKALELK--PDYSKVLLRRASANEGLGK   88 (514)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHHH---CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhccHHHHHHHHHHHHhc---CccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC--hHHHHHHHHHHHHHHHHhh
Confidence            4566789999999999999863   3789999999999999999999999999999875  4567899999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCc--------------------------------------------------------------
Q 041804           83 VNEAMGTFNKLDEFGLKD--------------------------------------------------------------  100 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~--------------------------------------------------------------  100 (403)
                      +++|+..|+++.+.++.+                                                              
T Consensus        89 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (514)
T 2gw1_A           89 FADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFF  168 (514)
T ss_dssp             HHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHH
Confidence            999999999998877532                                                              


Q ss_pred             -----------------HHHHHHHHHHHHh---cCCHHHHHHHHhcccc-----ccccccc--ccCcchHHHHHHHHHHH
Q 041804          101 -----------------EVSYCNLVDALCE---YKHVIEAQELCFGENK-----NVGFSGL--VEMNKTKIYNMILRGWF  153 (403)
Q Consensus       101 -----------------~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~-----~~~~~~~--~~~~~~~~~~~l~~~~~  153 (403)
                                       ...+......+..   .|++++|...++++..     .......  ..+.+..++..+...+.
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (514)
T 2gw1_A          169 GIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKF  248 (514)
T ss_dssp             TTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHH
Confidence                             3333334444443   8999999999988776     2000000  01456778899999999


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHH
Q 041804          154 KMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMR  233 (403)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  233 (403)
                      ..|++++|...|+++.+.+..  ..++..+..++...|++++|...++.+.... +.+..++..+...+...|+++.|..
T Consensus       249 ~~~~~~~A~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  325 (514)
T 2gw1_A          249 LKNDPLGAHEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGK  325 (514)
T ss_dssp             HSSCHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHH
T ss_pred             HCCCHHHHHHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            999999999999999887655  8889999999999999999999999998874 4467788999999999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH---hhCCHHHHHHHHHHHHHcCC
Q 041804          234 VYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR---CLEKPREILGLFDRMIESGI  310 (403)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~---~~~~~~~a~~~~~~~~~~~~  310 (403)
                      .++.+.+.... +...+..+...|...|++++|...++++.+... .+...+..+..   ..++.++|...++.+.+...
T Consensus       326 ~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~  403 (514)
T 2gw1_A          326 DFDKAKELDPE-NIFPYIQLACLAYRENKFDDCETLFSEAKRKFP-EAPEVPNFFAEILTDKNDFDKALKQYDLAIELEN  403 (514)
T ss_dssp             HHHHHHHTCSS-CSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHST-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhChh-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcc-cCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhh
Confidence            99999987543 677888999999999999999999999886521 13344443333   34889999999999886432


Q ss_pred             C-Cc----hhhHHHHHHHHHh---cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 041804          311 R-PK----MDTYVMLLRKFGR---WGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSA  382 (403)
Q Consensus       311 ~-~~----~~~~~~li~~~~~---~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p  382 (403)
                      . ++    ..++..+...+..   .|++++|...++++.+.. +.+..++..+..+|.+.|++++|...+++..+..  |
T Consensus       404 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~--~  480 (514)
T 2gw1_A          404 KLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD-PRSEQAKIGLAQMKLQQEDIDEAITLFEESADLA--R  480 (514)
T ss_dssp             TSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--S
T ss_pred             ccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhc--c
Confidence            2 12    3388899999999   999999999999998864 5578899999999999999999999999999853  5


Q ss_pred             Chhh
Q 041804          383 KPRE  386 (403)
Q Consensus       383 ~~~~  386 (403)
                      +...
T Consensus       481 ~~~~  484 (514)
T 2gw1_A          481 TMEE  484 (514)
T ss_dssp             SHHH
T ss_pred             ccHH
Confidence            5443

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.94  E-value=2.7e-23  Score=186.31  Aligned_cols=318  Identities=9%  Similarity=-0.017  Sum_probs=259.9

Q ss_pred             HHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           50 SWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        50 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      +...+.+.....  +.+...+..+...+.+.|++++|+.+|+++.+..+.+..++..+..++...|++++|...++++..
T Consensus        11 ~~~~~~~~~~~~--p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~   88 (450)
T 2y4t_A           11 VDLGTENLYFQS--MADVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQ   88 (450)
T ss_dssp             --------------CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cccccccccccc--HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            334444444433  456788999999999999999999999999998878999999999999999999999999999887


Q ss_pred             cccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH---HHHHHH------------HHHHHHcCChh
Q 041804          130 NVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL---HSYSIY------------MDIMCKSGKPW  194 (403)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l------------~~~~~~~~~~~  194 (403)
                             ..+.+..++..+...|.+.|++++|.+.|+++.+.++. +.   ..+..+            ...+...|+++
T Consensus        89 -------~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  160 (450)
T 2y4t_A           89 -------LKMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPS-ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYT  160 (450)
T ss_dssp             -------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             -------cCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHH
Confidence                   33567889999999999999999999999999987544 44   566555            44488999999


Q ss_pred             HHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      +|...|+++.+.. +.+..++..+..+|.+.|++++|..+|+.+.+.. +.+..++..+...|...|++++|...|+++.
T Consensus       161 ~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  238 (450)
T 2y4t_A          161 AAIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECL  238 (450)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999999999874 4577889999999999999999999999998864 3478899999999999999999999999998


Q ss_pred             hcCCCCChhh-HHH---------------HHHhhCCHHHHHHHHHHHHHcCCC-Cc--hhhHHHHHHHHHhcCCcchHHH
Q 041804          275 KKGCVPDVIT-YHC---------------FFRCLEKPREILGLFDRMIESGIR-PK--MDTYVMLLRKFGRWGFLRPVFV  335 (403)
Q Consensus       275 ~~~~~p~~~~-~~~---------------l~~~~~~~~~a~~~~~~~~~~~~~-~~--~~~~~~li~~~~~~g~~~~a~~  335 (403)
                      +.  .|+... +..               .....++.++|...++.+.+.... |.  ...+..+..++.+.|++++|..
T Consensus       239 ~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~  316 (450)
T 2y4t_A          239 KL--DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVEAIR  316 (450)
T ss_dssp             HH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             Hh--CCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence            65  454333 222               222338899999999999985432 11  3478888999999999999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCh
Q 041804          336 VWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKP  384 (403)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~  384 (403)
                      .++++.+.. +.+...|..+..+|...|++++|...++++.+  +.|+.
T Consensus       317 ~~~~a~~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~--~~p~~  362 (450)
T 2y4t_A          317 VCSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYETAQE--HNEND  362 (450)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT--TSSSC
T ss_pred             HHHHHHHhC-cccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH--hCcch
Confidence            999998763 45789999999999999999999999999988  44554

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.92  E-value=5.2e-22  Score=181.05  Aligned_cols=341  Identities=9%  Similarity=-0.093  Sum_probs=278.1

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ...+......+.+.|++++|+..|+++....   |+..+|..+..++...|++++|+..|+++.+.++.+..++..+..+
T Consensus         6 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~---p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~   82 (514)
T 2gw1_A            6 ALALKDKGNQFFRNKKYDDAIKYYNWALELK---EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASA   82 (514)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcC---ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHH
Confidence            5567888899999999999999999999965   7999999999999999999999999999999998899999999999


Q ss_pred             HHhcCCHHHHHHHHhcccccccccc-------------------------------------------------------
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSG-------------------------------------------------------  135 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~-------------------------------------------------------  135 (403)
                      +...|++++|...|+++....+...                                                       
T Consensus        83 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (514)
T 2gw1_A           83 NEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVT  162 (514)
T ss_dssp             HHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHH
T ss_pred             HHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhH
Confidence            9999999999999987754321000                                                       


Q ss_pred             -----------------cccCcchHHHHHHHHHHHh---cCChhHHHHHHHHHHh-----C--CC------CCcHHHHHH
Q 041804          136 -----------------LVEMNKTKIYNMILRGWFK---MSWWGKCREFWEEMDK-----R--GV------VKDLHSYSI  182 (403)
Q Consensus       136 -----------------~~~~~~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~-----~--~~------~~~~~~~~~  182 (403)
                                       ...+.+...+......+..   .|++++|...|+++.+     .  ..      +.+..++..
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (514)
T 2gw1_A          163 SMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEH  242 (514)
T ss_dssp             HHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHH
Confidence                             0001224444444444444   8999999999999987     3  11      124567888


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCc
Q 041804          183 YMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGR  262 (403)
Q Consensus       183 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~  262 (403)
                      +..++...|++++|...|+++.+..  |+..++..+...+...|+++.|...++.+.+... .+...+..+...|...|+
T Consensus       243 ~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~  319 (514)
T 2gw1_A          243 TGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKLDS-NNSSVYYHRGQMNFILQN  319 (514)
T ss_dssp             HHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCT-TCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCc-CCHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999874  3378888999999999999999999999988643 367789999999999999


Q ss_pred             HHHHHHHHHhchhcCCCCChhhHHHHHHhh---CCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHH
Q 041804          263 VREAYAVLAEMPKKGCVPDVITYHCFFRCL---EKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKK  339 (403)
Q Consensus       263 ~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  339 (403)
                      +++|...|++..+.... +...+..+...+   ++.++|...++.+.+.... +..++..+...+...|++++|...+++
T Consensus       320 ~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~  397 (514)
T 2gw1_A          320 YDQAGKDFDKAKELDPE-NIFPYIQLACLAYRENKFDDCETLFSEAKRKFPE-APEVPNFFAEILTDKNDFDKALKQYDL  397 (514)
T ss_dssp             TTHHHHHHHHHHHTCSS-CSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhChh-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccc-CHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            99999999999875322 344455444443   7899999999999886433 567889999999999999999999999


Q ss_pred             HHhcCC-CCC----HHHHHHHHHHHHh---cCCHHHHHHHHHHHHHcC
Q 041804          340 MEELGC-SPD----EFAYNALVDALID---KGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       340 ~~~~~~-~~~----~~~~~~l~~~~~~---~g~~~~a~~~~~~m~~~~  379 (403)
                      +.+... .++    ...|..+..++.+   .|++++|...++++....
T Consensus       398 a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~  445 (514)
T 2gw1_A          398 AIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD  445 (514)
T ss_dssp             HHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC
T ss_pred             HHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC
Confidence            876421 122    3488999999999   999999999999998853

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.92  E-value=6.9e-21  Score=165.21  Aligned_cols=307  Identities=13%  Similarity=0.061  Sum_probs=223.8

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      ++..+..+...+...|++++|...|+++.+..  +.+..++..+..++...|++++|+..|+++.+..+.+...+..+..
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD--PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHH
Confidence            45678888899999999999999999998865  4567889999999999999999999999999988778899999999


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccC---cchHHHHHH------------HHHHHhcCChhHHHHHHHHHHhCCCC
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEM---NKTKIYNMI------------LRGWFKMSWWGKCREFWEEMDKRGVV  174 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~  174 (403)
                      ++...|++++|...+++....       .+   .+...+..+            ...+...|++++|.+.++++.+..+.
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~-------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~  152 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKS-------NPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVW  152 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTS-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHcCChHHHHHHHHHHHhc-------CCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC
Confidence            999999999999999988763       23   344555544            57778888888888888888776554


Q ss_pred             CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHH--
Q 041804          175 KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNT--  252 (403)
Q Consensus       175 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--  252 (403)
                       +...+..+..++...|++++|...++.+.+.. +.+..++..+...+...|++++|...++.+.+.... +...+..  
T Consensus       153 -~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~~  229 (359)
T 3ieg_A          153 -DAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQD-HKRCFAHYK  229 (359)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             -chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcc-chHHHHHHH
Confidence             67778888888888888888888888887763 446677788888888888888888888888776322 2332221  


Q ss_pred             ----------HHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHH
Q 041804          253 ----------VIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLR  322 (403)
Q Consensus       253 ----------li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  322 (403)
                                +...+.+.|++++|...+++..+..  |+...+                           ....+..+..
T Consensus       230 ~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~---------------------------~~~~~~~la~  280 (359)
T 3ieg_A          230 QVKKLNKLIESAEELIRDGRYTDATSKYESVMKTE--PSVAEY---------------------------TVRSKERICH  280 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSSHHH---------------------------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCchHH---------------------------HHHHHHHHHH
Confidence                      2444556666666666666555431  221100                           0122444556


Q ss_pred             HHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          323 KFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       323 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      ++...|++++|...+++..+.. +.+..+|..+..+|.+.|++++|...+++..+.
T Consensus       281 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~  335 (359)
T 3ieg_A          281 CFSKDEKPVEAIRICSEVLQME-PDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEH  335 (359)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            6667777777777777776652 345666777777777777777777777776653

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.91  E-value=1.2e-21  Score=179.70  Aligned_cols=358  Identities=10%  Similarity=0.002  Sum_probs=276.0

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.+...  .+.++.++..+..++.+.|++++|+..|+++.+..  +.+..++..+..++...|+
T Consensus        33 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~  108 (537)
T 3fp2_A           33 NHFFTAKNFNEAIKYYQYAIEL--DPNEPVFYSNISACYISTGDLEKVIEFTTKALEIK--PDHSKALLRRASANESLGN  108 (537)
T ss_dssp             HHHHHTTCCC-CHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHhccHHHHHHHHHHHHhh--CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHHcCC
Confidence            3556778999999999998752  24568889999999999999999999999988865  4567888999999999999


Q ss_pred             hHHHHHHHHHHhhcCCC-cHH-----------------------------------------------------------
Q 041804           83 VNEAMGTFNKLDEFGLK-DEV-----------------------------------------------------------  102 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~-~~~-----------------------------------------------------------  102 (403)
                      +++|+..|+.+ ...+. ...                                                           
T Consensus       109 ~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  187 (537)
T 3fp2_A          109 FTDAMFDLSVL-SLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSS  187 (537)
T ss_dssp             HHHHHHHHHHH-C-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCC
T ss_pred             HHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhcc
Confidence            99999988643 22221 100                                                           


Q ss_pred             --------HHHHHHHHHH--------hcCCHHHHHHHHhcccccccccccccCcc-------hHHHHHHHHHHHhcCChh
Q 041804          103 --------SYCNLVDALC--------EYKHVIEAQELCFGENKNVGFSGLVEMNK-------TKIYNMILRGWFKMSWWG  159 (403)
Q Consensus       103 --------~~~~l~~~~~--------~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~  159 (403)
                              ....+...+.        ..+++++|...++++....       +.+       ..++..+...+...|+++
T Consensus       188 ~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~-------p~~~~~~~~~~~~~~~~g~~~~~~~~~~  260 (537)
T 3fp2_A          188 NYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN-------TVDDPLRENAALALCYTGIFHFLKNNLL  260 (537)
T ss_dssp             SSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC---------CCCHHHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             ccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC-------CCcchhhHHHHHHHHHHHHHHHhcccHH
Confidence                    1111111111        1247788888888877642       222       335777778889999999


Q ss_pred             HHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          160 KCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       160 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      +|.+.|++..+..  |+..++..+...+...|++++|...|+++.+.. +.+..++..+...+...|+++.|...++.+.
T Consensus       261 ~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  337 (537)
T 3fp2_A          261 DAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQ  337 (537)
T ss_dssp             HHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            9999999999875  457889999999999999999999999999874 4467889999999999999999999999999


Q ss_pred             HcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC-hhhHHHHHH---hhCCHHHHHHHHHHHHHcCCC----
Q 041804          240 EMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD-VITYHCFFR---CLEKPREILGLFDRMIESGIR----  311 (403)
Q Consensus       240 ~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~---~~~~~~~a~~~~~~~~~~~~~----  311 (403)
                      +.... +...+..+...|...|++++|...++++.+..  |+ ...+..+..   ..++.++|...++++.+....    
T Consensus       338 ~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~  414 (537)
T 3fp2_A          338 SLNPE-NVYPYIQLACLLYKQGKFTESEAFFNETKLKF--PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKI  414 (537)
T ss_dssp             HHCTT-CSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSC
T ss_pred             HhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhh
Confidence            87533 56788999999999999999999999998763  33 334444433   348899999999998864311    


Q ss_pred             -CchhhHHHHHHHHHhc----------CCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          312 -PKMDTYVMLLRKFGRW----------GFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       312 -~~~~~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                       .....+......+...          |++++|...++++.+.. +.+...+..+..+|.+.|++++|.+.|++..+..
T Consensus       415 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  492 (537)
T 3fp2_A          415 HVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILA  492 (537)
T ss_dssp             SSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence             1122244455677777          99999999999998864 5678899999999999999999999999999854

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=3e-20  Score=161.16  Aligned_cols=281  Identities=9%  Similarity=-0.013  Sum_probs=225.6

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      +...+..+...+...|++++|+..|+++.+..+.+..++..+..++...|++++|...++++..       ..+.+..++
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~   74 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIA-------LKMDFTAAR   74 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-------HCTTCHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHH-------hCCCcchHH
Confidence            4567888899999999999999999999999888999999999999999999999999999876       335567889


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCC---CCcHHHHHHH------------HHHHHHcCChhHHHHHHHHHHHcCCCC
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKRGV---VKDLHSYSIY------------MDIMCKSGKPWKAVKLYKEMKKKGIKM  210 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~  210 (403)
                      ..+...+...|++++|...|++..+..+   . +...+..+            ...+...|++++|...++++.+.. +.
T Consensus        75 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~  152 (359)
T 3ieg_A           75 LQRGHLLLKQGKLDEAEDDFKKVLKSNPSEQE-EKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VW  152 (359)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHTSCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHHHHHHHcCChHHHHHHHHHHHhcCCcccC-hHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CC
Confidence            9999999999999999999999998754   3 44555554            578888999999999999988874 45


Q ss_pred             ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH
Q 041804          211 DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR  290 (403)
Q Consensus       211 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  290 (403)
                      +..++..+...+...|+++.|...++.+.+.. +.+...+..+...+...|++++|...|++..+.  .|+...      
T Consensus       153 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~~~~------  223 (359)
T 3ieg_A          153 DAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKR------  223 (359)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHH------
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CccchH------
Confidence            67788888899999999999999999988764 346788888999999999999999999888764  233221      


Q ss_pred             hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCH----HHHHHHHHHHHhcCCHH
Q 041804          291 CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDE----FAYNALVDALIDKGMLD  366 (403)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~  366 (403)
                             +...+..+.      .......+...+.+.|++++|...++++.+.. +.+.    ..+..+..++.+.|+++
T Consensus       224 -------~~~~~~~~~------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~~~~~  289 (359)
T 3ieg_A          224 -------CFAHYKQVK------KLNKLIESAEELIRDGRYTDATSKYESVMKTE-PSVAEYTVRSKERICHCFSKDEKPV  289 (359)
T ss_dssp             -------HHHHHHHHH------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSSHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             -------HHHHHHHHH------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHHHHHccCHH
Confidence                   111111111      12233445677889999999999999998864 2233    23556788999999999


Q ss_pred             HHHHHHHHHHHc
Q 041804          367 MARKYDEEMFAK  378 (403)
Q Consensus       367 ~a~~~~~~m~~~  378 (403)
                      +|...+++..+.
T Consensus       290 ~A~~~~~~~~~~  301 (359)
T 3ieg_A          290 EAIRICSEVLQM  301 (359)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999999885

>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=99.90  E-value=1.6e-20  Score=160.98  Aligned_cols=294  Identities=10%  Similarity=-0.049  Sum_probs=215.9

Q ss_pred             CcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHH
Q 041804           27 FTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCN  106 (403)
Q Consensus        27 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  106 (403)
                      .+.++..+..+...+...|++++|..+|+++.+..  +.+...+..++.++...|++++|...++++.+..+.+..++..
T Consensus        18 ~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~   95 (330)
T 3hym_B           18 LQENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD--PFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPSNPVSWFA   95 (330)
T ss_dssp             --CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHH
T ss_pred             chhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHH
Confidence            45566777788888888888888888888887765  3445566677788888888888888888888877778888888


Q ss_pred             HHHHHHhcC-CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHH
Q 041804          107 LVDALCEYK-HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMD  185 (403)
Q Consensus       107 l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  185 (403)
                      +...+...| ++++|...+++....       .+.+..++..+...+...|++++|.+.|++..+.... +...+..+..
T Consensus        96 l~~~~~~~~~~~~~A~~~~~~a~~~-------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~  167 (330)
T 3hym_B           96 VGCYYLMVGHKNEHARRYLSKATTL-------EKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG-CHLPMLYIGL  167 (330)
T ss_dssp             HHHHHHHSCSCHHHHHHHHHHHHTT-------CTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTT-CSHHHHHHHH
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHh-------CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccc-cHHHHHHHHH
Confidence            888888888 888888888877663       3455667888888888888888888888888776544 4556667778


Q ss_pred             HHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC--------CCCCHHHHHHHHHHH
Q 041804          186 IMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG--------CQPSVVTCNTVIKLL  257 (403)
Q Consensus       186 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~li~~~  257 (403)
                      .|...|++++|...+++..+.. +.+..++..+...+...|++++|...++.+.+..        .+....++..+...|
T Consensus       168 ~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~  246 (330)
T 3hym_B          168 EYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVC  246 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHH
Confidence            8888888888888888877763 4456677777778888888888888887777642        123345677777777


Q ss_pred             HhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHH
Q 041804          258 CENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVW  337 (403)
Q Consensus       258 ~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~  337 (403)
                      ...|++++|...+++..+..                                 +.+...+..+...+.+.|++++|.+.+
T Consensus       247 ~~~g~~~~A~~~~~~a~~~~---------------------------------~~~~~~~~~la~~~~~~g~~~~A~~~~  293 (330)
T 3hym_B          247 RKLKKYAEALDYHRQALVLI---------------------------------PQNASTYSAIGYIHSLMGNFENAVDYF  293 (330)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS---------------------------------TTCSHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhhC---------------------------------ccchHHHHHHHHHHHHhccHHHHHHHH
Confidence            77777777777777665431                                 114556777788888888888888888


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHH-HhcCCH
Q 041804          338 KKMEELGCSPDEFAYNALVDAL-IDKGML  365 (403)
Q Consensus       338 ~~~~~~~~~~~~~~~~~l~~~~-~~~g~~  365 (403)
                      ++..+.. +.+...+..+..++ ...|+.
T Consensus       294 ~~al~~~-p~~~~~~~~l~~~~~~~~g~~  321 (330)
T 3hym_B          294 HTALGLR-RDDTFSVTMLGHCIEMYIGDS  321 (330)
T ss_dssp             HTTTTTC-SCCHHHHHHHHHHHHTTTTC-
T ss_pred             HHHHccC-CCchHHHHHHHHHHHHHhCch
Confidence            8887653 44677777777777 345554

>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=99.89  E-value=1.8e-19  Score=165.15  Aligned_cols=342  Identities=9%  Similarity=-0.038  Sum_probs=264.0

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      ....+..+...+.+.|++++|+..|+++....  +.+..+|..+..+|...|++++|++.|+++.+.++.+..++..+..
T Consensus        24 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~  101 (537)
T 3fp2_A           24 YAVQLKNRGNHFFTAKNFNEAIKYYQYAIELD--PNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRAS  101 (537)
T ss_dssp             HHHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhhC--CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHH
Confidence            35678889999999999999999999999875  4678899999999999999999999999999999889999999999


Q ss_pred             HHHhcCCHHHHHHHHhccccccccccc------------------------------ccCcchH----------------
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGL------------------------------VEMNKTK----------------  143 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~------------------------------~~~~~~~----------------  143 (403)
                      ++...|++++|...|+.+.........                              ...|+..                
T Consensus       102 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (537)
T 3fp2_A          102 ANESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVS  181 (537)
T ss_dssp             HHHHHTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHH
Confidence            999999999999988644222100000                              0001100                


Q ss_pred             --------------HHHHHHHHHHh--------cCChhHHHHHHHHHHhCCCCCc-------HHHHHHHHHHHHHcCChh
Q 041804          144 --------------IYNMILRGWFK--------MSWWGKCREFWEEMDKRGVVKD-------LHSYSIYMDIMCKSGKPW  194 (403)
Q Consensus       144 --------------~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~  194 (403)
                                    ....+...+..        .|++++|..+++++.+..+. +       ..++..+...+...|+++
T Consensus       182 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~  260 (537)
T 3fp2_A          182 SVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTV-DDPLRENAALALCYTGIFHFLKNNLL  260 (537)
T ss_dssp             TSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CC-CHHHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCC-cchhhHHHHHHHHHHHHHHHhcccHH
Confidence                          12222222222        24789999999999887544 3       235777778889999999


Q ss_pred             HHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          195 KAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       195 ~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      +|...|+...+.  .|+..++..+...+...|+++.|...++.+.+... .+..++..+...+...|++++|...|++..
T Consensus       261 ~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~  337 (537)
T 3fp2_A          261 DAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLNP-EYPPTYYHRGQMYFILQDYKNAKEDFQKAQ  337 (537)
T ss_dssp             HHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            999999999987  45678888999999999999999999999998753 367889999999999999999999999998


Q ss_pred             hcCCCCChhhHHHHHH---hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcC-----CC
Q 041804          275 KKGCVPDVITYHCFFR---CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELG-----CS  346 (403)
Q Consensus       275 ~~~~~p~~~~~~~l~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-----~~  346 (403)
                      +.... +...+..+..   ..++.++|...++++.+.... +...+..+...+...|++++|.+.++++.+..     ..
T Consensus       338 ~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~  415 (537)
T 3fp2_A          338 SLNPE-NVYPYIQLACLLYKQGKFTESEAFFNETKLKFPT-LPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIH  415 (537)
T ss_dssp             HHCTT-CSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCS
T ss_pred             HhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhH
Confidence            75321 2334444433   348899999999999987533 56788999999999999999999999987642     11


Q ss_pred             CCHHHHHHHHHHHHhc----------CCHHHHHHHHHHHHHcC
Q 041804          347 PDEFAYNALVDALIDK----------GMLDMARKYDEEMFAKG  379 (403)
Q Consensus       347 ~~~~~~~~l~~~~~~~----------g~~~~a~~~~~~m~~~~  379 (403)
                      .....+.....++.+.          |++++|...+++..+..
T Consensus       416 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~  458 (537)
T 3fp2_A          416 VGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD  458 (537)
T ss_dssp             STTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC
Confidence            2233345556777888          99999999999998853

>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=99.88  E-value=1.7e-20  Score=163.57  Aligned_cols=290  Identities=11%  Similarity=-0.025  Sum_probs=195.3

Q ss_pred             ccCChhHHHH-HHHHhhhCCCCCC--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHH
Q 041804           43 KFFEFDLSWN-LIHRMKDNPSSIP--NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIE  119 (403)
Q Consensus        43 ~~~~~~~a~~-~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  119 (403)
                      -.|++++|.. .+++........|  +...+..+...+...|++++|+..|+++.+..+.+..++..+..++...|++++
T Consensus        37 ~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~  116 (368)
T 1fch_A           37 WLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELL  116 (368)
T ss_dssp             ---------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHH
Confidence            4477888887 7776555431122  345677788888888888888888888888877788888888888888888888


Q ss_pred             HHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHH---------------HH
Q 041804          120 AQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSI---------------YM  184 (403)
Q Consensus       120 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---------------l~  184 (403)
                      |...++++..       ..+.+..++..+...|...|++++|.+.++++....+. +...+..               .+
T Consensus       117 A~~~~~~al~-------~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~  188 (368)
T 1fch_A          117 AISALRRCLE-------LKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRIL  188 (368)
T ss_dssp             HHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTT-TGGGCC---------------CTT
T ss_pred             HHHHHHHHHh-------cCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHH
Confidence            8888887776       33556777888888888888888888888888776544 2222221               12


Q ss_pred             HHHHHcCChhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 041804          185 DIMCKSGKPWKAVKLYKEMKKKGIKM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRV  263 (403)
Q Consensus       185 ~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  263 (403)
                      ..+...|++++|...|+++.+..... +..++..+...+...|++++|...++.+.+.. +.+...+..+...+...|++
T Consensus       189 ~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~  267 (368)
T 1fch_A          189 GSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQS  267 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCH
Confidence            33336667777777777766653111 35566666667777777777777777766653 22455666666667777777


Q ss_pred             HHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          264 REAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       264 ~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      ++|...|+++.+.                                . +.+..++..+..++.+.|++++|...++++.+.
T Consensus       268 ~~A~~~~~~al~~--------------------------------~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  314 (368)
T 1fch_A          268 EEAVAAYRRALEL--------------------------------Q-PGYIRSRYNLGISCINLGAHREAVEHFLEALNM  314 (368)
T ss_dssp             HHHHHHHHHHHHH--------------------------------C-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh--------------------------------C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            7766666665542                                1 124567788888888999999999999888764


Q ss_pred             CCC----------CCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 041804          344 GCS----------PDEFAYNALVDALIDKGMLDMARKYDEE  374 (403)
Q Consensus       344 ~~~----------~~~~~~~~l~~~~~~~g~~~~a~~~~~~  374 (403)
                      ...          ....+|..+..+|.+.|++++|..++++
T Consensus       315 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  355 (368)
T 1fch_A          315 QRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADAR  355 (368)
T ss_dssp             HHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTT
T ss_pred             CCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHH
Confidence            211          1267889999999999999999888764

>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=99.87  E-value=5.7e-20  Score=160.16  Aligned_cols=301  Identities=10%  Similarity=-0.041  Sum_probs=233.6

Q ss_pred             ccccHHHHHH-hhhhhcccCCCcC--CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            7 YANDWKRALE-FFNWVETDCHFTH--TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         7 ~~~~~~~A~~-~~~~~~~~~~~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      ..|++++|++ .|+.........|  +...+..+...+.+.|++++|...|+++.+..  +.+..+|..+..++...|++
T Consensus        37 ~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~  114 (368)
T 1fch_A           37 WLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD--PKHMEAWQYLGTTQAENEQE  114 (368)
T ss_dssp             ---------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCcCH
Confidence            4578888888 8876654222222  35678889999999999999999999999875  46788999999999999999


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHH---------------H
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNM---------------I  148 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------l  148 (403)
                      ++|+..|+++.+..+.+..++..+..++...|++++|...++++....       +.+...+..               .
T Consensus       115 ~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~  187 (368)
T 1fch_A          115 LLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYT-------PAYAHLVTPAEEGAGGAGLGPSKRI  187 (368)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-------TTTGGGCC---------------CT
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-------cCcHHHHHHHHHHhhhhcccHHHHH
Confidence            999999999999988899999999999999999999999999887642       222222211               2


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCC
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG  227 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  227 (403)
                      +..+...|++++|...|+++.+..+.. +..++..+..+|...|++++|...|+++.... +.+..++..+...+...|+
T Consensus       188 ~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~  266 (368)
T 1fch_A          188 LGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQ  266 (368)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCC
Confidence            333448899999999999998875442 57889999999999999999999999998873 4467889999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHH
Q 041804          228 VDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIE  307 (403)
Q Consensus       228 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~  307 (403)
                      +++|...|+.+.+.. +.+...+..+...|.+.|++++|...|++..+.  .|+...-                    ..
T Consensus       267 ~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~~~~~~~--------------------~~  323 (368)
T 1fch_A          267 SEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNM--QRKSRGP--------------------RG  323 (368)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HHTC-------------------------
T ss_pred             HHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCCCc--------------------cc
Confidence            999999999999874 346788999999999999999999999987753  1111000                    00


Q ss_pred             cCCCCchhhHHHHHHHHHhcCCcchHHHHHHHH
Q 041804          308 SGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKM  340 (403)
Q Consensus       308 ~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  340 (403)
                      ........+|..+..++...|++++|..++++.
T Consensus       324 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          324 EGGAMSENIWSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             -CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             cccchhhHHHHHHHHHHHHhCChHhHHHhHHHH
Confidence            001224678899999999999999999887643

>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=99.87  E-value=1.1e-19  Score=155.78  Aligned_cols=260  Identities=11%  Similarity=-0.037  Sum_probs=227.5

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC-C
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH-L   82 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~   82 (403)
                      .+...|++++|+++|+.+...  .+.+...+..++.++...|++++|..+++++.+..  +.+..+|..+...+...| +
T Consensus        31 ~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~  106 (330)
T 3hym_B           31 RHYYNCDFKMCYKLTSVVMEK--DPFHASCLPVHIGTLVELNKANELFYLSHKLVDLY--PSNPVSWFAVGCYYLMVGHK  106 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTSTHHHHHHHHHHHHSCSC
T ss_pred             HHHHcCCHHHHHHHHHHHHHc--CCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHhhhh
Confidence            345679999999999998853  24456677788899999999999999999999865  356788999999999999 9


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCR  162 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  162 (403)
                      +++|+..|++..+..+.+...+..+..++...|++++|...+++....       .+.+..++..+...|...|++++|.
T Consensus       107 ~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~-------~~~~~~~~~~l~~~~~~~~~~~~A~  179 (330)
T 3hym_B          107 NEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQL-------MKGCHLPMLYIGLEYGLTNNSKLAE  179 (330)
T ss_dssp             HHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-------TTTCSHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-------ccccHHHHHHHHHHHHHHhhHHHHH
Confidence            999999999999998888999999999999999999999999998773       3556677888999999999999999


Q ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC--------CCCChhhHHHHHHHHhhcCCHHHHHHH
Q 041804          163 EFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG--------IKMDVVAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      +.+++..+..+. +..++..+...+...|++++|...+++..+..        .+....++..+..++...|++++|...
T Consensus       180 ~~~~~al~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  258 (330)
T 3hym_B          180 RFFSQALSIAPE-DPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDY  258 (330)
T ss_dssp             HHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHhCCC-ChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence            999999988765 78899999999999999999999999988752        133456889999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          235 YREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      ++.+.+... .+...+..+...|...|++++|...|++..+.
T Consensus       259 ~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  299 (330)
T 3hym_B          259 HRQALVLIP-QNASTYSAIGYIHSLMGNFENAVDYFHTALGL  299 (330)
T ss_dssp             HHHHHHHST-TCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT
T ss_pred             HHHHHhhCc-cchHHHHHHHHHHHHhccHHHHHHHHHHHHcc
Confidence            999998753 36788999999999999999999999998865

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.86  E-value=4e-17  Score=147.64  Aligned_cols=337  Identities=11%  Similarity=0.019  Sum_probs=271.2

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHc----cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh----
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGK----FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT----   79 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----   79 (403)
                      .+++++|++.|+.... .   .++..+..+...|..    .+++++|..+|++..+.+    +..++..|...|..    
T Consensus        56 ~~~~~~A~~~~~~a~~-~---~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~----~~~a~~~Lg~~y~~g~g~  127 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAE-Q---GYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG----LPQAQQNLGVMYHEGNGV  127 (490)
T ss_dssp             CCCHHHHHHHHHHHHH-T---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSS
T ss_pred             CcCHHHHHHHHHHHHH-C---CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCC
Confidence            6789999999988875 2   457788888888888    899999999999988754    66777788888888    


Q ss_pred             cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh----cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh-
Q 041804           80 AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE----YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK-  154 (403)
Q Consensus        80 ~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-  154 (403)
                      .+++++|+++|++..+.+  ++..+..+...|..    .++.++|...|++....         .+...+..+...|.. 
T Consensus       128 ~~~~~~A~~~~~~a~~~~--~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~---------~~~~a~~~Lg~~y~~g  196 (490)
T 2xm6_A          128 KVDKAESVKWFRLAAEQG--RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQ---------GNVWSCNQLGYMYSRG  196 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT---------TCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHCC--CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC---------CCHHHHHHHHHHHhcC
Confidence            789999999999988754  66778888888887    78999999999887653         356778888888887 


Q ss_pred             ---cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh---
Q 041804          155 ---MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV---  224 (403)
Q Consensus       155 ---~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~---  224 (403)
                         .+++++|.+.|++..+.+   +..++..+...|..    .+++++|..+|++..+.|   +...+..+...|..   
T Consensus       197 ~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~  270 (490)
T 2xm6_A          197 LGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLA  270 (490)
T ss_dssp             SSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTT
T ss_pred             CCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCC
Confidence               889999999999988864   56677888888876    789999999999988765   45566667777776   


Q ss_pred             -cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc-----CcHHHHHHHHHhchhcCCCCChhhHHHHHHhh---C--
Q 041804          225 -SEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCEN-----GRVREAYAVLAEMPKKGCVPDVITYHCFFRCL---E--  293 (403)
Q Consensus       225 -~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~-----g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~---~--  293 (403)
                       .++.++|...|+...+.|   +...+..+...|...     ++.++|...|++..+.+.   ...+..+-..+   +  
T Consensus       271 ~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~~---~~a~~~lg~~y~~~g~~  344 (490)
T 2xm6_A          271 GAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQGD---ATAQANLGAIYFRLGSE  344 (490)
T ss_dssp             SSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHSCCH
T ss_pred             CCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhCCCc
Confidence             789999999999988764   566777788888877     899999999999887642   22333222222   2  


Q ss_pred             -CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHh----cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCC
Q 041804          294 -KPREILGLFDRMIESGIRPKMDTYVMLLRKFGR----WGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID----KGM  364 (403)
Q Consensus       294 -~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~  364 (403)
                       +.++|.++|++..+.+   +...+..+...|..    .+++++|...|++..+.+   ++..+..+...|.+    .++
T Consensus       345 ~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d  418 (490)
T 2xm6_A          345 EEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGLGVERD  418 (490)
T ss_dssp             HHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCC
T ss_pred             ccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCCCCC
Confidence             5788999999998864   56788888888888    889999999999998865   57788888888988    899


Q ss_pred             HHHHHHHHHHHHHcCCC
Q 041804          365 LDMARKYDEEMFAKGLS  381 (403)
Q Consensus       365 ~~~a~~~~~~m~~~~~~  381 (403)
                      .++|..+|++..+.+..
T Consensus       419 ~~~A~~~~~~A~~~~~~  435 (490)
T 2xm6_A          419 YVQAWAWFDTASTNDMN  435 (490)
T ss_dssp             HHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHCCCC
Confidence            99999999999987743

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.85  E-value=1.6e-19  Score=157.10  Aligned_cols=285  Identities=9%  Similarity=-0.082  Sum_probs=218.0

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      +...+..+...+.+.|++++|+.+|+++.+..  +.+..+|..+..++...|++++|+..|+++.+..+.+..++..+..
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~  141 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD--PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAV  141 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            45568899999999999999999999999875  4578899999999999999999999999999998889999999999


Q ss_pred             HHHhcCCHHHHHHHHhccccccccccccc---CcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-CcHHHHHHHHH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVE---MNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV-KDLHSYSIYMD  185 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~  185 (403)
                      +|...|++++|...++++....+......   ......+..+...+...|++++|.+.|+++.+..+. ++..++..+..
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            99999999999999998876321000000   001233445688899999999999999999887543 26788999999


Q ss_pred             HHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHH
Q 041804          186 IMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVRE  265 (403)
Q Consensus       186 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  265 (403)
                      .|...|++++|.+.|+++.+.. +.+..++..+..+|...|++++|...|+.+.+... .+..++..+..+|.+.|++++
T Consensus       222 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~  299 (365)
T 4eqf_A          222 LFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQP-GFIRSRYNLGISCINLGAYRE  299 (365)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CchHHHHHHHHHHHHCCCHHH
Confidence            9999999999999999998874 44678999999999999999999999999998743 357889999999999999999


Q ss_pred             HHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHH
Q 041804          266 AYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKK  339 (403)
Q Consensus       266 a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  339 (403)
                      |...|++..+.  .|+...-.                   .......+...|..+..++...|+.+.+..+.++
T Consensus       300 A~~~~~~al~~--~~~~~~~~-------------------~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          300 AVSNFLTALSL--QRKSRNQQ-------------------QVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHHHH--HHCC-------------------------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHh--CcccCCCc-------------------ccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            99999988753  12110000                   0000112456778888888888888887776654

>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=99.85  E-value=1.6e-19  Score=154.62  Aligned_cols=253  Identities=10%  Similarity=-0.035  Sum_probs=112.0

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHH
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEA   86 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a   86 (403)
                      ..|++++|+++|+.+...  .+.+..++..+..++...|++++|...++++.+..  +.+..++..+...+...|++++|
T Consensus        33 ~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~~~~~~A  108 (327)
T 3cv0_A           33 KLANLAEAALAFEAVCQA--APEREEAWRSLGLTQAENEKDGLAIIALNHARMLD--PKDIAVHAALAVSHTNEHNANAA  108 (327)
T ss_dssp             HTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HhccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--cCCHHHHHHHHHHHHHcCCHHHH
Confidence            344555555555444421  12234444444455555555555555555444432  22344444445555555555555


Q ss_pred             HHHHHHHhhcCCCcHHHHHHH--------------HH-HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHH
Q 041804           87 MGTFNKLDEFGLKDEVSYCNL--------------VD-ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG  151 (403)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (403)
                      ++.++++.+..+.+...+..+              .. .+...|++++|...++++..       ..+.+..++..+...
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~la~~  181 (327)
T 3cv0_A          109 LASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALE-------MNPNDAQLHASLGVL  181 (327)
T ss_dssp             HHHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHH-------HSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHh-------hCCCCHHHHHHHHHH
Confidence            555555544443333333222              11 23344444455444444443       122234444444445


Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHH
Q 041804          152 WFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFA  231 (403)
Q Consensus       152 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a  231 (403)
                      +...|++++|.+.++++.+..+. +..++..+..++...|++++|...|+++.+.. +.+..++..+...+...|++++|
T Consensus       182 ~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A  259 (327)
T 3cv0_A          182 YNLSNNYDSAAANLRRAVELRPD-DAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLA  259 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHH
Confidence            55555555555555544443322 34444444445555555555555555444432 22334444444444455555555


Q ss_pred             HHHHHHHHHcCCCC-----------CHHHHHHHHHHHHhcCcHHHHHHHHHh
Q 041804          232 MRVYREMREMGCQP-----------SVVTCNTVIKLLCENGRVREAYAVLAE  272 (403)
Q Consensus       232 ~~~~~~~~~~~~~~-----------~~~~~~~li~~~~~~g~~~~a~~~~~~  272 (403)
                      ...++.+.+.....           +...+..+..++.+.|++++|..++++
T Consensus       260 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  311 (327)
T 3cv0_A          260 AKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQ  311 (327)
T ss_dssp             HHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTC
T ss_pred             HHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            55554444432111           233444444445555555555444443

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.85  E-value=7.9e-20  Score=159.12  Aligned_cols=260  Identities=7%  Similarity=-0.076  Sum_probs=215.4

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.+...  .+.+..++..+..++.+.|++++|+..|+++.+..  +.+..+|..+..+|...|+
T Consensus        73 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~  148 (365)
T 4eqf_A           73 LKRLKEGDLPVTILFMEAAILQ--DPGDAEAWQFLGITQAENENEQAAIVALQRCLELQ--PNNLKALMALAVSYTNTSH  148 (365)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHcccc
Confidence            3456789999999999999852  34568899999999999999999999999999865  4568899999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHH----------HHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYC----------NLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~----------~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      +++|+..|+++.+..+.+...+.          .+...+...|++++|...++++....     ....+..++..+...|
T Consensus       149 ~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-----p~~~~~~~~~~l~~~~  223 (365)
T 4eqf_A          149 QQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQN-----GDMIDPDLQTGLGVLF  223 (365)
T ss_dssp             HHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHS-----CSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhC-----cCccCHHHHHHHHHHH
Confidence            99999999999987765444443          34888999999999999999988742     1122688999999999


Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHH
Q 041804          153 FKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAM  232 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~  232 (403)
                      ...|++++|.+.|++..+..+. +..+|..+..+|...|++++|...|+++.+.. +.+..++..+..+|...|++++|.
T Consensus       224 ~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~  301 (365)
T 4eqf_A          224 HLSGEFNRAIDAFNAALTVRPE-DYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREAV  301 (365)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHH
Confidence            9999999999999999987655 78899999999999999999999999999873 445788999999999999999999


Q ss_pred             HHHHHHHHcCCC-----------CCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          233 RVYREMREMGCQ-----------PSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       233 ~~~~~~~~~~~~-----------~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      ..|+++.+....           .+...|..+..++...|+.+.+..+..+-
T Consensus       302 ~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  353 (365)
T 4eqf_A          302 SNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLGD  353 (365)
T ss_dssp             HHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTTC
T ss_pred             HHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHhh
Confidence            999999875311           13678899999999999999998887763

>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=99.83  E-value=4.2e-18  Score=145.65  Aligned_cols=281  Identities=9%  Similarity=-0.044  Sum_probs=177.0

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      +...+..+...+...|++++|..+|+++.+..  +.+..++..+..++...|++++|...|+++.+..+.+..++..+..
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~   97 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAV   97 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHH
Confidence            34455666777777777777777777776654  3456667777777777777777777777777766556666666666


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHH-HH-HH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIY-MD-IM  187 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-~~-~~  187 (403)
                      .+...|++++|...+++.....       +.+...+..+...                      .|+......+ .. .+
T Consensus        98 ~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~  148 (327)
T 3cv0_A           98 SHTNEHNANAALASLRAWLLSQ-------PQYEQLGSVNLQA----------------------DVDIDDLNVQSEDFFF  148 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTS-------TTTTTC------------------------------------------CCT
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-------CccHHHHHHHhHH----------------------HHHHHHHHHHHHhHHH
Confidence            7777777777766666655421       1111111111000                      0011111111 11 25


Q ss_pred             HHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHH
Q 041804          188 CKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAY  267 (403)
Q Consensus       188 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~  267 (403)
                      ...|++++|...++++.+.. +.+..++..+...+...|++++|...++.+.+... .+...+..+...+...|++++|.
T Consensus       149 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~  226 (327)
T 3cv0_A          149 AAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRP-DDAQLWNKLGATLANGNRPQEAL  226 (327)
T ss_dssp             TSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHH
Confidence            55666777777777766653 33556666677777777777777777777766532 24566777777777777777777


Q ss_pred             HHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCC
Q 041804          268 AVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSP  347 (403)
Q Consensus       268 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~  347 (403)
                      ..|+++.+..  |                               .+..++..+...+...|++++|.+.++++.+.....
T Consensus       227 ~~~~~a~~~~--~-------------------------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~  273 (327)
T 3cv0_A          227 DAYNRALDIN--P-------------------------------GYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGG  273 (327)
T ss_dssp             HHHHHHHHHC--T-------------------------------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHcC--C-------------------------------CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCcc
Confidence            7777665431  1                               134567778888888899999999998887653111


Q ss_pred             -----------CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 041804          348 -----------DEFAYNALVDALIDKGMLDMARKYDEEMF  376 (403)
Q Consensus       348 -----------~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  376 (403)
                                 +...|..+..++.+.|++++|..++++..
T Consensus       274 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          274 TTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNV  313 (327)
T ss_dssp             CC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCS
T ss_pred             ccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence                       47788899999999999999998887543

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.83  E-value=3.7e-16  Score=142.80  Aligned_cols=355  Identities=8%  Similarity=0.060  Sum_probs=227.3

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHH-HhcCChH
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRY-VTAHLVN   84 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~~   84 (403)
                      ...|++++|..+|+.+..  -.+.+...|..++..+.+.|++++|..+|++.....   |+...|...+... ...|+.+
T Consensus        23 ~~~~~~~~a~~~~e~al~--~~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~---p~~~lw~~~~~~~~~~~~~~~   97 (530)
T 2ooe_A           23 AQNQPIDKARKTYERLVA--QFPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV---LHIDLWKCYLSYVRETKGKLP   97 (530)
T ss_dssp             HHSSCHHHHHHHHHHHHT--TCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC---CCHHHHHHHHHHHHHHTTTST
T ss_pred             HHhCCHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC---CChHHHHHHHHHHHHHccchh
Confidence            346899999999999984  346678899999999999999999999999999865   7888888777533 4567777


Q ss_pred             HHHH----HHHHHhhc-C--CCcHHHHHHHHHHHHh---------cCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           85 EAMG----TFNKLDEF-G--LKDEVSYCNLVDALCE---------YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        85 ~a~~----~~~~~~~~-~--~~~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .|.+    +|++.... |  +.+...|...+....+         .|+++.|..+|++.....      ..+....|...
T Consensus        98 ~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P------~~~~~~~~~~~  171 (530)
T 2ooe_A           98 SYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNP------MINIEQLWRDY  171 (530)
T ss_dssp             THHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSC------CTTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhch------hhhHHHHHHHH
Confidence            7665    77766543 3  2367788888777655         688999999998877631      11111222211


Q ss_pred             HHHH-------------HhcCChh--------------------------------------------------------
Q 041804          149 LRGW-------------FKMSWWG--------------------------------------------------------  159 (403)
Q Consensus       149 ~~~~-------------~~~~~~~--------------------------------------------------------  159 (403)
                      ....             .+.+++.                                                        
T Consensus       172 ~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~  251 (530)
T 2ooe_A          172 NKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQT  251 (530)
T ss_dssp             HHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSH
T ss_pred             HHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcch
Confidence            1100             0111222                                                        


Q ss_pred             ----HHHHHHHHHHhCCCCCcHHHHHHHHHHHHH-------cCChh-------HHHHHHHHHHHcCCCCChhhHHHHHHH
Q 041804          160 ----KCREFWEEMDKRGVVKDLHSYSIYMDIMCK-------SGKPW-------KAVKLYKEMKKKGIKMDVVAYNTVIRA  221 (403)
Q Consensus       160 ----~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~~~~ll~~  221 (403)
                          .+..+|++.....+. +...|..++..+.+       .|+++       +|..+|++..+.-.+-+...|..++..
T Consensus       252 ~~~~~a~~~y~~al~~~p~-~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~  330 (530)
T 2ooe_A          252 LITKRVMFAYEQCLLVLGH-HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADY  330 (530)
T ss_dssp             HHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence                344455555444332 45566666666554       56665       677777776652123345666777777


Q ss_pred             HhhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC-hhhHH--HHHH--hhCC
Q 041804          222 VGVSEGVDFAMRVYREMREMGCQPS--VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD-VITYH--CFFR--CLEK  294 (403)
Q Consensus       222 ~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~--~l~~--~~~~  294 (403)
                      +.+.|+++.|..+|+.+.+.  .|+  ...|..++..+.+.|++++|..+|++..+.  .|. ...|.  +.+.  ..++
T Consensus       331 ~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~--~~~~~~~~~~~a~~~~~~~~~  406 (530)
T 2ooe_A          331 EESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED--ARTRHHVYVTAALMEYYCSKD  406 (530)
T ss_dssp             HHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--TTCCTHHHHHHHHHHHHHTCC
T ss_pred             HHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--cCCchHHHHHHHHHHHHHcCC
Confidence            77777777777777777764  333  246666777777777777777777776654  222 11111  1221  2466


Q ss_pred             HHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcC-CCC--CHHHHHHHHHHHHhcCCHHHHHHH
Q 041804          295 PREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELG-CSP--DEFAYNALVDALIDKGMLDMARKY  371 (403)
Q Consensus       295 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~-~~~--~~~~~~~l~~~~~~~g~~~~a~~~  371 (403)
                      .++|..+|+...+... -+...|..++..+.+.|+.++|..+|++....+ ..|  ....|...+....+.|+.+.+..+
T Consensus       407 ~~~A~~~~e~al~~~p-~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~  485 (530)
T 2ooe_A          407 KSVAFKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKV  485 (530)
T ss_dssp             HHHHHHHHHHHHHHHT-TCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHCC-CCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            7777777777766432 245667777777777777777777777776652 122  234666667776777777777777


Q ss_pred             HHHHHH
Q 041804          372 DEEMFA  377 (403)
Q Consensus       372 ~~~m~~  377 (403)
                      .+++.+
T Consensus       486 ~~r~~~  491 (530)
T 2ooe_A          486 EKRRFT  491 (530)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            777665

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.82  E-value=9.3e-16  Score=138.73  Aligned_cols=336  Identities=12%  Similarity=0.079  Sum_probs=272.6

Q ss_pred             cCCHHhHHHHHHHHHc----cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHhhcCCC
Q 041804           28 THTTDTYNSVIDILGK----FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT----AHLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~   99 (403)
                      ..++..+..+...|..    .+++++|..+|++..+.+    +..++..|...|..    .+++++|+++|++..+.+  
T Consensus        36 ~g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~----~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~--  109 (490)
T 2xm6_A           36 SGEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG----YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG--  109 (490)
T ss_dssp             TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--
T ss_pred             CCCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC--
Confidence            4577888888888888    899999999999998864    67788889999998    999999999999998854  


Q ss_pred             cHHHHHHHHHHHHh----cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh----cCChhHHHHHHHHHHhC
Q 041804          100 DEVSYCNLVDALCE----YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK----MSWWGKCREFWEEMDKR  171 (403)
Q Consensus       100 ~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~  171 (403)
                      ++..+..|...|..    .+++++|...|++....         .+...+..+...|..    .+++++|.+.|++..+.
T Consensus       110 ~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~---------~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~  180 (490)
T 2xm6_A          110 LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQ---------GRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQ  180 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT---------TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC---------CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC
Confidence            66778888888888    78999999999987663         356678888888887    78999999999999887


Q ss_pred             CCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh----cCCHHHHHHHHHHHHHcCC
Q 041804          172 GVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV----SEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       172 ~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~  243 (403)
                      +   +..++..+...|..    .+++++|.++|++..+.|   +...+..+...|..    .+++++|..+|+...+.+ 
T Consensus       181 ~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~-  253 (490)
T 2xm6_A          181 G---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG-  253 (490)
T ss_dssp             T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT-
T ss_pred             C---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-
Confidence            4   67788899999988    899999999999998875   56677778777775    789999999999998764 


Q ss_pred             CCCHHHHHHHHHHHHh----cCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh-----CCHHHHHHHHHHHHHcCCCCch
Q 041804          244 QPSVVTCNTVIKLLCE----NGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL-----EKPREILGLFDRMIESGIRPKM  314 (403)
Q Consensus       244 ~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~-----~~~~~a~~~~~~~~~~~~~~~~  314 (403)
                        +...+..+...|..    .++.++|...|++..+.|...-......+....     .+.++|..++++..+.+   +.
T Consensus       254 --~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~  328 (490)
T 2xm6_A          254 --NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DA  328 (490)
T ss_dssp             --CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CH
T ss_pred             --CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CH
Confidence              56677778888887    899999999999988764321111112222222     57899999999999875   45


Q ss_pred             hhHHHHHHHHHhcC---CcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCChhhH
Q 041804          315 DTYVMLLRKFGRWG---FLRPVFVVWKKMEELGCSPDEFAYNALVDALID----KGMLDMARKYDEEMFAKGLSAKPREE  387 (403)
Q Consensus       315 ~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~  387 (403)
                      ..+..+...|...|   ++++|.+.|++..+.   .++..+..+...|..    .+++++|..+|++..+.|. |+....
T Consensus       329 ~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~---~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~~-~~a~~~  404 (490)
T 2xm6_A          329 TAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK---GEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQGL-SAAQVQ  404 (490)
T ss_dssp             HHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC-HHHHHH
T ss_pred             HHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCCC-HHHHHH
Confidence            57777777777766   789999999999886   467889999999998    8999999999999998863 555555


Q ss_pred             HHHHHHh
Q 041804          388 LGTKLVQ  394 (403)
Q Consensus       388 ~~~~~~~  394 (403)
                      ++.....
T Consensus       405 Lg~~y~~  411 (490)
T 2xm6_A          405 LGEIYYY  411 (490)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHc
Confidence            5555554

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.82  E-value=4e-17  Score=136.64  Aligned_cols=247  Identities=9%  Similarity=0.044  Sum_probs=118.8

Q ss_pred             HHhcCChHHHHHHHHHHhhcCCCc-HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           77 YVTAHLVNEAMGTFNKLDEFGLKD-EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        77 ~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      ....|++..|+..++......+.+ ......+.++|...|+++.|...++.          ..+|+..++..+...+...
T Consensus         9 ~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----------~~~~~~~a~~~la~~~~~~   78 (291)
T 3mkr_A            9 AFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----------SSAPELQAVRMFAEYLASH   78 (291)
T ss_dssp             HHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----------TSCHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----------cCChhHHHHHHHHHHHcCC
Confidence            344556666665555544433332 23444455566666666665554432          1234555555566666666


Q ss_pred             CChhHHHHHHHHHHhCCCCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHH
Q 041804          156 SWWGKCREFWEEMDKRGVVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      ++.++|.+.++++...+..| +...+..+...+...|++++|++.+++      +.+...+..+...+.+.|++++|...
T Consensus        79 ~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~  152 (291)
T 3mkr_A           79 SRRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKE  152 (291)
T ss_dssp             TTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            66666666666655544323 334444445556666666666665554      23445555555556666666666666


Q ss_pred             HHHHHHcCCCCCHHHH---HHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH---hhCCHHHHHHHHHHHHHc
Q 041804          235 YREMREMGCQPSVVTC---NTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR---CLEKPREILGLFDRMIES  308 (403)
Q Consensus       235 ~~~~~~~~~~~~~~~~---~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~---~~~~~~~a~~~~~~~~~~  308 (403)
                      |+.+.+..  |+....   ...+..+...|++++|..+|+++.+.. +.+...++.+..   ..+++++|...+++..+.
T Consensus       153 l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~  229 (291)
T 3mkr_A          153 LKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKC-SPTLLLLNGQAACHMAQGRWEAAEGVLQEALDK  229 (291)
T ss_dssp             HHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66655542  222111   111222223345555555555544431 112222222111   113333333333333332


Q ss_pred             CCCCchhhHHHHHHHHHhcCCcch-HHHHHHHHHhc
Q 041804          309 GIRPKMDTYVMLLRKFGRWGFLRP-VFVVWKKMEEL  343 (403)
Q Consensus       309 ~~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~~  343 (403)
                      ... +..++..++..+...|+.++ +.++++++.+.
T Consensus       230 ~p~-~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          230 DSG-HPETLINLVVLSQHLGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             CTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCC-CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            221 44556666666666666544 44566665554

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.82  E-value=3.7e-17  Score=147.37  Aligned_cols=364  Identities=13%  Similarity=-0.015  Sum_probs=243.0

Q ss_pred             cccccccccHHHHHHhhhhhcc-------cCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhC-----CCC-CCCHH
Q 041804            2 ETLSCYANDWKRALEFFNWVET-------DCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN-----PSS-IPNHA   68 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~~~-~~~~~   68 (403)
                      +.++...|++++|++.|+....       ....+....+|+.+..+|...|++++|...+++..+.     +.. .....
T Consensus        58 g~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~  137 (472)
T 4g1t_A           58 AYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPE  137 (472)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHH
Confidence            4567778999999999987643       1112334678999999999999999999999877542     101 12355


Q ss_pred             HHHHHHHHHHhc--CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH---hcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           69 TFRIMFKRYVTA--HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC---EYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        69 ~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      ++..+..++...  +++++|+..|++..+..+.++..+..+..++.   ..++.++|...+++...       ..+.+..
T Consensus       138 ~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~-------l~p~~~~  210 (472)
T 4g1t_A          138 LDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIR-------LNPDNQY  210 (472)
T ss_dssp             HHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHH-------HCSSCHH
T ss_pred             HHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhh-------cCCcchH
Confidence            677666666654  46899999999999999888888777766644   45677788888877665       3345566


Q ss_pred             HHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHH
Q 041804          144 IYNMILRGWFK----MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVI  219 (403)
Q Consensus       144 ~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll  219 (403)
                      ++..+...+..    .+++++|.+.+++.....+. +..++..+...|...|++++|...+++..+.. +-+..++..+.
T Consensus       211 ~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~-~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg  288 (472)
T 4g1t_A          211 LKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPG-VTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLHCQIG  288 (472)
T ss_dssp             HHHHHHHHHHHCC------CHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCcc-HHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHHHHHH
Confidence            66666655544    46788999999999887665 77889999999999999999999999998873 33555666665


Q ss_pred             HHHhh-------------------cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC
Q 041804          220 RAVGV-------------------SEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP  280 (403)
Q Consensus       220 ~~~~~-------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p  280 (403)
                      .+|..                   .+..+.|...++...+... .+...+..+...|...|++++|...|++..+....|
T Consensus       289 ~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~  367 (472)
T 4g1t_A          289 CCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAND-NLFRVCSILASLHALADQYEEAEYYFQKEFSKELTP  367 (472)
T ss_dssp             HHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCT-TTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCC-chhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCC
Confidence            55532                   2235678888888877643 356678889999999999999999999988764333


Q ss_pred             Chh--hH---HHH-HHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHH
Q 041804          281 DVI--TY---HCF-FRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNA  354 (403)
Q Consensus       281 ~~~--~~---~~l-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  354 (403)
                      ...  .+   ..+ ....++.++|+..|++..+.  .|+......         ....+..++++..+.. +.+..+|..
T Consensus       368 ~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i--~~~~~~~~~---------~~~~l~~~~~~~l~~~-p~~~~~~~~  435 (472)
T 4g1t_A          368 VAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKI--NQKSREKEK---------MKDKLQKIAKMRLSKN-GADSEALHV  435 (472)
T ss_dssp             HHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHS--CCCCHHHHH---------HHHHHHHHHHHHHHHC-C-CTTHHHH
T ss_pred             hHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CcccHHHHH---------HHHHHHHHHHHHHHhC-CCCHHHHHH
Confidence            221  11   111 12336788999999998874  344332222         2234455666665553 567889999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcC-CCCChhhH
Q 041804          355 LVDALIDKGMLDMARKYDEEMFAKG-LSAKPREE  387 (403)
Q Consensus       355 l~~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~~~  387 (403)
                      +..+|...|++++|++.|++.++.+ ..|+..+.
T Consensus       436 LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          436 LAFLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             HHHHHHHHHHCC----------------------
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence            9999999999999999999998863 34554443

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.82  E-value=1.8e-17  Score=138.67  Aligned_cols=255  Identities=10%  Similarity=0.057  Sum_probs=202.7

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCC--HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHT--TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      ...|++..|++.++.+..   ..|+  ......+.++|...|+++.|+..++..     .+|+..++..+...+...++.
T Consensus        10 ~~~g~y~~ai~~~~~~~~---~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~-----~~~~~~a~~~la~~~~~~~~~   81 (291)
T 3mkr_A           10 FYIGSYQQCINEAQRVKP---SSPERDVERDVFLYRAYLAQRKYGVVLDEIKPS-----SAPELQAVRMFAEYLASHSRR   81 (291)
T ss_dssp             HHTTCHHHHHHHHHHSCC---CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTT-----SCHHHHHHHHHHHHHHCSTTH
T ss_pred             HHHHHHHHHHHHHHhccc---CCchhhHHHHHHHHHHHHHCCCHHHHHHHhccc-----CChhHHHHHHHHHHHcCCCcH
Confidence            356899999999877653   2333  345567789999999999999866542     357788899999999999999


Q ss_pred             HHHHHHHHHHhhcC--CCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHH
Q 041804           84 NEAMGTFNKLDEFG--LKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC  161 (403)
Q Consensus        84 ~~a~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  161 (403)
                      ++|++.++++...+  +.+...+..+..++...|++++|.+.+++            +.+..++..+...+.+.|++++|
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------------~~~~~~~~~l~~~~~~~g~~~~A  149 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------------GDSLECMAMTVQILLKLDRLDLA  149 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------------CCSHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------------CCCHHHHHHHHHHHHHCCCHHHH
Confidence            99999999998775  44888888999999999999999999876            35667889999999999999999


Q ss_pred             HHHHHHHHhCCCCCcHHHH---HHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHH
Q 041804          162 REFWEEMDKRGVVKDLHSY---SIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREM  238 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  238 (403)
                      .+.|+++.+..  |+....   ..++..+...|++++|..+|+++.+. .+.+...++.+..++.+.|++++|...|+++
T Consensus       150 ~~~l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~a  226 (291)
T 3mkr_A          150 RKELKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEA  226 (291)
T ss_dssp             HHHHHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            99999998875  333211   12334444558999999999999988 4667888999999999999999999999999


Q ss_pred             HHcCCCCCHHHHHHHHHHHHhcCcHHH-HHHHHHhchhcCCCCChhhHH
Q 041804          239 REMGCQPSVVTCNTVIKLLCENGRVRE-AYAVLAEMPKKGCVPDVITYH  286 (403)
Q Consensus       239 ~~~~~~~~~~~~~~li~~~~~~g~~~~-a~~~~~~~~~~~~~p~~~~~~  286 (403)
                      .+... -+..++..++..+...|+.++ +.++++++.+.  .|+.....
T Consensus       227 l~~~p-~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~--~P~~~~~~  272 (291)
T 3mkr_A          227 LDKDS-GHPETLINLVVLSQHLGKPPEVTNRYLSQLKDA--HRSHPFIK  272 (291)
T ss_dssp             HHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             HHhCC-CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--CCCChHHH
Confidence            88753 377788889999999999875 57888888765  45544333

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.82  E-value=1.8e-20  Score=173.08  Aligned_cols=116  Identities=11%  Similarity=0.126  Sum_probs=62.6

Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHh---CCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHH
Q 041804          142 TKIYNMILRGWFKMSWWGKCREFWEEMDK---RGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTV  218 (403)
Q Consensus       142 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  218 (403)
                      ..+||++|.+|++.|++++|.++|++|.+   .|+.||..|||+||++|++.|++++|.++|++|.+.|+.||..||+++
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            34555555555555555555555544432   345555555555555555555555555555555555555555555555


Q ss_pred             HHHHhhcCC-HHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 041804          219 IRAVGVSEG-VDFAMRVYREMREMGCQPSVVTCNTVIKLL  257 (403)
Q Consensus       219 l~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  257 (403)
                      |.++++.|+ .+.|.++|++|.+.|+.||..+|++++..+
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~  246 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEE  246 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChh
Confidence            555555554 244555555555555555555555555433

>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=99.81  E-value=1.3e-18  Score=149.07  Aligned_cols=286  Identities=9%  Similarity=0.061  Sum_probs=128.8

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      +.|...-|+.++|.++++.+.       ++.+|..++.++.+.|++++|++.|.+.       +|..+|..++.++...|
T Consensus        10 ~~ll~~~~~ld~A~~fae~~~-------~~~vWs~La~A~l~~g~~~eAIdsfika-------~D~~~y~~V~~~ae~~g   75 (449)
T 1b89_A           10 QVLIEHIGNLDRAYEFAERCN-------EPAVWSQLAKAQLQKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSG   75 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHccCHHHHHHHHHhCC-------ChHHHHHHHHHHHHcCCHHHHHHHHHcC-------CCHHHHHHHHHHHHhCC
Confidence            456667788999999999884       2359999999999999999999999652       67779999999999999


Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHH
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC  161 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  161 (403)
                      ++++|+..++...+ ..+++.+.+.++.+|.+.|+++++.++++             .|+..+|+.+...|...|.+++|
T Consensus        76 ~~EeAi~yl~~ark-~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------------~pn~~a~~~IGd~~~~~g~yeeA  141 (449)
T 1b89_A           76 NWEELVKYLQMARK-KARESYVETELIFALAKTNRLAELEEFIN-------------GPNNAHIQQVGDRCYDEKMYDAA  141 (449)
T ss_dssp             ----------------------------------CHHHHTTTTT-------------CC----------------CTTTH
T ss_pred             CHHHHHHHHHHHHH-hCccchhHHHHHHHHHHhCCHHHHHHHHc-------------CCcHHHHHHHHHHHHHcCCHHHH
Confidence            99999997776666 34578889999999999999999887753             35667999999999999999999


Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ..+|..+         ..|..++.++.+.|++++|.+.++++      .++.+|..++.+|...|+++.|......    
T Consensus       142 ~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~----  202 (449)
T 1b89_A          142 KLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLH----  202 (449)
T ss_dssp             HHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTT----
T ss_pred             HHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHH----
Confidence            9999977         38999999999999999999999988      2789999999999999999999665443    


Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhh--CCHHHHHHHHHHHHH-cCCCC------
Q 041804          242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCL--EKPREILGLFDRMIE-SGIRP------  312 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~--~~~~~a~~~~~~~~~-~~~~~------  312 (403)
                       +...+.....++..|.+.|++++|..+++...... ......|+-+--.+  -++++..+.++.... ..++|      
T Consensus       203 -L~~~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~  280 (449)
T 1b89_A          203 -IVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAE  280 (449)
T ss_dssp             -TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHH
T ss_pred             -HHhCHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence             22344445678999999999999999999887543 33455555443333  344544444443322 22222      


Q ss_pred             chhhHHHHHHHHHhcCCcchHHHH
Q 041804          313 KMDTYVMLLRKFGRWGFLRPVFVV  336 (403)
Q Consensus       313 ~~~~~~~li~~~~~~g~~~~a~~~  336 (403)
                      +...|.-++-.|...++++.|...
T Consensus       281 ~~~~w~e~~~ly~~~~e~d~A~~t  304 (449)
T 1b89_A          281 QAHLWAELVFLYDKYEEYDNAIIT  304 (449)
T ss_dssp             TTTCHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhchHHHHHHH
Confidence            356788899999999999988874

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.80  E-value=1.7e-19  Score=166.71  Aligned_cols=154  Identities=10%  Similarity=0.136  Sum_probs=127.1

Q ss_pred             CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH---cCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHH
Q 041804          173 VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK---KGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVT  249 (403)
Q Consensus       173 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  249 (403)
                      ..--..||++||++|++.|++++|.++|++|.+   .|+.||..|||+||.+|++.|++++|.++|++|.+.|+.||..|
T Consensus       123 ~~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvT  202 (1134)
T 3spa_A          123 LSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLS  202 (1134)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHH
T ss_pred             HHhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHH
Confidence            344567999999999999999999999988764   48999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCc-HHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCc------hhhHHHHHH
Q 041804          250 CNTVIKLLCENGR-VREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPK------MDTYVMLLR  322 (403)
Q Consensus       250 ~~~li~~~~~~g~-~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~li~  322 (403)
                      ||++|.++++.|+ .++|.++|++|.+.|+.||..+|++++.+.++. .+++..+++ ..++.|+      ..+...|.+
T Consensus       203 YntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~-~vL~~Vrkv-~P~f~p~~~~~~~~~t~~LL~d  280 (1134)
T 3spa_A          203 YAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA-TVLKAVHKV-KPTFSLPPQLPPPVNTSKLLRD  280 (1134)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHH-HHHHHHGGG-CCCCCCCCCCCCCCCCCTTTHH
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHH-HHHHHHHHh-CcccCCCCCCcccccchHHHHH
Confidence            9999999999998 578999999999999999999999887655432 344444444 3344443      334445555


Q ss_pred             HHHhcC
Q 041804          323 KFGRWG  328 (403)
Q Consensus       323 ~~~~~g  328 (403)
                      .|.+.+
T Consensus       281 l~s~d~  286 (1134)
T 3spa_A          281 VYAKDG  286 (1134)
T ss_dssp             HHCCCS
T ss_pred             HHccCC
Confidence            665544

>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=99.78  E-value=2.8e-18  Score=146.94  Aligned_cols=280  Identities=14%  Similarity=0.085  Sum_probs=128.7

Q ss_pred             HccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHH
Q 041804           42 GKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ  121 (403)
Q Consensus        42 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  121 (403)
                      -+.|++++|.++++++..     |  .+|..++.++.+.|++++|++.|.+.     +|..+|..++.++...|++++|.
T Consensus        14 ~~~~~ld~A~~fae~~~~-----~--~vWs~La~A~l~~g~~~eAIdsfika-----~D~~~y~~V~~~ae~~g~~EeAi   81 (449)
T 1b89_A           14 EHIGNLDRAYEFAERCNE-----P--AVWSQLAKAQLQKGMVKEAIDSYIKA-----DDPSSYMEVVQAANTSGNWEELV   81 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHccCHHHHHHHHHhCCC-----h--HHHHHHHHHHHHcCCHHHHHHHHHcC-----CCHHHHHHHHHHHHhCCCHHHHH
Confidence            367889999999999832     3  49999999999999999999999652     47779999999999999999999


Q ss_pred             HHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHH
Q 041804          122 ELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYK  201 (403)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  201 (403)
                      ..++...+.        .+++.+.+.++.+|.+.|+++++.++++       .|+..+|..+...|...|.+++|...|.
T Consensus        82 ~yl~~ark~--------~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~  146 (449)
T 1b89_A           82 KYLQMARKK--------ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYN  146 (449)
T ss_dssp             -----------------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHH
T ss_pred             HHHHHHHHh--------CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            977766653        3457788999999999999999998885       3677899999999999999999999999


Q ss_pred             HHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC
Q 041804          202 EMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD  281 (403)
Q Consensus       202 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~  281 (403)
                      .+         ..|..++.++.+.|+++.|.+.++++      .++.+|..++.+|...|+++.|......+.   +.|+
T Consensus       147 ~a---------~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~---~~ad  208 (449)
T 1b89_A          147 NV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV---VHAD  208 (449)
T ss_dssp             HT---------TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT---TCHH
T ss_pred             Hh---------hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH---hCHh
Confidence            76         47899999999999999999999988      278999999999999999999977666543   2343


Q ss_pred             hhhHHHHHH---hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHh-cCCCC------CHHH
Q 041804          282 VITYHCFFR---CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEE-LGCSP------DEFA  351 (403)
Q Consensus       282 ~~~~~~l~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~------~~~~  351 (403)
                      .  ...++.   ..|+++++..+++...... +-....|+-+.-+|++- ++++..+.++...+ .+++|      +...
T Consensus       209 ~--l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky-~p~k~~ehl~~~~~~ini~k~~~~~~~~~~  284 (449)
T 1b89_A          209 E--LEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHL  284 (449)
T ss_dssp             H--HHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTT-CHHHHHHHHHHHSTTSCHHHHHHHHHTTTC
T ss_pred             h--HHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            3  333443   4488999999999988654 34566777777777664 34444444443322 23333      4667


Q ss_pred             HHHHHHHHHhcCCHHHHHH
Q 041804          352 YNALVDALIDKGMLDMARK  370 (403)
Q Consensus       352 ~~~l~~~~~~~g~~~~a~~  370 (403)
                      |.-++-.|.+.++++.|..
T Consensus       285 w~e~~~ly~~~~e~d~A~~  303 (449)
T 1b89_A          285 WAELVFLYDKYEEYDNAII  303 (449)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhhchHHHHHH
Confidence            9999999999999998876

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.77  E-value=9.5e-17  Score=128.48  Aligned_cols=198  Identities=12%  Similarity=-0.006  Sum_probs=125.4

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      ++++..+..+...+.+.|++++|...|++..+..  +.+...+..+..++.+.|++++|+..|++..+..+.+...+..+
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~l   79 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN--PQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVL   79 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS--SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHH
Confidence            5677889999999999999999999999999876  46788999999999999999999999999999998899999999


Q ss_pred             HHHHHhc-----------CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCc
Q 041804          108 VDALCEY-----------KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKD  176 (403)
Q Consensus       108 ~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  176 (403)
                      ..++...           |++++|...+++...       ..|.+..++..+...+...|++++|...|++..+.+  .+
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~-------~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~  150 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAER-------VNPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DT  150 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CC
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHH-------hCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cc
Confidence            9998887           555555555555444       223334445555555555555555555555554444  24


Q ss_pred             HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHH
Q 041804          177 LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYRE  237 (403)
Q Consensus       177 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~  237 (403)
                      ...+..+..+|...|++++|...|++..+.. +.+...+..+..++...|++++|...+++
T Consensus       151 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          151 PEIRSALAELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAAL  210 (217)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC-------------
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            4445555555555555555555555554442 22334444444444455555555444443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.77  E-value=1e-16  Score=128.34  Aligned_cols=201  Identities=10%  Similarity=-0.070  Sum_probs=168.0

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           64 IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      +++...+..+...+.+.|++++|+..|++..+..+.+...+..+..++.+.|++++|...+++...       ..|.+..
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~-------~~P~~~~   74 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVA-------RTPRYLG   74 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCCCcHH
Confidence            467778999999999999999999999999999988999999999999999999999999999887       4466788


Q ss_pred             HHHHHHHHHHhc-----------CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh
Q 041804          144 IYNMILRGWFKM-----------SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV  212 (403)
Q Consensus       144 ~~~~l~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  212 (403)
                      .+..+...+...           |++++|...|++..+..+. +...+..+..++...|++++|+..|++..+..  .+.
T Consensus        75 a~~~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~  151 (217)
T 2pl2_A           75 GYMVLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPR-YAPLHLQRGLVYALLGERDKAEASLKQALALE--DTP  151 (217)
T ss_dssp             HHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCH
T ss_pred             HHHHHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cch
Confidence            899999999999           9999999999999988766 78899999999999999999999999999987  688


Q ss_pred             hhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          213 VAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       213 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      ..+..+..++...|++++|...|+.+.+..+ .+...+..+...+.+.|++++|...|++...
T Consensus       152 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~P-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  213 (217)
T 2pl2_A          152 EIRSALAELYLSMGRLDEALAQYAKALEQAP-KDLDLRVRYASALLLKGKAEEAARAAALEHH  213 (217)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHTC----------------
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHccCHHHHHHHHHHHhh
Confidence            8999999999999999999999999998743 3678888899999999999999999987653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.76  E-value=1.2e-14  Score=132.74  Aligned_cols=339  Identities=9%  Similarity=-0.005  Sum_probs=238.0

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      +-+...|..++.. .+.|++++|..+|+++.+..  +.+...|...+..+.+.|++++|..+|++.....+ +...|...
T Consensus        10 P~~~~~w~~l~~~-~~~~~~~~a~~~~e~al~~~--P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p-~~~lw~~~   85 (530)
T 2ooe_A           10 PYDLDAWSILIRE-AQNQPIDKARKTYERLVAQF--PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVL-HIDLWKCY   85 (530)
T ss_dssp             TTCHHHHHHHHHH-HHSSCHHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCC-CHHHHHHH
T ss_pred             CCCHHHHHHHHHH-HHhCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-ChHHHHHH
Confidence            4578899999984 78999999999999999875  45678899999999999999999999999999875 66677777


Q ss_pred             HHHH-HhcCCHHHHHH----HHhcccccccccccccCcchHHHHHHHHHHHh---------cCChhHHHHHHHHHHhCCC
Q 041804          108 VDAL-CEYKHVIEAQE----LCFGENKNVGFSGLVEMNKTKIYNMILRGWFK---------MSWWGKCREFWEEMDKRGV  173 (403)
Q Consensus       108 ~~~~-~~~~~~~~a~~----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~  173 (403)
                      +... ...|+.+.|.+    +|+......+    ..+++...|...+....+         .|+++.|..+|++..+...
T Consensus        86 ~~~~~~~~~~~~~a~~~~~~~~~~al~~~g----~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~  161 (530)
T 2ooe_A           86 LSYVRETKGKLPSYKEKMAQAYDFALDKIG----MEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPM  161 (530)
T ss_dssp             HHHHHHHTTTSTTHHHHHHHHHHHHHHHTT----TSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHccchhhHHHHHHHHHHHHHHHCC----CCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchh
Confidence            7543 34566666554    6665544321    123456778877776654         6889999999999887311


Q ss_pred             CCcHHHHHHHHHHHH-------------HcCChh----------------------------------------------
Q 041804          174 VKDLHSYSIYMDIMC-------------KSGKPW----------------------------------------------  194 (403)
Q Consensus       174 ~~~~~~~~~l~~~~~-------------~~~~~~----------------------------------------------  194 (403)
                      .+....|........             ..+++.                                              
T Consensus       162 ~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~  241 (530)
T 2ooe_A          162 INIEQLWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEK  241 (530)
T ss_dssp             TTHHHHHHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHH
Confidence            111223322111000             011122                                              


Q ss_pred             --------------HHHHHHHHHHHcCCCCChhhHHHHHHHHhh-------cCCHH-------HHHHHHHHHHHcCCCCC
Q 041804          195 --------------KAVKLYKEMKKKGIKMDVVAYNTVIRAVGV-------SEGVD-------FAMRVYREMREMGCQPS  246 (403)
Q Consensus       195 --------------~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~  246 (403)
                                    .+..+|++.... .+-+...|..+...+.+       .|+++       .|..+|+...+.-.+.+
T Consensus       242 ~~~~~~~~~~~~~~~a~~~y~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~  320 (530)
T 2ooe_A          242 SNPLRTEDQTLITKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKN  320 (530)
T ss_dssp             HCSSCCSCSHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSC
T ss_pred             cCCccCCcchhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCccc
Confidence                          333445544443 12345566666666654       68876       88999998886323346


Q ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCCh--hhHHHHHH---hhCCHHHHHHHHHHHHHcCCCCchhhHHHHH
Q 041804          247 VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDV--ITYHCFFR---CLEKPREILGLFDRMIESGIRPKMDTYVMLL  321 (403)
Q Consensus       247 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~--~~~~~l~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  321 (403)
                      ...|..++..+.+.|++++|..+|+++.+.  .|+.  ..|.....   ..++.++|.++|++..+.... +...|....
T Consensus       321 ~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~-~~~~~~~~a  397 (530)
T 2ooe_A          321 MLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART-RHHVYVTAA  397 (530)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTC-CTHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCC-chHHHHHHH
Confidence            788899999999999999999999999875  4542  35555444   346788999999999875322 233333322


Q ss_pred             HH-HHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          322 RK-FGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       322 ~~-~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                      .. +...|++++|..+|++..+.. +.++..|..++..+.+.|+.++|..+|++.+..+
T Consensus       398 ~~~~~~~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~  455 (530)
T 2ooe_A          398 LMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  455 (530)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSC
T ss_pred             HHHHHHcCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhcc
Confidence            22 346899999999999998763 4568999999999999999999999999999874

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.74  E-value=8.9e-16  Score=126.42  Aligned_cols=225  Identities=14%  Similarity=-0.022  Sum_probs=191.5

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc-------HHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD-------EVS  103 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-------~~~  103 (403)
                      ...+..+...+...|++++|...|++..+..   ++..+|..+..++...|++++|+..|++..+..+.+       ..+
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~   81 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH---KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKS   81 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS---CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh---ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHH
Confidence            5678888999999999999999999998865   677889999999999999999999999988765443       688


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHH
Q 041804          104 YCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIY  183 (403)
Q Consensus       104 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  183 (403)
                      +..+..++...|++++|...+++....        .|+.       ..+.+.|++++|.+.++++....+. +...+..+
T Consensus        82 ~~~l~~~~~~~~~~~~A~~~~~~a~~~--------~~~~-------~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~  145 (258)
T 3uq3_A           82 FARIGNAYHKLGDLKKTIEYYQKSLTE--------HRTA-------DILTKLRNAEKELKKAEAEAYVNPE-KAEEARLE  145 (258)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--------CCCH-------HHHHHHHHHHHHHHHHHHHHHCCHH-HHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhc--------Cchh-------HHHHHHhHHHHHHHHHHHHHHcCcc-hHHHHHHH
Confidence            999999999999999999999888764        2332       3566778899999999999887544 66788889


Q ss_pred             HHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcH
Q 041804          184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRV  263 (403)
Q Consensus       184 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~  263 (403)
                      ...+...|++++|...|++..+.. +.+..++..+..++...|++++|...++.+.+... .+...+..+...+...|++
T Consensus       146 ~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~l~~~~~~~g~~  223 (258)
T 3uq3_A          146 GKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKATAQIAVKEY  223 (258)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCH-HHHHHHHHHHHHHHHHhhH
Confidence            999999999999999999998874 44678888999999999999999999999988743 3578888899999999999


Q ss_pred             HHHHHHHHhchhc
Q 041804          264 REAYAVLAEMPKK  276 (403)
Q Consensus       264 ~~a~~~~~~~~~~  276 (403)
                      ++|...|++..+.
T Consensus       224 ~~A~~~~~~a~~~  236 (258)
T 3uq3_A          224 ASALETLDAARTK  236 (258)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999987754

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.74  E-value=9.9e-17  Score=133.59  Aligned_cols=226  Identities=8%  Similarity=-0.117  Sum_probs=127.8

Q ss_pred             cccccccHHHHHHhhhhhcccCCC--cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            4 LSCYANDWKRALEFFNWVETDCHF--THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      +...+|++++|++.|+.+......  +.+..++..+...+...|++++|...|++..+..  +.+..+|..+..++...|
T Consensus        14 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~   91 (275)
T 1xnf_A           14 PLQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAG   91 (275)
T ss_dssp             CCCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTT
T ss_pred             ccCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHcc
Confidence            344557777777777766642111  1235566677777777777777777777766654  245666777777777777


Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHH
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC  161 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  161 (403)
                      ++++|+..|++..+..+.+..++..+..++...|++++|...++++...        .|+.......+..+...|++++|
T Consensus        92 ~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--------~~~~~~~~~~~~~~~~~~~~~~A  163 (275)
T 1xnf_A           92 NFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--------DPNDPFRSLWLYLAEQKLDEKQA  163 (275)
T ss_dssp             CHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--------CTTCHHHHHHHHHHHHHHCHHHH
T ss_pred             CHHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--------CCCChHHHHHHHHHHHhcCHHHH
Confidence            7777777777777666556666666666666677777776666665542        12222233333344445666666


Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCC---CChhhHHHHHHHHhhcCCHHHHHHHHHHH
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK---MDVVAYNTVIRAVGVSEGVDFAMRVYREM  238 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~~  238 (403)
                      ...+++....... +...+. ++..+...++.++|...++........   .+..++..+...|...|++++|...|+.+
T Consensus       164 ~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  241 (275)
T 1xnf_A          164 KEVLKQHFEKSDK-EQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLA  241 (275)
T ss_dssp             HHHHHHHHHHSCC-CSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCc-chHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            6666555443222 222222 444455555555565555555433110   01244455555555555555555555555


Q ss_pred             HHc
Q 041804          239 REM  241 (403)
Q Consensus       239 ~~~  241 (403)
                      .+.
T Consensus       242 l~~  244 (275)
T 1xnf_A          242 VAN  244 (275)
T ss_dssp             HTT
T ss_pred             HhC
Confidence            543

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.73  E-value=3.9e-15  Score=123.68  Aligned_cols=226  Identities=11%  Similarity=0.034  Sum_probs=128.6

Q ss_pred             ccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC--HHHHHHHHHHHHhcCC
Q 041804            5 SCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN--HATFRIMFKRYVTAHL   82 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~   82 (403)
                      +...|++++|++.|+.+...  .+.+...+..+..++...|++++|+..+++..+.+ ..|+  ..+|..+...+...|+
T Consensus        13 ~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~lg~~~~~~~~   89 (272)
T 3u4t_A           13 LFKNNNYAEAIEVFNKLEAK--KYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKV-NATKAKSADFEYYGKILMKKGQ   89 (272)
T ss_dssp             HHTTTCHHHHHHHHHHHHHT--TCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTS-CTTTCCHHHHHHHHHHHHHTTC
T ss_pred             HHHhcCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcc-CchhHHHHHHHHHHHHHHHccc
Confidence            44556666666666666532  12234456666666666666666666666666532 1111  2346666666666666


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCR  162 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  162 (403)
                      +++|+..|++..+..+.+..++..+..++...|++++|...+++....       .+.+..++..+...+...+++++|.
T Consensus        90 ~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-------~~~~~~~~~~l~~~~~~~~~~~~A~  162 (272)
T 3u4t_A           90 DSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP-------TTTDPKVFYELGQAYYYNKEYVKAD  162 (272)
T ss_dssp             HHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS-------SCCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc-------CCCcHHHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666556666666666666666666666666666552       2344455555552333334666666


Q ss_pred             HHHHHHHhCCCCCcHHHHHHHHHHHHHcCC---hhHHHHHHHHHHHcC-CCCC------hhhHHHHHHHHhhcCCHHHHH
Q 041804          163 EFWEEMDKRGVVKDLHSYSIYMDIMCKSGK---PWKAVKLYKEMKKKG-IKMD------VVAYNTVIRAVGVSEGVDFAM  232 (403)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~-~~~~------~~~~~~ll~~~~~~~~~~~a~  232 (403)
                      +.|++..+..+. +...+..+..++...++   +++|...+++..+.. -.|+      ..++..+...|...|++++|.
T Consensus       163 ~~~~~a~~~~p~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  241 (272)
T 3u4t_A          163 SSFVKVLELKPN-IYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVKAD  241 (272)
T ss_dssp             HHHHHHHHHSTT-CHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHhCcc-chHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            666666655433 34555556666666565   555666666655431 1122      134445555555566666666


Q ss_pred             HHHHHHHHc
Q 041804          233 RVYREMREM  241 (403)
Q Consensus       233 ~~~~~~~~~  241 (403)
                      ..++++.+.
T Consensus       242 ~~~~~al~~  250 (272)
T 3u4t_A          242 AAWKNILAL  250 (272)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            666665554

>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=99.73  E-value=7.6e-15  Score=120.47  Aligned_cols=202  Identities=12%  Similarity=0.032  Sum_probs=119.1

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ...+..+...+...|++++|...|+++.+..  +.+..++..+...+...|++++|++.|+++.+..+.+...+..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID--PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC--CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHH
Confidence            4455666666666666666666666666543  23455666666666666666666666666666655566666666666


Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      +...|++++|...++++....     ..+.+..++..+...+...|++++|.+.|++..+.... +...+..+...+...
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~-----~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~  188 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDT-----LYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRN-QPSVALEMADLLYKE  188 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCT-----TCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHT
T ss_pred             HHHHhHHHHHHHHHHHHHhCc-----cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHc
Confidence            666666666666666655410     11234455556666666666666666666666554433 455555666666666


Q ss_pred             CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      |++++|...++.+.+.. +.+...+..+...+...|+.+.|.++++.+.+.
T Consensus       189 g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  238 (252)
T 2ho1_A          189 REYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL  238 (252)
T ss_dssp             TCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            66666666666655542 234445555555555666666666666665554

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.73  E-value=5.4e-16  Score=127.71  Aligned_cols=220  Identities=15%  Similarity=0.082  Sum_probs=188.6

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCC-CCC----HHHHHHHHHH
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSS-IPN----HATFRIMFKR   76 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~~----~~~~~~l~~~   76 (403)
                      +..+...|++++|++.|+.+... .  .+..++..+..++...|++++|...+++..+..+. .|+    ..++..+..+
T Consensus        12 g~~~~~~~~~~~A~~~~~~a~~~-~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~   88 (258)
T 3uq3_A           12 GNKFYKARQFDEAIEHYNKAWEL-H--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFARIGNA   88 (258)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH-S--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHh-h--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHHH
Confidence            34566789999999999999863 3  77889999999999999999999999998875310 112    5789999999


Q ss_pred             HHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC
Q 041804           77 YVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS  156 (403)
Q Consensus        77 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  156 (403)
                      +...|++++|+..|++..+..+.        ...+...|++++|...+++...       ..+.+..++..+...+...|
T Consensus        89 ~~~~~~~~~A~~~~~~a~~~~~~--------~~~~~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~  153 (258)
T 3uq3_A           89 YHKLGDLKKTIEYYQKSLTEHRT--------ADILTKLRNAEKELKKAEAEAY-------VNPEKAEEARLEGKEYFTKS  153 (258)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCC--------HHHHHHHHHHHHHHHHHHHHHH-------CCHHHHHHHHHHHHHHHHTT
T ss_pred             HHHcccHHHHHHHHHHHHhcCch--------hHHHHHHhHHHHHHHHHHHHHH-------cCcchHHHHHHHHHHHHHhc
Confidence            99999999999999999987654        2346677889999999998876       33556788999999999999


Q ss_pred             ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHH
Q 041804          157 WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYR  236 (403)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  236 (403)
                      ++++|.+.|++..+..+. +..+|..+..++...|++++|...++...+.. +.+..++..+..++...|++++|...++
T Consensus       154 ~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  231 (258)
T 3uq3_A          154 DWPNAVKAYTEMIKRAPE-DARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALETLD  231 (258)
T ss_dssp             CHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            999999999999987665 78899999999999999999999999999874 4467889999999999999999999999


Q ss_pred             HHHHc
Q 041804          237 EMREM  241 (403)
Q Consensus       237 ~~~~~  241 (403)
                      ...+.
T Consensus       232 ~a~~~  236 (258)
T 3uq3_A          232 AARTK  236 (258)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            98875

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.73  E-value=4.7e-14  Score=127.05  Aligned_cols=325  Identities=8%  Similarity=-0.099  Sum_probs=189.7

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhC-------CCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcC----
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN-------PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFG----   97 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----   97 (403)
                      .....|+.+..++...|++++|++.|++..+.       ...+....+|+.+..+|...|++++|+..+++..+..    
T Consensus        49 ~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~  128 (472)
T 4g1t_A           49 FKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFS  128 (472)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSC
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcc
Confidence            34567888888888888888888888765431       0012345678888888888888888888888765431    


Q ss_pred             ----CCcHHHHHHHHHHHHhc--CCHHHHHHHHhcccccccccccccCcchHHHHHHHHH---HHhcCChhHHHHHHHHH
Q 041804           98 ----LKDEVSYCNLVDALCEY--KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG---WFKMSWWGKCREFWEEM  168 (403)
Q Consensus        98 ----~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~---~~~~~~~~~a~~~~~~~  168 (403)
                          +....++..+..++...  +++++|...|++....       .|.+...+..+...   +...++.++|++.+++.
T Consensus       129 ~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~-------~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~a  201 (472)
T 4g1t_A          129 SPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK-------KPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQA  201 (472)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-------STTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHH
T ss_pred             cccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence                12455666666555543  4678888888877653       23444455544444   33456677788888877


Q ss_pred             HhCCCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC
Q 041804          169 DKRGVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ  244 (403)
Q Consensus       169 ~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  244 (403)
                      .+.++. +..++..+...+..    .+++++|.+.+++..... +.+..++..+...|...|+++.|...++++.+..+.
T Consensus       202 l~l~p~-~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~  279 (472)
T 4g1t_A          202 IRLNPD-NQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPN  279 (472)
T ss_dssp             HHHCSS-CHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT
T ss_pred             hhcCCc-chHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCC
Confidence            776544 55556555554443    456778888888877663 445667777888888888888888888888776332


Q ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHH
Q 041804          245 PSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKF  324 (403)
Q Consensus       245 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  324 (403)
                       +..++..+..+|...+....+....          ..   ..........++|...++...+.... +..++..+...+
T Consensus       280 -~~~~~~~lg~~y~~~~~~~~~~~~~----------~~---~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~lg~~~  344 (472)
T 4g1t_A          280 -NAYLHCQIGCCYRAKVFQVMNLREN----------GM---YGKRKLLELIGHAVAHLKKADEANDN-LFRVCSILASLH  344 (472)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHC-------------------CHHHHHHHHHHHHHHHHHHHHHCTT-TCCCHHHHHHHH
T ss_pred             -hHHHHHHHHHHHHHHHHHhhhHHHH----------HH---HHHHHHHhhHHHHHHHHHHHhhcCCc-hhhhhhhHHHHH
Confidence             4555666655553321111000000          00   00001112234556666665554322 345566666677


Q ss_pred             HhcCCcchHHHHHHHHHhcCCCCCH--HHHHHHHH-HHHhcCCHHHHHHHHHHHHH
Q 041804          325 GRWGFLRPVFVVWKKMEELGCSPDE--FAYNALVD-ALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       325 ~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~-~~~~~g~~~~a~~~~~~m~~  377 (403)
                      ...|++++|.+.|++..+....+..  ..+..+.. .+.+.|++++|+..+++.++
T Consensus       345 ~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~  400 (472)
T 4g1t_A          345 ALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK  400 (472)
T ss_dssp             HHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            7777777777777776654322211  11222222 23456667777776666655

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.72  E-value=6.5e-15  Score=118.51  Aligned_cols=204  Identities=7%  Similarity=-0.075  Sum_probs=124.6

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      ++..+..+...+...|++++|...|+++.+..  +.+...+..+...+...|++++|.+.|+++.+..+.+..++..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD--PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHH
Confidence            45566666777777777777777777666643  2345666667777777777777777777776666556666666666


Q ss_pred             HHHhc-CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          110 ALCEY-KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       110 ~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      .+... |++++|...++++....     ..+.+..++..+...+...|++++|.+.++++.+..+. +...+..+..++.
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~  158 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADP-----TYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQ-FPPAFKELARTKM  158 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTST-----TCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHH
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCc-----CCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CchHHHHHHHHHH
Confidence            66666 67777666666655410     12233455666666666666666666666666555433 4555666666666


Q ss_pred             HcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          189 KSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       189 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ..|++++|...++.+.+.....+...+..+...+...|+.+.+..+++.+.+.
T Consensus       159 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          159 LAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Confidence            66666666666666655421134445555555555666666666666665543

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.72  E-value=1.1e-15  Score=124.81  Aligned_cols=203  Identities=8%  Similarity=0.060  Sum_probs=138.6

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      .....|..+...+...|++++|...|+++.+..  +.+..++..+...+...|++++|+..|+++.+..+.+..++..+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la   98 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN--KEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAG   98 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHH
Confidence            345667777888888888888888888887754  356777888888888888888888888888887766778888888


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      ..+...|++++|...+++...       ..+.+..++..+...+...|++++|.+.++++.+.... +...+..+...+.
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~  170 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALR-------AGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNEN-DTEARFQFGMCLA  170 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH-------HTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHH
Confidence            888888888888888877766       33455667777778888888888888888887766544 5667777777788


Q ss_pred             HcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          189 KSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       189 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      ..|++++|...|+++.+.. +.+..++..+..++...|++++|...++.+.+..
T Consensus       171 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          171 NEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            8888888888887777663 3356677777777777777778877777777653

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.72  E-value=7.5e-15  Score=118.14  Aligned_cols=212  Identities=11%  Similarity=-0.039  Sum_probs=180.2

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      .+...+..+...+...|++++|++.|+++.+..+.+...+..+..++...|++++|...+++...       ..+.+..+
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~-------~~~~~~~~   78 (225)
T 2vq2_A            6 QVSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALS-------IKPDSAEI   78 (225)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHH
T ss_pred             ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHH-------hCCCChHH
Confidence            45678889999999999999999999999998877899999999999999999999999998876       33557788


Q ss_pred             HHHHHHHHHhc-CChhHHHHHHHHHHhCCCCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHH
Q 041804          145 YNMILRGWFKM-SWWGKCREFWEEMDKRGVVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV  222 (403)
Q Consensus       145 ~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~  222 (403)
                      +..+...+... |++++|.+.++++.+.+..| +...+..+..++...|++++|...++++.+.. +.+...+..+...+
T Consensus        79 ~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~  157 (225)
T 2vq2_A           79 NNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTK  157 (225)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHH
Confidence            99999999999 99999999999998832223 36788889999999999999999999998874 34577888999999


Q ss_pred             hhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHH
Q 041804          223 GVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYH  286 (403)
Q Consensus       223 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~  286 (403)
                      ...|++++|...++.+.+.....+...+..+...+...|+.+.|..+++.+.+.  .|+.....
T Consensus       158 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~  219 (225)
T 2vq2_A          158 MLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN--FPYSEELQ  219 (225)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHH
Confidence            999999999999999988744246777888888889999999999999988754  35544433

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.71  E-value=9.9e-16  Score=127.49  Aligned_cols=249  Identities=8%  Similarity=-0.101  Sum_probs=192.5

Q ss_pred             HHccCChhHHHHHHHHhhhCCCCC--CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH
Q 041804           41 LGKFFEFDLSWNLIHRMKDNPSSI--PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI  118 (403)
Q Consensus        41 ~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  118 (403)
                      +...|++++|+..|+++.+.....  .+..++..+...+...|++++|+..|+++.+..+.+..++..+..++...|+++
T Consensus        15 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~   94 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFD   94 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHH
T ss_pred             cCccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCHH
Confidence            345688999999999998863111  246688899999999999999999999999998889999999999999999999


Q ss_pred             HHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHH
Q 041804          119 EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVK  198 (403)
Q Consensus       119 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  198 (403)
                      +|...+++...       ..+.+..++..+...|...|++++|.+.|+++.+..+  +.......+..+...|++++|..
T Consensus        95 ~A~~~~~~al~-------~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~--~~~~~~~~~~~~~~~~~~~~A~~  165 (275)
T 1xnf_A           95 AAYEAFDSVLE-------LDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDP--NDPFRSLWLYLAEQKLDEKQAKE  165 (275)
T ss_dssp             HHHHHHHHHHH-------HCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHCHHHHHH
T ss_pred             HHHHHHHHHHh-------cCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC--CChHHHHHHHHHHHhcCHHHHHH
Confidence            99999999887       3355678899999999999999999999999988643  33344455556677899999999


Q ss_pred             HHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC---CCHHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          199 LYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ---PSVVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      .++...... +++...+ .++..+...++.+.|...++...+....   .+...+..+...|...|++++|...|++..+
T Consensus       166 ~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  243 (275)
T 1xnf_A          166 VLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA  243 (275)
T ss_dssp             HHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            998887763 3444444 4677777888889999998887654211   1257788899999999999999999999887


Q ss_pred             cCCCC-ChhhHHHHHHhhCCHHHHHHHH
Q 041804          276 KGCVP-DVITYHCFFRCLEKPREILGLF  302 (403)
Q Consensus       276 ~~~~p-~~~~~~~l~~~~~~~~~a~~~~  302 (403)
                      .  .| +...+...+...++.++|++.+
T Consensus       244 ~--~p~~~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          244 N--NVHNFVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             T--CCTTCHHHHHHHHHHHHHHHC----
T ss_pred             C--CchhHHHHHHHHHHHHHHHhhHHHH
Confidence            5  34 3444444444455666555443

>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=99.71  E-value=4.8e-15  Score=128.19  Aligned_cols=233  Identities=10%  Similarity=0.039  Sum_probs=196.3

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC-hHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL-VNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      +..+|..+..++.+.|++++|+..+++.....  +-+..+|+.+..++...|+ +++|+..|++..+..+.+..+|..+.
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~--P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g  173 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC--ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            35678888999999999999999999999875  3567889999999999996 99999999999999988999999999


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      .++...|++++|+..++++..       ..+.+..+|..+..++.+.|++++|+..|+++.+.++. +...|+.+..++.
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~-------ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~-~~~a~~~lg~~l~  245 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILN-------QDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVIS  245 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHH-------hCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHH
Confidence            999999999999999999887       45778889999999999999999999999999998777 8889999999999


Q ss_pred             H-cCChhHH-----HHHHHHHHHcCCCCChhhHHHHHHHHhhcC--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 041804          189 K-SGKPWKA-----VKLYKEMKKKGIKMDVVAYNTVIRAVGVSE--GVDFAMRVYREMREMGCQPSVVTCNTVIKLLCEN  260 (403)
Q Consensus       189 ~-~~~~~~a-----~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  260 (403)
                      . .|..++|     +..|++.+... +-+...|..+...+...|  ++++|...+..+ +. .+.+...+..+...|.+.
T Consensus       246 ~l~~~~~eA~~~~el~~~~~Al~l~-P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~  322 (382)
T 2h6f_A          246 NTTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDM  322 (382)
T ss_dssp             HTTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHH
T ss_pred             HhcCcchHHHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHH
Confidence            8 6665777     48888888763 335678888888888877  688898888887 33 234667888888888886


Q ss_pred             C---------cHHHHHHHHHhc-hh
Q 041804          261 G---------RVREAYAVLAEM-PK  275 (403)
Q Consensus       261 g---------~~~~a~~~~~~~-~~  275 (403)
                      |         ..++|.++|+++ .+
T Consensus       323 ~~~~~~~~~~~~~~A~~~~~~l~~~  347 (382)
T 2h6f_A          323 LENQCDNKEDILNKALELCEILAKE  347 (382)
T ss_dssp             HHTTCSSHHHHHHHHHHHHHHHHHT
T ss_pred             hcccccchHHHHHHHHHHHHHHHHH
Confidence            4         257888888887 44

>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=99.71  E-value=9.8e-15  Score=119.82  Aligned_cols=208  Identities=10%  Similarity=-0.006  Sum_probs=179.1

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHH
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYN  146 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (403)
                      ...|..+...+...|++++|+..|+++.+..+.+..++..+..++...|++++|...++++...       .+.+..++.
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~-------~~~~~~~~~  109 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALAS-------DSRNARVLN  109 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTCHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-------CcCcHHHHH
Confidence            5678889999999999999999999999988778999999999999999999999999988763       355778899


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKRGVVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS  225 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  225 (403)
                      .+...|...|++++|.+.++++.+.+..| +...+..+..++...|++++|...+++..+.. +.+...+..+...+...
T Consensus       110 ~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~  188 (252)
T 2ho1_A          110 NYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKE  188 (252)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHc
Confidence            99999999999999999999998833333 56788889999999999999999999998874 44677888999999999


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhH
Q 041804          226 EGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITY  285 (403)
Q Consensus       226 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~  285 (403)
                      |++++|...++.+.+.. +.+...+..+...+...|+.++|...++++.+.  .|+...+
T Consensus       189 g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~  245 (252)
T 2ho1_A          189 REYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRL--YPGSLEY  245 (252)
T ss_dssp             TCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTSHHH
T ss_pred             CCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH--CCCCHHH
Confidence            99999999999998763 346778888899999999999999999998875  3544433

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.71  E-value=4.4e-15  Score=123.38  Aligned_cols=236  Identities=10%  Similarity=-0.001  Sum_probs=191.4

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCN  106 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~  106 (403)
                      |+..+......+...|++++|+..|++..+..  +.+..++..+..++...|++++|+..|++..+.+..   ...+|..
T Consensus         2 n~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~   79 (272)
T 3u4t_A            2 NDDVEFRYADFLFKNNNYAEAIEVFNKLEAKK--YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEY   79 (272)
T ss_dssp             ---CHHHHHHHHHTTTCHHHHHHHHHHHHHTT--CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHH
T ss_pred             cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHH
Confidence            34566777889999999999999999999875  344558889999999999999999999999984321   3445899


Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHH
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDI  186 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  186 (403)
                      +..++...|++++|...+++...       ..+.+..++..+...|...|++++|.+.|++..+..+. +...|..+...
T Consensus        80 lg~~~~~~~~~~~A~~~~~~a~~-------~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~l~~~  151 (272)
T 3u4t_A           80 YGKILMKKGQDSLAIQQYQAAVD-------RDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTT-DPKVFYELGQA  151 (272)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH-------HSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCC-CHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHh-------cCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCC-cHHHHHHHHHH
Confidence            99999999999999999999887       34556788999999999999999999999999887554 67777777734


Q ss_pred             HHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCC---HHHHHHHHHHHHHcC-CCCC------HHHHHHHHHH
Q 041804          187 MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG---VDFAMRVYREMREMG-CQPS------VVTCNTVIKL  256 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~-~~~~------~~~~~~li~~  256 (403)
                      +...+++++|.+.|++..+.. +.+...+..+..++...++   .+.|...++++.+.. -.|+      ...|..+...
T Consensus       152 ~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  230 (272)
T 3u4t_A          152 YYYNKEYVKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYY  230 (272)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHH
Confidence            455569999999999999873 3346777778888888888   888999998887652 1233      2577888899


Q ss_pred             HHhcCcHHHHHHHHHhchhc
Q 041804          257 LCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       257 ~~~~g~~~~a~~~~~~~~~~  276 (403)
                      |...|++++|...|++..+.
T Consensus       231 ~~~~~~~~~A~~~~~~al~~  250 (272)
T 3u4t_A          231 YTINRDKVKADAAWKNILAL  250 (272)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhc
Confidence            99999999999999998875

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.70  E-value=2.1e-15  Score=123.01  Aligned_cols=194  Identities=11%  Similarity=0.037  Sum_probs=163.6

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      +..+...|++++|++.|+.+..  ..+.+...+..+..++...|++++|...++++.+..  +.+..++..+...+...|
T Consensus        30 a~~~~~~~~~~~A~~~~~~~l~--~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~  105 (243)
T 2q7f_A           30 MGRGSEFGDYEKAAEAFTKAIE--ENKEDAIPYINFANLLSSVNELERALAFYDKALELD--SSAATAYYGAGNVYVVKE  105 (243)
T ss_dssp             ------------CCTTHHHHHT--TCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhhCHHHHHHHHHHHHH--hCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CcchHHHHHHHHHHHHhc
Confidence            4456778999999999999884  234568899999999999999999999999998865  357888999999999999


Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHH
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC  161 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  161 (403)
                      ++++|++.|+++.+..+.+...+..+...+...|++++|...+++...       ..+.+..++..+...+.+.|++++|
T Consensus       106 ~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~A  178 (243)
T 2q7f_A          106 MYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVE-------LNENDTEARFQFGMCLANEGMLDEA  178 (243)
T ss_dssp             CHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             cHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH-------hCCccHHHHHHHHHHHHHcCCHHHH
Confidence            999999999999998888889999999999999999999999999876       3355778899999999999999999


Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG  207 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  207 (403)
                      .+.|+++.+.... +..++..+..+|...|++++|...++++.+..
T Consensus       179 ~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          179 LSQFAAVTEQDPG-HADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhCcc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            9999999887655 67889999999999999999999999998873

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.69  E-value=2.5e-15  Score=130.00  Aligned_cols=241  Identities=8%  Similarity=-0.035  Sum_probs=201.2

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCC-hhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhc
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFE-FDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTA   80 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   80 (403)
                      +.++...|++++|++.|+.+...  .+.+..+|+.+..++...|+ +++|+..|++.....  +.+..+|+.+..++...
T Consensus       104 g~~~~~~g~~~~Al~~~~~al~l--~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~--P~~~~a~~~~g~~~~~~  179 (382)
T 2h6f_A          104 RAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ--PKNYQVWHHRRVLVEWL  179 (382)
T ss_dssp             HHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCChHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHc
Confidence            34566779999999999998852  24467899999999999997 999999999999976  45788999999999999


Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh-cCChh
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK-MSWWG  159 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~  159 (403)
                      |++++|+..|+++.+.++.+..+|..+..++...|++++|+..++++..       ..+.+..+|+.+..++.. .|..+
T Consensus       180 g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~-------l~P~~~~a~~~lg~~l~~l~~~~~  252 (382)
T 2h6f_A          180 RDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLK-------EDVRNNSVWNQRYFVISNTTGYND  252 (382)
T ss_dssp             TCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCSCS
T ss_pred             cCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhcCcch
Confidence            9999999999999999988999999999999999999999999999887       446788999999999999 66658


Q ss_pred             HH-----HHHHHHHHhCCCCCcHHHHHHHHHHHHHcC--ChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcC------
Q 041804          160 KC-----REFWEEMDKRGVVKDLHSYSIYMDIMCKSG--KPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSE------  226 (403)
Q Consensus       160 ~a-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~------  226 (403)
                      +|     ++.|++.....+. +...|..+..++...|  ++++|++.+..+ +. .+.+...+..+..+|.+.+      
T Consensus       253 eA~~~~el~~~~~Al~l~P~-~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~~~~~~~~  329 (382)
T 2h6f_A          253 RAVLEREVQYTLEMIKLVPH-NESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDMLENQCDN  329 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHHhcccccc
Confidence            87     5889998887766 7889999999999888  689999999888 33 3446678888888888864      


Q ss_pred             ---CHHHHHHHHHHH-HHcCCCCC-HHHHHHHHHHHH
Q 041804          227 ---GVDFAMRVYREM-REMGCQPS-VVTCNTVIKLLC  258 (403)
Q Consensus       227 ---~~~~a~~~~~~~-~~~~~~~~-~~~~~~li~~~~  258 (403)
                         ..++|..+++.+ .+.  .|. ...|..+...+.
T Consensus       330 ~~~~~~~A~~~~~~l~~~~--DP~r~~~w~~~~~~l~  364 (382)
T 2h6f_A          330 KEDILNKALELCEILAKEK--DTIRKEYWRYIGRSLQ  364 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHTT--CGGGHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHh--CchhHHHHHHHHHHHH
Confidence               358999999998 554  343 445555555443

>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=99.69  E-value=3.1e-13  Score=129.60  Aligned_cols=329  Identities=11%  Similarity=0.108  Sum_probs=169.7

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      .++...|.+++|..+|+....      .....+.++.   ..+++++|.++.++.       -+..+|..+..++...|+
T Consensus      1057 ~Iai~lglyEEAf~IYkKa~~------~~~A~~VLie---~i~nldrAiE~Aerv-------n~p~vWsqLAKAql~~G~ 1120 (1630)
T 1xi4_A         1057 NIAISNELFEEAFAIFRKFDV------NTSAVQVLIE---HIGNLDRAYEFAERC-------NEPAVWSQLAKAQLQKGM 1120 (1630)
T ss_pred             HHHHhCCCHHHHHHHHHHcCC------HHHHHHHHHH---HHhhHHHHHHHHHhc-------CCHHHHHHHHHHHHhCCC
Confidence            345555666666666665431      1111122211   445555555555533       123445555555555555


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhccccccccc--------------------ccccCcch
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFS--------------------GLVEMNKT  142 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--------------------~~~~~~~~  142 (403)
                      +++|+..|.+.     .|...|..++.++.+.|++++|.+.+....+.....                    .....++.
T Consensus      1121 ~kEAIdsYiKA-----dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~e~~Idt~LafaYAKl~rleele~fI~~~n~ 1195 (1630)
T 1xi4_A         1121 VKEAIDSYIKA-----DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNN 1195 (1630)
T ss_pred             HHHHHHHHHhc-----CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcccccccHHHHHHHHhhcCHHHHHHHHhCCCH
Confidence            55555555332     344555555555555555555555554433320000                    00001222


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHH
Q 041804          143 KIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV  222 (403)
Q Consensus       143 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~  222 (403)
                      ..|..+...|...|++++|..+|...         ..|..+..+|.+.|++++|.+.+++.      .+..+|..+-.+|
T Consensus      1196 ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~~ac 1260 (1630)
T 1xi4_A         1196 AHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFAC 1260 (1630)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHHHHH
Confidence            33334444444555555555555442         14455555555555555555554443      1334555555555


Q ss_pred             hhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH--hhCCHHHHHH
Q 041804          223 GVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR--CLEKPREILG  300 (403)
Q Consensus       223 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~--~~~~~~~a~~  300 (403)
                      ...|++..|......     +..++..+..++..|.+.|.+++|+.+++...... ......|+-+..  +--++++..+
T Consensus      1261 ve~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftELaiLyaKy~peklmE 1334 (1630)
T 1xi4_A         1261 VDGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMRE 1334 (1630)
T ss_pred             hhhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHHHHHHHhCCHHHHHH
Confidence            555555444443332     22355667788889999999999999997766432 223334433333  3234444444


Q ss_pred             HHHHHHHcC-CCC------chhhHHHHHHHHHhcCCcchHHHHHHHHH----------h-cCCCCCHHHHHHHHHHHHhc
Q 041804          301 LFDRMIESG-IRP------KMDTYVMLLRKFGRWGFLRPVFVVWKKME----------E-LGCSPDEFAYNALVDALIDK  362 (403)
Q Consensus       301 ~~~~~~~~~-~~~------~~~~~~~li~~~~~~g~~~~a~~~~~~~~----------~-~~~~~~~~~~~~l~~~~~~~  362 (403)
                      .++...+.. ++|      +...|.-++-.|.+.|+++.|....-+-.          + ..-..|+..|...+..|...
T Consensus      1335 hlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~~h~~~a~~~~~Fk~~i~kv~n~elyykai~Fyl~~ 1414 (1630)
T 1xi4_A         1335 HLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEF 1414 (1630)
T ss_pred             HHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHhccHhhhhhHHHHHHhcccccHHHHHHHHHHHHhh
Confidence            433333322 222      45678889999999999999884321110          0 01245777787777777766


Q ss_pred             C---------------CHHHHHHHHH
Q 041804          363 G---------------MLDMARKYDE  373 (403)
Q Consensus       363 g---------------~~~~a~~~~~  373 (403)
                      +               +.+++.++|.
T Consensus      1415 ~P~~lndLl~~l~~rlD~~R~V~l~~ 1440 (1630)
T 1xi4_A         1415 KPLLLNDLLMVLSPRLDHTRAVNYFS 1440 (1630)
T ss_pred             ChHHHHHHHHHhhhcCChHHHHHHHH
Confidence            6               6666666654

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.68  E-value=1.4e-13  Score=114.45  Aligned_cols=225  Identities=10%  Similarity=-0.004  Sum_probs=185.7

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHhhcCCCcHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT----AHLVNEAMGTFNKLDEFGLKDEVSY  104 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  104 (403)
                      .++.++..+...+...|++++|...|++..+.    .+..++..+...|..    .+++++|+..|++..+.+  +..++
T Consensus         4 ~~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~----~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~--~~~a~   77 (273)
T 1ouv_A            4 QDPKELVGLGAKSYKEKDFTQAKKYFEKACDL----KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN--YSNGC   77 (273)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHH
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC----CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC--CHHHH
Confidence            35678888888999999999999999998883    356778888888998    999999999999988865  77888


Q ss_pred             HHHHHHHHh----cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCc
Q 041804          105 CNLVDALCE----YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK----MSWWGKCREFWEEMDKRGVVKD  176 (403)
Q Consensus       105 ~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~  176 (403)
                      ..+...|..    .+++++|...+++....         .+..++..+...|..    .+++++|.+.|++..+.+   +
T Consensus        78 ~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~---------~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~  145 (273)
T 1ouv_A           78 HLLGNLYYSGQGVSQNTNKALQYYSKACDL---------KYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---D  145 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHT---------TCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---C
T ss_pred             HHHHHHHhCCCCcccCHHHHHHHHHHHHHc---------CCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---c
Confidence            888888888    99999999999887663         266778888888888    899999999999988875   5


Q ss_pred             HHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh----cCCHHHHHHHHHHHHHcCCCCCHH
Q 041804          177 LHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV----SEGVDFAMRVYREMREMGCQPSVV  248 (403)
Q Consensus       177 ~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~  248 (403)
                      ...+..+...|..    .+++++|...|++..+.+   +...+..+...|..    .+++++|...|+...+.+   +..
T Consensus       146 ~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~  219 (273)
T 1ouv_A          146 GDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGG  219 (273)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHH
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHH
Confidence            6677788888887    889999999999888774   45677778888888    889999999999888864   366


Q ss_pred             HHHHHHHHHHh----cCcHHHHHHHHHhchhcC
Q 041804          249 TCNTVIKLLCE----NGRVREAYAVLAEMPKKG  277 (403)
Q Consensus       249 ~~~~li~~~~~----~g~~~~a~~~~~~~~~~~  277 (403)
                      .+..+...|..    .+++++|...|++..+.+
T Consensus       220 a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          220 GCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            77778888888    888888988888877653

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.67  E-value=5.7e-15  Score=131.66  Aligned_cols=341  Identities=11%  Similarity=0.001  Sum_probs=178.8

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCCh---hHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhc
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEF---DLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTA   80 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   80 (403)
                      +..++|++++|++.|+.... .+   ++.++..+...|...|+.   ++|..+|++..+.     +...+..+...+...
T Consensus        12 ~~~~~g~~~~A~~~~~~aa~-~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~-----~~~A~~~Lg~~~~~~   82 (452)
T 3e4b_A           12 EALKRGDTVTAQQNYQQLAE-LG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT-----SPRAQARLGRLLAAK   82 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH-HT---CCTGGGTCC---------------------------------CHHHHHHHHHTC
T ss_pred             HHHhCCCHHHHHHHHHHHHH-CC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC-----CHHHHHHHHHHHHhC
Confidence            44567888999998888764 32   344555666667777777   8888888887752     555666666655554


Q ss_pred             C-----ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHH---HHHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           81 H-----LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIE---AQELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        81 ~-----~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      +     ++++|+.+|++..+.|.++  .+..|...|...+..++   +...+.....         ..+......+...|
T Consensus        83 ~~~~~~~~~~A~~~~~~Aa~~g~~~--A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~---------~g~~~a~~~Lg~~y  151 (452)
T 3e4b_A           83 PGATEAEHHEAESLLKKAFANGEGN--TLIPLAMLYLQYPHSFPNVNAQQQISQWQA---------AGYPEAGLAQVLLY  151 (452)
T ss_dssp             --CCHHHHHHHHHHHHHHHHTTCSS--CHHHHHHHHHHCGGGCTTCCHHHHHHHHHH---------HTCTTHHHHHHHHH
T ss_pred             CCCCCcCHHHHHHHHHHHHHCCCHH--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHH---------CCCHHHHHHHHHHH
Confidence            4     6788888888888755443  66666666666554332   3333332222         12234455666666


Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcC---ChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc----
Q 041804          153 FKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSG---KPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS----  225 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~----  225 (403)
                      ...+.++.+......+.+.-...+...+..|...|...|   ++++|++.|+...+.| .++...+..+...|...    
T Consensus       152 ~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~  230 (452)
T 3e4b_A          152 RTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGT  230 (452)
T ss_dssp             HHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSS
T ss_pred             HcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCC
Confidence            666644444333222222111123336666777777777   6777777777777665 33444444555555443    


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-H--HhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH--hhC-----CH
Q 041804          226 EGVDFAMRVYREMREMGCQPSVVTCNTVIKL-L--CENGRVREAYAVLAEMPKKGCVPDVITYHCFFR--CLE-----KP  295 (403)
Q Consensus       226 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~-~--~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~--~~~-----~~  295 (403)
                      +++++|...|+... .   -+...+..+... |  ...+++++|...|++..+.|   +...+..+-.  ..+     +.
T Consensus       231 ~d~~~A~~~~~~aa-~---g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~G~g~~~d~  303 (452)
T 3e4b_A          231 PDEKTAQALLEKIA-P---GYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYYEGKWVPADA  303 (452)
T ss_dssp             CCHHHHHHHHHHHG-G---GSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCH
T ss_pred             CCHHHHHHHHHHHc-C---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCH
Confidence            56777777777765 2   244455555554 3  34667777777777766654   2222222211  123     56


Q ss_pred             HHHHHHHHHHHHcCCCCchhhHHHHHHHHHh----cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCCHHH
Q 041804          296 REILGLFDRMIESGIRPKMDTYVMLLRKFGR----WGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID----KGMLDM  367 (403)
Q Consensus       296 ~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~  367 (403)
                      ++|..+|++.. .   -+......|...|..    ..++++|...|++..+.|.   ......|...|..    ..+.++
T Consensus       304 ~~A~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~---~~A~~~Lg~~y~~G~g~~~d~~~  376 (452)
T 3e4b_A          304 KAAEAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ---NSADFAIAQLFSQGKGTKPDPLN  376 (452)
T ss_dssp             HHHHHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC---TTHHHHHHHHHHSCTTBCCCHHH
T ss_pred             HHHHHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh---HHHHHHHHHHHHhCCCCCCCHHH
Confidence            67777776665 2   244455555555544    3367777777777766542   2344445555543    346677


Q ss_pred             HHHHHHHHHHcC
Q 041804          368 ARKYDEEMFAKG  379 (403)
Q Consensus       368 a~~~~~~m~~~~  379 (403)
                      |..+++...+.|
T Consensus       377 A~~~~~~A~~~g  388 (452)
T 3e4b_A          377 AYVFSQLAKAQD  388 (452)
T ss_dssp             HHHHHHHHHTTC
T ss_pred             HHHHHHHHHHCC
Confidence            777777666655

>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=99.66  E-value=6e-13  Score=127.65  Aligned_cols=283  Identities=11%  Similarity=0.091  Sum_probs=194.1

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      ...+...+...|.+++|..+|++...      ...+.+.++.   ..+++++|.++.++.     .++.+|..+..++..
T Consensus      1052 ~~eIA~Iai~lglyEEAf~IYkKa~~------~~~A~~VLie---~i~nldrAiE~Aerv-----n~p~vWsqLAKAql~ 1117 (1630)
T 1xi4_A         1052 APDIANIAISNELFEEAFAIFRKFDV------NTSAVQVLIE---HIGNLDRAYEFAERC-----NEPAVWSQLAKAQLQ 1117 (1630)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHcCC------HHHHHHHHHH---HHhhHHHHHHHHHhc-----CCHHHHHHHHHHHHh
Confidence            34478889999999999999999642      2223333333   778999999999855     468999999999999


Q ss_pred             cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCCh
Q 041804          114 YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKP  193 (403)
Q Consensus       114 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  193 (403)
                      .|++++|...|.+.            .+...|..++.++.+.|++++|.+++....+...  +....+.++.+|++.+++
T Consensus      1118 ~G~~kEAIdsYiKA------------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~--e~~Idt~LafaYAKl~rl 1183 (1630)
T 1xi4_A         1118 KGMVKEAIDSYIKA------------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKAR--ESYVETELIFALAKTNRL 1183 (1630)
T ss_pred             CCCHHHHHHHHHhc------------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcc--cccccHHHHHHHHhhcCH
Confidence            99999999999653            4566788899999999999999999998877653  333334588899999888


Q ss_pred             hHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          194 WKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       194 ~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      ++...+    ..   .++...|..+...|...|+++.|..+|..+         ..|..+..+|.+.|++++|.+.+++.
T Consensus      1184 eele~f----I~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA 1247 (1630)
T 1xi4_A         1184 AELEEF----IN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA 1247 (1630)
T ss_pred             HHHHHH----Hh---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh
Confidence            854433    22   345667777888889999999999999875         37888889999999999999888876


Q ss_pred             hhcCCCCChhhHHHHHHhh---------------------------------CCHHHHHHHHHHHHHcCCCCchhhHHHH
Q 041804          274 PKKGCVPDVITYHCFFRCL---------------------------------EKPREILGLFDRMIESGIRPKMDTYVML  320 (403)
Q Consensus       274 ~~~~~~p~~~~~~~l~~~~---------------------------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (403)
                      .      +..+|..+-.+|                                 |.+++|+.+++...... +-....|+-+
T Consensus      1248 ~------n~~aWkev~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftEL 1320 (1630)
T 1xi4_A         1248 N------STRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTEL 1320 (1630)
T ss_pred             C------CHHHHHHHHHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHH
Confidence            3      334443332222                                 44555555554444322 1122334334


Q ss_pred             HHHHHhc--CCcchHHHHHHHHHhcCCCC------CHHHHHHHHHHHHhcCCHHHHH
Q 041804          321 LRKFGRW--GFLRPVFVVWKKMEELGCSP------DEFAYNALVDALIDKGMLDMAR  369 (403)
Q Consensus       321 i~~~~~~--g~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~g~~~~a~  369 (403)
                      ...+++.  ++..++.+.|..-.  +++|      +...|.-++-.|.+.|+++.|.
T Consensus      1321 aiLyaKy~peklmEhlk~f~~ri--ni~k~~r~~e~~~lW~elv~LY~~~~e~dnA~ 1375 (1630)
T 1xi4_A         1321 AILYSKFKPQKMREHLELFWSRV--NIPKVLRAAEQAHLWAELVFLYDKYEEYDNAI 1375 (1630)
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhc--ccchHhHHHHHHHHHHHHHHHHHhcccHHHHH
Confidence            4443332  22223333322111  1222      4556777788888888888777

>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=99.64  E-value=7.1e-13  Score=110.10  Aligned_cols=222  Identities=9%  Similarity=0.030  Sum_probs=189.6

Q ss_pred             cchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhH
Q 041804          140 NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAY  215 (403)
Q Consensus       140 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~  215 (403)
                      .+..++..+...|...|++++|.+.|++..+.   -+..++..+...|..    .+++++|...|++..+.+   +...+
T Consensus         4 ~~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~   77 (273)
T 1ouv_A            4 QDPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGC   77 (273)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            35667888999999999999999999999884   256788889999999    999999999999999886   67788


Q ss_pred             HHHHHHHhh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHHHHHHHHHhchhcCCCCChhhHHH
Q 041804          216 NTVIRAVGV----SEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCE----NGRVREAYAVLAEMPKKGCVPDVITYHC  287 (403)
Q Consensus       216 ~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~p~~~~~~~  287 (403)
                      ..+...|..    .+++++|...|+...+.+   +...+..+...|..    .+++++|...|++..+.+   +...+..
T Consensus        78 ~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~  151 (273)
T 1ouv_A           78 HLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTI  151 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHH
Confidence            889999999    999999999999999874   77888999999999    999999999999998875   2233322


Q ss_pred             H---HHh----hCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHh----cCCcchHHHHHHHHHhcCCCCCHHHHHHHH
Q 041804          288 F---FRC----LEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGR----WGFLRPVFVVWKKMEELGCSPDEFAYNALV  356 (403)
Q Consensus       288 l---~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  356 (403)
                      +   ...    .++.++|...+++..+.+   +...+..+...|..    .+++++|.+.+++..+.+   +...+..+.
T Consensus       152 lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~l~  225 (273)
T 1ouv_A          152 LGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLG  225 (273)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC---CHHHHHHHH
Confidence            2   222    467899999999998874   45778888889999    999999999999998864   377888889


Q ss_pred             HHHHh----cCCHHHHHHHHHHHHHcC
Q 041804          357 DALID----KGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       357 ~~~~~----~g~~~~a~~~~~~m~~~~  379 (403)
                      ..|.+    .+++++|.+++++..+.|
T Consensus       226 ~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          226 AMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             HHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            99999    999999999999999876

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.63  E-value=2e-13  Score=121.75  Aligned_cols=340  Identities=12%  Similarity=0.039  Sum_probs=220.9

Q ss_pred             CcccccccccH---HHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccC-----ChhHHHHHHHHhhhCCCCCCCHHHHHH
Q 041804            1 RETLSCYANDW---KRALEFFNWVETDCHFTHTTDTYNSVIDILGKFF-----EFDLSWNLIHRMKDNPSSIPNHATFRI   72 (403)
Q Consensus         1 L~~l~~~~~~~---~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~~   72 (403)
                      |+.++...|++   ++|++.|+.... .    ++..+..+...+...+     ++++|..+|++..+.+  .++  ++..
T Consensus        41 Lg~~y~~~g~~~d~~~A~~~~~~A~~-~----~~~A~~~Lg~~~~~~~~~~~~~~~~A~~~~~~Aa~~g--~~~--A~~~  111 (452)
T 3e4b_A           41 LADIQVGTRDPAQIKQAEATYRAAAD-T----SPRAQARLGRLLAAKPGATEAEHHEAESLLKKAFANG--EGN--TLIP  111 (452)
T ss_dssp             CC---------------------------------CHHHHHHHHHTC--CCHHHHHHHHHHHHHHHHTT--CSS--CHHH
T ss_pred             HHHHHHccCCCCCHHHHHHHHHHHHh-C----CHHHHHHHHHHHHhCCCCCCcCHHHHHHHHHHHHHCC--CHH--HHHH
Confidence            45566677888   899999998874 1    6677777777565555     7899999999999876  233  7777


Q ss_pred             HHHHHHhcCChHH---HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH----HHHHHHHhcccccccccccccCcchHHH
Q 041804           73 MFKRYVTAHLVNE---AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV----IEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        73 l~~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      |...|...+..+.   +.+.+......|  ++..+..+...|...+.+    +.+..++.....          .+..++
T Consensus       112 Lg~~y~~~~~~~~~~~a~~~~~~a~~~g--~~~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~----------~~~~a~  179 (452)
T 3e4b_A          112 LAMLYLQYPHSFPNVNAQQQISQWQAAG--YPEAGLAQVLLYRTQGTYDQHLDDVERICKAALN----------TTDICY  179 (452)
T ss_dssp             HHHHHHHCGGGCTTCCHHHHHHHHHHHT--CTTHHHHHHHHHHHHTCGGGGHHHHHHHHHHHTT----------TCTTHH
T ss_pred             HHHHHHhCCCCCCCHHHHHHHHHHHHCC--CHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHc----------CCHHHH
Confidence            8888887665444   444454444433  566777888888887744    444444444333          223378


Q ss_pred             HHHHHHHHhcC---ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc----CChhHHHHHHHHHHHcCCCCChhhHHHH
Q 041804          146 NMILRGWFKMS---WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS----GKPWKAVKLYKEMKKKGIKMDVVAYNTV  218 (403)
Q Consensus       146 ~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~~~~l  218 (403)
                      ..+...|.+.|   +.++|.+.|++..+.|.. +...+..+...|...    +++++|+.+|+... .|   +...+..+
T Consensus       180 ~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~-~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a~~~L  254 (452)
T 3e4b_A          180 VELATVYQKKQQPEQQAELLKQMEAGVSRGTV-TAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPASWVSL  254 (452)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCS-CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHHHHHH
T ss_pred             HHHHHHHHHcCCcccHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHHHHHH
Confidence            88999999999   999999999999998866 666556777777554    68999999999987 43   55566666


Q ss_pred             HHH-H--hhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC-----cHHHHHHHHHhchhcCCCCChhhHHHHHH
Q 041804          219 IRA-V--GVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENG-----RVREAYAVLAEMPKKGCVPDVITYHCFFR  290 (403)
Q Consensus       219 l~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g-----~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  290 (403)
                      ... +  ...+++++|...|++..+.|   +...+..|...|. .|     ++++|...|++.. .|   +......+-.
T Consensus       255 g~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g---~~~A~~~Lg~  326 (452)
T 3e4b_A          255 AQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GR---EVAADYYLGQ  326 (452)
T ss_dssp             HHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TT---CHHHHHHHHH
T ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CC---CHHHHHHHHH
Confidence            665 3  56899999999999999876   6777788888887 55     9999999999988 43   3333332222


Q ss_pred             hh--C-----CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHh----cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHH
Q 041804          291 CL--E-----KPREILGLFDRMIESGIRPKMDTYVMLLRKFGR----WGFLRPVFVVWKKMEELGCSPDEFAYNALVDAL  359 (403)
Q Consensus       291 ~~--~-----~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  359 (403)
                      .+  +     +.++|..+|++..+.|.   ......|...|..    ..++.+|...|+...+.|. ++.......+...
T Consensus       327 ~y~~G~g~~~d~~~A~~~~~~Aa~~g~---~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g~-~~a~~~l~~l~~~  402 (452)
T 3e4b_A          327 IYRRGYLGKVYPQKALDHLLTAARNGQ---NSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQDT-PEANDLATQLEAP  402 (452)
T ss_dssp             HHHTTTTSSCCHHHHHHHHHHHHTTTC---TTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTCC-HHHHHHHHHHHTT
T ss_pred             HHHCCCCCCcCHHHHHHHHHHHHhhCh---HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCCC-HHHHHHHHHHHHh
Confidence            22  2     68899999999988764   3455556666653    4689999999999998773 3333332223333


Q ss_pred             HhcCCHHHHHHHHHHHHHc
Q 041804          360 IDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       360 ~~~g~~~~a~~~~~~m~~~  378 (403)
                      ...++..+|..+.++..+.
T Consensus       403 ~~~~~~~~a~~~~~~~~~~  421 (452)
T 3e4b_A          403 LTPAQRAEGQRLVQQELAA  421 (452)
T ss_dssp             CCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHh
Confidence            3345667788887776653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.63  E-value=4.9e-14  Score=124.17  Aligned_cols=309  Identities=13%  Similarity=-0.012  Sum_probs=217.8

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC--HHHHHHHHHHHHhcCChHHHHHHHHHHhhc----CC-C-
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN--HATFRIMFKRYVTAHLVNEAMGTFNKLDEF----GL-K-   99 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~-   99 (403)
                      ......+......+...|++++|...|++..+..+..|.  ..++..+...+...|++++|+..|++....    +. + 
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   85 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG   85 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH
Confidence            345667778889999999999999999999886511111  357888999999999999999999987554    21 2 


Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC--------------------hh
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW--------------------WG  159 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--------------------~~  159 (403)
                      ...++..+...+...|++++|...+++........+ .......++..+...|...|+                    ++
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~  164 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELN-DKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQ  164 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHH
Confidence            566888899999999999999999887765321000 111224578888899999999                    99


Q ss_pred             HHHHHHHHHHhC----CCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC-CCC----hhhHHHHHHHHhhcCCHH
Q 041804          160 KCREFWEEMDKR----GVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI-KMD----VVAYNTVIRAVGVSEGVD  229 (403)
Q Consensus       160 ~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~ll~~~~~~~~~~  229 (403)
                      +|.+.+++..+.    +.. ....++..+...|...|++++|...+++..+... .++    ..++..+...+...|+++
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            999888876542    111 1235678888889999999999999988765410 111    236777888888999999


Q ss_pred             HHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHH
Q 041804          230 FAMRVYREMREMGCQ-PS----VVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDR  304 (403)
Q Consensus       230 ~a~~~~~~~~~~~~~-~~----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~  304 (403)
                      +|...+++..+.... ++    ..++..+...|...|++++|...+++..+..                         . 
T Consensus       245 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~-------------------------~-  298 (406)
T 3sf4_A          245 TASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIA-------------------------Q-  298 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-------------------------H-
T ss_pred             HHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHH-------------------------H-
Confidence            999999887754111 11    4567778888888899988888888765320                         0 


Q ss_pred             HHHcCCC-CchhhHHHHHHHHHhcCCcchHHHHHHHHHhc----CCC-CCHHHHHHHHHHHHhcCCH
Q 041804          305 MIESGIR-PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL----GCS-PDEFAYNALVDALIDKGML  365 (403)
Q Consensus       305 ~~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~g~~  365 (403)
                        ..+.. ....++..+...|...|++++|.+.+++..+.    +.. ....++..+...+...|+.
T Consensus       299 --~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          299 --ELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             --HTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             --hcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence              00000 11346677778888888999988888887542    211 1245566677777777765

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.62  E-value=8.9e-14  Score=108.17  Aligned_cols=167  Identities=18%  Similarity=0.070  Sum_probs=97.6

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      ++.+|..+..++.+.|++++|++.|++..+..  +-+..+|..+..+|.+.|++++|+..+.......+.+...+..+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD--PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHH
Confidence            34556666666666666666666666665543  2345556666666666666666666666666655555555666666


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                      .+...++++.+...+.+...       ..+.+..++..+...|.+.|++++|.+.|++..+..+. +..+|..+..+|.+
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~-------~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~lg~~~~~  153 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIA-------LNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPG-FIRAYQSIGLAYEG  153 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH-------hCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcch-hhhHHHHHHHHHHH
Confidence            66666666666666555544       22344555555556666666666666666665555443 45555556666666


Q ss_pred             cCChhHHHHHHHHHHHc
Q 041804          190 SGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~  206 (403)
                      .|++++|++.|++..+.
T Consensus       154 ~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          154 KGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             TTCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHhC
Confidence            66666666666655543

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.62  E-value=1.5e-13  Score=121.03  Aligned_cols=286  Identities=12%  Similarity=0.012  Sum_probs=209.3

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc----HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccC
Q 041804           64 IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD----EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEM  139 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  139 (403)
                      .+....+......+...|++++|+..|++..+..+.+    ..++..+...+...|++++|...+++........+ ..+
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~   84 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIG-DQL   84 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT-CHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcc-ccH
Confidence            4566778888999999999999999999999987765    35788899999999999999999887654311000 123


Q ss_pred             cchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC-----CCcHHHHHHHHHHHHHcCC--------------------hh
Q 041804          140 NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGV-----VKDLHSYSIYMDIMCKSGK--------------------PW  194 (403)
Q Consensus       140 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~--------------------~~  194 (403)
                      ....++..+...|...|++++|...+++..+...     .....++..+...|...|+                    ++
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            3456788889999999999999999988765321     1114478888888999999                    88


Q ss_pred             HHHHHHHHHHHc----CCCC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCcHH
Q 041804          195 KAVKLYKEMKKK----GIKM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ-PS----VVTCNTVIKLLCENGRVR  264 (403)
Q Consensus       195 ~a~~~~~~~~~~----~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~li~~~~~~g~~~  264 (403)
                      +|...+++....    +..| ...++..+...+...|+++.|...+++..+.... ++    ..++..+...|...|+++
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            888888876543    1111 1346777778888889999999888887654111 11    236777788888888888


Q ss_pred             HHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCC-CchhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          265 EAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIR-PKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       265 ~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      +|...+++..+..                         .   ..+.. ....++..+...+...|++++|...+++..+.
T Consensus       245 ~A~~~~~~al~~~-------------------------~---~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  296 (406)
T 3sf4_A          245 TASEYYKKTLLLA-------------------------R---QLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAI  296 (406)
T ss_dssp             HHHHHHHHHHHHH-------------------------H---HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH-------------------------H---hCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence            8888887765320                         0   00101 12456778888999999999999999988653


Q ss_pred             CC-CCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          344 GC-SPD----EFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       344 ~~-~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .- .++    ..++..+...|.+.|++++|...+++..+.
T Consensus       297 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  336 (406)
T 3sf4_A          297 AQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  336 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            10 112    567888899999999999999999987764

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.62  E-value=6.6e-13  Score=112.28  Aligned_cols=218  Identities=10%  Similarity=-0.064  Sum_probs=154.4

Q ss_pred             hHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh-------cCCh-------HHHHHHHHHHhh-cCCCcHHHHHHHHHHHH
Q 041804           48 DLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT-------AHLV-------NEAMGTFNKLDE-FGLKDEVSYCNLVDALC  112 (403)
Q Consensus        48 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~-------~~a~~~~~~~~~-~~~~~~~~~~~l~~~~~  112 (403)
                      ++|..+|++.....  +.+...|..++..+..       .|++       ++|..+|++..+ ..+.+...|..++..+.
T Consensus        33 ~~a~~~~~~al~~~--p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLVL--GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            57777888777754  3456677777766653       4775       788888888887 46557778888888888


Q ss_pred             hcCCHHHHHHHHhcccccccccccccCcchH-HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH-Hc
Q 041804          113 EYKHVIEAQELCFGENKNVGFSGLVEMNKTK-IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC-KS  190 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~  190 (403)
                      ..|++++|..+|++....       .+.+.. +|..++..+.+.|++++|..+|++..+.+.. +...|........ ..
T Consensus       111 ~~~~~~~A~~~~~~al~~-------~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~-~~~~~~~~a~~~~~~~  182 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLLAI-------EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART-RHHVYVTAALMEYYCS  182 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTS-------SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTC-CTHHHHHHHHHHHHTS
T ss_pred             hcCCHHHHHHHHHHHHhc-------cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHc
Confidence            888888888888877763       122333 6777888888888888888888888776543 4444544333322 25


Q ss_pred             CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC-CCC--CHHHHHHHHHHHHhcCcHHHHH
Q 041804          191 GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG-CQP--SVVTCNTVIKLLCENGRVREAY  267 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~li~~~~~~g~~~~a~  267 (403)
                      |++++|.++|+...+.. +-+...|..++..+.+.|+++.|..+|+...+.. .+|  ....|..++..+.+.|+.+.|.
T Consensus       183 ~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~  261 (308)
T 2ond_A          183 KDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASIL  261 (308)
T ss_dssp             CCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            88888888888877662 3356677777777888888888888888888752 343  3567777777777888888888


Q ss_pred             HHHHhchhc
Q 041804          268 AVLAEMPKK  276 (403)
Q Consensus       268 ~~~~~~~~~  276 (403)
                      .+++++.+.
T Consensus       262 ~~~~~a~~~  270 (308)
T 2ond_A          262 KVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888877654

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.62  E-value=2.7e-13  Score=114.72  Aligned_cols=219  Identities=10%  Similarity=0.012  Sum_probs=181.9

Q ss_pred             HHHHHhhhhhcccCCCcCCHHhHHHHHHHHH-------ccCCh-------hHHHHHHHHhhhC-CCCCCCHHHHHHHHHH
Q 041804           12 KRALEFFNWVETDCHFTHTTDTYNSVIDILG-------KFFEF-------DLSWNLIHRMKDN-PSSIPNHATFRIMFKR   76 (403)
Q Consensus        12 ~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~-------~~~~~-------~~a~~~~~~~~~~-~~~~~~~~~~~~l~~~   76 (403)
                      ++|+.+|+.+...  .+.++..|..++..+.       +.|++       ++|..+|++..+. .  +.+...|..++..
T Consensus        33 ~~a~~~~~~al~~--~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~--p~~~~~~~~~~~~  108 (308)
T 2ond_A           33 KRVMFAYEQCLLV--LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLL--KKNMLLYFAYADY  108 (308)
T ss_dssp             HHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTT--TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--cCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhC--cccHHHHHHHHHH
Confidence            6888999988752  3556888888888876       35886       9999999999983 4  3466789999999


Q ss_pred             HHhcCChHHHHHHHHHHhhcCCCcHH-HHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHH-h
Q 041804           77 YVTAHLVNEAMGTFNKLDEFGLKDEV-SYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWF-K  154 (403)
Q Consensus        77 ~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~  154 (403)
                      +.+.|++++|..+|++..+..+.+.. +|..++..+.+.|++++|..+|++....       .+.+...|........ .
T Consensus       109 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~-------~p~~~~~~~~~a~~~~~~  181 (308)
T 2ond_A          109 EESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED-------ARTRHHVYVTAALMEYYC  181 (308)
T ss_dssp             HHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTS-------TTCCTHHHHHHHHHHHHT
T ss_pred             HHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhc-------CCCCHHHHHHHHHHHHHH
Confidence            99999999999999999998776665 8999999999999999999999998874       2344555554444432 3


Q ss_pred             cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC-CCC--ChhhHHHHHHHHhhcCCHHHH
Q 041804          155 MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG-IKM--DVVAYNTVIRAVGVSEGVDFA  231 (403)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~ll~~~~~~~~~~~a  231 (403)
                      .|++++|.++|++..+..+. +...|..++..+.+.|++++|..+|++..... ++|  ....|..++....+.|+.+.|
T Consensus       182 ~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a  260 (308)
T 2ond_A          182 SKDKSVAFKIFELGLKKYGD-IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASI  260 (308)
T ss_dssp             SCCHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            69999999999999887555 78899999999999999999999999999863 455  356888889999999999999


Q ss_pred             HHHHHHHHHcC
Q 041804          232 MRVYREMREMG  242 (403)
Q Consensus       232 ~~~~~~~~~~~  242 (403)
                      ..+++.+.+..
T Consensus       261 ~~~~~~a~~~~  271 (308)
T 2ond_A          261 LKVEKRRFTAF  271 (308)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHc
Confidence            99999998864

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.62  E-value=4.2e-14  Score=124.93  Aligned_cols=282  Identities=13%  Similarity=0.018  Sum_probs=201.3

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcH----HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE----VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      ..+..+...+...|++++|+..|++..+..+.+.    .++..+..++...|++++|...+++........+ ..+....
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~~~  127 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMN-DRLGEAK  127 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTT-CHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc-CchHHHH
Confidence            3455667788889999999999999888876654    5778888888899999999988887654310000 1244567


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCC-----CCCcHHHHHHHHHHHHHcCC-----------------hhHHHHHHH
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDKRG-----VVKDLHSYSIYMDIMCKSGK-----------------PWKAVKLYK  201 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~~  201 (403)
                      ++..+...|...|++++|.+.+++..+..     ......++..+...|...|+                 +++|.+.++
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            78889999999999999999998876531     11234578888889999999                 888888888


Q ss_pred             HHHHc----CCCC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHHhcCcHHHHHHHHH
Q 041804          202 EMKKK----GIKM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ-PS----VVTCNTVIKLLCENGRVREAYAVLA  271 (403)
Q Consensus       202 ~~~~~----~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~li~~~~~~g~~~~a~~~~~  271 (403)
                      +..+.    +..+ ...++..+...+...|++++|...+++..+.... ++    ...+..+...|...|++++|...++
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            76543    1111 2346777788888899999999998887754211 11    2367778888888888888888887


Q ss_pred             hchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCC-CCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc----CC-
Q 041804          272 EMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGI-RPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL----GC-  345 (403)
Q Consensus       272 ~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~-  345 (403)
                      +..+..                         .   ..+. .....++..+...+...|++++|...+++..+.    +. 
T Consensus       288 ~al~~~-------------------------~---~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  339 (411)
T 4a1s_A          288 RTLALA-------------------------V---ELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDR  339 (411)
T ss_dssp             HHHHHH-------------------------H---HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHH-------------------------H---HcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCh
Confidence            765420                         0   0000 012346777788888899999999988887653    11 


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          346 SPDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       346 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .....++..+..+|.+.|++++|..++++..+.
T Consensus       340 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          340 IGEARACWSLGNAHSAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            112446777888889999999999999888774

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.62  E-value=7.7e-14  Score=123.24  Aligned_cols=283  Identities=11%  Similarity=-0.035  Sum_probs=212.5

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHhhc------CCCc
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH----ATFRIMFKRYVTAHLVNEAMGTFNKLDEF------GLKD  100 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~  100 (403)
                      ...+..+...+...|++++|+..|++..+..  +.+.    .+|..+...|...|++++|+..|++..+.      .+..
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  125 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAG--TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGE  125 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhc--ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHH
Confidence            3455667788899999999999999998865  2233    47888999999999999999999988765      1226


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC-----------------hhHHHH
Q 041804          101 EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW-----------------WGKCRE  163 (403)
Q Consensus       101 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----------------~~~a~~  163 (403)
                      ..++..+...|...|++++|...+++........+ ..+....++..+...|...|+                 +++|.+
T Consensus       126 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~  204 (411)
T 4a1s_A          126 AKSSGNLGNTLKVMGRFDEAAICCERHLTLARQLG-DRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVE  204 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh-chHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHH
Confidence            67889999999999999999999988765321000 123445678899999999999                 999999


Q ss_pred             HHHHHHhC----CC-CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCC-CC----hhhHHHHHHHHhhcCCHHHHHH
Q 041804          164 FWEEMDKR----GV-VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK-MD----VVAYNTVIRAVGVSEGVDFAMR  233 (403)
Q Consensus       164 ~~~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~ll~~~~~~~~~~~a~~  233 (403)
                      .+++..+.    +. .....++..+...|...|++++|...+++..+.... ++    ..++..+...|...|++++|..
T Consensus       205 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  284 (411)
T 4a1s_A          205 FYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAE  284 (411)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHH
Confidence            98876542    11 113357888899999999999999999998764111 11    2377888899999999999999


Q ss_pred             HHHHHHHcCCC-----CCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHc
Q 041804          234 VYREMREMGCQ-----PSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIES  308 (403)
Q Consensus       234 ~~~~~~~~~~~-----~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~  308 (403)
                      .+++..+....     ....++..+...|...|++++|...+++..+.                         .....  
T Consensus       285 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~-------------------------~~~~~--  337 (411)
T 4a1s_A          285 HYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAI-------------------------AQELG--  337 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------------------------HHHHT--
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-------------------------HHHCC--
Confidence            99988764211     12467788889999999999999999876542                         01000  


Q ss_pred             CCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          309 GIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       309 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      .......++..+...|...|++++|.+.+++..+.
T Consensus       338 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  372 (411)
T 4a1s_A          338 DRIGEARACWSLGNAHSAIGGHERALKYAEQHLQL  372 (411)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            00112346777888889999999999999888764

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.61  E-value=2.1e-13  Score=105.97  Aligned_cols=168  Identities=12%  Similarity=0.016  Sum_probs=133.3

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      .+...|..+...|...|++++|++.|++..+..+.+..++..+..++...|++++|...+.....       ..+.+..+
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~-------~~~~~~~~   75 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVV-------LDTTSAEA   75 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCCCCHHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-------cCchhHHH
Confidence            45677888888888899999999999998888877888888888888888888888888887766       33556667


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV  224 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  224 (403)
                      +..+...+...++++.+.+.+.+.....+. +...+..+..+|.+.|++++|++.|++..+.. +.+..++..+..+|.+
T Consensus        76 ~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~-~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~  153 (184)
T 3vtx_A           76 YYILGSANFMIDEKQAAIDALQRAIALNTV-YADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEG  153 (184)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHH
Confidence            777778888888888888888888776555 67777888888888888888888888877763 3456677777788888


Q ss_pred             cCCHHHHHHHHHHHHHc
Q 041804          225 SEGVDFAMRVYREMREM  241 (403)
Q Consensus       225 ~~~~~~a~~~~~~~~~~  241 (403)
                      .|++++|...|++..+.
T Consensus       154 ~g~~~~A~~~~~~al~~  170 (184)
T 3vtx_A          154 KGLRDEAVKYFKKALEK  170 (184)
T ss_dssp             TTCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHhC
Confidence            88888888888877764

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.60  E-value=9.6e-15  Score=125.09  Aligned_cols=273  Identities=10%  Similarity=0.014  Sum_probs=200.0

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCC--HHhHHHHHHHHHccCChhHHHHHHHHhhhC----CCCCCCHHHHHHHHHH
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHT--TDTYNSVIDILGKFFEFDLSWNLIHRMKDN----PSSIPNHATFRIMFKR   76 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~l~~~   76 (403)
                      ..+...|++++|++.|+.+.......+.  ...+..+...+...|++++|...+++....    +..+....++..+...
T Consensus        13 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~   92 (338)
T 3ro2_A           13 ERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNT   92 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence            3456789999999999998863211111  467889999999999999999999886543    1011225578889999


Q ss_pred             HHhcCChHHHHHHHHHHhhcCCC------cHHHHHHHHHHHHhcCC--------------------HHHHHHHHhccccc
Q 041804           77 YVTAHLVNEAMGTFNKLDEFGLK------DEVSYCNLVDALCEYKH--------------------VIEAQELCFGENKN  130 (403)
Q Consensus        77 ~~~~~~~~~a~~~~~~~~~~~~~------~~~~~~~l~~~~~~~~~--------------------~~~a~~~~~~~~~~  130 (403)
                      +...|++++|+..+++..+....      ...++..+...+...|+                    +++|...+.+....
T Consensus        93 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~  172 (338)
T 3ro2_A           93 LKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSL  172 (338)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence            99999999999999987664322      24478889999999999                    99998888775542


Q ss_pred             ccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC-----CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          131 VGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGV-----VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      ....+ ..+....++..+...+...|++++|.+.+++..+...     .....++..+...+...|++++|...+++...
T Consensus       173 ~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  251 (338)
T 3ro2_A          173 VTALG-DRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLL  251 (338)
T ss_dssp             HHHHT-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhcC-CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            10000 1123345788888999999999999999988764311     11234788888899999999999999988765


Q ss_pred             cCCC-CC----hhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC-----CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          206 KGIK-MD----VVAYNTVIRAVGVSEGVDFAMRVYREMREMGC-----QPSVVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       206 ~~~~-~~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      .... .+    ..++..+...+...|++++|...++...+...     .....++..+...|...|++++|...+++..+
T Consensus       252 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  331 (338)
T 3ro2_A          252 LARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  331 (338)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            4111 11    45677788888999999999999988765411     11144677788899999999999999988765


Q ss_pred             c
Q 041804          276 K  276 (403)
Q Consensus       276 ~  276 (403)
                      .
T Consensus       332 ~  332 (338)
T 3ro2_A          332 I  332 (338)
T ss_dssp             C
T ss_pred             H
Confidence            3

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.60  E-value=7.3e-14  Score=119.55  Aligned_cols=281  Identities=12%  Similarity=0.007  Sum_probs=185.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc----HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD----EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      .+......+...|++++|+..|+++.+..+.+    ...+..+...+...|++++|...+++........+ ..+....+
T Consensus         7 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~~~~   85 (338)
T 3ro2_A            7 ELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIG-DQLGEAKA   85 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT-CHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccc-ccHHHHHH
Confidence            34445556666667777777776666665443    34566666666677777777766665443210000 11233556


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCC-Cc----HHHHHHHHHHHHHcCC--------------------hhHHHHH
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVV-KD----LHSYSIYMDIMCKSGK--------------------PWKAVKL  199 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~--------------------~~~a~~~  199 (403)
                      +..+...|...|++++|.+.+++..+.... ++    ..++..+...+...|+                    +++|...
T Consensus        86 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~  165 (338)
T 3ro2_A           86 SGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDL  165 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHH
Confidence            788888888999999999888876543111 11    3477788888888888                    8888888


Q ss_pred             HHHHHHc----CCCC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC-C----CHHHHHHHHHHHHhcCcHHHHHHH
Q 041804          200 YKEMKKK----GIKM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ-P----SVVTCNTVIKLLCENGRVREAYAV  269 (403)
Q Consensus       200 ~~~~~~~----~~~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~----~~~~~~~li~~~~~~g~~~~a~~~  269 (403)
                      +++....    +..+ ...++..+...+...|+++.|...++...+.... +    ...++..+...+...|++++|...
T Consensus       166 ~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  245 (338)
T 3ro2_A          166 YEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEY  245 (338)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            8776543    1111 2336677777888888888888888877653110 1    123667777888888888888888


Q ss_pred             HHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCC-CCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc----C
Q 041804          270 LAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGI-RPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL----G  344 (403)
Q Consensus       270 ~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~  344 (403)
                      +++..+..                         .   ..+. .....++..+...+...|++++|...+++..+.    +
T Consensus       246 ~~~al~~~-------------------------~---~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~  297 (338)
T 3ro2_A          246 YKKTLLLA-------------------------R---QLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELK  297 (338)
T ss_dssp             HHHHHHHH-------------------------H---HTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHH-------------------------H---hhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcC
Confidence            87755320                         0   0000 012446777888899999999999999888653    1


Q ss_pred             CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          345 CS-PDEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       345 ~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      -. ....++..+...|.+.|++++|...+++..+.
T Consensus       298 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          298 DRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            11 12447778889999999999999999998874

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.60  E-value=1.5e-13  Score=123.35  Aligned_cols=216  Identities=10%  Similarity=-0.035  Sum_probs=189.4

Q ss_pred             ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh-HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHH
Q 041804           46 EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV-NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELC  124 (403)
Q Consensus        46 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  124 (403)
                      .+++++..++......  +.+...+..+...+...|++ ++|++.|++..+..+.+..+|..+..+|...|++++|...|
T Consensus        83 ~~~~al~~l~~~~~~~--~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~  160 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSA--QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCF  160 (474)
T ss_dssp             HHHHHHHHHHHHHTTC--CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccC--chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            3667777787776654  35788999999999999999 99999999999999889999999999999999999999999


Q ss_pred             hcccccccccccccCcchHHHHHHHHHHHhc---------CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc-----
Q 041804          125 FGENKNVGFSGLVEMNKTKIYNMILRGWFKM---------SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS-----  190 (403)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----  190 (403)
                      ++....        .|+..++..+...+...         |++++|.+.|++..+..+. +...|..+..+|...     
T Consensus       161 ~~al~~--------~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~  231 (474)
T 4abn_A          161 SGALTH--------CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVL-DGRSWYILGNAYLSLYFNTG  231 (474)
T ss_dssp             HHHHTT--------CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhh--------CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHhhc
Confidence            998864        35578899999999999         9999999999999988766 788999999999998     


Q ss_pred             ---CChhHHHHHHHHHHHcCCC---CChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHH
Q 041804          191 ---GKPWKAVKLYKEMKKKGIK---MDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVR  264 (403)
Q Consensus       191 ---~~~~~a~~~~~~~~~~~~~---~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~  264 (403)
                         |++++|+..|++..+.. +   -+...+..+..+|...|++++|...|++..+.... +...+..+...+...|+++
T Consensus       232 ~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~a~~~l~~~~~~lg~~~  309 (474)
T 4abn_A          232 QNPKISQQALSAYAQAEKVD-RKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPA-WPEPQQREQQLLEFLSRLT  309 (474)
T ss_dssp             CCHHHHHHHHHHHHHHHHHC-GGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHHHHhC-CCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHH
Confidence               99999999999999873 2   47788999999999999999999999999987533 5677888899999999999


Q ss_pred             HHHHHHHhch
Q 041804          265 EAYAVLAEMP  274 (403)
Q Consensus       265 ~a~~~~~~~~  274 (403)
                      +|...+..+.
T Consensus       310 eAi~~~~~~~  319 (474)
T 4abn_A          310 SLLESKGKTK  319 (474)
T ss_dssp             HHHHHTTTCC
T ss_pred             HHHHHhcccc
Confidence            9998776653

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.58  E-value=9.8e-14  Score=124.46  Aligned_cols=217  Identities=8%  Similarity=-0.021  Sum_probs=185.6

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCCh-hHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEF-DLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      +++++++..++....  ..+.+...+..+..++...|++ ++|+..|++..+..  +.+..+|..+..+|...|++++|+
T Consensus        82 ~~~~~al~~l~~~~~--~~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~  157 (474)
T 4abn_A           82 EEMEKTLQQMEEVLG--SAQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE--PELVEAWNQLGEVYWKKGDVTSAH  157 (474)
T ss_dssp             HHHHHHHHHHHHHHT--TCCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHhc--cCchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHcCCHHHHH
Confidence            456777777776653  2345788999999999999999 99999999998875  345889999999999999999999


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHHhc---------CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc---
Q 041804           88 GTFNKLDEFGLKDEVSYCNLVDALCEY---------KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM---  155 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---  155 (403)
                      +.|++..+..+. ..++..+..++...         |++++|...+++...       ..+.+...|..+..+|...   
T Consensus       158 ~~~~~al~~~p~-~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~-------~~p~~~~~~~~lg~~~~~~~~~  229 (474)
T 4abn_A          158 TCFSGALTHCKN-KVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQ-------MDVLDGRSWYILGNAYLSLYFN  229 (474)
T ss_dssp             HHHHHHHTTCCC-HHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCCC-HHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHHHHh
Confidence            999999998865 68999999999999         999999999999887       4466788899999999998   


Q ss_pred             -----CChhHHHHHHHHHHhCCCC--CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCH
Q 041804          156 -----SWWGKCREFWEEMDKRGVV--KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGV  228 (403)
Q Consensus       156 -----~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  228 (403)
                           |++++|.+.|++..+..+.  -+...|..+..+|...|++++|.+.|++..+.. +.+...+..+..++...|++
T Consensus       230 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~a~~~l~~~~~~lg~~  308 (474)
T 4abn_A          230 TGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALD-PAWPEPQQREQQLLEFLSRL  308 (474)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHH
T ss_pred             hccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHH
Confidence                 9999999999999987541  278899999999999999999999999998874 34566788888888888988


Q ss_pred             HHHHHHHHHH
Q 041804          229 DFAMRVYREM  238 (403)
Q Consensus       229 ~~a~~~~~~~  238 (403)
                      ++|...+..+
T Consensus       309 ~eAi~~~~~~  318 (474)
T 4abn_A          309 TSLLESKGKT  318 (474)
T ss_dssp             HHHHHHTTTC
T ss_pred             HHHHHHhccc
Confidence            8888755433

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.57  E-value=4.5e-13  Score=117.13  Aligned_cols=301  Identities=7%  Similarity=-0.048  Sum_probs=184.4

Q ss_pred             ccccccHHHHHHhhhhhcccC-CC--cCCHHhHHHHHHHH--HccCChhHHH-----------HHHHHhhhCCCCCCCHH
Q 041804            5 SCYANDWKRALEFFNWVETDC-HF--THTTDTYNSVIDIL--GKFFEFDLSW-----------NLIHRMKDNPSSIPNHA   68 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~-~~--~~~~~~~~~li~~~--~~~~~~~~a~-----------~~~~~~~~~~~~~~~~~   68 (403)
                      ..+++++++|..+++.+.... ..  .++...|..++..-  .-.+.++.+.           +.++.+....   ++..
T Consensus        22 ~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~---~~~~   98 (383)
T 3ulq_A           22 YIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQ---ARLT   98 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHT---HHHH
T ss_pred             HHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcC---CCch
Confidence            346789999999998886522 11  23334444444332  2234444444           6777765532   2222


Q ss_pred             H------HHHHHHHHHhcCChHHHHHHHHHHhhc----CCC--cHHHHHHHHHHHHhcCCHHHHHHHHhccccccccccc
Q 041804           69 T------FRIMFKRYVTAHLVNEAMGTFNKLDEF----GLK--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGL  136 (403)
Q Consensus        69 ~------~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  136 (403)
                      .      +......+...|++++|+..|++..+.    +.+  ...++..+..++...|++++|...+.+........+.
T Consensus        99 ~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~  178 (383)
T 3ulq_A           99 GLLEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEA  178 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCST
T ss_pred             hHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcc
Confidence            2      223667788999999999999998775    211  5578899999999999999999998876653211100


Q ss_pred             ccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-----CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc----C
Q 041804          137 VEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV-----KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK----G  207 (403)
Q Consensus       137 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~  207 (403)
                      ..+....+++.+...|...|++++|.+.|++..+....     ....++..+..+|...|++++|.+.+++..+.    +
T Consensus       179 ~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~  258 (383)
T 3ulq_A          179 YNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESN  258 (383)
T ss_dssp             THHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             chHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhc
Confidence            02233456788888888888888888888776543111     11246777777888888888888888777662    2


Q ss_pred             C-CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHhcCc---HHHHHHHHHhchhcCCC
Q 041804          208 I-KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG----CQPSVVTCNTVIKLLCENGR---VREAYAVLAEMPKKGCV  279 (403)
Q Consensus       208 ~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~  279 (403)
                      . +....++..+...+.+.|++++|...+++..+..    -+.....+..+...|...|+   .++|..++++...    
T Consensus       259 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~----  334 (383)
T 3ulq_A          259 ILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKML----  334 (383)
T ss_dssp             CGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTC----
T ss_pred             cchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcC----
Confidence            2 2234466677777777777777777777765431    11112223445555555555   3444444433210    


Q ss_pred             CChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHh
Q 041804          280 PDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEE  342 (403)
Q Consensus       280 p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  342 (403)
                                                    .......+..+...|...|++++|.+.+++..+
T Consensus       335 ------------------------------~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          335 ------------------------------YADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             ------------------------------HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ------------------------------HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                                          001223455666677777777777777776654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.56  E-value=5.1e-14  Score=119.24  Aligned_cols=246  Identities=11%  Similarity=0.030  Sum_probs=174.5

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhC-------CCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhc----
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN-------PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEF----   96 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----   96 (403)
                      +.+..++..+...+...|++++|..+++++.+.       . .+....++..+...|...|++++|+..|++..+.    
T Consensus        24 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  102 (311)
T 3nf1_A           24 PARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHD-HPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKT  102 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSS-SHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            345678999999999999999999999998872       1 1234567889999999999999999999998765    


Q ss_pred             --C-CC-cHHHHHHHHHHHHhcCCHHHHHHHHhccccccccc-ccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804           97 --G-LK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFS-GLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus        97 --~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                        + .+ ...++..+...+...|++++|...+++........ +...+....++..+...+...|++++|.+++++..+.
T Consensus       103 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  182 (311)
T 3nf1_A          103 LGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEI  182 (311)
T ss_dssp             HCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             hCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence              2 23 67889999999999999999999998877531000 0022445677889999999999999999999998764


Q ss_pred             ------CCCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHc-------CCCCChhhH-------HHHHHHHhhcCCHHH
Q 041804          172 ------GVVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-------GIKMDVVAY-------NTVIRAVGVSEGVDF  230 (403)
Q Consensus       172 ------~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~-------~~ll~~~~~~~~~~~  230 (403)
                            +..| ...++..+..+|...|++++|...++++.+.       ...+.....       ..+...+...+.+..
T Consensus       183 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (311)
T 3nf1_A          183 YQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGE  262 (311)
T ss_dssp             HHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCC
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHH
Confidence                  2122 3467888999999999999999999998763       112222211       222222333445555


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          231 AMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       231 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      +...+....... +....++..+...|.+.|++++|...|++..+
T Consensus       263 a~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          263 YGGWYKACKVDS-PTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             CC---------C-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhcCCCC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            556666655432 23566788899999999999999999998764

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.55  E-value=1.2e-12  Score=114.51  Aligned_cols=307  Identities=7%  Similarity=-0.035  Sum_probs=207.5

Q ss_pred             HHHccCChhHHHHHHHHhhhCCC-C--CCCHHHHHHHHHH--HHhcCChHHHH-----------HHHHHHhhcCCC-c--
Q 041804           40 ILGKFFEFDLSWNLIHRMKDNPS-S--IPNHATFRIMFKR--YVTAHLVNEAM-----------GTFNKLDEFGLK-D--  100 (403)
Q Consensus        40 ~~~~~~~~~~a~~~~~~~~~~~~-~--~~~~~~~~~l~~~--~~~~~~~~~a~-----------~~~~~~~~~~~~-~--  100 (403)
                      .+.+.+++++|..+++++.+.-. .  .++...|-.++..  ....++++.+.           +.++.+.....+ +  
T Consensus        21 ~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~y~~ll~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~i~~~~~~~~~~  100 (383)
T 3ulq_A           21 MYIRRFSIPDAEYLRREIKQELDQMEEDQDLHLYYSLMEFRHNLMLEYLEPLEKMRIEEQPRLSDLLLEIDKKQARLTGL  100 (383)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSCGGGSCCHHHHHHHHHHHTHHHHHH
T ss_pred             HHHHHcCHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHHhhcCcccccccccccchhhHHHHHHhcCCCchhH
Confidence            35578999999999998866421 1  1333333443332  22334444444           677766553322 1  


Q ss_pred             --HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC----
Q 041804          101 --EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV----  174 (403)
Q Consensus       101 --~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----  174 (403)
                        ...+......+...|++++|...+++........+ .......++..+...|...|+++.|...+++..+....    
T Consensus       101 l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~  179 (383)
T 3ulq_A          101 LEYYFNFFRGMYELDQREYLSAIKFFKKAESKLIFVK-DRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAY  179 (383)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCC-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTT
T ss_pred             HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhhCC-CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccc
Confidence              11223366777889999999999988765321000 11124577889999999999999999999887653111    


Q ss_pred             --CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCC-CC----hhhHHHHHHHHhhcCCHHHHHHHHHHHHHc----CC
Q 041804          175 --KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK-MD----VVAYNTVIRAVGVSEGVDFAMRVYREMREM----GC  243 (403)
Q Consensus       175 --~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~  243 (403)
                        ....+++.+..+|...|++++|...|++..+.... ++    ..++..+...|...|++++|...+++..+.    +.
T Consensus       180 ~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~  259 (383)
T 3ulq_A          180 NIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNI  259 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcc
Confidence              12457888889999999999999999887754111 11    236778888899999999999999988763    22


Q ss_pred             -CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHH
Q 041804          244 -QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLR  322 (403)
Q Consensus       244 -~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  322 (403)
                       +....++..+...|.+.|++++|...+++..+.                         ...   .+.......+..+..
T Consensus       260 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-------------------------~~~---~~~~~~~~~~~~l~~  311 (383)
T 3ulq_A          260 LPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAY-------------------------SQK---AGDVIYLSEFEFLKS  311 (383)
T ss_dssp             GGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------------------------HHH---HTCHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-------------------------HHH---cCCHHHHHHHHHHHH
Confidence             334567888889999999999999998876542                         000   011111223566777


Q ss_pred             HHHhcCC---cchHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 041804          323 KFGRWGF---LRPVFVVWKKMEELGCSP-DEFAYNALVDALIDKGMLDMARKYDEEMFAK  378 (403)
Q Consensus       323 ~~~~~g~---~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  378 (403)
                      .+...|+   +++|..++++.   +..| ....+..+...|.+.|++++|...+++..+.
T Consensus       312 ~~~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~~  368 (383)
T 3ulq_A          312 LYLSGPDEEAIQGFFDFLESK---MLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQV  368 (383)
T ss_dssp             HHTSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHhCCCcHHHHHHHHHHHHHC---cCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            7888888   67777777665   2223 3456778899999999999999999998763

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.52  E-value=2.1e-12  Score=100.22  Aligned_cols=166  Identities=8%  Similarity=-0.091  Sum_probs=107.4

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ...+..+...+...|++++|...++++.+..  +.+..++..+...+...|++++|...++++.+..+.+...+..+...
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~   85 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDAD--AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            3455666667777777777777777766653  34566667777777777777777777777776665566666667777


Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      +...|++++|...+++...       ..+.+..++..+...+...|++++|.+.+++..+.... +...+..+..++...
T Consensus        86 ~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~  157 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAE-------ANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPN-EGKVHRAIAFSYEQM  157 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHT
T ss_pred             HHHhcCHHHHHHHHHHHHh-------cCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHc
Confidence            7777777777776666554       22344555666666666666666666666666655433 455666666666666


Q ss_pred             CChhHHHHHHHHHHHc
Q 041804          191 GKPWKAVKLYKEMKKK  206 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~  206 (403)
                      |++++|...++...+.
T Consensus       158 ~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          158 GRHEEALPHFKKANEL  173 (186)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHc
Confidence            6666666666665543

>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=99.50  E-value=1.4e-12  Score=121.78  Aligned_cols=166  Identities=10%  Similarity=-0.051  Sum_probs=152.2

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      +..+|+.+..++.+.|++++|+..|++..+..  +-+..+|+.+..+|.+.|++++|+..|++..+..+.+..+|..+..
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~--P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P~~~~a~~nLg~   85 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVF--PEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            47899999999999999999999999999865  3457899999999999999999999999999999889999999999


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                      ++...|++++|.+.|++..+       ..+.+..+|+.+...|.+.|++++|++.|++..+..+. +...+..+..++..
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~-------l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~-~~~a~~~L~~~l~~  157 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQ-------INPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPD-FPDAYCNLAHCLQI  157 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHhhhhhHHHh
Confidence            99999999999999999887       44667889999999999999999999999999998766 78899999999999


Q ss_pred             cCChhHHHHHHHHHHH
Q 041804          190 SGKPWKAVKLYKEMKK  205 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~  205 (403)
                      .|++++|.+.++++.+
T Consensus       158 ~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          158 VCDWTDYDERMKKLVS  173 (723)
T ss_dssp             TTCCTTHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHH
Confidence            9999999999888765

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.50  E-value=6.5e-13  Score=112.43  Aligned_cols=240  Identities=9%  Similarity=-0.019  Sum_probs=167.0

Q ss_pred             ccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC-------CCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc---
Q 041804          137 VEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR-------GVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK---  206 (403)
Q Consensus       137 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---  206 (403)
                      ..+.+..++..+...+...|++++|..+|+++.+.       .......++..+...|...|++++|...+++....   
T Consensus        22 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~  101 (311)
T 3nf1_A           22 EIPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREK  101 (311)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            44566788999999999999999999999998773       23335677888999999999999999999998765   


Q ss_pred             ---CC-CCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc------CC-CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          207 ---GI-KMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM------GC-QPSVVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       207 ---~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                         +- +....++..+...|...|++++|...++++.+.      +. ......+..+...|...|++++|..++++..+
T Consensus       102 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~  181 (311)
T 3nf1_A          102 TLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALE  181 (311)
T ss_dssp             HHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               22 223557888899999999999999999998865      21 22345688889999999999999999998865


Q ss_pred             c------CCCCC-hhhHHHHHH---hhCCHHHHHHHHHHHHHc-------CCCCch-------hhHHHHHHHHHhcCCcc
Q 041804          276 K------GCVPD-VITYHCFFR---CLEKPREILGLFDRMIES-------GIRPKM-------DTYVMLLRKFGRWGFLR  331 (403)
Q Consensus       276 ~------~~~p~-~~~~~~l~~---~~~~~~~a~~~~~~~~~~-------~~~~~~-------~~~~~li~~~~~~g~~~  331 (403)
                      .      +..|. ...+..+..   ..++.++|...++++.+.       ...+..       ..+..+...+...+.+.
T Consensus       182 ~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  261 (311)
T 3nf1_A          182 IYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFG  261 (311)
T ss_dssp             HHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSC
T ss_pred             HHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHH
Confidence            3      21232 223333333   338899999999888753       111221       12223333445566777


Q ss_pred             hHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          332 PVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      ++...++...... +.+..++..+..+|.+.|++++|.+++++..+
T Consensus       262 ~a~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          262 EYGGWYKACKVDS-PTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             CCC---------C-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCCCC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7777777776542 34567888999999999999999999998876

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.49  E-value=9e-10  Score=101.77  Aligned_cols=362  Identities=8%  Similarity=0.021  Sum_probs=237.0

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCC---hhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFE---FDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      ..++++.+..+|+.+...  ++.+...|...+..-.+.++   ++.+..+|++.......+|+...|..-+....+.++.
T Consensus        78 ~~~~~~~aR~vyEraL~~--fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW~~Yl~f~~~~~~~  155 (679)
T 4e6h_A           78 SLKQWKQVYETFDKLHDR--FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLWLSYITYVRKKNDI  155 (679)
T ss_dssp             HTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHHHHHHHHHHHHSCS
T ss_pred             hcCcHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhccc
Confidence            346778888888888743  55667788888888888888   8888888888887642247888887777766555543


Q ss_pred             --------HHHHHHHHHHhh-cCC---CcHHHHHHHHHHHHh---------cCCHHHHHHHHhcccccccccccccCcch
Q 041804           84 --------NEAMGTFNKLDE-FGL---KDEVSYCNLVDALCE---------YKHVIEAQELCFGENKNVGFSGLVEMNKT  142 (403)
Q Consensus        84 --------~~a~~~~~~~~~-~~~---~~~~~~~~l~~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  142 (403)
                              +.+.++|+.... .|.   .+...|...+.....         .++.+.+.++|++.....      ...-.
T Consensus       156 ~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~iP------~~~~~  229 (679)
T 4e6h_A          156 ITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLCQP------MDCLE  229 (679)
T ss_dssp             TTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTTSC------CSSHH
T ss_pred             ccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHHHhCc------cHHHH
Confidence                    334467766543 233   255677777665432         334566777776665421      00001


Q ss_pred             -------------------------------------------------------------------------HHHHHHH
Q 041804          143 -------------------------------------------------------------------------KIYNMIL  149 (403)
Q Consensus       143 -------------------------------------------------------------------------~~~~~l~  149 (403)
                                                                                               ..|...+
T Consensus       230 ~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~ql~lW~~yi  309 (679)
T 4e6h_A          230 SMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYDVQQLLIWLEWI  309 (679)
T ss_dssp             HHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhHHHHHHHHHHHH
Confidence                                                                                     1111111


Q ss_pred             HHHHhcC-------ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHH-HHHHHHHHcCCCCChhhHHHHHHH
Q 041804          150 RGWFKMS-------WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAV-KLYKEMKKKGIKMDVVAYNTVIRA  221 (403)
Q Consensus       150 ~~~~~~~-------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~-~~~~~~~~~~~~~~~~~~~~ll~~  221 (403)
                      ..--..+       ..+.+..+|++.....+. +...|...+..+...|+.++|. ++|++.... .+.+...|-..+..
T Consensus       310 ~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p~-~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~  387 (679)
T 4e6h_A          310 RWESDNKLELSDDLHKARMTYVYMQAAQHVCF-APEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQ  387 (679)
T ss_dssp             HHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTT-CHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHH
T ss_pred             HHHHhCCccccchhhHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHH
Confidence            1111111       011223445554444333 5556666677777788888886 999998875 44566667777888


Q ss_pred             HhhcCCHHHHHHHHHHHHHcCC---------CCC------------HHHHHHHHHHHHhcCcHHHHHHHHHhchhc-C-C
Q 041804          222 VGVSEGVDFAMRVYREMREMGC---------QPS------------VVTCNTVIKLLCENGRVREAYAVLAEMPKK-G-C  278 (403)
Q Consensus       222 ~~~~~~~~~a~~~~~~~~~~~~---------~~~------------~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-~-~  278 (403)
                      .-+.|+++.|..+|+.+.+...         .|+            ..+|...+....+.|+.+.|..+|.+..+. + .
T Consensus       388 ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~  467 (679)
T 4e6h_A          388 YELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLV  467 (679)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGS
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCC
Confidence            8889999999999998876410         132            236777788888889999999999998765 2 1


Q ss_pred             CCChhhHHHHHHh-hC-CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCC--CHHHHHH
Q 041804          279 VPDVITYHCFFRC-LE-KPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSP--DEFAYNA  354 (403)
Q Consensus       279 ~p~~~~~~~l~~~-~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~--~~~~~~~  354 (403)
                      .+......+.+.. ++ +.+.|..+|+...+. ..-+...+...+......|+.+.|..+|++.......+  ....|..
T Consensus       468 ~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~  546 (679)
T 4e6h_A          468 TPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQK  546 (679)
T ss_dssp             CTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            2223333333332 23 478999999998876 23355667788888888899999999999988764221  3567888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcC
Q 041804          355 LVDALIDKGMLDMARKYDEEMFAKG  379 (403)
Q Consensus       355 l~~~~~~~g~~~~a~~~~~~m~~~~  379 (403)
                      +++.-.+.|+.+.+.++.+++.+.-
T Consensus       547 ~~~fE~~~G~~~~~~~v~~R~~~~~  571 (679)
T 4e6h_A          547 VIFFESKVGSLNSVRTLEKRFFEKF  571 (679)
T ss_dssp             HHHHHHHTCCSHHHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            8888889999999999999998864

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.49  E-value=2.3e-11  Score=106.05  Aligned_cols=319  Identities=8%  Similarity=-0.006  Sum_probs=201.1

Q ss_pred             CcCCHHhHHHHHHHH--HccCChhHHHHHHHHhhhCCC-C--CCCHHHHHHHHHH--HHhcCChHHHH---------HHH
Q 041804           27 FTHTTDTYNSVIDIL--GKFFEFDLSWNLIHRMKDNPS-S--IPNHATFRIMFKR--YVTAHLVNEAM---------GTF   90 (403)
Q Consensus        27 ~~~~~~~~~~li~~~--~~~~~~~~a~~~~~~~~~~~~-~--~~~~~~~~~l~~~--~~~~~~~~~a~---------~~~   90 (403)
                      ..|+..+-+.+-..|  ...+++++|..+++++.+... .  .++...|-.++..  ....+.+..+.         ..+
T Consensus         6 ~~~~~~v~~~l~~wy~~i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l   85 (378)
T 3q15_A            6 AIPSSRVGVKINEWYKMIRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELL   85 (378)
T ss_dssp             CBCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHHHHHHHHHTCCC--------CHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhhcCcccccccccchHHHH
Confidence            345666666666666  789999999999998755320 1  1233334444332  12223333333         666


Q ss_pred             HHHhhcCCC-cH----HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           91 NKLDEFGLK-DE----VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        91 ~~~~~~~~~-~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      +.+.....+ +.    ..+......+...|++++|...+++........+ ..+....++..+...|...|+++.|...+
T Consensus        86 ~~i~~~~~~~~~~l~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~a~~~~~lg~~y~~~~~~~~A~~~~  164 (378)
T 3q15_A           86 ETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVS-DDIEKAEFHFKVAEAYYHMKQTHVSMYHI  164 (378)
T ss_dssp             HHHHGGGHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCC-CHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHhccCCCCccHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCC-ChHHHHHHHHHHHHHHHHcCCcHHHHHHH
Confidence            666543322 11    1334455667789999999999988765421100 11234567888999999999999999999


Q ss_pred             HHHHhCC----C-CC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHc----CCCC-ChhhHHHHHHHHhhcCCHHHHHHH
Q 041804          166 EEMDKRG----V-VK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK----GIKM-DVVAYNTVIRAVGVSEGVDFAMRV  234 (403)
Q Consensus       166 ~~~~~~~----~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~ll~~~~~~~~~~~a~~~  234 (403)
                      ++..+..    . .+ ...+++.+..+|...|++++|.+.|++..+.    +..+ ...++..+..+|...|+++.|...
T Consensus       165 ~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~  244 (378)
T 3q15_A          165 LQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEH  244 (378)
T ss_dssp             HHHHHHHHTSTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHhCCCchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHH
Confidence            8876531    1 11 2457788889999999999999999887663    1111 234677788888999999999999


Q ss_pred             HHHHHHc----CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCC
Q 041804          235 YREMREM----GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGI  310 (403)
Q Consensus       235 ~~~~~~~----~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~  310 (403)
                      +++..+.    +.+....++..+...|.+.|++++|...+++..+.....+.                            
T Consensus       245 ~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~----------------------------  296 (378)
T 3q15_A          245 FQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSH----------------------------  296 (378)
T ss_dssp             HHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCC----------------------------
T ss_pred             HHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCC----------------------------
Confidence            9988762    22223677888889999999999999999887653111110                            


Q ss_pred             CCchhhHHHHHHHHHhcCC---cchHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          311 RPKMDTYVMLLRKFGRWGF---LRPVFVVWKKMEELGCSP-DEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       311 ~~~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      +.....+..+...+...++   +.+|...+++.   +..| ....+..+...|.+.|++++|...+++..+
T Consensus       297 ~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~---~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          297 KFYKELFLFLQAVYKETVDERKIHDLLSYFEKK---NLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             SCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC---CChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            0111223334444445555   55555555542   1112 234556677777788888888887777654

>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=99.48  E-value=7e-12  Score=97.22  Aligned_cols=164  Identities=11%  Similarity=-0.025  Sum_probs=100.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHH
Q 041804          102 VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYS  181 (403)
Q Consensus       102 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  181 (403)
                      ..+..+...+...|++++|...++++..       ..+.+..++..+...+...|++++|.+.++++.+.... +...+.
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~   80 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYD-------ADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPD-NVKVAT   80 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCC-------TTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHH-------hCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-CHHHHH
Confidence            3455555555666666666666665554       22334555666666666666666666666666555333 455666


Q ss_pred             HHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcC
Q 041804          182 IYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENG  261 (403)
Q Consensus       182 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g  261 (403)
                      .+...+...|++++|.+.++++.+.. +.+...+..+...+...|++++|...++.+.+.. +.+...+..+...+...|
T Consensus        81 ~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  158 (186)
T 3as5_A           81 VLGLTYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMG  158 (186)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcC
Confidence            66666666666666666666666552 3345566666666666677777777776666653 224566666666777777


Q ss_pred             cHHHHHHHHHhchh
Q 041804          262 RVREAYAVLAEMPK  275 (403)
Q Consensus       262 ~~~~a~~~~~~~~~  275 (403)
                      ++++|...+++..+
T Consensus       159 ~~~~A~~~~~~~~~  172 (186)
T 3as5_A          159 RHEEALPHFKKANE  172 (186)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            77777777766654

>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=99.46  E-value=3.7e-12  Score=118.88  Aligned_cols=167  Identities=12%  Similarity=-0.021  Sum_probs=151.7

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      -+..+|+.+...|.+.|++++|++.|++..+..+.+..++..+..+|.+.|++++|+..|++..+       ..+.+..+
T Consensus         7 ~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~-------l~P~~~~a   79 (723)
T 4gyw_A            7 THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIR-------ISPTFADA   79 (723)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCCCCHHH
Confidence            34678999999999999999999999999999988999999999999999999999999999887       44667889


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV  224 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~  224 (403)
                      |..+...|.+.|++++|.+.|++..+.+.. +..+|+.+..+|...|++++|++.|++..+.. +-+...+..+..++..
T Consensus        80 ~~nLg~~l~~~g~~~~A~~~~~kAl~l~P~-~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~-P~~~~a~~~L~~~l~~  157 (723)
T 4gyw_A           80 YSNMGNTLKEMQDVQGALQCYTRAIQINPA-FADAHSNLASIHKDSGNIPEAIASYRTALKLK-PDFPDAYCNLAHCLQI  157 (723)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHhhhhhHHHh
Confidence            999999999999999999999999988766 78899999999999999999999999999874 3356789999999999


Q ss_pred             cCCHHHHHHHHHHHHH
Q 041804          225 SEGVDFAMRVYREMRE  240 (403)
Q Consensus       225 ~~~~~~a~~~~~~~~~  240 (403)
                      .|++++|.+.++++.+
T Consensus       158 ~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          158 VCDWTDYDERMKKLVS  173 (723)
T ss_dssp             TTCCTTHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHH
Confidence            9999999998888765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.46  E-value=1.5e-11  Score=107.01  Aligned_cols=269  Identities=12%  Similarity=0.012  Sum_probs=159.4

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCH----HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC----HHHHHHHHH
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTT----DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN----HATFRIMFK   75 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~   75 (403)
                      ++...|++++|++.++....... ..+.    .+++.+...+...|++++|...+++........++    ..++..+..
T Consensus        23 ~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~  101 (373)
T 1hz4_A           23 VAINDGNPDEAERLAKLALEELP-PGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSE  101 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCC-TTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHcCC-CCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            44556788888888777654221 1122    24556666777788888888887776542101112    223556677


Q ss_pred             HHHhcCChHHHHHHHHHHhhcC----C---C-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHH
Q 041804           76 RYVTAHLVNEAMGTFNKLDEFG----L---K-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNM  147 (403)
Q Consensus        76 ~~~~~~~~~~a~~~~~~~~~~~----~---~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (403)
                      .+...|++++|+..+++..+..    .   + ....+..+...+...|++++|...+++........  +.+....++..
T Consensus       102 ~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~--~~~~~~~~~~~  179 (373)
T 1hz4_A          102 ILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSY--QPQQQLQCLAM  179 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTS--CGGGGHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcc--CcHHHHHHHHH
Confidence            7778888888888887765532    1   2 34456667777778888888888777655432111  11113356667


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCcH-HHHH-----HHHHHHHHcCChhHHHHHHHHHHHcCCCCC---hhhHHHH
Q 041804          148 ILRGWFKMSWWGKCREFWEEMDKRGVVKDL-HSYS-----IYMDIMCKSGKPWKAVKLYKEMKKKGIKMD---VVAYNTV  218 (403)
Q Consensus       148 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l  218 (403)
                      +...+...|++++|...+++.......++. ..+.     ..+..+...|++++|...+++.......++   ...+..+
T Consensus       180 la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~l  259 (373)
T 1hz4_A          180 LIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNI  259 (373)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHH
Confidence            777777888888888888776543211111 1111     223346677888888877777654321111   2234556


Q ss_pred             HHHHhhcCCHHHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          219 IRAVGVSEGVDFAMRVYREMREM----GCQPSV-VTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       219 l~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      ...+...|++++|...++.....    |..++. ..+..+..++...|+.++|...+++...
T Consensus       260 a~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          260 ARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            66777778888887777776543    111122 2455556667777777777777776553

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.45  E-value=9.8e-11  Score=101.86  Aligned_cols=281  Identities=7%  Similarity=-0.085  Sum_probs=182.2

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC------cHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH----ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK------DEV  102 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~~~  102 (403)
                      ........+...|++++|...+++..... ...+.    .+++.+...+...|++++|...+++.......      ...
T Consensus        16 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~   94 (373)
T 1hz4_A           16 FNALRAQVAINDGNPDEAERLAKLALEEL-PPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALW   94 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTC-CTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHH
Confidence            34455667778999999999999987754 12222    25677778889999999999999987764322      234


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhcccccccccccc-cCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC----cH
Q 041804          103 SYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLV-EMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK----DL  177 (403)
Q Consensus       103 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~  177 (403)
                      ++..+...+...|++++|...+++........+.. .+....++..+...+...|++++|...+++........    ..
T Consensus        95 ~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  174 (373)
T 1hz4_A           95 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  174 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHH
Confidence            46778888999999999999998776532100000 02234566778888888999999999998876543221    23


Q ss_pred             HHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh-hhHH-----HHHHHHhhcCCHHHHHHHHHHHHHcCCCC---CHH
Q 041804          178 HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV-VAYN-----TVIRAVGVSEGVDFAMRVYREMREMGCQP---SVV  248 (403)
Q Consensus       178 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~-----~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~  248 (403)
                      .++..+...+...|++++|...+++.......++. ..+.     ..+..+...|+++.|...++........+   ...
T Consensus       175 ~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~  254 (373)
T 1hz4_A          175 QCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQG  254 (373)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHH
Confidence            46777778888888888888888887654212111 1111     22234667888888888887766432211   122


Q ss_pred             HHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCch-hhHHHHHHHHHhc
Q 041804          249 TCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKM-DTYVMLLRKFGRW  327 (403)
Q Consensus       249 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~li~~~~~~  327 (403)
                      .+..+...+...|++++|...+++.....                            ...+..++. ..+..+..++...
T Consensus       255 ~~~~la~~~~~~g~~~~A~~~l~~a~~~~----------------------------~~~~~~~~~~~~~~~la~~~~~~  306 (373)
T 1hz4_A          255 QWRNIARAQILLGEFEPAEIVLEELNENA----------------------------RSLRLMSDLNRNLLLLNQLYWQA  306 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH----------------------------HHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHH----------------------------HhCcchhhHHHHHHHHHHHHHHh
Confidence            45566677777788888877777654320                            011111111 2444556667777


Q ss_pred             CCcchHHHHHHHHHh
Q 041804          328 GFLRPVFVVWKKMEE  342 (403)
Q Consensus       328 g~~~~a~~~~~~~~~  342 (403)
                      |+.++|...+++...
T Consensus       307 g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          307 GRKSDAQRVLLDALK  321 (373)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            888888877777654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.45  E-value=2.2e-11  Score=106.12  Aligned_cols=301  Identities=9%  Similarity=-0.078  Sum_probs=198.9

Q ss_pred             cccccHHHHHHhhhhhcccC-CC--cCCHHhHHHHHHHH--HccCChhHHH---------HHHHHhhhCCCCCCCH----
Q 041804            6 CYANDWKRALEFFNWVETDC-HF--THTTDTYNSVIDIL--GKFFEFDLSW---------NLIHRMKDNPSSIPNH----   67 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~-~~--~~~~~~~~~li~~~--~~~~~~~~a~---------~~~~~~~~~~~~~~~~----   67 (403)
                      ..++++++|.++++.+.+.. ..  ..+...|..++..-  .-.+.+..+.         +.++.+....  .+..    
T Consensus        23 i~~~~~~~A~~l~~~i~~~~~~~~~~~~~~~yy~l~~~r~~~~~~~~~~~~~~~~~~~~~~~l~~i~~~~--~~~~~~l~  100 (378)
T 3q15_A           23 IRQFSVPDAEILKAEVEQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLETIETPQ--KKLTGLLK  100 (378)
T ss_dssp             HHTTCHHHHHHHHHHHHHHGGGBCCCHHHHHHHHHHHHHHHHHHHTCCC--------CHHHHHHHHHGGG--HHHHHHHH
T ss_pred             HHHcCHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHhhcCcccccccccchHHHHHHHhccC--CCCccHHH
Confidence            45788999999998875421 11  22334445544431  1123333333         6666665422  1111    


Q ss_pred             -HHHHHHHHHHHhcCChHHHHHHHHHHhhcCC-----C-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           68 -ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL-----K-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        68 -~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                       ..+......+...|++++|+..|++..+...     + ...++..+..+|...|+++.|...+.+..............
T Consensus       101 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~  180 (378)
T 3q15_A          101 YYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIR  180 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHH
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhh
Confidence             1233455667889999999999999876521     1 55688899999999999999999988776532110000112


Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHHHHHhC----CCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc----CCCCC
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWEEMDKR----GVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK----GIKMD  211 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~  211 (403)
                      ...+++.+...|...|++++|.+.|++..+.    +.. ....++..+..+|...|++++|...+++..+.    +.+..
T Consensus       181 ~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~  260 (378)
T 3q15_A          181 TIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLL  260 (378)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhH
Confidence            4567889999999999999999999887653    111 12357888999999999999999999998872    22333


Q ss_pred             hhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHHHhcCc---HHHHHHHHHhchhcCCCCChhh
Q 041804          212 VVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ----PSVVTCNTVIKLLCENGR---VREAYAVLAEMPKKGCVPDVIT  284 (403)
Q Consensus       212 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~p~~~~  284 (403)
                      ..++..+...+.+.|++++|...+++..+....    .....+..+...|...++   ..+|...+++...   .     
T Consensus       261 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~---~-----  332 (378)
T 3q15_A          261 PKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNL---H-----  332 (378)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTC---H-----
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCC---h-----
Confidence            667888999999999999999999999875321    123344555555556666   5555555544211   0     


Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHh
Q 041804          285 YHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEE  342 (403)
Q Consensus       285 ~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  342 (403)
                                                ......+..+...|...|++++|...|++..+
T Consensus       333 --------------------------~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          333 --------------------------AYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             --------------------------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             --------------------------hHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                                      01123455677788888888888888887754

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.44  E-value=1.2e-09  Score=101.04  Aligned_cols=357  Identities=8%  Similarity=-0.026  Sum_probs=232.8

Q ss_pred             HHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC---hHHHHH
Q 041804           12 KRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL---VNEAMG   88 (403)
Q Consensus        12 ~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~   88 (403)
                      .+.+..|+.....  .+.|...|..++..+.+.+.++.+..+|+++...-  +.+...|..-+..-.+.++   ++.+.+
T Consensus        49 ~d~i~~lE~~l~~--np~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~f--P~~~~lW~~Yi~~E~~~~~~~~~~~v~~  124 (679)
T 4e6h_A           49 SDVIGKLNDMIEE--QPTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDRF--PLMANIWCMRLSLEFDKMEELDAAVIEP  124 (679)
T ss_dssp             SCHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTC--CCCHHHHHH
T ss_pred             HHHHHHHHHHHHH--CcCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHhhCCcchHHHHHH
Confidence            3344455554432  35689999999999999999999999999999874  5677889988988888888   999999


Q ss_pred             HHHHHhhcCC--CcHHHHHHHHHHHHhcCCH--------HHHHHHHhccccccccccccc--CcchHHHHHHHHHHHh--
Q 041804           89 TFNKLDEFGL--KDEVSYCNLVDALCEYKHV--------IEAQELCFGENKNVGFSGLVE--MNKTKIYNMILRGWFK--  154 (403)
Q Consensus        89 ~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~--------~~a~~~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~--  154 (403)
                      +|++.....+  ++...|...+....+.++.        +...++|+......     |.  ..+...|...+.....  
T Consensus       125 lfeRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~v-----G~~d~~s~~iW~~Yi~f~~~~~  199 (679)
T 4e6h_A          125 VLARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKC-----AIFEPKSIQFWNEYLHFLEHWK  199 (679)
T ss_dssp             HHHHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHT-----TTTCSSCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHh-----CcccccchHHHHHHHHHHHhcc
Confidence            9999998874  5777888888776665543        33446777665543     32  2345677777765442  


Q ss_pred             -------cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH-------------cCChhH-------------------
Q 041804          155 -------MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK-------------SGKPWK-------------------  195 (403)
Q Consensus       155 -------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------------~~~~~~-------------------  195 (403)
                             .++++.+.++|++........-..+|......-..             ..+++.                   
T Consensus       200 ~~~~~eeq~~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~  279 (679)
T 4e6h_A          200 PVNKFEEQQRVQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNL  279 (679)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCC
T ss_pred             ccCcHHHHhHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhcc
Confidence                   33456677777777653111111222111110000             001111                   


Q ss_pred             ------------------------------------------------HHHHHHHHHHcCCCCChhhHHHHHHHHhhcCC
Q 041804          196 ------------------------------------------------AVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG  227 (403)
Q Consensus       196 ------------------------------------------------a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  227 (403)
                                                                      +..+|++.... .+-+...|-..+..+...|+
T Consensus       280 p~~~~~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~  358 (679)
T 4e6h_A          280 PITLNQATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNT  358 (679)
T ss_dssp             CSSSTTCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSC
T ss_pred             ccccccchhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCc
Confidence                                                            22233333332 12233444445555556778


Q ss_pred             HHHHH-HHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcC---------CCCC------------hhhH
Q 041804          228 VDFAM-RVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKG---------CVPD------------VITY  285 (403)
Q Consensus       228 ~~~a~-~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~---------~~p~------------~~~~  285 (403)
                      .+.|. .+|+..... .+.+...|-..+...-+.|+++.|..+|+.+....         -.|+            ...|
T Consensus       359 ~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vW  437 (679)
T 4e6h_A          359 DSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVY  437 (679)
T ss_dssp             CTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHH
Confidence            88886 999998875 34466677778888889999999999999887531         0132            1234


Q ss_pred             HHHHH---hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhc-CCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Q 041804          286 HCFFR---CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRW-GFLRPVFVVWKKMEELGCSPDEFAYNALVDALID  361 (403)
Q Consensus       286 ~~l~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~-g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (403)
                      ...+.   ..+..+.|..+|.+..+....+....|...+..-.+. ++++.|..+|+...+. ++.+...|..+++....
T Consensus       438 i~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~fe~~  516 (679)
T 4e6h_A          438 CVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-FATDGEYINKYLDFLIY  516 (679)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCchHHHHHHHHHHHh
Confidence            43333   3366789999999998761112233444333333344 4589999999999876 45577788899998899


Q ss_pred             cCCHHHHHHHHHHHHHcCC
Q 041804          362 KGMLDMARKYDEEMFAKGL  380 (403)
Q Consensus       362 ~g~~~~a~~~~~~m~~~~~  380 (403)
                      .|+.+.|..+|++.+....
T Consensus       517 ~~~~~~AR~lferal~~~~  535 (679)
T 4e6h_A          517 VNEESQVKSLFESSIDKIS  535 (679)
T ss_dssp             HTCHHHHHHHHHHHTTTSS
T ss_pred             CCCHHHHHHHHHHHHHhcC
Confidence            9999999999999887654

>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=99.42  E-value=5.5e-11  Score=95.73  Aligned_cols=196  Identities=8%  Similarity=-0.039  Sum_probs=156.5

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      .++..+......+...|++++|+..|++..+.. .+++...+..+..++...|++++|+..|++..+..+.+..++..+.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLT-NNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHH
Confidence            466888999999999999999999999999875 2267788888999999999999999999999999988999999999


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccCcch-------HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCc---HH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEMNKT-------KIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKD---LH  178 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~  178 (403)
                      .++...|++++|...+++....       .+.+.       .+|..+...+...|++++|.+.|++..+.  .|+   ..
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~-------~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~  154 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKA-------VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTD  154 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-------STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHH-------CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHH
Confidence            9999999999999999998873       23444       56888889999999999999999999886  344   46


Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      .|..+..+|...|     ...++.+...+ ..+...|....  ....+.+++|...+++..+..
T Consensus       155 ~~~~l~~~~~~~~-----~~~~~~a~~~~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~  210 (228)
T 4i17_A          155 ALYSLGVLFYNNG-----ADVLRKATPLA-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTLS  210 (228)
T ss_dssp             HHHHHHHHHHHHH-----HHHHHHHGGGT-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHH-----HHHHHHHHhcc-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcC
Confidence            7777777776554     33445555443 22344443333  234567899999999999874

>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=99.42  E-value=4.3e-12  Score=105.65  Aligned_cols=233  Identities=11%  Similarity=-0.026  Sum_probs=160.9

Q ss_pred             cccHHHHHHhhhhhcc------cCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhC------CCCCCCHHHHHHHHH
Q 041804            8 ANDWKRALEFFNWVET------DCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN------PSSIPNHATFRIMFK   75 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~------~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~~~~~~l~~   75 (403)
                      .|++++|++.|+....      ....+....++..+..++...|++++|...+++..+.      +..+....++..+..
T Consensus        14 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~   93 (283)
T 3edt_B           14 LVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAV   93 (283)
T ss_dssp             CSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHH
Confidence            4666666666665553      1122345678999999999999999999999988764      211234568899999


Q ss_pred             HHHhcCChHHHHHHHHHHhhcC--------CCcHHHHHHHHHHHHhcCCHHHHHHHHhccccccccc-ccccCcchHHHH
Q 041804           76 RYVTAHLVNEAMGTFNKLDEFG--------LKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFS-GLVEMNKTKIYN  146 (403)
Q Consensus        76 ~~~~~~~~~~a~~~~~~~~~~~--------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~  146 (403)
                      +|...|++++|+..|++..+..        +....++..+..++...|++++|...+++........ +...+....++.
T Consensus        94 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  173 (283)
T 3edt_B           94 LYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKN  173 (283)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence            9999999999999999988761        2267889999999999999999999998877631000 001344567889


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhC-------CCCCc-HHHHHHHHHHHHHcCChhHHHHHHHHHHH---c-C--CCCCh
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKR-------GVVKD-LHSYSIYMDIMCKSGKPWKAVKLYKEMKK---K-G--IKMDV  212 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~-~--~~~~~  212 (403)
                      .+...|...|++++|.+.+++..+.       ...+. ...|..+...+...+....+.. +.....   . +  .+...
T Consensus       174 ~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  252 (283)
T 3edt_B          174 NLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAP-YGEYGSWYKACKVDSPTVN  252 (283)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC-------------CCCCCCHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHH-HHHHHHHHHhcCCCCHHHH
Confidence            9999999999999999999988753       11222 2334444444443333333322 222211   1 1  12234


Q ss_pred             hhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          213 VAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       213 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      .++..+...|...|++++|..++++..+.
T Consensus       253 ~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          253 TTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            57888899999999999999999988753

>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=99.40  E-value=7.4e-11  Score=94.98  Aligned_cols=204  Identities=13%  Similarity=-0.013  Sum_probs=159.7

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC-CcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL-KDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      .++..+......+...|++++|+..|++..+..+ ++...+..+..++...|++++|...+++...       ..+.+..
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~-------~~p~~~~   77 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIK-------KNYNLAN   77 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------TTCSHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHH-------hCcchHH
Confidence            5678889999999999999999999999999998 6888888899999999999999999999887       4456788


Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH-------HHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC---hh
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL-------HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD---VV  213 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~  213 (403)
                      ++..+...|...|++++|.+.|++..+..+. +.       ..|..+...+...|++++|+..|++..+.  .|+   ..
T Consensus        78 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~  154 (228)
T 4i17_A           78 AYIGKSAAYRDMKNNQEYIATLTEGIKAVPG-NATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTD  154 (228)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHH
Confidence            8999999999999999999999999887654 44       56888888999999999999999999876  444   45


Q ss_pred             hHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHH
Q 041804          214 AYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCF  288 (403)
Q Consensus       214 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l  288 (403)
                      .+..+..+|...|     ..+++.+...+. .+...|....  ....+.+++|...|++..+.  .|+......+
T Consensus       155 ~~~~l~~~~~~~~-----~~~~~~a~~~~~-~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l--~p~~~~~~~~  219 (228)
T 4i17_A          155 ALYSLGVLFYNNG-----ADVLRKATPLAS-SNKEKYASEK--AKADAAFKKAVDYLGEAVTL--SPNRTEIKQM  219 (228)
T ss_dssp             HHHHHHHHHHHHH-----HHHHHHHGGGTT-TCHHHHHHHH--HHHHHHHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHHHHHHHHH-----HHHHHHHHhccc-CCHHHHHHHH--HHHHHHHHHHHHHHHHHhhc--CCCCHHHHHH
Confidence            6666766765443     344555554432 2344444433  33467789999999998875  4654444333

>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=99.40  E-value=1.4e-11  Score=102.45  Aligned_cols=232  Identities=13%  Similarity=0.019  Sum_probs=159.0

Q ss_pred             HccCChhHHHHHHHHhhh-------CCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhc------C-CC-cHHHHHH
Q 041804           42 GKFFEFDLSWNLIHRMKD-------NPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEF------G-LK-DEVSYCN  106 (403)
Q Consensus        42 ~~~~~~~~a~~~~~~~~~-------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~-~~-~~~~~~~  106 (403)
                      ...|++++|+.++++..+       .. .+....++..+...|...|++++|+..|++..+.      + .+ ...++..
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~   90 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHD-HPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNN   90 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSS-SHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHH
Confidence            345677777776666554       12 1234668899999999999999999999998865      2 22 7788999


Q ss_pred             HHHHHHhcCCHHHHHHHHhccccccccc-ccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC------CCCC-cHH
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNVGFS-GLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR------GVVK-DLH  178 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~  178 (403)
                      +..++...|++++|...+.+........ +...+....++..+...|...|++++|.+.+++..+.      +..| ...
T Consensus        91 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  170 (283)
T 3edt_B           91 LAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAK  170 (283)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHH
Confidence            9999999999999999998876531000 0012455778899999999999999999999988765      1122 456


Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHc-------CCCCChh-hHHHHHHHHhhcCCHH------HHHHHHHHHHHcCCC
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKK-------GIKMDVV-AYNTVIRAVGVSEGVD------FAMRVYREMREMGCQ  244 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~-~~~~ll~~~~~~~~~~------~a~~~~~~~~~~~~~  244 (403)
                      ++..+..+|...|++++|...+++..+.       ...+... .+..+...+...+...      .+...++.... ..+
T Consensus       171 ~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~  249 (283)
T 3edt_B          171 TKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV-DSP  249 (283)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC-CCH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC-CCH
Confidence            7888999999999999999999998764       1222322 3333333332222222      22222211111 111


Q ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          245 PSVVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       245 ~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      ....++..+...|...|++++|..+|++..+
T Consensus       250 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          250 TVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2345788889999999999999999998764

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.34  E-value=1.3e-11  Score=92.02  Aligned_cols=146  Identities=10%  Similarity=0.005  Sum_probs=119.1

Q ss_pred             CcccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhc
Q 041804            1 RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTA   80 (403)
Q Consensus         1 L~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   80 (403)
                      |+.++..+|++++|+..++....  ..+.++..+..+..+|.+.|++++|++.|++..+..  +.+..+|..+..+|...
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~--~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~   78 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTP--SPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ--ERDPKAHRFLGLLYELE   78 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSC--SHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHcChHHHHHHHHHHhcc--cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHc
Confidence            67889999999999999998874  223346677789999999999999999999999875  45788999999999999


Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHH-HhcccccccccccccCcchHHHHHHHHHHHhcCC
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQEL-CFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW  157 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  157 (403)
                      |++++|+..|++..+..+.+..++..+..++.+.|+.+++... +++..+       ..|.+..+|......+...|+
T Consensus        79 ~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~-------l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           79 ENTDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAK-------LFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHH-------HSTTCHHHHHHHHHHHHTCCC
T ss_pred             CchHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHH-------hCcCCHHHHHHHHHHHHHhCc
Confidence            9999999999999999988999999999999999998776654 466665       335567777777777666654

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.30  E-value=2.3e-10  Score=94.13  Aligned_cols=189  Identities=8%  Similarity=-0.087  Sum_probs=126.1

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVS  103 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~  103 (403)
                      +.+...+..+...+.+.|++++|+..|+.+.+..+..|. ..++..+..+|...|++++|+..|++..+..+.   ...+
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            345778888899999999999999999999987511111 678889999999999999999999999998664   4667


Q ss_pred             HHHHHHHHHh--------cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 041804          104 YCNLVDALCE--------YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK  175 (403)
Q Consensus       104 ~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  175 (403)
                      +..+..++..        .|++++|...|+++....       +.+......+              ..+..+...    
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-------p~~~~~~~a~--------------~~~~~~~~~----  146 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY-------PNHELVDDAT--------------QKIRELRAK----  146 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC-------TTCTTHHHHH--------------HHHHHHHHH----
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC-------cCchhHHHHH--------------HHHHHHHHH----
Confidence            8888889988        999999999999887642       2222222111              111111100    


Q ss_pred             cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCC--ChhhHHHHHHHHhhc----------CCHHHHHHHHHHHHHc
Q 041804          176 DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKM--DVVAYNTVIRAVGVS----------EGVDFAMRVYREMREM  241 (403)
Q Consensus       176 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~ll~~~~~~----------~~~~~a~~~~~~~~~~  241 (403)
                      -...+..+..+|...|++++|+..|+.+.+.....  ....+..+..+|...          |++++|...|+.+.+.
T Consensus       147 ~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          147 LARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            11124455556666666666666666666542111  123444555555544          6666666666666665

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.29  E-value=4.4e-10  Score=92.48  Aligned_cols=195  Identities=11%  Similarity=-0.016  Sum_probs=145.9

Q ss_pred             CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc---HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           64 IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD---EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                      +.+...+..+...+.+.|++++|+..|+++.+..+.+   ..++..+..++...|++++|...|++.....+    ..+.
T Consensus        12 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p----~~~~   87 (261)
T 3qky_A           12 HSSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQ----IDPR   87 (261)
T ss_dssp             CSSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT----TCTT
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCC----CCch
Confidence            3567788888999999999999999999999988766   78899999999999999999999999887421    1223


Q ss_pred             chHHHHHHHHHHHh--------cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh
Q 041804          141 KTKIYNMILRGWFK--------MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV  212 (403)
Q Consensus       141 ~~~~~~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  212 (403)
                      ...++..+..++..        .|++++|...|+++.+..+. +......+..              +......    -.
T Consensus        88 ~~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~a~~~--------------~~~~~~~----~~  148 (261)
T 3qky_A           88 VPQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPN-HELVDDATQK--------------IRELRAK----LA  148 (261)
T ss_dssp             HHHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTT-CTTHHHHHHH--------------HHHHHHH----HH
T ss_pred             hHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcC-chhHHHHHHH--------------HHHHHHH----HH
Confidence            35667788888888        99999999999999886543 2222222211              1111110    01


Q ss_pred             hhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHhc----------CcHHHHHHHHHhchhcCCCC
Q 041804          213 VAYNTVIRAVGVSEGVDFAMRVYREMREMGCQP--SVVTCNTVIKLLCEN----------GRVREAYAVLAEMPKKGCVP  280 (403)
Q Consensus       213 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~li~~~~~~----------g~~~~a~~~~~~~~~~~~~p  280 (403)
                      ..+..+...|.+.|+++.|...|+.+.+.....  ....+..+..+|...          |++++|...|+++.+.  .|
T Consensus       149 ~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~--~p  226 (261)
T 3qky_A          149 RKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI--FP  226 (261)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH--CT
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH--CC
Confidence            124567788999999999999999999874332  245677788888866          8999999999999876  45


Q ss_pred             Chh
Q 041804          281 DVI  283 (403)
Q Consensus       281 ~~~  283 (403)
                      +..
T Consensus       227 ~~~  229 (261)
T 3qky_A          227 DSP  229 (261)
T ss_dssp             TCT
T ss_pred             CCh
Confidence            543

>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=99.28  E-value=3.3e-10  Score=82.54  Aligned_cols=127  Identities=13%  Similarity=0.133  Sum_probs=54.7

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      ..+...+...|++++|+.+|+++.+.++.+...+..+...+...|++++|...++++...       .+.+...+..+..
T Consensus         5 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-------~~~~~~~~~~l~~   77 (136)
T 2fo7_A            5 YNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL-------DPRSAEAWYNLGN   77 (136)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-------CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHH-------CCCchHHHHHHHH
Confidence            334444444444444444444444443334444444444444444444444444443321       1222333444444


Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          151 GWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       151 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      .+...|++++|.+.++++.+.... +...+..+...+...|++++|...++++..
T Consensus        78 ~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           78 AYYKQGDYDEAIEYYQKALELDPR-SAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            444444444444444444443222 333444444444444444444444444443

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.27  E-value=2.4e-10  Score=90.42  Aligned_cols=162  Identities=6%  Similarity=-0.121  Sum_probs=84.8

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHH----------------HHHHHHhcCChHHHHHHHHHHhh
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRI----------------MFKRYVTAHLVNEAMGTFNKLDE   95 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~----------------l~~~~~~~~~~~~a~~~~~~~~~   95 (403)
                      .+......+...|++++|+..|++..+..   |+ ...|..                +..+|.+.|++++|+..|++..+
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~---p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   82 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIALN---IDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQ   82 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC---HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC---CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33344455566677777777776666643   32 334444                55566666666666666666666


Q ss_pred             cCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC--hhHHHHHHHHHHhCCC
Q 041804           96 FGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW--WGKCREFWEEMDKRGV  173 (403)
Q Consensus        96 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~  173 (403)
                      ..+.+...+..+..++...|++++|...|++...       ..|.+..++..+...|...|+  .+.+...+.....  .
T Consensus        83 ~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-------~~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~--~  153 (208)
T 3urz_A           83 KAPNNVDCLEACAEMQVCRGQEKDALRMYEKILQ-------LEADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSS--P  153 (208)
T ss_dssp             HCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---C--C
T ss_pred             HCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------cCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC--C
Confidence            6655666666666666666666666666665554       224445555555555544332  2233333333321  1


Q ss_pred             CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          174 VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       174 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      .|....+..+..++...|++++|...|++..+.
T Consensus       154 ~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l  186 (208)
T 3urz_A          154 TKMQYARYRDGLSKLFTTRYEKARNSLQKVILR  186 (208)
T ss_dssp             CHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT
T ss_pred             CchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            222223333344444555666666666655543

>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=99.27  E-value=2.8e-10  Score=82.90  Aligned_cols=132  Identities=11%  Similarity=0.114  Sum_probs=114.4

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL  111 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  111 (403)
                      ..+..+...+...|++++|..+++++.+..  +.+...+..+...+...|++++|...|+++...++.+...+..+...+
T Consensus         2 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~   79 (136)
T 2fo7_A            2 EAWYNLGNAYYKQGDYDEAIEYYQKALELD--PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAY   79 (136)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHcCcHHHHHHHHHHHHHcC--CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHH
Confidence            357778889999999999999999988764  356778888999999999999999999999988877888899999999


Q ss_pred             HhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 041804          112 CEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG  172 (403)
Q Consensus       112 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  172 (403)
                      ...|++++|...++++...       .+.+..++..+...+...|++++|.+.++++.+.+
T Consensus        80 ~~~~~~~~A~~~~~~~~~~-------~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  133 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALEL-------DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD  133 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHS
T ss_pred             HHhcCHHHHHHHHHHHHHh-------CCCChHHHHHHHHHHHHHccHHHHHHHHHHHHccC
Confidence            9999999999999888763       34567788889999999999999999999987653

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.26  E-value=5.6e-09  Score=85.90  Aligned_cols=145  Identities=8%  Similarity=-0.001  Sum_probs=71.3

Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      |+..|++..+.+.++..++..+..++...|++++|++++.+.....     ....+...+..++..+.+.|+.+.|.+.+
T Consensus        85 a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~-----~~~~~lea~~l~vqi~L~~~r~d~A~k~l  159 (310)
T 3mv2_B           85 NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGIDND-----EAEGTTELLLLAIEVALLNNNVSTASTIF  159 (310)
T ss_dssp             CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSS-----CSTTHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-----CCcCcHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4555555554443333444455555555666666666655543320     00234455555556666666666666666


Q ss_pred             HHHHhCCCCC-----cHHHHHHHHHH--HHHcC--ChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHH
Q 041804          166 EEMDKRGVVK-----DLHSYSIYMDI--MCKSG--KPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYR  236 (403)
Q Consensus       166 ~~~~~~~~~~-----~~~~~~~l~~~--~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~  236 (403)
                      ++|.+.  .|     +..+...+..+  ....|  ++++|..+|+++.+.  .|+..+-..++.++.+.|++++|...++
T Consensus       160 ~~~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~  235 (310)
T 3mv2_B          160 DNYTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVE  235 (310)
T ss_dssp             HHHHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHH
Confidence            665543  22     13334444433  22223  556666666665443  2332222333335555666666666665


Q ss_pred             HHH
Q 041804          237 EMR  239 (403)
Q Consensus       237 ~~~  239 (403)
                      .+.
T Consensus       236 ~l~  238 (310)
T 3mv2_B          236 LLL  238 (310)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.23  E-value=8e-09  Score=84.99  Aligned_cols=175  Identities=9%  Similarity=-0.014  Sum_probs=105.2

Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC-CCChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          161 CREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI-KMDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      |...|++..+.+ .++..++..+..++...|++++|++++.+.+..+. .-+...+..++..+.+.|+.+.|.+.++.|.
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            566677666554 33455556777777778888888888877765542 1245566677777788888888888888877


Q ss_pred             HcCCCC-----CHHHHHHHHHH--HHhcC--cHHHHHHHHHhchhcCCCCCh----hhHHHHHHhhCCHHHHHHHHHHHH
Q 041804          240 EMGCQP-----SVVTCNTVIKL--LCENG--RVREAYAVLAEMPKKGCVPDV----ITYHCFFRCLEKPREILGLFDRMI  306 (403)
Q Consensus       240 ~~~~~~-----~~~~~~~li~~--~~~~g--~~~~a~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~~~a~~~~~~~~  306 (403)
                      +.  .|     +..+...+..+  ....|  +..+|..+|+++.+.  .|+.    ..++ .....+++++|.+.++.+.
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--FPTWKTQLGLLN-LHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             HH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHH-HHHHHTCHHHHHHHHHHHH
T ss_pred             hc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHH-HHHHcCCHHHHHHHHHHHH
Confidence            65  34     23444444444  22223  777788888877654  3331    2233 2223366667766666554


Q ss_pred             HcC---------CCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhc
Q 041804          307 ESG---------IRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEEL  343 (403)
Q Consensus       307 ~~~---------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  343 (403)
                      +..         -+-++.++..+|......|+  +|.++++++.+.
T Consensus       239 ~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~  282 (310)
T 3mv2_B          239 SDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL  282 (310)
T ss_dssp             SHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT
T ss_pred             HhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh
Confidence            321         02245555455555555665  677777777765

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.23  E-value=5.9e-10  Score=88.17  Aligned_cols=187  Identities=10%  Similarity=0.046  Sum_probs=108.0

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHH
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYN  146 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (403)
                      ...+......+...|++++|+..|++..+..+.+...+...-                  ...       ..........
T Consensus         4 ~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~------------------~~~-------~~~~~~~~~~   58 (208)
T 3urz_A            4 VDEMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTN------------------VDK-------NSEISSKLAT   58 (208)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHH------------------SCT-------TSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhh------------------hcc-------hhhhhHHHHH
Confidence            344555667788999999999999999988766666555410                  000       1112223344


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcC
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSE  226 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  226 (403)
                      .+...|.+.|++++|...|++..+..+. +...+..+..++...|++++|...|++..+.. +-+..++..+..+|...+
T Consensus        59 ~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~  136 (208)
T 3urz_A           59 ELALAYKKNRNYDKAYLFYKELLQKAPN-NVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYLTA  136 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHHh
Confidence            5666666677777777777766666554 56666666677777777777777777766653 334555666655554443


Q ss_pred             C--HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhh
Q 041804          227 G--VDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVIT  284 (403)
Q Consensus       227 ~--~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~  284 (403)
                      +  ...+...++....  ..|....+.....++...|++++|...|++..+.  .|+...
T Consensus       137 ~~~~~~~~~~~~~~~~--~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l--~P~~~~  192 (208)
T 3urz_A          137 EQEKKKLETDYKKLSS--PTKMQYARYRDGLSKLFTTRYEKARNSLQKVILR--FPSTEA  192 (208)
T ss_dssp             HHHHHHHHHHHC---C--CCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTT--SCCHHH
T ss_pred             HHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCHHH
Confidence            2  2334444444321  1222223333445555566777777777776654  455443

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.23  E-value=1.8e-10  Score=107.94  Aligned_cols=153  Identities=7%  Similarity=-0.168  Sum_probs=77.8

Q ss_pred             HccCChhHHHHHHHHhh--------hCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           42 GKFFEFDLSWNLIHRMK--------DNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        42 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      ...|++++|++.+++..        +..  +.+...+..+..++...|++++|+..|++..+.++.+...|..+..++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~--p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF--SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC--TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc--ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHH
Confidence            44555555555555554        222  22334455555555555555555555555555554455555555555555


Q ss_pred             cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCCh
Q 041804          114 YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKP  193 (403)
Q Consensus       114 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  193 (403)
                      .|++++|...|++...       ..+.+...+..+..+|.+.|++++ .+.|++..+.++. +...|..+..++.+.|++
T Consensus       480 ~g~~~~A~~~~~~al~-------l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~  550 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLD-------TFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDG-VISAAFGLARARSAEGDR  550 (681)
T ss_dssp             HTCHHHHHHHHHHHHH-------HSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             cCCHHHHHHHHHHHHH-------hCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCc-hHHHHHHHHHHHHHcCCH
Confidence            5555555555555444       223344445555555555555555 5555555544433 444555555555555555


Q ss_pred             hHHHHHHHHHHH
Q 041804          194 WKAVKLYKEMKK  205 (403)
Q Consensus       194 ~~a~~~~~~~~~  205 (403)
                      ++|++.|++..+
T Consensus       551 ~~A~~~~~~al~  562 (681)
T 2pzi_A          551 VGAVRTLDEVPP  562 (681)
T ss_dssp             HHHHHHHHTSCT
T ss_pred             HHHHHHHHhhcc
Confidence            555555554443

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.23  E-value=1.3e-08  Score=84.65  Aligned_cols=224  Identities=6%  Similarity=-0.054  Sum_probs=181.4

Q ss_pred             HHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC--ChHHHHHHHHHHhhcCCCcHHHHHHHHHHH----Hhc
Q 041804           41 LGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH--LVNEAMGTFNKLDEFGLKDEVSYCNLVDAL----CEY  114 (403)
Q Consensus        41 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~----~~~  114 (403)
                      ..+....++|+.+++.+...+  +-+..+|+.--.++...+  ++++++.+++.+....+.+..+|+.-..++    ...
T Consensus        43 ~~~~e~s~~aL~~t~~~L~~n--P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l  120 (306)
T 3dra_A           43 MKAEEYSERALHITELGINEL--ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELN  120 (306)
T ss_dssp             HHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHT
T ss_pred             HHcCCCCHHHHHHHHHHHHHC--cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhc
Confidence            334444579999999999876  345678999888888888  999999999999999988888888776666    555


Q ss_pred             ---CCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChh--HHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          115 ---KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWG--KCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       115 ---~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                         +++++++..++++..       ..+.+..+|+.-.-...+.|.++  ++++.++++.+.++. |..+|+.-...+..
T Consensus       121 ~~~~~~~~EL~~~~~~l~-------~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll~~  192 (306)
T 3dra_A          121 NNDFDPYREFDILEAMLS-------SDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK-NNSAWSHRFFLLFS  192 (306)
T ss_dssp             TTCCCTHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHS
T ss_pred             cccCCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHh
Confidence               788999999998887       55788899999888888899888  999999999998887 88899888777777


Q ss_pred             cCC------hhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHH-HHHHHHHHHHcC--CCCCHHHHHHHHHHHHhc
Q 041804          190 SGK------PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDF-AMRVYREMREMG--CQPSVVTCNTVIKLLCEN  260 (403)
Q Consensus       190 ~~~------~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~li~~~~~~  260 (403)
                      .+.      ++++++.++.+.... +-|...|+.+-..+.+.|+... +..+...+.+.+  -..+...+..+...|.+.
T Consensus       193 l~~~~~~~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~  271 (306)
T 3dra_A          193 KKHLATDNTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQ  271 (306)
T ss_dssp             SGGGCCHHHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHT
T ss_pred             ccccchhhhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHcc
Confidence            776      888999999988875 4588888888888877777433 445555554432  134678888899999999


Q ss_pred             CcHHHHHHHHHhchh
Q 041804          261 GRVREAYAVLAEMPK  275 (403)
Q Consensus       261 g~~~~a~~~~~~~~~  275 (403)
                      |+.++|.++++.+.+
T Consensus       272 ~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          272 KKYNESRTVYDLLKS  286 (306)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHh
Confidence            999999999999875

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.22  E-value=6.2e-11  Score=88.39  Aligned_cols=146  Identities=10%  Similarity=-0.079  Sum_probs=97.1

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH  116 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  116 (403)
                      |..++...|++++|+..+.......  +.+...+..+...|.+.|++++|++.|++..+..+.+..+|..+..++...|+
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~~~--p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTPSP--RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSCSH--HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHcChHHHHHHHHHHhcccC--cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCc
Confidence            3445556677778877777776643  12234556677778888888888888888887777777788888888888888


Q ss_pred             HHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHH-HHHHHhCCCCCcHHHHHHHHHHHHHcCC
Q 041804          117 VIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREF-WEEMDKRGVVKDLHSYSIYMDIMCKSGK  192 (403)
Q Consensus       117 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~  192 (403)
                      +++|...|++...       ..+.+..++..+...|.+.|++++|.+. +++..+..+. +..+|......+...|+
T Consensus        81 ~~~A~~~~~~al~-------~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~-~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           81 TDKAVECYRRSVE-------LNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPG-SPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTCCC
T ss_pred             hHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHhCc
Confidence            8888877777665       3345566777777777777777665544 4666665544 55666666555555543

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.20  E-value=4.9e-08  Score=87.50  Aligned_cols=342  Identities=7%  Similarity=-0.006  Sum_probs=218.1

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCC-hhHHHHHHHHhhhCCC-CCCCHHHHHHHHHHHH----hcCC
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFE-FDLSWNLIHRMKDNPS-SIPNHATFRIMFKRYV----TAHL   82 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~~~~~~~-~~~~~~~~~~l~~~~~----~~~~   82 (403)
                      ++++.+..+|+....   ..|+...|...+....+.++ .+....+|+.....-+ .+++...|...+..+.    ..++
T Consensus        28 ~~~e~~~~iferal~---~~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~  104 (493)
T 2uy1_A           28 KDYRSLESLFGRCLK---KSYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTR  104 (493)
T ss_dssp             TCHHHHHHHHHHHST---TCCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHH
T ss_pred             CCHHHHHHHHHHHhc---cCCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHH
Confidence            678899999988875   35799999998888877764 4667788887776421 2356778888777654    3467


Q ss_pred             hHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhc-------------CCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           83 VNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEY-------------KHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~-------------~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .+.+.++|++....+.. -...|......-...             +.+..|..++......      ....+...|...
T Consensus       105 ~~~vR~iy~rAL~~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~------~~~~s~~~W~~y  178 (493)
T 2uy1_A          105 IEKIRNGYMRALQTPMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPL------IRGWSVKNAARL  178 (493)
T ss_dssp             HHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHTCSHHHHHHH
T ss_pred             HHHHHHHHHHHHhChhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHH------HhhccHHHHHHH
Confidence            88899999999886444 333333332221111             1222333333333221      001123355555


Q ss_pred             HHHHHhcC--C-----hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHH
Q 041804          149 LRGWFKMS--W-----WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRA  221 (403)
Q Consensus       149 ~~~~~~~~--~-----~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~  221 (403)
                      +..-...+  -     .+.+..+|+++....+. +...|...+..+...|+++.|..+|++....  +.+...+.    .
T Consensus       179 ~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~p~-~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~----~  251 (493)
T 2uy1_A          179 IDLEMENGMKLGGRPHESRMHFIHNYILDSFYY-AEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSL----Y  251 (493)
T ss_dssp             HHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHH----H
T ss_pred             HHHHhcCCccCcchhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHH----H
Confidence            44432221  1     34567789988876544 6788999999999999999999999999988  33333332    2


Q ss_pred             HhhcCCHHHHHHHHHHHHHcC------------CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHH--H
Q 041804          222 VGVSEGVDFAMRVYREMREMG------------CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYH--C  287 (403)
Q Consensus       222 ~~~~~~~~~a~~~~~~~~~~~------------~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~--~  287 (403)
                      |+...+.+..   ++.+.+.-            .......|...+..+.+.++.+.|..+|++. ... ..+...|.  +
T Consensus       252 y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~-~~~~~v~i~~A  326 (493)
T 2uy1_A          252 YGLVMDEEAV---YGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNE-GVGPHVFIYCA  326 (493)
T ss_dssp             HHHHTTCTHH---HHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTS-CCCHHHHHHHH
T ss_pred             HHhhcchhHH---HHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCC-CCChHHHHHHH
Confidence            3222221221   23332210            0112345667777777788899999999998 321 12333332  2


Q ss_pred             HHH-hhC-CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCH
Q 041804          288 FFR-CLE-KPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGML  365 (403)
Q Consensus       288 l~~-~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  365 (403)
                      .+. .++ +.+.|..+|+...+.... ++..+...+....+.|+.+.|..+|+++.     .....|...+..-...|+.
T Consensus       327 ~lE~~~~~d~~~ar~ife~al~~~~~-~~~~~~~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~  400 (493)
T 2uy1_A          327 FIEYYATGSRATPYNIFSSGLLKHPD-STLLKEEFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSM  400 (493)
T ss_dssp             HHHHHHHCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCH
T ss_pred             HHHHHHCCChHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCH
Confidence            222 223 588999999999875422 34456667777788999999999999973     3578899999888889999


Q ss_pred             HHHHHHHHHHHH
Q 041804          366 DMARKYDEEMFA  377 (403)
Q Consensus       366 ~~a~~~~~~m~~  377 (403)
                      +.+..++++...
T Consensus       401 ~~~r~v~~~~~~  412 (493)
T 2uy1_A          401 ELFRELVDQKMD  412 (493)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999988875

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.20  E-value=2.9e-10  Score=87.39  Aligned_cols=159  Identities=13%  Similarity=-0.023  Sum_probs=78.8

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHH
Q 041804           72 IMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG  151 (403)
Q Consensus        72 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (403)
                      .+...+...|++++|+..|++..+..+.+...+..+..++...|++++|...+++....       .+ +...+..+...
T Consensus        11 ~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~-------~p-~~~~~~~~~~~   82 (176)
T 2r5s_A           11 KQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLE-------YQ-DNSYKSLIAKL   82 (176)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG-------GC-CHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc-------cC-ChHHHHHHHHH
Confidence            34444555555555555555555544445555555555555555555555555554432       11 22222111111


Q ss_pred             -HHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCC-ChhhHHHHHHHHhhcCCHH
Q 041804          152 -WFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKM-DVVAYNTVIRAVGVSEGVD  229 (403)
Q Consensus       152 -~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~ll~~~~~~~~~~  229 (403)
                       +...+....|...+++..+..+. +...+..+..++...|++++|...|+++.+....+ +...+..+...+...|+.+
T Consensus        83 ~~~~~~~~~~a~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  161 (176)
T 2r5s_A           83 ELHQQAAESPELKRLEQELAANPD-NFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGN  161 (176)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSC
T ss_pred             HHHhhcccchHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCC
Confidence             11112223345555555554433 45555566666666666666666666655543221 2335555556666666666


Q ss_pred             HHHHHHHHHH
Q 041804          230 FAMRVYREMR  239 (403)
Q Consensus       230 ~a~~~~~~~~  239 (403)
                      +|...|+...
T Consensus       162 ~A~~~y~~al  171 (176)
T 2r5s_A          162 AIASKYRRQL  171 (176)
T ss_dssp             HHHHHHHHHH
T ss_pred             cHHHHHHHHH
Confidence            6666655544

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.20  E-value=1.1e-09  Score=84.21  Aligned_cols=163  Identities=10%  Similarity=-0.040  Sum_probs=112.3

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH-
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL-  111 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~-  111 (403)
                      .+..+...+.+.|++++|...|++..+..  +.+...+..+..++...|++++|+..|++..+..+ ++..+..+.... 
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~   84 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDEL--QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQ-DNSYKSLIAKLEL   84 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHH--HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC-ChHHHHHHHHHHH
Confidence            45566777788888888888888777654  34567778888888888888888888888777666 554433332221 


Q ss_pred             HhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-cHHHHHHHHHHHHHc
Q 041804          112 CEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK-DLHSYSIYMDIMCKS  190 (403)
Q Consensus       112 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~  190 (403)
                      ...+....+...+++...       ..+.+...+..+...+...|++++|...|+++.+..+.+ +...+..+..++...
T Consensus        85 ~~~~~~~~a~~~~~~al~-------~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~  157 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELA-------ANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSAL  157 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHH-------HSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHH
T ss_pred             HhhcccchHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHh
Confidence            122222345666666655       334567777888888888888888888888887776543 355777788888888


Q ss_pred             CChhHHHHHHHHHHH
Q 041804          191 GKPWKAVKLYKEMKK  205 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~  205 (403)
                      |+.++|...|++...
T Consensus       158 g~~~~A~~~y~~al~  172 (176)
T 2r5s_A          158 GQGNAIASKYRRQLY  172 (176)
T ss_dssp             CSSCHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHH
Confidence            888888888876653

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.20  E-value=2.2e-09  Score=86.01  Aligned_cols=189  Identities=7%  Similarity=-0.117  Sum_probs=126.4

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHH---HHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEV---SYC  105 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~  105 (403)
                      ++..+..+...+.+.|++++|+..|+++....+..|. ..++..+..+|.+.|++++|+..|+++.+..+.+..   ++.
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            3456667778888899999999999998875422222 357788888999999999999999999888776432   455


Q ss_pred             HHHHHHHh------------------cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHH
Q 041804          106 NLVDALCE------------------YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEE  167 (403)
Q Consensus       106 ~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  167 (403)
                      .+..++..                  .|+.++|...|+++....       |.+..++......          ..+...
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-------P~~~~a~~a~~~l----------~~~~~~  145 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-------PNSQYTTDATKRL----------VFLKDR  145 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC-------TTCTTHHHHHHHH----------HHHHHH
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-------cCChhHHHHHHHH----------HHHHHH
Confidence            55555543                  578999999999888742       2232222221110          011111


Q ss_pred             HHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCC--ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          168 MDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKM--DVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       168 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      +.        .....+...|.+.|++++|+..|+.+.+.....  ....+..+..++.+.|+.++|...++.+...++
T Consensus       146 ~~--------~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~  215 (225)
T 2yhc_A          146 LA--------KYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS  215 (225)
T ss_dssp             HH--------HHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCS
T ss_pred             HH--------HHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCC
Confidence            11        122345677888888888888888888762111  124577778888888888888888888877643

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.20  E-value=2.3e-09  Score=89.31  Aligned_cols=167  Identities=8%  Similarity=-0.056  Sum_probs=111.4

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      .+...+..+...+...|++++|+..|++..+..+.+...+..+..++.+.|++++|...++++...       .+.....
T Consensus       115 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~-------~p~~~~~  187 (287)
T 3qou_A          115 REEELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ-------DQDTRYQ  187 (287)
T ss_dssp             CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG-------GCSHHHH
T ss_pred             CchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh-------hcchHHH
Confidence            344556667777777788888888888877777777777777777777888888888777776653       1222222


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCC-CChhhHHHHHHHHh
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK-MDVVAYNTVIRAVG  223 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~ll~~~~  223 (403)
                      .......+...++.+.|.+.+++.....+. +...+..+...+...|++++|...|.++.+.... .+...+..+...+.
T Consensus       188 ~~~~~~~l~~~~~~~~a~~~l~~al~~~P~-~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~  266 (287)
T 3qou_A          188 GLVAQIELLXQAADTPEIQQLQQQVAENPE-DAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILA  266 (287)
T ss_dssp             HHHHHHHHHHHHTSCHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcccCccHHHHHHHHhcCCc-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHH
Confidence            223333355666677777777777766554 6667777777777777777777777777766321 12456677777777


Q ss_pred             hcCCHHHHHHHHHHHH
Q 041804          224 VSEGVDFAMRVYREMR  239 (403)
Q Consensus       224 ~~~~~~~a~~~~~~~~  239 (403)
                      ..|+.+.|...+++..
T Consensus       267 ~~g~~~~a~~~~r~al  282 (287)
T 3qou_A          267 ALGTGDALASXYRRQL  282 (287)
T ss_dssp             HHCTTCHHHHHHHHHH
T ss_pred             HcCCCCcHHHHHHHHH
Confidence            7777777776666554

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.20  E-value=6.6e-10  Score=93.00  Aligned_cols=171  Identities=9%  Similarity=-0.036  Sum_probs=121.7

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhC----CCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC------cH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDN----PSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK------DE  101 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~~  101 (403)
                      .|......|...|++++|...|++....    + .+++ ..+|+.+..+|...|++++|+..|++..+..+.      ..
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a  117 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAG-NEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGA  117 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhC-CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            4666677888999999999999877653    2 1122 568999999999999999999999988765432      24


Q ss_pred             HHHHHHHHHHHhc-CCHHHHHHHHhcccccccccccccCc-chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH--
Q 041804          102 VSYCNLVDALCEY-KHVIEAQELCFGENKNVGFSGLVEMN-KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL--  177 (403)
Q Consensus       102 ~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--  177 (403)
                      .++..+..+|... |++++|...+++........  +..+ ...++..+...+.+.|++++|...|++..+.......  
T Consensus       118 ~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~--~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  195 (292)
T 1qqe_A          118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQD--QSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQ  195 (292)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTG
T ss_pred             HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhC--CChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCccc
Confidence            5788899999996 99999999988876531000  0000 1345777777888888888888888887775443221  


Q ss_pred             ----HHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          178 ----HSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       178 ----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                          ..|..+..++...|++++|...|++..+.
T Consensus       196 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l  228 (292)
T 1qqe_A          196 WSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (292)
T ss_dssp             GGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence                14566666777777777777777776543

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.20  E-value=1.1e-09  Score=91.39  Aligned_cols=169  Identities=6%  Similarity=-0.054  Sum_probs=142.1

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      +.+...+..+...+.+.|++++|...|++..+..  +.+...+..+...+...|++++|+..++++....+.........
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~  191 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLS--NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVA  191 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHH
Confidence            4456778888899999999999999999998875  35678899999999999999999999999988776544444445


Q ss_pred             HHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-cHHHHHHHHHH
Q 041804          108 VDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK-DLHSYSIYMDI  186 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~  186 (403)
                      ...+...++.++|...+++...       ..+.+...+..+...+...|++++|.+.|.++.+..+.. +...+..++..
T Consensus       192 ~~~l~~~~~~~~a~~~l~~al~-------~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~  264 (287)
T 3qou_A          192 QIELLXQAADTPEIQQLQQQVA-------ENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEI  264 (287)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHH
T ss_pred             HHHHHhhcccCccHHHHHHHHh-------cCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHH
Confidence            5556777888888888888776       447788899999999999999999999999999876552 36789999999


Q ss_pred             HHHcCChhHHHHHHHHHHH
Q 041804          187 MCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~  205 (403)
                      +...|+.++|...|++...
T Consensus       265 ~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          265 LAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             HHHHCTTCHHHHHHHHHHH
T ss_pred             HHHcCCCCcHHHHHHHHHH
Confidence            9999999999999887654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.19  E-value=3e-09  Score=89.00  Aligned_cols=210  Identities=10%  Similarity=0.060  Sum_probs=141.2

Q ss_pred             ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcC----CC--cHHHHHHHHHHHHhcCCHHH
Q 041804           46 EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFG----LK--DEVSYCNLVDALCEYKHVIE  119 (403)
Q Consensus        46 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~--~~~~~~~l~~~~~~~~~~~~  119 (403)
                      ++++|...|++.                ...|...|++++|...|.+..+..    .+  ...+|+.+..+|...|++++
T Consensus        32 ~~~~A~~~~~~a----------------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~   95 (292)
T 1qqe_A           32 KFEEAADLCVQA----------------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVN   95 (292)
T ss_dssp             HHHHHHHHHHHH----------------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             cHHHHHHHHHHH----------------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHH
Confidence            488888887776                456788999999999999886642    22  35789999999999999999


Q ss_pred             HHHHHhcccccccccccccC-cchHHHHHHHHHHHhc-CChhHHHHHHHHHHhCCCCC-c----HHHHHHHHHHHHHcCC
Q 041804          120 AQELCFGENKNVGFSGLVEM-NKTKIYNMILRGWFKM-SWWGKCREFWEEMDKRGVVK-D----LHSYSIYMDIMCKSGK  192 (403)
Q Consensus       120 a~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~~~  192 (403)
                      |...+++........  +.. .-..+++.+...|... |++++|...|++..+..... +    ..++..+...+...|+
T Consensus        96 A~~~~~~Al~l~~~~--g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~  173 (292)
T 1qqe_A           96 AVDSLENAIQIFTHR--GQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQ  173 (292)
T ss_dssp             HHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHc--CCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCC
Confidence            999988776532000  101 1145677888888885 88888888888776532110 1    3467777888888888


Q ss_pred             hhHHHHHHHHHHHcCCCCChh------hHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCH------HHHHHHHHHHH--
Q 041804          193 PWKAVKLYKEMKKKGIKMDVV------AYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSV------VTCNTVIKLLC--  258 (403)
Q Consensus       193 ~~~a~~~~~~~~~~~~~~~~~------~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~li~~~~--  258 (403)
                      +++|+..|++..+........      .+..+..++...|+++.|...|++..+.  .|+.      ..+..++.+|.  
T Consensus       174 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~l~~l~~~~~~~  251 (292)
T 1qqe_A          174 YIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSE--DPNFADSRESNFLKSLIDAVNEG  251 (292)
T ss_dssp             HHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC-----------HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCCCcHHHHHHHHHHHHHHcC
Confidence            888888888887763222211      4556666777788888888888877653  2221      12334455553  


Q ss_pred             hcCcHHHHHHHHHhchh
Q 041804          259 ENGRVREAYAVLAEMPK  275 (403)
Q Consensus       259 ~~g~~~~a~~~~~~~~~  275 (403)
                      ..+++++|...|+.+..
T Consensus       252 ~~~~~~~A~~~~~~~~~  268 (292)
T 1qqe_A          252 DSEQLSEHCKEFDNFMR  268 (292)
T ss_dssp             CTTTHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHHHhccCCc
Confidence            34567777777766544

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.19  E-value=5.8e-10  Score=104.56  Aligned_cols=185  Identities=11%  Similarity=-0.038  Sum_probs=142.2

Q ss_pred             HhcCChHHHHHHHHHHh--------hcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           78 VTAHLVNEAMGTFNKLD--------EFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        78 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      ...|++++|++.|++..        +..+.+...+..+..++...|++++|...+++...       ..+.+...|..+.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~-------~~p~~~~a~~~lg  474 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAE-------RVGWRWRLVWYRA  474 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHH-------HHCCCHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhc-------cCcchHHHHHHHH
Confidence            66788999999999888        66666888888888889999999999998888876       4466778888888


Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHH
Q 041804          150 RGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVD  229 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~  229 (403)
                      ..+...|++++|.+.|++..+..+. +...|..+..+|.+.|++++ ++.|++..+.+ +-+...+..+..++.+.|+++
T Consensus       475 ~~~~~~g~~~~A~~~~~~al~l~P~-~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~  551 (681)
T 2pzi_A          475 VAELLTGDYDSATKHFTEVLDTFPG-ELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRV  551 (681)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHH
Confidence            8899999999999999988887665 67788888888899999998 88898888774 346678888888888999999


Q ss_pred             HHHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCc--------HHHHHHHHHhch
Q 041804          230 FAMRVYREMREMGCQPS-VVTCNTVIKLLCENGR--------VREAYAVLAEMP  274 (403)
Q Consensus       230 ~a~~~~~~~~~~~~~~~-~~~~~~li~~~~~~g~--------~~~a~~~~~~~~  274 (403)
                      +|...|+++.+.  .|+ ...+..+..++...++        +++|.+.+..+.
T Consensus       552 ~A~~~~~~al~l--~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~  603 (681)
T 2pzi_A          552 GAVRTLDEVPPT--SRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALP  603 (681)
T ss_dssp             HHHHHHHTSCTT--STTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHhhccc--CcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCC
Confidence            999988887765  343 4566666666655443        555555555443

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.16  E-value=1.2e-09  Score=100.53  Aligned_cols=164  Identities=10%  Similarity=-0.076  Sum_probs=119.8

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      .|++++|++.|+...+.  .+.+...+..+...+...|++++|...+++..+..  +.+..++..+..+|...|++++|+
T Consensus         2 ~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~   77 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH--RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH--PGHPEAVARLGRVRWTQQRHAEAA   77 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS--TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            57889999999888742  24457888889999999999999999999988865  346778888999999999999999


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc---CChhHHHHH
Q 041804           88 GTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM---SWWGKCREF  164 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~  164 (403)
                      +.|++..+..+.+...+..+..++...|++++|.+.+++...       ..+.+..++..+...+...   |++++|.+.
T Consensus        78 ~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~  150 (568)
T 2vsy_A           78 VLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQ-------LLPEEPYITAQLLNWRRRLCDWRALDVLSAQ  150 (568)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCCTTHHHHHHH
T ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhhccccHHHHHHH
Confidence            999999988877888999999999999999999999988776       3355677888888888888   899999999


Q ss_pred             HHHHHhCCCCCcHHHHHHH
Q 041804          165 WEEMDKRGVVKDLHSYSIY  183 (403)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~l  183 (403)
                      +++..+.+.. +...|..+
T Consensus       151 ~~~al~~~p~-~~~~~~~l  168 (568)
T 2vsy_A          151 VRAAVAQGVG-AVEPFAFL  168 (568)
T ss_dssp             HHHHHHHTCC-CSCHHHHT
T ss_pred             HHHHHhcCCc-ccChHHHh
Confidence            9988887654 33344433

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.15  E-value=9.9e-10  Score=101.15  Aligned_cols=154  Identities=4%  Similarity=-0.148  Sum_probs=123.1

Q ss_pred             cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHH
Q 041804           44 FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQEL  123 (403)
Q Consensus        44 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  123 (403)
                      .|++++|...+++..+..  +.+...|..+...+...|++++|++.|++..+..+.+..++..+..++...|++++|...
T Consensus         2 ~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR--PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            478899999999988865  346788999999999999999999999999999888999999999999999999999999


Q ss_pred             HhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc---CChhHHHHHH
Q 041804          124 CFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS---GKPWKAVKLY  200 (403)
Q Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~  200 (403)
                      +++...       ..+.+...+..+...|.+.|++++|.+.|++..+.... +...+..+..++...   |++++|.+.+
T Consensus        80 ~~~al~-------~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~g~~~~A~~~~  151 (568)
T 2vsy_A           80 LQQASD-------AAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPE-EPYITAQLLNWRRRLCDWRALDVLSAQV  151 (568)
T ss_dssp             HHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCTTHHHHHHHH
T ss_pred             HHHHHh-------cCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence            999887       34567788999999999999999999999999988665 778899999999999   9999999999


Q ss_pred             HHHHHcC
Q 041804          201 KEMKKKG  207 (403)
Q Consensus       201 ~~~~~~~  207 (403)
                      ++..+.+
T Consensus       152 ~~al~~~  158 (568)
T 2vsy_A          152 RAAVAQG  158 (568)
T ss_dssp             HHHHHHT
T ss_pred             HHHHhcC
Confidence            9998874

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.14  E-value=7.6e-09  Score=82.88  Aligned_cols=188  Identities=7%  Similarity=-0.155  Sum_probs=130.1

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc---HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcc-
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD---EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNK-  141 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-  141 (403)
                      +...+..+...+...|++++|+..|+++.+..+.+   ...+..+..++.+.|++++|...|+++....     +..+. 
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~-----P~~~~~   77 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN-----PTHPNI   77 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-----TTCTTH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC-----cCCCcH
Confidence            44566677888999999999999999999877653   4688889999999999999999999987642     11121 


Q ss_pred             hHHHHHHHHHHHh------------------cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 041804          142 TKIYNMILRGWFK------------------MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEM  203 (403)
Q Consensus       142 ~~~~~~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  203 (403)
                      ..++..+..++..                  .|++++|...|+++.+..+. +..++.......          .+...+
T Consensus        78 ~~a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~-~~~a~~a~~~l~----------~~~~~~  146 (225)
T 2yhc_A           78 DYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPN-SQYTTDATKRLV----------FLKDRL  146 (225)
T ss_dssp             HHHHHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTT-CTTHHHHHHHHH----------HHHHHH
T ss_pred             HHHHHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcC-ChhHHHHHHHHH----------HHHHHH
Confidence            1244445555543                  46677777777777765433 222222211100          000000


Q ss_pred             HHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCcHHHHHHHHHhchhcC
Q 041804          204 KKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPS--VVTCNTVIKLLCENGRVREAYAVLAEMPKKG  277 (403)
Q Consensus       204 ~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  277 (403)
                      .        .....+...|.+.|+++.|...|+.+.+..+...  ...+..+..+|.+.|+.++|.+.++.+...+
T Consensus       147 ~--------~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          147 A--------KYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             H--------HHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             H--------HHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            0        0113456788899999999999999998743211  2568889999999999999999999888763

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.10  E-value=1.9e-08  Score=83.51  Aligned_cols=220  Identities=6%  Similarity=-0.041  Sum_probs=180.5

Q ss_pred             ccHHHHHHhhhhhcccCCCcC-CHHhHHHHHHHHHccC--ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHH----Hhc-
Q 041804            9 NDWKRALEFFNWVETDCHFTH-TTDTYNSVIDILGKFF--EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRY----VTA-   80 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~-   80 (403)
                      ...++|++.++.+..   +.| +..+|+.--.++...|  +++++++.++.+....  +.+..+|+.-...+    ... 
T Consensus        47 e~s~~aL~~t~~~L~---~nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n--Pk~y~aW~~R~~iL~~~~~~l~  121 (306)
T 3dra_A           47 EYSERALHITELGIN---ELASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN--EKNYQIWNYRQLIIGQIMELNN  121 (306)
T ss_dssp             CCSHHHHHHHHHHHH---HCTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC--TTCCHHHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHH---HCcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC--cccHHHHHHHHHHHHHHHHhcc
Confidence            344689999988875   334 4667888888998888  9999999999999876  45666777665555    555 


Q ss_pred             --CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH--HHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC
Q 041804           81 --HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI--EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS  156 (403)
Q Consensus        81 --~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  156 (403)
                        +++++++.+++++.+.++.+..+|+.-..++...+.++  ++++.+.++..       ..+.|..+|+.-.......+
T Consensus       122 ~~~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~-------~d~~N~sAW~~R~~ll~~l~  194 (306)
T 3dra_A          122 NDFDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVID-------TDLKNNSAWSHRFFLLFSKK  194 (306)
T ss_dssp             TCCCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHSSG
T ss_pred             ccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHhcc
Confidence              78999999999999999999999999998888889888  99999998887       55778888988888887777


Q ss_pred             C------hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhH-HHHHHHHHHHcC--CCCChhhHHHHHHHHhhcCC
Q 041804          157 W------WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWK-AVKLYKEMKKKG--IKMDVVAYNTVIRAVGVSEG  227 (403)
Q Consensus       157 ~------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~ll~~~~~~~~  227 (403)
                      .      ++++++.++++....+. |...|+-+...+.+.|+... +..+..++...+  -+.+...+..+...|.+.|+
T Consensus       195 ~~~~~~~~~eEl~~~~~aI~~~p~-n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~  273 (306)
T 3dra_A          195 HLATDNTIDEELNYVKDKIVKCPQ-NPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKK  273 (306)
T ss_dssp             GGCCHHHHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTC
T ss_pred             ccchhhhHHHHHHHHHHHHHhCCC-CccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCC
Confidence            6      89999999999998888 99999999999999888554 555666655432  13467888999999999999


Q ss_pred             HHHHHHHHHHHHHc
Q 041804          228 VDFAMRVYREMREM  241 (403)
Q Consensus       228 ~~~a~~~~~~~~~~  241 (403)
                      .++|.++++.+.+.
T Consensus       274 ~~~A~~~~~~l~~~  287 (306)
T 3dra_A          274 YNESRTVYDLLKSK  287 (306)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhc
Confidence            99999999999863

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=99.10  E-value=1.9e-08  Score=79.73  Aligned_cols=163  Identities=10%  Similarity=-0.041  Sum_probs=73.1

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC----CHHHHHHHHhcccccccccccccCcc
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK----HVIEAQELCFGENKNVGFSGLVEMNK  141 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~~~~~~~~~~~~~~~~~~  141 (403)
                      +..++..+...|...+++++|+.+|++..+.+  ++..+..+...|.. +    +.++|...|++....         .+
T Consensus        17 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g--~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~---------g~   84 (212)
T 3rjv_A           17 DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG--DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEA---------GS   84 (212)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT--CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHT---------TC
T ss_pred             CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC--CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHC---------CC
Confidence            34444444444444445555555554444422  33344444444444 3    444444444444221         22


Q ss_pred             hHHHHHHHHHHHh----cCChhHHHHHHHHHHhCCCC-CcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCCh
Q 041804          142 TKIYNMILRGWFK----MSWWGKCREFWEEMDKRGVV-KDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDV  212 (403)
Q Consensus       142 ~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~  212 (403)
                      ..++..|...|..    .+++++|.++|++..+.+.. .+..++..|...|..    .+++++|+.+|++..+.  ..+.
T Consensus        85 ~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~  162 (212)
T 3rjv_A           85 KSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL--SRTG  162 (212)
T ss_dssp             HHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT--SCTT
T ss_pred             HHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc--CCCH
Confidence            3334444444443    44555555555555544321 013444555555554    44555555555555544  1122


Q ss_pred             hhHHHHHHHHhhc------CCHHHHHHHHHHHHHcC
Q 041804          213 VAYNTVIRAVGVS------EGVDFAMRVYREMREMG  242 (403)
Q Consensus       213 ~~~~~ll~~~~~~------~~~~~a~~~~~~~~~~~  242 (403)
                      ..+..|...|...      .+.++|...|+...+.|
T Consensus       163 ~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          163 YAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            3344444444322      14555555555555543

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=99.07  E-value=2.1e-08  Score=79.48  Aligned_cols=178  Identities=9%  Similarity=-0.029  Sum_probs=145.2

Q ss_pred             HHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC----ChHHHH
Q 041804           12 KRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH----LVNEAM   87 (403)
Q Consensus        12 ~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~   87 (403)
                      .+|++.|+....    ..++.++..+...|...+++++|..+|++..+.+    +..++..+...|.. +    ++++|+
T Consensus         3 ~eA~~~~~~aa~----~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g----~~~a~~~lg~~y~~-~g~~~~~~~A~   73 (212)
T 3rjv_A            3 TEPGSQYQQQAE----AGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG----DGDALALLAQLKIR-NPQQADYPQAR   73 (212)
T ss_dssp             -CTTHHHHHHHH----TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT----CHHHHHHHHHHTTS-STTSCCHHHHH
T ss_pred             chHHHHHHHHHH----CCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC----CHHHHHHHHHHHHc-CCCCCCHHHHH
Confidence            357777777764    3578889999999999999999999999998864    67788888888887 6    899999


Q ss_pred             HHHHHHhhcCCCcHHHHHHHHHHHHh----cCCHHHHHHHHhcccccccccccccC-cchHHHHHHHHHHHh----cCCh
Q 041804           88 GTFNKLDEFGLKDEVSYCNLVDALCE----YKHVIEAQELCFGENKNVGFSGLVEM-NKTKIYNMILRGWFK----MSWW  158 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~  158 (403)
                      ++|++..+.+  ++.++..|...|..    .+++++|...|++....      +.. .+..++..|...|..    .+++
T Consensus        74 ~~~~~A~~~g--~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~------~~~~~~~~a~~~Lg~~y~~g~g~~~d~  145 (212)
T 3rjv_A           74 QLAEKAVEAG--SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARD------SESDAAVDAQMLLGLIYASGVHGPEDD  145 (212)
T ss_dssp             HHHHHHHHTT--CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSS------TTSHHHHHHHHHHHHHHHHTSSSSCCH
T ss_pred             HHHHHHHHCC--CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHc------CCCcchHHHHHHHHHHHHcCCCCCCCH
Confidence            9999997743  67788888888887    88999999999998875      211 236788889999988    8899


Q ss_pred             hHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc-C-----ChhHHHHHHHHHHHcCC
Q 041804          159 GKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS-G-----KPWKAVKLYKEMKKKGI  208 (403)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-----~~~~a~~~~~~~~~~~~  208 (403)
                      ++|...|++..+.+  .+...+..|...|... |     ++++|..+|+...+.|.
T Consensus       146 ~~A~~~~~~A~~~~--~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          146 VKASEYFKGSSSLS--RTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHHHHHHHHTS--CTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcC--CCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            99999999998872  2445677787777653 3     89999999999998873

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=99.03  E-value=9e-09  Score=86.75  Aligned_cols=120  Identities=9%  Similarity=-0.017  Sum_probs=57.4

Q ss_pred             ccccHHHHHHhhhhhcccCC-----CcCC----HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCC--CC--CHHHHHHH
Q 041804            7 YANDWKRALEFFNWVETDCH-----FTHT----TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSS--IP--NHATFRIM   73 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~-----~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~--~~--~~~~~~~l   73 (403)
                      .+|++++|.++++...+...     +.++    ...|......|...|++++|...|.+..+....  .+  -..+|+.+
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~l   82 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQA   82 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            46889999999987664111     1122    123444455555556666555555544331100  00  12345555


Q ss_pred             HHHHHhcCChHHHHHHHHHHhhcC----CC--cHHHHHHHHHHHHhcCCHHHHHHHHhcc
Q 041804           74 FKRYVTAHLVNEAMGTFNKLDEFG----LK--DEVSYCNLVDALCEYKHVIEAQELCFGE  127 (403)
Q Consensus        74 ~~~~~~~~~~~~a~~~~~~~~~~~----~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~  127 (403)
                      ..+|...|++++|+..|++..+..    -+  ...++..+..+|.. |++++|...+++.
T Consensus        83 g~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~A  141 (307)
T 2ifu_A           83 GMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQA  141 (307)
T ss_dssp             HHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHH
Confidence            555555555555555555543321    11  12334444444444 4444444444443

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=99.02  E-value=2.7e-08  Score=78.86  Aligned_cols=137  Identities=9%  Similarity=-0.069  Sum_probs=109.7

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      .+..+...+...|++++|...|++..     .|+..+|..+..+|...|++++|+..|++..+..+.+..++..+..++.
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~-----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~   82 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYY   82 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc-----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHH
Confidence            45567778888999999999998874     3678889999999999999999999999998888778888999999999


Q ss_pred             hcCCHHHHHHHHhcccccccccc---------cccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC
Q 041804          113 EYKHVIEAQELCFGENKNVGFSG---------LVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV  174 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~---------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  174 (403)
                      ..|++++|...+++.....+...         ...+....++..+...|.+.|++++|.+.|++..+....
T Consensus        83 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~  153 (213)
T 1hh8_A           83 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  153 (213)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCcc
Confidence            99999999999888776321000         001123477888999999999999999999999887554

>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=99.01  E-value=3.2e-07  Score=77.09  Aligned_cols=233  Identities=10%  Similarity=0.021  Sum_probs=177.6

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC-ChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH-LVNEAMGTFNKLDEFGLKDEVSYCNLVDAL  111 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  111 (403)
                      +++.+-....+.+..++|+++++.+...+  +-+..+|+.--..+...| .+++++.+++.+....+++..+|+.-..++
T Consensus        56 ~~~~~r~~~~~~e~se~AL~lt~~~L~~n--P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL  133 (349)
T 3q7a_A           56 AMDYFRAIAAKEEKSERALELTEIIVRMN--PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLL  133 (349)
T ss_dssp             HHHHHHHHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHhC--chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHH
Confidence            34444444455566689999999999976  456678998888888888 599999999999999999999999988888


Q ss_pred             Hhc-C-CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChh--------HHHHHHHHHHhCCCCCcHHHHH
Q 041804          112 CEY-K-HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWG--------KCREFWEEMDKRGVVKDLHSYS  181 (403)
Q Consensus       112 ~~~-~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~  181 (403)
                      ... + ++++++..++++..       ..+.|..+|+.-.-...+.|.++        ++++.++++.+.++. |..+|+
T Consensus       134 ~~l~~~~~~~EL~~~~k~L~-------~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp~-N~SAW~  205 (349)
T 3q7a_A          134 DRISPQDPVSEIEYIHGSLL-------PDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDGR-NNSAWG  205 (349)
T ss_dssp             HHHCCSCCHHHHHHHHHHTS-------SCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCTT-CHHHHH
T ss_pred             HHhcCCChHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCCC-CHHHHH
Confidence            877 7 88999999999887       55778888888777777777777        899999999998877 889999


Q ss_pred             HHHHHHHHcCC-------hhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCH--------------------HHHHHH
Q 041804          182 IYMDIMCKSGK-------PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGV--------------------DFAMRV  234 (403)
Q Consensus       182 ~l~~~~~~~~~-------~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~--------------------~~a~~~  234 (403)
                      .....+.+.+.       ++++++.++++.... +-|...|+.+-..+.+.|+.                    ......
T Consensus       206 ~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (349)
T 3q7a_A          206 WRWYLRVSRPGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAF  284 (349)
T ss_dssp             HHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC-------------
T ss_pred             HHHHHHHhccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHH
Confidence            98888888776       678899998888874 44777887766666655543                    222222


Q ss_pred             HHHHHHcC-----CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          235 YREMREMG-----CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       235 ~~~~~~~~-----~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      ...+...+     -.++......++..|...|+.++|.++++.+.+.
T Consensus       285 ~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          285 GFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             -CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            22222221     1356778888899999999999999999988643

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.95  E-value=2.5e-08  Score=71.54  Aligned_cols=94  Identities=9%  Similarity=-0.081  Sum_probs=42.5

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      .+......+.+.|++++|++.|++..+..  +.+..+|..+..+|.+.|++++|+..|++..+.++.+..+|..+..++.
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~   92 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRD--PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLV   92 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence            34444444444444444444444444432  2234444444444444444444444444444444444444444444444


Q ss_pred             hcCCHHHHHHHHhccc
Q 041804          113 EYKHVIEAQELCFGEN  128 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~  128 (403)
                      ..|++++|...|++..
T Consensus        93 ~~~~~~~A~~~~~~al  108 (126)
T 4gco_A           93 AMREWSKAQRAYEDAL  108 (126)
T ss_dssp             HTTCHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHH
Confidence            4444444444444433

>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=98.95  E-value=1.4e-08  Score=85.49  Aligned_cols=193  Identities=8%  Similarity=-0.087  Sum_probs=105.1

Q ss_pred             cCChhHHHHHHHHhhhCCC---C--CCCH----HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC------cHHHHHHHH
Q 041804           44 FFEFDLSWNLIHRMKDNPS---S--IPNH----ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK------DEVSYCNLV  108 (403)
Q Consensus        44 ~~~~~~a~~~~~~~~~~~~---~--~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~~~~~~~l~  108 (403)
                      .|++++|.+++++..+...   .  .++.    ..|+.....|...|++++|...|.+..+....      -..+|..+.
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg   83 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTSFMKWKPDYDSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAG   83 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCCSSSCSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHccccccCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4677778887776654210   0  1232    24566666777778888887777776553221      234566666


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccC-cchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC-----cHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEM-NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK-----DLHSYSI  182 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~  182 (403)
                      .+|...|++++|...+++........  +.+ ....+++.+...|.. |++++|.+.|++..+.....     ...++..
T Consensus        84 ~~~~~~g~~~~A~~~~~~Al~l~~~~--g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~  160 (307)
T 2ifu_A           84 MMLKDLQRMPEAVQYIEKASVMYVEN--GTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGK  160 (307)
T ss_dssp             HHHHHTTCGGGGHHHHHHHHHHHHTT--TCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHHc--CCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHH
Confidence            77777777777776666544321000  111 123455666666666 67777766666654321100     1345556


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHc----CCCCC-hhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          183 YMDIMCKSGKPWKAVKLYKEMKKK----GIKMD-VVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       183 l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      +..+|...|++++|+..|++....    +..+. ...+..+..++...|+++.|...|++..
T Consensus       161 lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          161 ASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            666666666666666666665543    11111 1133444445555566666666666655

>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=98.95  E-value=8e-08  Score=80.34  Aligned_cols=166  Identities=13%  Similarity=0.033  Sum_probs=122.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcch----HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC-Cc--
Q 041804          104 YCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKT----KIYNMILRGWFKMSWWGKCREFWEEMDKRGVV-KD--  176 (403)
Q Consensus       104 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~--  176 (403)
                      +...+..+...|++++|...+++.....     ...|+.    ..+..+...+...+++++|...|++..+.... ++  
T Consensus        78 l~~~i~~~~~~~~y~~a~~~~~~~l~~~-----~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~  152 (293)
T 3u3w_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKE-----EYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVY  152 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTC-----CCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTT
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHhccc-----cCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHH
Confidence            3344677788899999999988876642     222332    23445777777888999999999999874322 22  


Q ss_pred             --HHHHHHHHHHHHHcCChhHHHHHHHHHHHc-----CCCCC-hhhHHHHHHHHhhcCCHHHHHHHHHHHHHc----CCC
Q 041804          177 --LHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-----GIKMD-VVAYNTVIRAVGVSEGVDFAMRVYREMREM----GCQ  244 (403)
Q Consensus       177 --~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~  244 (403)
                        ..+++.+..+|...|++++|+..|+++.+.     +..+. ..++..+...|.+.|++++|...+++..+.    +..
T Consensus       153 ~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~  232 (293)
T 3u3w_A          153 QNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSM  232 (293)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBC
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcH
Confidence              236889999999999999999999998742     11222 237788888999999999999999988754    222


Q ss_pred             CC-HHHHHHHHHHHHhcCc-HHHHHHHHHhch
Q 041804          245 PS-VVTCNTVIKLLCENGR-VREAYAVLAEMP  274 (403)
Q Consensus       245 ~~-~~~~~~li~~~~~~g~-~~~a~~~~~~~~  274 (403)
                      +. ..+|..+..+|.+.|+ +++|.+.+++..
T Consensus       233 ~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          233 ALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             TTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            22 5678889999999994 699999888765

>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=98.94  E-value=5.1e-10  Score=95.55  Aligned_cols=175  Identities=10%  Similarity=0.009  Sum_probs=96.1

Q ss_pred             cccHHHHHHhhhh----hcccCCCcCCHHhHHHHHHHHH------------ccCChhHHHHHHHHhhhCCCCCCCHHHHH
Q 041804            8 ANDWKRALEFFNW----VETDCHFTHTTDTYNSVIDILG------------KFFEFDLSWNLIHRMKDNPSSIPNHATFR   71 (403)
Q Consensus         8 ~~~~~~A~~~~~~----~~~~~~~~~~~~~~~~li~~~~------------~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   71 (403)
                      .+.+++|+..++.    ...   ++|+. .|........            ..+++++|...++......  +.+...+.
T Consensus        78 ~~~~e~al~~~~~Ge~~~l~---i~p~~-ayg~~g~~~~~i~~~~~l~f~~~L~~~~~A~~~~~~a~~~~--p~~a~~~~  151 (336)
T 1p5q_A           78 PYGLERAIQRMEKGEHSIVY---LKPSY-AFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMNSEEK--LEQSTIVK  151 (336)
T ss_dssp             CHHHHHHHTTCCTTCEEEEE---ECTTT-TTTTTCBGGGTBCSSCCEEEEEEEEEEECCCCGGGCCHHHH--HHHHHHHH
T ss_pred             chHHHHHHhcCCCCCeEEEE---ECCcc-ccCcCCCCccCCCCCCeEEEEEEEeecccccchhcCCHHHH--HHHHHHHH
Confidence            4578888888776    332   23432 3322221111            3345566666665544422  12456788


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhcCCCc---------------HHHHHHHHHHHHhcCCHHHHHHHHhccccccccccc
Q 041804           72 IMFKRYVTAHLVNEAMGTFNKLDEFGLKD---------------EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGL  136 (403)
Q Consensus        72 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  136 (403)
                      .+...+.+.|++++|+..|++..+..+.+               ..+|..+..++.+.|++++|...+++...       
T Consensus       152 ~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~-------  224 (336)
T 1p5q_A          152 ERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALE-------  224 (336)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------
Confidence            88999999999999999999998877664               34455555555555555555555544443       


Q ss_pred             ccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHH
Q 041804          137 VEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKA  196 (403)
Q Consensus       137 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  196 (403)
                      ..+.+..++..+..+|...|++++|...|++..+..+. +...+..+..++...|+++++
T Consensus       225 ~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          225 LDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-NKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHH
Confidence            22334444444445555555555555555544444333 334444444444444444444

>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=98.94  E-value=4.1e-08  Score=74.23  Aligned_cols=127  Identities=12%  Similarity=-0.013  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .+..+...+...|++++|...|++..+..+.+..++..+..++...|++++|...+.+...       ..+.+..++..+
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~-------~~~~~~~~~~~~   87 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIE-------LDKKYIKGYYRR   87 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCcccHHHHHHH
Confidence            3444445555555555555555555554444555555555555555555555555554443       223334445555


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHH--HHHHHHHHHcCChhHHHHHHHHH
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSY--SIYMDIMCKSGKPWKAVKLYKEM  203 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~~~~~~  203 (403)
                      ...+...|++++|.+.|++..+.... +...+  ..+...+...|++++|+..+...
T Consensus        88 a~~~~~~~~~~~A~~~~~~a~~~~p~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           88 AASNMALGKFRAALRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            55555555555555555555444332 22233  22222244455555555555443

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.93  E-value=1.4e-06  Score=78.12  Aligned_cols=312  Identities=6%  Similarity=-0.080  Sum_probs=185.9

Q ss_pred             CChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC-hHHHHHHHHHHhhc-C--CCcHHHHHHHHHHHH----hcCC
Q 041804           45 FEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL-VNEAMGTFNKLDEF-G--LKDEVSYCNLVDALC----EYKH  116 (403)
Q Consensus        45 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~-~--~~~~~~~~~l~~~~~----~~~~  116 (403)
                      |+++.+..+|++....-   |+...|..-+....+.++ .+....+|+..... |  +.+...|...+..+.    .+++
T Consensus        28 ~~~e~~~~iferal~~~---ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~  104 (493)
T 2uy1_A           28 KDYRSLESLFGRCLKKS---YNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTR  104 (493)
T ss_dssp             TCHHHHHHHHHHHSTTC---CCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHH
T ss_pred             CCHHHHHHHHHHHhccC---CCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHH
Confidence            88999999999999853   899999998888877764 45677788877654 3  347788888887754    3567


Q ss_pred             HHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh-------------cCChhHHHHHHHHHHhCCCCCcHHHHHHH
Q 041804          117 VIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK-------------MSWWGKCREFWEEMDKRGVVKDLHSYSIY  183 (403)
Q Consensus       117 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  183 (403)
                      .+.+.++|++....      +...-...|......-..             .+.+..|..+++.+...-...+...|...
T Consensus       105 ~~~vR~iy~rAL~~------P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~s~~~W~~y  178 (493)
T 2uy1_A          105 IEKIRNGYMRALQT------PMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGWSVKNAARL  178 (493)
T ss_dssp             HHHHHHHHHHHHTS------CCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSHHHHHHH
T ss_pred             HHHHHHHHHHHHhC------hhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhccHHHHHHH
Confidence            88899999988763      111112223222221111             12233344444444321000133456555


Q ss_pred             HHHHHHcC--C-----hhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 041804          184 MDIMCKSG--K-----PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKL  256 (403)
Q Consensus       184 ~~~~~~~~--~-----~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  256 (403)
                      +..-...+  -     .+.+..+|+++... .+.+...|...+.-+.+.|+++.|..+++.....  +.+...+.    .
T Consensus       179 ~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~-~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~----~  251 (493)
T 2uy1_A          179 IDLEMENGMKLGGRPHESRMHFIHNYILDS-FYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSL----Y  251 (493)
T ss_dssp             HHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHH----H
T ss_pred             HHHHhcCCccCcchhhHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHH----H
Confidence            55432211  1     23567889998876 3556778888888888999999999999999988  33333332    2


Q ss_pred             HHhcCcHHHH-HHHHHhchhc-----CCCCC---hhhHHHHHHh---hCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHH
Q 041804          257 LCENGRVREA-YAVLAEMPKK-----GCVPD---VITYHCFFRC---LEKPREILGLFDRMIESGIRPKMDTYVMLLRKF  324 (403)
Q Consensus       257 ~~~~g~~~~a-~~~~~~~~~~-----~~~p~---~~~~~~l~~~---~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~  324 (403)
                      |+...+.++. ..+.+.....     +..+.   ...|...+..   .+..+.|..+|++. .. ...+...|......-
T Consensus       252 y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~-~~~~~~v~i~~A~lE  329 (493)
T 2uy1_A          252 YGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GN-EGVGPHVFIYCAFIE  329 (493)
T ss_dssp             HHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TT-SCCCHHHHHHHHHHH
T ss_pred             HHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hC-CCCChHHHHHHHHHH
Confidence            2222111111 1111111000     00011   1223333332   35578899999988 32 122334444322222


Q ss_pred             Hh-cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 041804          325 GR-WGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEM  375 (403)
Q Consensus       325 ~~-~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  375 (403)
                      .. .++.+.|..+|+...+.. +.++..|...++...+.|+.+.|..+|++.
T Consensus       330 ~~~~~d~~~ar~ife~al~~~-~~~~~~~~~yid~e~~~~~~~~aR~l~er~  380 (493)
T 2uy1_A          330 YYATGSRATPYNIFSSGLLKH-PDSTLLKEEFFLFLLRIGDEENARALFKRL  380 (493)
T ss_dssp             HHHHCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHS
T ss_pred             HHHCCChHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            22 337999999999998753 334667777888888999999999888875

>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=98.92  E-value=4.6e-08  Score=81.82  Aligned_cols=171  Identities=11%  Similarity=-0.063  Sum_probs=123.7

Q ss_pred             HHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHH----HHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--c----HHHH
Q 041804           35 NSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHA----TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--D----EVSY  104 (403)
Q Consensus        35 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~----~~~~  104 (403)
                      ...+..+...|++++|..+++.........|+..    .+..+...+...+++++|+..|++..+....  +    ..++
T Consensus        79 ~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~  158 (293)
T 3u3w_A           79 KDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIE  158 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHH
Confidence            3446778899999999999999988653334422    3345677777888999999999999885443  3    3378


Q ss_pred             HHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC----CCCC-cHHH
Q 041804          105 CNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR----GVVK-DLHS  179 (403)
Q Consensus       105 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~  179 (403)
                      +.+..+|...|++++|...++++.......+...+....++..+...|.+.|++++|.+.+++..+.    +..+ -..+
T Consensus       159 ~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~  238 (293)
T 3u3w_A          159 NAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQL  238 (293)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHH
Confidence            9999999999999999999988774211000022233447888888888999999998888876542    2111 2567


Q ss_pred             HHHHHHHHHHcCC-hhHHHHHHHHHHH
Q 041804          180 YSIYMDIMCKSGK-PWKAVKLYKEMKK  205 (403)
Q Consensus       180 ~~~l~~~~~~~~~-~~~a~~~~~~~~~  205 (403)
                      |..+..+|.+.|+ +++|.+.|++...
T Consensus       239 ~~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          239 YYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            7888888888884 5888888877654

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.92  E-value=5e-08  Score=81.56  Aligned_cols=173  Identities=10%  Similarity=-0.063  Sum_probs=123.7

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH----HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC------cHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH----ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK------DEV  102 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~~~  102 (403)
                      .+...+..+...|++++|.+.+....+.....++.    ..+..+...+...|++++|+..|++..+....      ...
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            34456778889999999999999887754221211    23445666778889999999999998764332      245


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC----CC-CcH
Q 041804          103 SYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG----VV-KDL  177 (403)
Q Consensus       103 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~-~~~  177 (403)
                      +++.+...|...|++++|...+++........+........++..+...|.+.|++++|.+.+++..+..    .. .-.
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~  236 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            8899999999999999999999887632100000101123578888999999999999999998876432    11 115


Q ss_pred             HHHHHHHHHHHHcCChhHH-HHHHHHHHH
Q 041804          178 HSYSIYMDIMCKSGKPWKA-VKLYKEMKK  205 (403)
Q Consensus       178 ~~~~~l~~~~~~~~~~~~a-~~~~~~~~~  205 (403)
                      .+|..+..+|.+.|++++| ...+++...
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            6788888888999999988 776776553

>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=98.91  E-value=2.5e-07  Score=77.73  Aligned_cols=224  Identities=8%  Similarity=-0.033  Sum_probs=174.1

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccC-ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhc-C-C
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFF-EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTA-H-L   82 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-~   82 (403)
                      ......++|+++++.+...  .+-+..+|+.--.++...| .+++++..++.+....  +.+..+|+.-..++.+. + +
T Consensus        65 ~~~e~se~AL~lt~~~L~~--nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n--PKny~aW~hR~wlL~~l~~~~  140 (349)
T 3q7a_A           65 AKEEKSERALELTEIIVRM--NPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN--LKSYQVWHHRLLLLDRISPQD  140 (349)
T ss_dssp             HTTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT--CCCHHHHHHHHHHHHHHCCSC
T ss_pred             HhCCCCHHHHHHHHHHHHh--CchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHhcCCC
Confidence            3445567899999888752  2345677888888888888 5999999999999976  56788999888888877 7 8


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH--------HHHHHHhcccccccccccccCcchHHHHHHHHHHHh
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI--------EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK  154 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  154 (403)
                      +++++++++++.+.++.+..+|+.-..++.+.+.++        ++++.+.++..       ..+.|..+|+.....+.+
T Consensus       141 ~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~-------~dp~N~SAW~~R~~lL~~  213 (349)
T 3q7a_A          141 PVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLR-------VDGRNNSAWGWRWYLRVS  213 (349)
T ss_dssp             CHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHh
Confidence            999999999999999889999988777777666665        88888888877       457788899998888888


Q ss_pred             cCC-------hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCCh--------------------hHHHHHHHHHHHcC
Q 041804          155 MSW-------WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKP--------------------WKAVKLYKEMKKKG  207 (403)
Q Consensus       155 ~~~-------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------------------~~a~~~~~~~~~~~  207 (403)
                      .+.       ++++++.+++.....+. |...|+-+-..+.+.|+.                    ........++...+
T Consensus       214 l~~~~~~~~~~~eELe~~~~aI~~~P~-n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  292 (349)
T 3q7a_A          214 RPGAETSSRSLQDELIYILKSIHLIPH-NVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDP  292 (349)
T ss_dssp             STTCCCCHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-C
T ss_pred             ccccccchHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcc
Confidence            876       68899999999988777 889999888888777765                    12222222222221


Q ss_pred             -----CCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          208 -----IKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       208 -----~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                           -.++......++..|...|+.++|.++++.+.+.
T Consensus       293 ~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          293 LPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             CCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             cccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence                 1357778889999999999999999999998754

>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=98.91  E-value=1.2e-08  Score=84.77  Aligned_cols=194  Identities=7%  Similarity=0.014  Sum_probs=103.2

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      +...+..+...+...|++++|+..|++..+..+.+...+..+..++...|++++|...+++...       ..+.+...+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~-------~~p~~~~~~   75 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE-------LDGQSVKAH   75 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT-------SCTTCHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-------hCCCCHHHH
Confidence            3445556666666666666666666666666655666666666666666666666666666555       234455566


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS  225 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  225 (403)
                      ..+..+|...|++++|...|++..+.++. +...+...+....+.   .+... +........+.+......+ ..+ ..
T Consensus        76 ~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~i~~~l-~~l-~~  148 (281)
T 2c2l_A           76 FFLGQCQLEMESYDEAIANLQRAYSLAKE-QRLNFGDDIPSALRI---AKKKR-WNSIEERRIHQESELHSYL-TRL-IA  148 (281)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHH-TTCCCCSHHHHHHHH---HHHHH-HHHHHHTCCCCCCHHHHHH-HHH-HH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHHH---HHHHH-HHHHHHHHHhhhHHHHHHH-HHH-HH
Confidence            66666666667777776666665543211 000111111111111   11111 1222223333344433333 222 25


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhc-CcHHHHHHHHHhchh
Q 041804          226 EGVDFAMRVYREMREMGCQPSV-VTCNTVIKLLCEN-GRVREAYAVLAEMPK  275 (403)
Q Consensus       226 ~~~~~a~~~~~~~~~~~~~~~~-~~~~~li~~~~~~-g~~~~a~~~~~~~~~  275 (403)
                      |+.+.|.+.++...+.  .|+. .....+...+.+. +.+++|.++|....+
T Consensus       149 ~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          149 AERERELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HHHHHHHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            7777887777766654  3433 3333333334443 567888888887764

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.90  E-value=4.3e-08  Score=70.94  Aligned_cols=96  Identities=7%  Similarity=-0.095  Sum_probs=46.8

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ...+..+...+...|++++|...|++..+..  +.+..++..+..++...|++++|+..+++..+..+.+...+..+..+
T Consensus        16 ~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   93 (133)
T 2lni_A           16 ALMVKNKGNECFQKGDYPQAMKHYTEAIKRN--PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAA   93 (133)
T ss_dssp             HHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC--TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            4444455555555555555555555554432  22344444555555555555555555555554444444444444444


Q ss_pred             HHhcCCHHHHHHHHhccc
Q 041804          111 LCEYKHVIEAQELCFGEN  128 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~  128 (403)
                      +...|++++|...+++..
T Consensus        94 ~~~~~~~~~A~~~~~~~~  111 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKAL  111 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            444445444444444433

>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=98.90  E-value=5.5e-08  Score=73.49  Aligned_cols=131  Identities=9%  Similarity=-0.055  Sum_probs=109.3

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ...+..+...+...|++++|...|++..+..  +.+..++..+..++...|++++|+..|++..+..+.+..++..+..+
T Consensus        13 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~   90 (166)
T 1a17_A           13 AEELKTQANDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            4567888889999999999999999988865  35688899999999999999999999999999887789999999999


Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCcchHHH--HHHHHHHHhcCChhHHHHHHHHHHh
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY--NMILRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      +...|++++|...+++....       .+.+...+  ......+.+.|++++|.+.+.....
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~-------~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKV-------KPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH-------STTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            99999999999999988763       23344444  3444447788999999998877643

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.90  E-value=3.8e-08  Score=70.60  Aligned_cols=105  Identities=10%  Similarity=0.021  Sum_probs=91.1

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      |..+.+.|++++|++.|+.....  .+.+..+|..+..++.+.|++++|+..|++..+.+  +.+..+|..+..++...|
T Consensus        20 G~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~   95 (126)
T 4gco_A           20 GNEYFKKGDYPTAMRHYNEAVKR--DPENAILYSNRAACLTKLMEFQRALDDCDTCIRLD--SKFIKGYIRKAACLVAMR   95 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh--hhhhHHHHHHHHHHHHCC
Confidence            34567889999999999998752  24568899999999999999999999999999875  456889999999999999


Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ++++|++.|++..+..|.+..++..+..+
T Consensus        96 ~~~~A~~~~~~al~l~P~~~~a~~~l~~~  124 (126)
T 4gco_A           96 EWSKAQRAYEDALQVDPSNEEAREGVRNC  124 (126)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHCcCCHHHHHHHHHh
Confidence            99999999999999998888887776543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.90  E-value=4.1e-08  Score=79.68  Aligned_cols=189  Identities=7%  Similarity=-0.110  Sum_probs=131.1

Q ss_pred             ccCChhHHHHHHHHhhhCCCCCCCHHHHHHH-------HHHHHhcCChHHHHHHHHHHhhcCCC------c---------
Q 041804           43 KFFEFDLSWNLIHRMKDNPSSIPNHATFRIM-------FKRYVTAHLVNEAMGTFNKLDEFGLK------D---------  100 (403)
Q Consensus        43 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~a~~~~~~~~~~~~~------~---------  100 (403)
                      ..++...|.+.|.+.....  +-....|..+       ...+.+.++..+++..+..-....+.      +         
T Consensus        18 ~~~d~~~A~~~F~~a~~~d--P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~~~   95 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD--ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGDIT   95 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCCCE
T ss_pred             cCCCHHHHHHHHHHHHHhC--hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCcccccc
Confidence            5799999999999999876  3456788877       56666766677777777766552221      1         


Q ss_pred             ------HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC
Q 041804          101 ------EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV  174 (403)
Q Consensus       101 ------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  174 (403)
                            ......+...+...|++++|.++|..+...        .|+......+...+.+.+++++|+..|+...... .
T Consensus        96 ~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~--------~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d  166 (282)
T 4f3v_A           96 YPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVA--------GSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-D  166 (282)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCT--------TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-C
T ss_pred             cccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-C
Confidence                  234455667778888999998888887763        2332266666678888888888888887554431 1


Q ss_pred             Cc--HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC--hhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          175 KD--LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD--VVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       175 ~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      |.  ...+..+..++...|++++|+..|++.......|.  .........++.+.|+.++|..+|+++....
T Consensus       167 ~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          167 KFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             cccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            11  23667777788888888888888888775433243  2345556667777888888888888888763

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.89  E-value=7.4e-08  Score=68.73  Aligned_cols=95  Identities=15%  Similarity=0.186  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .|..+...+...|++++|++.|+++.+..+.+..++..+..++...|++++|...++++..       ..+.+..++..+
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~l   83 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALE-------LDPNNAEAWYNL   83 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-------hCCccHHHHHHH
Confidence            3444444444444444444444444443333334444444444444444444444443332       112223333444


Q ss_pred             HHHHHhcCChhHHHHHHHHHHh
Q 041804          149 LRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      ...+...|++++|...|+++.+
T Consensus        84 a~~~~~~~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           84 GNAYYKQGDYDEAIEYYQKALE  105 (125)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHH
Confidence            4444444444444444444433

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.89  E-value=4.5e-08  Score=70.54  Aligned_cols=115  Identities=11%  Similarity=0.040  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .+..+...+...|++++|+..|++.....+.+...+..+..++...|++++|...+.+...       ..+.+..++..+
T Consensus        14 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~~~   86 (131)
T 2vyi_A           14 RLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAIC-------IDPAYSKAYGRM   86 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHh-------cCccCHHHHHHH
Confidence            3333444444444444444444444443333344444444444444444444444443333       112223334444


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcC
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSG  191 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  191 (403)
                      ...+...|++++|.+.|++..+..+. +...+..+..++...|
T Consensus        87 ~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~  128 (131)
T 2vyi_A           87 GLALSSLNKHVEAVAYYKKALELDPD-NETYKSNLKIAELKLR  128 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHh
Confidence            44444444444444444444433222 3333444444444333

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.88  E-value=6.1e-08  Score=70.14  Aligned_cols=109  Identities=9%  Similarity=0.038  Sum_probs=90.2

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.....  .+.+...+..+..++...|++++|...+++..+..  +.+...+..+..++...|+
T Consensus        24 ~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~~~   99 (133)
T 2lni_A           24 NECFQKGDYPQAMKHYTEAIKR--NPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE--PTFIKGYTRKAAALEAMKD   99 (133)
T ss_dssp             HHHHHTTCSHHHHHHHHHHHTT--CTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHHHhh
Confidence            3456789999999999988742  34467888999999999999999999999988865  3567888899999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK  115 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  115 (403)
                      +++|++.|++..+..+.+...+..+..++...|
T Consensus       100 ~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A          100 YTKAMDVYQKALDLDSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhc
Confidence            999999999998887767778888777776655

>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=98.88  E-value=3.1e-08  Score=76.00  Aligned_cols=84  Identities=5%  Similarity=0.021  Sum_probs=37.0

Q ss_pred             ccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH-HHhcCCH--HH
Q 041804           43 KFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA-LCEYKHV--IE  119 (403)
Q Consensus        43 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--~~  119 (403)
                      ..|++++|...++......  +.+...|..+..+|...|++++|+..|++..+..+.+...+..+..+ +...|++  ++
T Consensus        22 ~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~   99 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQ   99 (177)
T ss_dssp             -----CCCCHHHHHHHHHC--CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHH
T ss_pred             hccCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHH
Confidence            4445555555555444432  23344455555555555555555555555554444444444444444 3344444  44


Q ss_pred             HHHHHhccc
Q 041804          120 AQELCFGEN  128 (403)
Q Consensus       120 a~~~~~~~~  128 (403)
                      |...+++..
T Consensus       100 A~~~~~~al  108 (177)
T 2e2e_A          100 TRAMIDKAL  108 (177)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            444444433

>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=98.87  E-value=5.3e-09  Score=89.22  Aligned_cols=149  Identities=9%  Similarity=-0.055  Sum_probs=125.7

Q ss_pred             cccHHHHHHhhhhhcccCCCcC-CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC----------------HHHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTH-TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN----------------HATF   70 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----------------~~~~   70 (403)
                      .+++++|++.|+....   ..| +...+..+...+.+.|++++|+..|++..+..   |+                ..+|
T Consensus       126 L~~~~~A~~~~~~a~~---~~p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~---p~~~~~~~~~~~~~~~~~~~~~  199 (336)
T 1p5q_A          126 LKSFEKAKESWEMNSE---EKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWL---EYESSFSNEEAQKAQALRLASH  199 (336)
T ss_dssp             EEEEECCCCGGGCCHH---HHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT---TTCCCCCSHHHHHHHHHHHHHH
T ss_pred             EeecccccchhcCCHH---HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh---hccccCChHHHHHHHHHHHHHH
Confidence            3566677777766543   133 46788899999999999999999999998865   33                4789


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      ..+..+|.+.|++++|+..|++..+..+.+..++..+..++...|++++|...|++...       ..+.+..++..+..
T Consensus       200 ~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~-------l~P~~~~a~~~l~~  272 (336)
T 1p5q_A          200 LNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ-------LYPNNKAAKTQLAV  272 (336)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCSSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-------HCCCCHHHHHHHHH
Confidence            99999999999999999999999999988999999999999999999999999999887       44667788999999


Q ss_pred             HHHhcCChhHH-HHHHHHHH
Q 041804          151 GWFKMSWWGKC-REFWEEMD  169 (403)
Q Consensus       151 ~~~~~~~~~~a-~~~~~~~~  169 (403)
                      .+.+.|+++++ ...+..|.
T Consensus       273 ~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          273 CQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            99999999988 44566554

>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=98.86  E-value=4.3e-07  Score=71.82  Aligned_cols=129  Identities=12%  Similarity=-0.100  Sum_probs=102.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHH
Q 041804          103 SYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSI  182 (403)
Q Consensus       103 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  182 (403)
                      .+..+...+...|++++|...+++..          .|+..++..+...|...|++++|.+.|++..+.... +...|..
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~----------~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~   76 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQ----------DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQ   76 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSS----------SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc----------CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHH
Confidence            45566777888899999999888764          246678888899999999999999999988877654 6778888


Q ss_pred             HHHHHHHcCChhHHHHHHHHHHHcCCC--------------C-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcC
Q 041804          183 YMDIMCKSGKPWKAVKLYKEMKKKGIK--------------M-DVVAYNTVIRAVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       183 l~~~~~~~~~~~~a~~~~~~~~~~~~~--------------~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      +..+|...|++++|...|+...+....              | ....+..+..++...|+++.|...|+...+..
T Consensus        77 lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           77 RGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            888999999999999999988875311              1 12567778888888888888888888888753

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.85  E-value=3.9e-08  Score=77.19  Aligned_cols=160  Identities=8%  Similarity=-0.025  Sum_probs=96.9

Q ss_pred             HccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhc----CC-C-cHHHHHHHHHHHHhcC
Q 041804           42 GKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEF----GL-K-DEVSYCNLVDALCEYK  115 (403)
Q Consensus        42 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~-~~~~~~~l~~~~~~~~  115 (403)
                      ...|++++|.++++.+...  ......++..+...+...|++++|+..+++..+.    +. + ...++..+...+...|
T Consensus         3 ~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g   80 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH--PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAG   80 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS--TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             cccccHHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcC
Confidence            3456777777744444332  1234556777777777777777777777776551    11 1 5566777778888888


Q ss_pred             CHHHHHHHHhcccccccccccc-cC-cchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC---CCCc--HHHHHHHHHHHH
Q 041804          116 HVIEAQELCFGENKNVGFSGLV-EM-NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG---VVKD--LHSYSIYMDIMC  188 (403)
Q Consensus       116 ~~~~a~~~~~~~~~~~~~~~~~-~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~--~~~~~~l~~~~~  188 (403)
                      ++++|...+++........  + .+ ....++..+...+...|++++|...+++.....   ..+.  ..++..+..++.
T Consensus        81 ~~~~A~~~~~~al~~~~~~--~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~  158 (203)
T 3gw4_A           81 NWDAARRCFLEERELLASL--PEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQ  158 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHS--CCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHc--CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence            8888888777655431100  1 11 224456777778888888888888887765321   1111  233566667777


Q ss_pred             HcCChhHHHHHHHHHHH
Q 041804          189 KSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       189 ~~~~~~~a~~~~~~~~~  205 (403)
                      ..|++++|.+.+++..+
T Consensus       159 ~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          159 QEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HCcCHHHHHHHHHHHHH
Confidence            77777777777766554

>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=98.85  E-value=9.3e-09  Score=85.37  Aligned_cols=196  Identities=8%  Similarity=-0.057  Sum_probs=133.3

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      .+...+..+...+.+.|++++|+..|++.....  +.+...|..+..+|.+.|++++|+..+++..+..+.+...+..+.
T Consensus         2 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg   79 (281)
T 2c2l_A            2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLG   79 (281)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            356778888999999999999999999998865  347888999999999999999999999999999888999999999


Q ss_pred             HHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMC  188 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  188 (403)
                      .++...|++++|...+.+.....+..  ........+..+  ..      ..+. -+..........+......+.. + 
T Consensus        80 ~~~~~~g~~~~A~~~~~~al~l~p~~--~~~~~~~~~~~~--~~------~~~~-~~~~~~~~~~~~~~~i~~~l~~-l-  146 (281)
T 2c2l_A           80 QCQLEMESYDEAIANLQRAYSLAKEQ--RLNFGDDIPSAL--RI------AKKK-RWNSIEERRIHQESELHSYLTR-L-  146 (281)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHT--TCCCCSHHHHHH--HH------HHHH-HHHHHHHTCCCCCCHHHHHHHH-H-
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCccc--hhhHHHHHHHHH--HH------HHHH-HHHHHHHHHHhhhHHHHHHHHH-H-
Confidence            99999999999999998876532100  000011111111  11      1111 1222333333334444444433 2 


Q ss_pred             HcCChhHHHHHHHHHHHcCCCCChh-hHHHHHHHHhhc-CCHHHHHHHHHHHHHc
Q 041804          189 KSGKPWKAVKLYKEMKKKGIKMDVV-AYNTVIRAVGVS-EGVDFAMRVYREMREM  241 (403)
Q Consensus       189 ~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~ll~~~~~~-~~~~~a~~~~~~~~~~  241 (403)
                      ..|++++|++.++...+.  .|+.. ....+...+.+. +.+++|.++|..+.+.
T Consensus       147 ~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          147 IAAERERELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             HHHHHHHHHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HHHHHHHHHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            368889998888877765  44443 333333334444 5678888888877653

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.85  E-value=6.3e-08  Score=71.67  Aligned_cols=101  Identities=9%  Similarity=-0.063  Sum_probs=69.7

Q ss_pred             CcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHH
Q 041804          139 MNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTV  218 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  218 (403)
                      |.+...+..+...+.+.|++++|...|++....++. +...|..+..+|...|++++|+..|++..+.. +-+...+..+
T Consensus        33 p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~l  110 (151)
T 3gyz_A           33 DDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY-NVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHT  110 (151)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHH
Confidence            344556666677777777777777777777766555 66677777777777777777777777777663 3345566667


Q ss_pred             HHHHhhcCCHHHHHHHHHHHHHc
Q 041804          219 IRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       219 l~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ..+|...|++++|...|+...+.
T Consensus       111 g~~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          111 GQCQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            77777777777777777777765

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.85  E-value=8.6e-08  Score=68.36  Aligned_cols=115  Identities=14%  Similarity=0.074  Sum_probs=96.3

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ...+..+...+...|++++|.++++++....  +.+..++..+...+...|++++|+..|+++.+..+.+..++..+..+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHH
Confidence            5678889999999999999999999998765  35678899999999999999999999999999887788999999999


Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK  154 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  154 (403)
                      +...|++++|...+++....       .+.+...+..+...+..
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~-------~~~~~~~~~~l~~~~~~  123 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALEL-------DPNNAEAKQNLGNAKQK  123 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHh-------CCCcHHHHHHHHHHHHh
Confidence            99999999999999987763       24445555555554443

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.85  E-value=5.7e-08  Score=69.96  Aligned_cols=122  Identities=10%  Similarity=-0.029  Sum_probs=104.0

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      +.+...+..+...+...|++++|...+++.....  +.+...+..+..++...|++++|+..+++..+..+.+...+..+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~   86 (131)
T 2vyi_A            9 SAEAERLKTEGNEQMKVENFEAAVHFYGKAIELN--PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRM   86 (131)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHccCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHH
Confidence            3456778888999999999999999999988764  35678899999999999999999999999999887788999999


Q ss_pred             HHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCCh
Q 041804          108 VDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWW  158 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  158 (403)
                      ..++...|++++|...+++....       .+.+...+..+...+.+.|++
T Consensus        87 ~~~~~~~~~~~~A~~~~~~~~~~-------~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           87 GLALSSLNKHVEAVAYYKKALEL-------DPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH-------STTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhc-------CccchHHHHHHHHHHHHHhcC
Confidence            99999999999999999988763       345667778888888777664

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.84  E-value=3.3e-07  Score=74.41  Aligned_cols=194  Identities=8%  Similarity=-0.099  Sum_probs=147.2

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHH-------HHHHHccCChhHHHHHHHHhhhCCCCCCC-------------
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSV-------IDILGKFFEFDLSWNLIHRMKDNPSSIPN-------------   66 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l-------i~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------------   66 (403)
                      +.+++..|.+.|..+...  .+-....|..+       ..++.+.++..++...+..-....   |+             
T Consensus        18 ~~~d~~~A~~~F~~a~~~--dP~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~---p~~l~a~~~~~g~y~   92 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNY--DESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQIS---MSTLNARIAIGGLYG   92 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCC---GGGGCCEEECCTTTC
T ss_pred             cCCCHHHHHHHHHHHHHh--ChhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCC---hhhhhhhhccCCccc
Confidence            468999999999999862  23347788887       567777777777777776665521   21             


Q ss_pred             ---------HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccc
Q 041804           67 ---------HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLV  137 (403)
Q Consensus        67 ---------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  137 (403)
                               ...+-.....+...|++++|.++|+.+...++.+. ....+...+.+.+++++|+..|......      .
T Consensus        93 ~~~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~p~~~-~~~~~a~l~~~~~r~~dA~~~l~~a~~~------~  165 (282)
T 4f3v_A           93 DITYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAGSEHL-VAWMKAVVYGAAERWTDVIDQVKSAGKW------P  165 (282)
T ss_dssp             CCEEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTTCHHH-HHHHHHHHHHHTTCHHHHHHHHTTGGGC------S
T ss_pred             ccccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCchH-HHHHHHHHHHHcCCHHHHHHHHHHhhcc------C
Confidence                     22344567888899999999999999988775566 7777777899999999999999865442      1


Q ss_pred             cCc--chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC--cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChh
Q 041804          138 EMN--KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK--DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVV  213 (403)
Q Consensus       138 ~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  213 (403)
                       .|  ...++..+..++...|++++|++.|++.......|  ..........++.+.|+.++|..+|+++...  .|+..
T Consensus       166 -d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~~~  242 (282)
T 4f3v_A          166 -DKFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPEPK  242 (282)
T ss_dssp             -CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCCHH
T ss_pred             -CcccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcHH
Confidence             12  13478888999999999999999999998654324  3446777788899999999999999999987  45533


Q ss_pred             hH
Q 041804          214 AY  215 (403)
Q Consensus       214 ~~  215 (403)
                      ..
T Consensus       243 ~~  244 (282)
T 4f3v_A          243 VA  244 (282)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.83  E-value=1.1e-06  Score=73.33  Aligned_cols=170  Identities=7%  Similarity=-0.144  Sum_probs=85.7

Q ss_pred             HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcH------HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcc
Q 041804           68 ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE------VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNK  141 (403)
Q Consensus        68 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  141 (403)
                      ..+...+..+...|++++|++.+.+..+......      ..+..+...+...|++++|...+++......... .....
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~-~~~~~  154 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGI-DVYQN  154 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSS-CTTHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCC-chHHH
Confidence            3445566667777777777777777666543311      1233344455566666666666655443210000 00011


Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHh---CCC-CC--cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC----CCC-
Q 041804          142 TKIYNMILRGWFKMSWWGKCREFWEEMDK---RGV-VK--DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG----IKM-  210 (403)
Q Consensus       142 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~-~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~~-  210 (403)
                      ..+++.+...|...|++++|...|++..+   ... .+  ...++..+..+|...|++++|+..+++..+..    ... 
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            33566666666666666666666665542   111 11  11355555566666666666666665554321    000 


Q ss_pred             ChhhHHHHHHHHhhcCCHHHH-HHHHHHH
Q 041804          211 DVVAYNTVIRAVGVSEGVDFA-MRVYREM  238 (403)
Q Consensus       211 ~~~~~~~ll~~~~~~~~~~~a-~~~~~~~  238 (403)
                      -..+|..+..+|.+.|+.++| ...++..
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            023444455555555555555 4444443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.83  E-value=1.8e-08  Score=74.58  Aligned_cols=99  Identities=10%  Similarity=-0.088  Sum_probs=91.7

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      +...+..+...+.+.|++++|+..|++.....  +.+...|..+..+|...|++++|+..|++..+..+.++..|..+..
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~--P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~  112 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD--FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQ  112 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHHH
Confidence            46688899999999999999999999999876  4578899999999999999999999999999999889999999999


Q ss_pred             HHHhcCCHHHHHHHHhccccc
Q 041804          110 ALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      ++...|++++|...|++....
T Consensus       113 ~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          113 CQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh
Confidence            999999999999999988764

>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=98.82  E-value=2.6e-08  Score=73.79  Aligned_cols=57  Identities=11%  Similarity=-0.093  Sum_probs=23.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhc
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFG  126 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  126 (403)
                      +..+...+...|++++|+..|++.....+.+...|..+..++...|++++|...+++
T Consensus        24 ~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~   80 (148)
T 2vgx_A           24 LYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSY   80 (148)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            333333444444444444444444443333334444444444444444444444333

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.82  E-value=5.2e-08  Score=76.43  Aligned_cols=162  Identities=8%  Similarity=-0.043  Sum_probs=118.5

Q ss_pred             cccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhC----CCCCCCHHHHHHHHHHHHhcC
Q 041804            6 CYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDN----PSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         6 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      ...|++++|.+.++.+..  .......++..+...+...|++++|...+++....    +..+....++..+...+...|
T Consensus         3 ~~~g~~~~A~~~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g   80 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLA--HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAG   80 (203)
T ss_dssp             ----CHHHHHHHHHHHHT--STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             cccccHHHHHHHHHHhcC--ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcC
Confidence            357999999996665543  12235778999999999999999999999987761    101223567888999999999


Q ss_pred             ChHHHHHHHHHHhhc---CC--C--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh
Q 041804           82 LVNEAMGTFNKLDEF---GL--K--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK  154 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~---~~--~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  154 (403)
                      ++++|+..+++..+.   ..  +  ...++..+...+...|++++|...+++........+ .......++..+...+..
T Consensus        81 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~~la~~~~~  159 (203)
T 3gw4_A           81 NWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQAD-DQVAIACAFRGLGDLAQQ  159 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcc-chHHHHHHHHHHHHHHHH
Confidence            999999999987765   21  1  355688899999999999999999988764311000 111223456888899999


Q ss_pred             cCChhHHHHHHHHHHh
Q 041804          155 MSWWGKCREFWEEMDK  170 (403)
Q Consensus       155 ~~~~~~a~~~~~~~~~  170 (403)
                      .|++++|.+.+++..+
T Consensus       160 ~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          160 EKNLLEAQQHWLRARD  175 (203)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHH
Confidence            9999999999987754

>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=98.81  E-value=2.9e-08  Score=76.15  Aligned_cols=118  Identities=8%  Similarity=-0.039  Sum_probs=59.6

Q ss_pred             cccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHH-HHhcCCh--H
Q 041804            8 ANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKR-YVTAHLV--N   84 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--~   84 (403)
                      .|++++|++.|+.....  .+.+...+..+..++...|++++|...|++..+..  +.+...+..+..+ +...|++  +
T Consensus        23 ~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           23 QQNPEAQLQALQDKIRA--NPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR--GENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             ----CCCCHHHHHHHHH--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--CSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             ccCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhcCCcchH
Confidence            45555555555554431  12344555555555555555555555555555433  2344445555555 4455555  5


Q ss_pred             HHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           85 EAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      +|+..|++..+..+.+...+..+..++...|++++|...+++...
T Consensus        99 ~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A           99 QTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            555555555555544555555555555555555555555554443

>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=98.81  E-value=6.2e-08  Score=71.74  Aligned_cols=100  Identities=8%  Similarity=-0.064  Sum_probs=90.9

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      .+...+..+...+.+.|++++|...|+......  +.+...|..+..+|...|++++|+..|++.....+.++..+..+.
T Consensus        19 ~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg   96 (148)
T 2vgx_A           19 DTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD--HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAA   96 (148)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC--cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHH
Confidence            356678888999999999999999999998865  457889999999999999999999999999999988999999999


Q ss_pred             HHHHhcCCHHHHHHHHhccccc
Q 041804          109 DALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      .++...|++++|...|++....
T Consensus        97 ~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           97 ECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            9999999999999999887764

>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=98.75  E-value=1.5e-08  Score=79.39  Aligned_cols=144  Identities=11%  Similarity=0.065  Sum_probs=67.9

Q ss_pred             HHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcH----------------HHH
Q 041804           41 LGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDE----------------VSY  104 (403)
Q Consensus        41 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----------------~~~  104 (403)
                      ....|+++++.+.++.-....  ......+..+...+...|++++|+..|++..+..+.+.                .++
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (198)
T 2fbn_A           14 RENLYFQGAKKSIYDYTDEEK--VQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCN   91 (198)
T ss_dssp             --------CCCSGGGCCHHHH--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHH
T ss_pred             hhhhhhccccCchhhCCHHHH--HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHH
Confidence            334455555555554332211  12344566677777777888888888877776554432                444


Q ss_pred             HHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHH
Q 041804          105 CNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYM  184 (403)
Q Consensus       105 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  184 (403)
                      ..+..++...|++++|...+++...       ..+.+..++..+..+|...|++++|.+.|++..+..+. +...+..+.
T Consensus        92 ~~la~~~~~~~~~~~A~~~~~~al~-------~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~  163 (198)
T 2fbn_A           92 LNLATCYNKNKDYPKAIDHASKVLK-------IDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPN-NLDIRNSYE  163 (198)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH-------HSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHH-------hCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHH
Confidence            4444455555555555555444443       12333444444444455555555555555444443322 333444444


Q ss_pred             HHHHHcCChh
Q 041804          185 DIMCKSGKPW  194 (403)
Q Consensus       185 ~~~~~~~~~~  194 (403)
                      .++...++.+
T Consensus       164 ~~~~~~~~~~  173 (198)
T 2fbn_A          164 LCVNKLKEAR  173 (198)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            4444333333

>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=98.75  E-value=2.3e-07  Score=66.47  Aligned_cols=94  Identities=12%  Similarity=-0.092  Sum_probs=45.3

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      .+..+...+.+.|++++|+..|++..+..  +.+...|..+..++...|++++|+..|++..+.++.+...+..+..++.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   83 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA--PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            34444444555555555555555444432  2234444455555555555555555555555444444444444444444


Q ss_pred             hcCCHHHHHHHHhccc
Q 041804          113 EYKHVIEAQELCFGEN  128 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~  128 (403)
                      ..|++++|...+++..
T Consensus        84 ~~~~~~~A~~~~~~al   99 (126)
T 3upv_A           84 AVKEYASALETLDAAR   99 (126)
T ss_dssp             HTTCHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHH
Confidence            5555555444444433

>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=98.74  E-value=2.4e-07  Score=66.46  Aligned_cols=105  Identities=10%  Similarity=0.030  Sum_probs=88.2

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.....  .+.+...|..+..++.+.|++++|+..+++..+..  +.+...|..+..++...|+
T Consensus        12 ~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~   87 (126)
T 3upv_A           12 KEYFTKSDWPNAVKAYTEMIKR--APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD--PNFVRAYIRKATAQIAVKE   87 (126)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHhcCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHhC
Confidence            4566789999999999998852  24568899999999999999999999999999875  3567889999999999999


Q ss_pred             hHHHHHHHHHHhhcC------CCcHHHHHHHHHHH
Q 041804           83 VNEAMGTFNKLDEFG------LKDEVSYCNLVDAL  111 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~------~~~~~~~~~l~~~~  111 (403)
                      +++|+..|++..+..      +.+...+..+..+.
T Consensus        88 ~~~A~~~~~~al~~~p~~~~~p~~~~~~~~l~~~~  122 (126)
T 3upv_A           88 YASALETLDAARTKDAEVNNGSSAREIDQLYYKAS  122 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcccCCchhHHHHHHHHHHHH
Confidence            999999999999877      55666666655543

>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=98.73  E-value=5.3e-07  Score=63.41  Aligned_cols=91  Identities=12%  Similarity=-0.078  Sum_probs=36.7

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      +..+...+...|++++|...|+......  +.+...+..+..++...|++++|...+++..+..+.+...+..+..++..
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~   84 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCYSEAIKLD--PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEF   84 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            3334444444444444444444443322  12333344444444444444444444444444333333333344444444


Q ss_pred             cCCHHHHHHHHhc
Q 041804          114 YKHVIEAQELCFG  126 (403)
Q Consensus       114 ~~~~~~a~~~~~~  126 (403)
                      .|++++|...+++
T Consensus        85 ~~~~~~A~~~~~~   97 (118)
T 1elw_A           85 LNRFEEAKRTYEE   97 (118)
T ss_dssp             TTCHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHH
Confidence            4444444443333

>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=98.73  E-value=3.8e-08  Score=77.03  Aligned_cols=156  Identities=11%  Similarity=-0.057  Sum_probs=112.1

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC--------------HHHHHH
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN--------------HATFRI   72 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--------------~~~~~~   72 (403)
                      ..++++.+.+.++....+  .......+..+...+.+.|++++|...|++.....+..|+              ..+|..
T Consensus        16 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (198)
T 2fbn_A           16 NLYFQGAKKSIYDYTDEE--KVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLN   93 (198)
T ss_dssp             ------CCCSGGGCCHHH--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccccCchhhCCHHH--HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHH
Confidence            346677777777644321  1223557788889999999999999999999875422221              278889


Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           73 MFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        73 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      +..+|...|++++|+..+++..+..+.+..++..+..++...|++++|...|++...       ..+.+..++..+..++
T Consensus        94 la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~  166 (198)
T 2fbn_A           94 LATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAAS-------LNPNNLDIRNSYELCV  166 (198)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH-------HSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHH-------HCCCcHHHHHHHHHHH
Confidence            999999999999999999999999888999999999999999999999999998876       3355677788888888


Q ss_pred             HhcCChhHHH-HHHHHHHhC
Q 041804          153 FKMSWWGKCR-EFWEEMDKR  171 (403)
Q Consensus       153 ~~~~~~~~a~-~~~~~~~~~  171 (403)
                      ...++..++. ..|..+...
T Consensus       167 ~~~~~~~~~~~~~~~~~f~~  186 (198)
T 2fbn_A          167 NKLKEARKKDKLTFGGMFDK  186 (198)
T ss_dssp             HHHHHHHC------------
T ss_pred             HHHHHHHHHHHHHHHHHhcc
Confidence            7777777666 455555443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.71  E-value=9.2e-08  Score=70.32  Aligned_cols=97  Identities=5%  Similarity=-0.082  Sum_probs=55.2

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ...+..+...+.+.|++++|...|+......  +.+...|..+..++...|++++|+..|++....++.++..+..+..+
T Consensus        18 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~   95 (142)
T 2xcb_A           18 LEQLYALGFNQYQAGKWDDAQKIFQALCMLD--HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAEC   95 (142)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHH
Confidence            3444455555556666666666666555543  23455555555666666666666666666665555555555555566


Q ss_pred             HHhcCCHHHHHHHHhcccc
Q 041804          111 LCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~  129 (403)
                      +...|++++|...|++...
T Consensus        96 ~~~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           96 HLQLGDLDGAESGFYSARA  114 (142)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            6666666666555555443

>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=98.69  E-value=3.7e-05  Score=64.35  Aligned_cols=170  Identities=10%  Similarity=-0.018  Sum_probs=118.9

Q ss_pred             HccCChh-HHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC----------hHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           42 GKFFEFD-LSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL----------VNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        42 ~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      .+.|.++ +|+++++.+...+  +-+..+|+.--..+...+.          +++++.+++.+....+.+..+|+.-..+
T Consensus        40 ~~~~e~s~eaL~~t~~~L~~n--P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wl  117 (331)
T 3dss_A           40 RQAGELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWL  117 (331)
T ss_dssp             HHTTCCSHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            3556654 7899999998876  3445567765444444333          5788888888888888888888888888


Q ss_pred             HHhcC--CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC-hhHHHHHHHHHHhCCCCCcHHHHHHHHHHH
Q 041804          111 LCEYK--HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW-WGKCREFWEEMDKRGVVKDLHSYSIYMDIM  187 (403)
Q Consensus       111 ~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  187 (403)
                      +...+  .+++++..+.++..       ..+.|..+|+.-.......|. ++++++.++.+.+.++. |..+|+.....+
T Consensus       118 L~~l~~~~~~~EL~~~~k~l~-------~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~-N~SAW~~R~~ll  189 (331)
T 3dss_A          118 LSRLPEPNWARELELCARFLE-------ADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLL  189 (331)
T ss_dssp             HHHCSSCCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHH
T ss_pred             HhccCcccHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHH
Confidence            77777  47888888888777       456777888877777777777 58888888888887777 777887777666


Q ss_pred             HHc--------------CChhHHHHHHHHHHHcCCCCChhhHHHHHHHH
Q 041804          188 CKS--------------GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV  222 (403)
Q Consensus       188 ~~~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~  222 (403)
                      ...              +.++++++.+....... +-|...|+-+-..+
T Consensus       190 ~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll  237 (331)
T 3dss_A          190 PQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLL  237 (331)
T ss_dssp             HHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHH
T ss_pred             HHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            655              23556666666666553 33555555443333

>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=98.69  E-value=7e-07  Score=62.77  Aligned_cols=104  Identities=10%  Similarity=-0.041  Sum_probs=87.9

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.....  .+.+...+..+..++...|++++|...+++..+..  +.+...+..+..++...|+
T Consensus        12 ~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~   87 (118)
T 1elw_A           12 NKALSVGNIDDALQCYSEAIKL--DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK--PDWGKGYSRKAAALEFLNR   87 (118)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHHhh
Confidence            3456789999999999998752  24468889999999999999999999999998865  3467889999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      +++|...|++..+.++.+...+..+..+
T Consensus        88 ~~~A~~~~~~~~~~~~~~~~~~~~l~~~  115 (118)
T 1elw_A           88 FEEAKRTYEEGLKHEANNPQLKEGLQNM  115 (118)
T ss_dssp             HHHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHHh
Confidence            9999999999999887777777666554

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.68  E-value=3.6e-07  Score=67.06  Aligned_cols=98  Identities=7%  Similarity=-0.100  Sum_probs=81.5

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.+...  .+.+...|..+..++.+.|++++|+..|++.....  +.+...+..+..+|...|+
T Consensus        26 ~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~  101 (142)
T 2xcb_A           26 FNQYQAGKWDDAQKIFQALCML--DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD--INEPRFPFHAAECHLQLGD  101 (142)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHHccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC--CCCcHHHHHHHHHHHHcCC
Confidence            3556789999999999998752  24568889999999999999999999999999875  3566788899999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSY  104 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~  104 (403)
                      +++|+..|+...+..+.++...
T Consensus       102 ~~~A~~~~~~al~~~p~~~~~~  123 (142)
T 2xcb_A          102 LDGAESGFYSARALAAAQPAHE  123 (142)
T ss_dssp             HHHHHHHHHHHHHHHHTCGGGH
T ss_pred             HHHHHHHHHHHHHhCCCCcchH
Confidence            9999999999988765544433

>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=98.66  E-value=1.2e-05  Score=67.21  Aligned_cols=218  Identities=6%  Similarity=-0.059  Sum_probs=158.4

Q ss_pred             ccH-HHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCC----------hhHHHHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 041804            9 NDW-KRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFE----------FDLSWNLIHRMKDNPSSIPNHATFRIMFKRY   77 (403)
Q Consensus         9 ~~~-~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~   77 (403)
                      |.+ ++|++.++.+..  -.+-+..+|+.--.++...+.          +++++.+++.+....  +.+..+|+.-..++
T Consensus        43 ~e~s~eaL~~t~~~L~--~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~--PKny~aW~hR~wlL  118 (331)
T 3dss_A           43 GELDESVLELTSQILG--ANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN--PKSYGTWHHRCWLL  118 (331)
T ss_dssp             TCCSHHHHHHHHHHHT--TCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH--HCchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHH
Confidence            444 478999988884  223345667766666555444          688999999998865  56888999988888


Q ss_pred             HhcCC--hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC-HHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh
Q 041804           78 VTAHL--VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH-VIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK  154 (403)
Q Consensus        78 ~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  154 (403)
                      .+.++  +++++.+++++.+.++.+..+|+.-..++...|. ++++++.+.++..       ..+.|..+|+.....+.+
T Consensus       119 ~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~-------~~p~N~SAW~~R~~ll~~  191 (331)
T 3dss_A          119 SRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLIT-------RNFSNYSSWHYRSCLLPQ  191 (331)
T ss_dssp             HHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-------HCSCCHHHHHHHHHHHHH
T ss_pred             hccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHH-------HCCCCHHHHHHHHHHHHH
Confidence            88884  8999999999999999999999998888888888 5899999888887       457788888877777665


Q ss_pred             c--------------CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc-----------CChhHHHHHHHHHHHcCCC
Q 041804          155 M--------------SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS-----------GKPWKAVKLYKEMKKKGIK  209 (403)
Q Consensus       155 ~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----------~~~~~a~~~~~~~~~~~~~  209 (403)
                      .              +.++++++.+.......+. |..+|+-+-..+.+.           +.++++++.++++.+.  .
T Consensus       192 l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~-d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~--~  268 (331)
T 3dss_A          192 LHPQPDSGPQGRLPENVLLKELELVQNAFFTDPN-DQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQEL--E  268 (331)
T ss_dssp             HSCCC------CCCHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHH--C
T ss_pred             hhhccccccccccchHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhh--C
Confidence            5              4578899999999888777 888888666555554           3456777777777765  3


Q ss_pred             CChhhHHHHH-----HHHhhcCCHHHHHHHHHHHHHc
Q 041804          210 MDVVAYNTVI-----RAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       210 ~~~~~~~~ll-----~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ||. .|..+.     ......+..+++...+.++.+.
T Consensus       269 pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          269 PEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             TTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             ccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence            443 232211     1122345556666666666654

>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=98.65  E-value=2.4e-07  Score=66.52  Aligned_cols=105  Identities=10%  Similarity=-0.038  Sum_probs=74.2

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHH
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYN  146 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (403)
                      ..++..+...+.+.|++++|+..|++..+..+.+..+|..+..+|...|++++|+..+++.....+........-..+|.
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~   87 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMS   87 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHH
Confidence            34677788888888888888888888888887788888888888888888888888887765431000000001123566


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      .+..++...|++++|.+.|++....
T Consensus        88 ~lg~~~~~~~~~~~A~~~~~kal~~  112 (127)
T 4gcn_A           88 RAGNAFQKQNDLSLAVQWFHRSLSE  112 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            6677777778888888887777664

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.64  E-value=1.3e-06  Score=64.40  Aligned_cols=99  Identities=10%  Similarity=-0.131  Sum_probs=89.9

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN----HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVS  103 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  103 (403)
                      +.+...+..+...+...|++++|...|++..+..   |+    ...|..+..+|...|++++|+..+++..+..+.+...
T Consensus        25 ~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~---~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  101 (148)
T 2dba_A           25 ASSVEQLRKEGNELFKCGDYGGALAAYTQALGLD---ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKA  101 (148)
T ss_dssp             CCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSC---CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHc---ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHH
Confidence            3467788999999999999999999999999865   65    6788899999999999999999999999988778999


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804          104 YCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       104 ~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      +..+..++...|++++|...+++...
T Consensus       102 ~~~~a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          102 LYRRSQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999999999998876

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.63  E-value=4.9e-07  Score=68.20  Aligned_cols=101  Identities=13%  Similarity=-0.034  Sum_probs=90.9

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      +.+...+..+...+.+.|++++|+..|++..+..  +.+...|..+..+|...|++++|+..|++..+..+.+...|..+
T Consensus         8 ~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l   85 (164)
T 3sz7_A            8 TPESDKLKSEGNAAMARKEYSKAIDLYTQALSIA--PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRL   85 (164)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            3456788899999999999999999999998865  34788899999999999999999999999999998899999999


Q ss_pred             HHHHHhcCCHHHHHHHHhccccc
Q 041804          108 VDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      ..++...|++++|...|++....
T Consensus        86 g~~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           86 GLARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHccCHHHHHHHHHHHHHh
Confidence            99999999999999999988764

>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=98.62  E-value=6.3e-07  Score=65.16  Aligned_cols=101  Identities=9%  Similarity=-0.111  Sum_probs=91.7

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      +.+...+..+...+...|++++|...|+......  +.+...|..+..++...|++++|+..|++..+..+.+...+..+
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l   83 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFL   83 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC--cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHH
Confidence            4567889999999999999999999999988865  35678999999999999999999999999999988899999999


Q ss_pred             HHHHHhcCCHHHHHHHHhccccc
Q 041804          108 VDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      ..++...|++++|...+.+....
T Consensus        84 ~~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           84 GQCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHH
Confidence            99999999999999999887654

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.62  E-value=6.9e-07  Score=79.94  Aligned_cols=121  Identities=8%  Similarity=-0.030  Sum_probs=100.9

Q ss_pred             CcccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhc
Q 041804            1 RETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTA   80 (403)
Q Consensus         1 L~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~   80 (403)
                      ++..+...|++++|++.|+...+.  .+.+..+|..+..++.+.|++++|+..+++..+..  +.+..+|..+..+|...
T Consensus        12 lg~~~~~~g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~lg~~~~~~   87 (477)
T 1wao_1           12 QANDYFKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD--KKYIKGYYRRAASNMAL   87 (477)
T ss_dssp             SSSSTTTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHc
Confidence            355677889999999999998852  24458899999999999999999999999999975  45678999999999999


Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHH--HHhcCCHHHHHHHHh
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDA--LCEYKHVIEAQELCF  125 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~a~~~~~  125 (403)
                      |++++|++.|++..+..+.+...+..+..+  +.+.|++++|.+.++
T Consensus        88 g~~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           88 GKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            999999999999999887777777777766  888899999999988

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.61  E-value=6e-07  Score=67.72  Aligned_cols=102  Identities=12%  Similarity=0.061  Sum_probs=80.5

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      .+...|..+...+...|++++|+..|++..+..+.+...|..+..+|...|++++|...+++...       ..+.+..+
T Consensus         9 ~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~-------~~p~~~~~   81 (164)
T 3sz7_A            9 PESDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATV-------VDPKYSKA   81 (164)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHH-------hCCCCHHH
Confidence            34567778888888888888888888888888777888888888888888888888888887776       33556777


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGV  173 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  173 (403)
                      |..+..+|...|++++|.+.|++..+...
T Consensus        82 ~~~lg~~~~~~g~~~~A~~~~~~al~~~p  110 (164)
T 3sz7_A           82 WSRLGLARFDMADYKGAKEAYEKGIEAEG  110 (164)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            88888888888888888888887776543

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.61  E-value=3.4e-07  Score=63.78  Aligned_cols=97  Identities=12%  Similarity=-0.004  Sum_probs=48.2

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--cHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--DEVSYCNLV  108 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~l~  108 (403)
                      ...+..+...+...|++++|...|++..+..  +.+...|..+..++...|++++|+..|++..+..+.  +...+..+.
T Consensus         6 ~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~   83 (112)
T 2kck_A            6 PEEYYLEGVLQYDAGNYTESIDLFEKAIQLD--PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKA   83 (112)
T ss_dssp             TTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC--cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHH
Confidence            3444445555555555555555555554432  233444555555555555555555555555554444  444455555


Q ss_pred             HHHHhc-CCHHHHHHHHhcccc
Q 041804          109 DALCEY-KHVIEAQELCFGENK  129 (403)
Q Consensus       109 ~~~~~~-~~~~~a~~~~~~~~~  129 (403)
                      .++... |++++|.+.+.+...
T Consensus        84 ~~~~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           84 DALRYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             HHHTTCSSCSHHHHHHHHHHGG
T ss_pred             HHHHHHhCCHHHHHHHHHHHhh
Confidence            555555 555555555444443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.58  E-value=5.6e-07  Score=62.64  Aligned_cols=93  Identities=8%  Similarity=-0.067  Sum_probs=80.6

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC--CHHHHHHHHHHHHhc
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP--NHATFRIMFKRYVTA   80 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~   80 (403)
                      .++...|++++|+..|+.....  .+.+...+..+..++...|++++|...+++..+..  +.  +...+..+..++...
T Consensus        14 ~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~l~~~~~~~   89 (112)
T 2kck_A           14 VLQYDAGNYTESIDLFEKAIQL--DPEESKYWLMKGKALYNLERYEEAVDCYNYVINVI--EDEYNKDVWAAKADALRYI   89 (112)
T ss_dssp             HHHHSSCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--CCTTCHHHHHHHHHHHTTC
T ss_pred             HHHHHhhhHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--cccchHHHHHHHHHHHHHH
Confidence            4566789999999999998752  24567889999999999999999999999999875  33  588999999999999


Q ss_pred             -CChHHHHHHHHHHhhcCCC
Q 041804           81 -HLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        81 -~~~~~a~~~~~~~~~~~~~   99 (403)
                       |++++|++.++......+.
T Consensus        90 ~~~~~~A~~~~~~~~~~~p~  109 (112)
T 2kck_A           90 EGKEVEAEIAEARAKLEHHH  109 (112)
T ss_dssp             SSCSHHHHHHHHHHGGGCCC
T ss_pred             hCCHHHHHHHHHHHhhcccC
Confidence             9999999999999987765

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.57  E-value=1.9e-06  Score=63.46  Aligned_cols=100  Identities=7%  Similarity=-0.087  Sum_probs=63.6

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc---HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcc
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD---EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNK  141 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  141 (403)
                      .+...+..+...+...|++++|+..|++..+..+.+   ...+..+..++...|++++|...+++...       ..+.+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~-------~~~~~   98 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIE-------KDGGD   98 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HTSCC
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHh-------hCccC
Confidence            355667777777777777777777777777766544   55666666666666666666666665554       22334


Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          142 TKIYNMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       142 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      ...+..+..++...|++++|.+.|++..+.
T Consensus        99 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A           99 VKALYRRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            455555566666666666666666665554

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.56  E-value=8.5e-07  Score=63.67  Aligned_cols=113  Identities=12%  Similarity=0.095  Sum_probs=79.6

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcc----h
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNK----T  142 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----~  142 (403)
                      ...|..+...+...|++++|+..|++..+..+.+...+..+..++...|++++|...+++.....+    ...++    .
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~~~~~   79 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGR----ENREDYRQIA   79 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH----HSTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhcc----ccchhHHHHH
Confidence            345667777778888888888888888777766777788888888888888888888777665310    00111    5


Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHH
Q 041804          143 KIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMD  185 (403)
Q Consensus       143 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  185 (403)
                      .++..+...+...|++++|.+.|++..+..  |+......+..
T Consensus        80 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~  120 (131)
T 1elr_A           80 KAYARIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDVLKKCQQ  120 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CCHHHHHHHHH
Confidence            667778888888888888888888887754  34444444443

>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=98.55  E-value=1.6e-06  Score=62.97  Aligned_cols=99  Identities=11%  Similarity=0.040  Sum_probs=66.7

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      .+...|..+...+...|++++|+..|+...+..+.+...+..+..++...|++++|...+++...       ..+.+..+
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~-------~~p~~~~~   79 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE-------LDGQSVKA   79 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-------hCchhHHH
Confidence            45666777777777777777777777777776666667777777777777777777777666655       22345556


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHh
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      +..+..++...|++++|...|++..+
T Consensus        80 ~~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           80 HFFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            66666666666666666666666554

>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=98.53  E-value=3.4e-06  Score=60.39  Aligned_cols=99  Identities=10%  Similarity=0.086  Sum_probs=64.0

Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC--CCCC----hhhH
Q 041804          142 TKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG--IKMD----VVAY  215 (403)
Q Consensus       142 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~----~~~~  215 (403)
                      ..++..+...+.+.|++++|++.|++..+..+. +...|..+..+|...|++++|++.+++.++..  ..++    ..+|
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~-~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPS-NITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            345666777777777777777777777776555 66677777777777777777777777766542  1111    1244


Q ss_pred             HHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          216 NTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       216 ~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ..+..++...|+++.|...|++..+.
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal~~  112 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSLSE  112 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            44555566666666666666666553

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.52  E-value=1.1e-05  Score=71.41  Aligned_cols=171  Identities=9%  Similarity=-0.070  Sum_probs=113.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc-chHHHHHHHHHHHhcCChhHHHHHHHHHHh----CCCCC-c
Q 041804          103 SYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN-KTKIYNMILRGWFKMSWWGKCREFWEEMDK----RGVVK-D  176 (403)
Q Consensus       103 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~-~  176 (403)
                      ++..+...|...|++++|.+.+..+.......  +... ...+.+.+-..+...|+++.|.++++....    .+..+ -
T Consensus        57 al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  134 (434)
T 4b4t_Q           57 SILELGQLYVTMGAKDKLREFIPHSTEYMMQF--AKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLK  134 (434)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTS--CHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc--cchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHH
Confidence            35667777888888888887777665432100  0011 112334444445567888898888877643    22222 3


Q ss_pred             HHHHHHHHHHHHHcCChhHHHHHHHHHHHc--CC--CC-ChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc--CCC-C-C-
Q 041804          177 LHSYSIYMDIMCKSGKPWKAVKLYKEMKKK--GI--KM-DVVAYNTVIRAVGVSEGVDFAMRVYREMREM--GCQ-P-S-  246 (403)
Q Consensus       177 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~--~~-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~--~~~-~-~-  246 (403)
                      ..++..+...|...|++++|..+++++...  +.  .+ ...++..++..|...|++++|..+++.....  .+. | . 
T Consensus       135 ~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~  214 (434)
T 4b4t_Q          135 HSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQT  214 (434)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHH
Confidence            457788889999999999999999887654  11  11 2347788888999999999999999887653  121 1 1 


Q ss_pred             -HHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          247 -VVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       247 -~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                       ...+..+...+...|+++.|...|.+..+
T Consensus       215 ~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          215 VAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             HHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence             24566667777888999999888877653

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.51  E-value=1e-06  Score=62.54  Aligned_cols=96  Identities=8%  Similarity=-0.141  Sum_probs=86.5

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      .+..+...+.+.|++++|+..|++..+..  +.+...|..+..++...|++++|+..|++..+..+.+...+..+..++.
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~   96 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHT   96 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            45667788999999999999999999875  3578899999999999999999999999999999889999999999999


Q ss_pred             hcCCHHHHHHHHhccccc
Q 041804          113 EYKHVIEAQELCFGENKN  130 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~  130 (403)
                      ..|++++|...+++....
T Consensus        97 ~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           97 NEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC-
T ss_pred             HcCCHHHHHHHHHHHHHh
Confidence            999999999999887653

>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=98.51  E-value=2.5e-06  Score=61.15  Aligned_cols=110  Identities=10%  Similarity=0.044  Sum_probs=73.4

Q ss_pred             hHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC--CCC----hhhH
Q 041804          142 TKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI--KMD----VVAY  215 (403)
Q Consensus       142 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~----~~~~  215 (403)
                      ...+..+...+...|++++|...|++..+.... +...+..+..++...|++++|...++.......  .++    ..++
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   82 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAY   82 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHH
Confidence            345667777777788888888888877766543 566777777777778888888887777766521  111    4566


Q ss_pred             HHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 041804          216 NTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVI  254 (403)
Q Consensus       216 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  254 (403)
                      ..+..++...|+++.|...|+.+.+..  |+......+.
T Consensus        83 ~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~  119 (131)
T 1elr_A           83 ARIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDVLKKCQ  119 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhC--CCHHHHHHHH
Confidence            666677777777777777777777653  3444444333

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.51  E-value=5e-06  Score=73.58  Aligned_cols=202  Identities=8%  Similarity=-0.071  Sum_probs=141.6

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCC---------------HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--c
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPN---------------HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--D  100 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~---------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~  100 (403)
                      ...+.+.|++++|++.|..+.+......+               ..++..+...|...|++++|.+.+..+.+.-..  +
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            45677889999999999888875422111               124778889999999999999999887654322  2


Q ss_pred             H----HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC----
Q 041804          101 E----VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG----  172 (403)
Q Consensus       101 ~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----  172 (403)
                      .    .+.+.+...+...|+.+.+..++........... .......++..+...|...|++++|..+++++...-    
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~  169 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREK-RVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD  169 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSS-CCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc
Confidence            1    2333444445567888999888876554221100 223345678899999999999999999998875421    


Q ss_pred             C-CCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc--CCC-C-C--hhhHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          173 V-VKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK--GIK-M-D--VVAYNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       173 ~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~-~-~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      - .....++..++..|...|++++|..++++....  .+. | .  ...+..+...+...++++.|...|....+
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            1 113467888999999999999999999887653  122 1 1  23556666777889999999998887764

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.50  E-value=1.6e-07  Score=83.63  Aligned_cols=151  Identities=9%  Similarity=-0.080  Sum_probs=116.6

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-------------HHHHHHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-------------HATFRIMFK   75 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------------~~~~~~l~~   75 (403)
                      +++++|++.|+.....  .+.....+..+...+.+.|++++|+..|++..+.....++             ..+|..+..
T Consensus       248 ~~~~~A~~~~~~~~~~--~~~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~  325 (457)
T 1kt0_A          248 KSFEKAKESWEMDTKE--KLEQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAM  325 (457)
T ss_dssp             EEEECCCCGGGSCHHH--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhcccCcchhhcCHHH--HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHH
Confidence            4566666666554421  1223567888999999999999999999998885411111             578999999


Q ss_pred             HHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           76 RYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        76 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      +|.+.|++++|+..|++..+..+.+..+|..+..+|...|++++|...|++....       .+.+..++..+..++.+.
T Consensus       326 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l-------~P~~~~a~~~l~~~~~~~  398 (457)
T 1kt0_A          326 CYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV-------NPQNKAARLQISMCQKKA  398 (457)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-------C----CHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999889999999999999999999999999998773       355667788888888888


Q ss_pred             CChhHHHH-HHHHH
Q 041804          156 SWWGKCRE-FWEEM  168 (403)
Q Consensus       156 ~~~~~a~~-~~~~~  168 (403)
                      ++++++.+ .+..|
T Consensus       399 ~~~~~a~~~~~~~~  412 (457)
T 1kt0_A          399 KEHNERDRRIYANM  412 (457)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHH
Confidence            88877653 34444

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.50  E-value=1e-06  Score=62.59  Aligned_cols=95  Identities=7%  Similarity=-0.179  Sum_probs=68.1

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      +..+...+.+.|++++|+..|++..+..+.+...|..+..++...|++++|...+++...       ..+.+..++..+.
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~-------l~P~~~~~~~~la   92 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARM-------LDPKDIAVHAALA   92 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCCCCHHHHHHHH
Confidence            445566677778888888888887777766777777777777777777777777777665       3344566677777


Q ss_pred             HHHHhcCChhHHHHHHHHHHhC
Q 041804          150 RGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      .++...|++++|...|++..+.
T Consensus        93 ~~~~~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           93 VSHTNEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh
Confidence            7777777777777777776654

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.45  E-value=3.2e-06  Score=60.58  Aligned_cols=94  Identities=13%  Similarity=-0.106  Sum_probs=69.7

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH---HHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc---HHHHHHH
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH---ATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD---EVSYCNL  107 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~l  107 (403)
                      +..+...+...|++++|...|+...+..  +.+.   .++..+..++...|++++|+..|++..+..+.+   ..++..+
T Consensus         5 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~l   82 (129)
T 2xev_A            5 AYNVAFDALKNGKYDDASQLFLSFLELY--PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKL   82 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHH
Confidence            4455667777888888888888877754  1222   467777778888888888888888888777665   6677778


Q ss_pred             HHHHHhcCCHHHHHHHHhcccc
Q 041804          108 VDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      ..++...|++++|...++++..
T Consensus        83 a~~~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           83 GLSQYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            8888888888888888877765

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.43  E-value=8.9e-06  Score=58.21  Aligned_cols=93  Identities=5%  Similarity=-0.123  Sum_probs=54.0

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhcCCCcH---HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcc---hHHH
Q 041804           72 IMFKRYVTAHLVNEAMGTFNKLDEFGLKDE---VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNK---TKIY  145 (403)
Q Consensus        72 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---~~~~  145 (403)
                      .+...+...|++++|+..|+.+.+..+.+.   ..+..+..++...|++++|...+++....       .+.+   ..++
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~-------~p~~~~~~~~~   79 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSR-------YPTHDKAAGGL   79 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTSTTHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHH-------CCCCcccHHHH
Confidence            345556666777777777776666555433   45556666666666666666666655542       1222   3445


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhC
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKR  171 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~  171 (403)
                      ..+..++...|++++|...|+++.+.
T Consensus        80 ~~la~~~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           80 LKLGLSQYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            55555566666666666666655554

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.39  E-value=1.8e-06  Score=73.60  Aligned_cols=96  Identities=13%  Similarity=-0.053  Sum_probs=62.6

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHH------------------HHHHHHHHHHhcCChHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHA------------------TFRIMFKRYVTAHLVNEAMGTFNK   92 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~------------------~~~~l~~~~~~~~~~~~a~~~~~~   92 (403)
                      ...+..+...+.+.|++++|...|++.....   |+..                  .|..+..+|.+.|++++|+..|++
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~---p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~  255 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYM---GDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNI  255 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHS---CHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHh---ccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            4456677778888888999998888877643   5443                  555556666666666666666666


Q ss_pred             HhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           93 LDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        93 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      ..+..+.+..+|..+..+|...|++++|...|++...
T Consensus       256 al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          256 VLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             HHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             HHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6665555556666666666666666666666655544

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.38  E-value=7.8e-07  Score=62.74  Aligned_cols=89  Identities=6%  Similarity=-0.084  Sum_probs=42.0

Q ss_pred             cccHHHHHHhhhhhcccCC--CcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804            8 ANDWKRALEFFNWVETDCH--FTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~--~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      .|++++|++.|+.... .+  .+.+..++..+..++...|++++|+..|++..+..  +.+..++..+..++...|++++
T Consensus         3 ~g~~~~A~~~~~~al~-~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~   79 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIA-SGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF--PNHQALRVFYAMVLYNLGRYEQ   79 (117)
T ss_dssp             ----CCCHHHHHHHHS-SCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHH
T ss_pred             CCcHHHHHHHHHHHHH-cCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchHHHHHHHHHHHHcCCHHH
Confidence            3455555555555543 11  12233445555555555555555555555555443  2234445555555555555555


Q ss_pred             HHHHHHHHhhcCCC
Q 041804           86 AMGTFNKLDEFGLK   99 (403)
Q Consensus        86 a~~~~~~~~~~~~~   99 (403)
                      |+..|++..+..+.
T Consensus        80 A~~~~~~al~~~p~   93 (117)
T 3k9i_A           80 GVELLLKIIAETSD   93 (117)
T ss_dssp             HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHhCCC
Confidence            55555555544433

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.37  E-value=8.8e-07  Score=79.24  Aligned_cols=88  Identities=10%  Similarity=-0.037  Sum_probs=43.6

Q ss_pred             HHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH
Q 041804           39 DILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI  118 (403)
Q Consensus        39 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  118 (403)
                      ..+.+.|++++|.+.|++..+..  +.+..+|..+..+|.+.|++++|++.+++..+..+.+..++..+..+|...|+++
T Consensus        14 ~~~~~~g~~~~A~~~~~~Al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           14 NDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             SSTTTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHH
Confidence            34444555555555555554432  2234455555555555555555555555555544444444555555555555555


Q ss_pred             HHHHHHhccc
Q 041804          119 EAQELCFGEN  128 (403)
Q Consensus       119 ~a~~~~~~~~  128 (403)
                      +|.+.+++..
T Consensus        92 eA~~~~~~al  101 (477)
T 1wao_1           92 AALRDYETVV  101 (477)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5544444433

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.37  E-value=7.9e-07  Score=62.73  Aligned_cols=108  Identities=6%  Similarity=-0.135  Sum_probs=86.9

Q ss_pred             ccCChhHHHHHHHHhhhCCCC-CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHH
Q 041804           43 KFFEFDLSWNLIHRMKDNPSS-IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQ  121 (403)
Q Consensus        43 ~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  121 (403)
                      ..|++++|+..|++..+.+.. +.+..++..+..+|...|++++|+..|++..+..+.+..++..+..++...|++++|.
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHH
Confidence            468999999999999986311 2345688999999999999999999999999999889999999999999999999999


Q ss_pred             HHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804          122 ELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      ..+++.....     ...|+...|...+..|.+.
T Consensus        82 ~~~~~al~~~-----p~~~~~~~~~~ai~~~~~~  110 (117)
T 3k9i_A           82 ELLLKIIAET-----SDDETIQSYKQAILFYADK  110 (117)
T ss_dssp             HHHHHHHHHH-----CCCHHHHHTHHHHHHHTTC
T ss_pred             HHHHHHHHhC-----CCcHHHHHHHHHHHHHHHH
Confidence            9999877654     4566777777777777653

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.37  E-value=3.9e-06  Score=74.73  Aligned_cols=157  Identities=8%  Similarity=-0.066  Sum_probs=83.0

Q ss_pred             ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHh
Q 041804           46 EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCF  125 (403)
Q Consensus        46 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  125 (403)
                      ++++|...|+......  +.....|..+...+.+.|++++|+..|++..+..+.+...            ..+....   
T Consensus       249 ~~~~A~~~~~~~~~~~--~~~a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~------------~~~~~~~---  311 (457)
T 1kt0_A          249 SFEKAKESWEMDTKEK--LEQAAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGL------------SEKESKA---  311 (457)
T ss_dssp             EEECCCCGGGSCHHHH--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSC------------CHHHHHH---
T ss_pred             hcccCcchhhcCHHHH--HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccC------------ChHHHHH---
Confidence            4455555554443321  1234578888899999999999999999988866553110            0000000   


Q ss_pred             cccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          126 GENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                                 ..+....+|..+..+|.+.|++++|+..+++..+.... +..+|..+..+|...|++++|...|++..+
T Consensus       312 -----------~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~~g~a~~~~g~~~~A~~~~~~al~  379 (457)
T 1kt0_A          312 -----------SESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLE  379 (457)
T ss_dssp             -----------HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             -----------HHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence                       00112234455555555555555555555555554433 455555555555555555555555555554


Q ss_pred             cCCCCChhhHHHHHHHHhhcCCHHHHH
Q 041804          206 KGIKMDVVAYNTVIRAVGVSEGVDFAM  232 (403)
Q Consensus       206 ~~~~~~~~~~~~ll~~~~~~~~~~~a~  232 (403)
                      .. +-+...+..+..++.+.++.+++.
T Consensus       380 l~-P~~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          380 VN-PQNKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             TC-----CHHHHHHHHHHHHHHHHHHH
T ss_pred             hC-CCCHHHHHHHHHHHHHHHHHHHHH
Confidence            42 223334455555555555554443

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.35  E-value=5.2e-06  Score=71.55  Aligned_cols=137  Identities=9%  Similarity=-0.050  Sum_probs=79.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .+..+...+.+.|++++|+..|++..+.-....           .....+++.       .       ..+.+..+|..+
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~-----------~~~~~~~~~-------~-------~~~~~~~~~~nl  279 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSR-----------AAAEDADGA-------K-------LQPVALSCVLNI  279 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHH-----------HHSCHHHHG-------G-------GHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCc-----------cccChHHHH-------H-------HHHHHHHHHHHH
Confidence            466777788888888888888887765210000           000111110       0       112344556666


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCH
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGV  228 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~  228 (403)
                      ..+|.+.|++++|.+.+++..+.... +...|..+..+|...|++++|++.|++..+.. +.+...+..+..++...++.
T Consensus       280 a~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~-P~~~~~~~~l~~~~~~~~~~  357 (370)
T 1ihg_A          280 GACKLKMSDWQGAVDSCLEALEIDPS-NTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLKVKQKIKAQ  357 (370)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccCHHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHH
Confidence            66666667777777777666665443 55666666666777777777777776666652 22444555555555555555


Q ss_pred             HHHH
Q 041804          229 DFAM  232 (403)
Q Consensus       229 ~~a~  232 (403)
                      +++.
T Consensus       358 ~~a~  361 (370)
T 1ihg_A          358 KDKE  361 (370)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.34  E-value=2.7e-06  Score=63.59  Aligned_cols=98  Identities=7%  Similarity=-0.027  Sum_probs=63.9

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC----HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC------c
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN----HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK------D  100 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~  100 (403)
                      ..++..+...+...|++++|...+++..+.....++    ..++..+...+...|++++|...+++..+....      .
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~   88 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVE   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHH
Confidence            346777778888888888888888776653200111    136777778888888888888888776543211      2


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHhccc
Q 041804          101 EVSYCNLVDALCEYKHVIEAQELCFGEN  128 (403)
Q Consensus       101 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~  128 (403)
                      ..++..+..++...|++++|...+++..
T Consensus        89 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~  116 (164)
T 3ro3_A           89 AQSCYSLGNTYTLLQDYEKAIDYHLKHL  116 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            3455666666667777777766665544

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.34  E-value=4.9e-05  Score=69.32  Aligned_cols=173  Identities=10%  Similarity=-0.037  Sum_probs=125.4

Q ss_pred             cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC----------hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           44 FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL----------VNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        44 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      ....++|++.++.+....  +.+..+|+.--.++...|+          ++++++.++.+.+..+++..+|..-..++.+
T Consensus        42 ~~~~eeal~~~~~~l~~n--P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~  119 (567)
T 1dce_A           42 GELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSR  119 (567)
T ss_dssp             TCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            334567788898888865  3456678877777777766          8889999999998888888888888888888


Q ss_pred             cC--CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC-ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          114 YK--HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS-WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       114 ~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      .+  +++++++.++++.+       ..+.+..+|+.-.....+.| .++++.+.++++.+.++. |..+|+.....+.+.
T Consensus       120 l~~~~~~~el~~~~k~l~-------~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~-n~saW~~r~~ll~~l  191 (567)
T 1dce_A          120 LPEPNWARELELCARFLE-------ADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQL  191 (567)
T ss_dssp             CSSCCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC-CHHHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHh-------hccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCC-CccHHHHHHHHHHhh
Confidence            88  66888888888877       44677888888877777888 788888888888887777 778888877776663


Q ss_pred             --------------CChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCC
Q 041804          191 --------------GKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEG  227 (403)
Q Consensus       191 --------------~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~  227 (403)
                                    +.++++++.+++..... +-|...|..+-..+.+.++
T Consensus       192 ~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~ll~~~~~  241 (567)
T 1dce_A          192 HPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGRAEP  241 (567)
T ss_dssp             SCCCCSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHHHHSCCCC
T ss_pred             cccccccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHHHHhcCCC
Confidence                          33455666666655542 3344555555444444443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.33  E-value=6.6e-06  Score=61.40  Aligned_cols=137  Identities=8%  Similarity=-0.077  Sum_probs=77.9

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC------cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK------DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                      ..++..+...+...|++++|+..+++..+....      ...++..+...+...|++++|...+++........+ ....
T Consensus         9 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~-~~~~   87 (164)
T 3ro3_A            9 GRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLK-DRAV   87 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT-CHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhC-CcHH
Confidence            346777888888899999999998887664322      224666777777777888877777766544210000 0011


Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHHHHHhC----CCC-CcHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWEEMDKR----GVV-KDLHSYSIYMDIMCKSGKPWKAVKLYKEMK  204 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  204 (403)
                      ...++..+...+...|++++|.+.+++..+.    +.. ....++..+...+...|++++|.+.+++..
T Consensus        88 ~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  156 (164)
T 3ro3_A           88 EAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL  156 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            1334555556666666666666666554432    100 012334444555555555555555555443

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.33  E-value=4.5e-06  Score=71.95  Aligned_cols=124  Identities=6%  Similarity=-0.088  Sum_probs=102.7

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhh----------------CCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHh
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKD----------------NPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLD   94 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~----------------~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~   94 (403)
                      ...+..+...+.+.|++++|+..|++..+                ..  +.+..+|..+..+|.+.|++++|+..+++..
T Consensus       223 a~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~--~~~~~~~~nla~~~~~~g~~~~A~~~~~~al  300 (370)
T 1ihg_A          223 SEDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQ--PVALSCVLNIGACKLKMSDWQGAVDSCLEAL  300 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGH--HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHH--HHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            34577888899999999999999998876                22  2345688999999999999999999999999


Q ss_pred             hcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHH
Q 041804           95 EFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCRE  163 (403)
Q Consensus        95 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  163 (403)
                      +..+.+..++..+..+|...|++++|...+++....       .+.+..++..+...+...++.+++.+
T Consensus       301 ~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l-------~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          301 EIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI-------APEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            998889999999999999999999999999988763       34566677777777777776666544

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.32  E-value=5e-06  Score=62.45  Aligned_cols=100  Identities=13%  Similarity=-0.032  Sum_probs=83.7

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhC--------CCC--------CCCHHHHHHHHHHHHhcCChHHHHHHHHHHh
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDN--------PSS--------IPNHATFRIMFKRYVTAHLVNEAMGTFNKLD   94 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~--------~~~--------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~   94 (403)
                      ...+......+.+.|++++|+..|......        ...        +.+...|..+..+|.+.|++++|+..+++..
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            456778888899999999999999887764        100        1234678889999999999999999999999


Q ss_pred             hcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhccccc
Q 041804           95 EFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus        95 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      +.++.+..+|..+..++...|++++|...|++....
T Consensus        91 ~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           91 KREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            998889999999999999999999999999887763

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.31  E-value=5.8e-06  Score=62.07  Aligned_cols=117  Identities=11%  Similarity=-0.013  Sum_probs=62.5

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      ....+......+.+.|++++|+..|.+....-..           ............  ..          ..+.+..+|
T Consensus        10 ~a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~-----------~~~~~~~~~~~~--~~----------~~~~~~~~~   66 (162)
T 3rkv_A           10 SVEALRQKGNELFVQKDYKEAIDAYRDALTRLDT-----------LILREKPGEPEW--VE----------LDRKNIPLY   66 (162)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-----------HHHTSCTTSHHH--HH----------HHHTHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH-----------hcccCCCCHHHH--HH----------HHHHHHHHH
Confidence            3456778888999999999999999988775000           000000000000  00          112333445


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..+..+|.+.|++++|...+++..+.++. +...|..+..+|...|++++|...|+...+.
T Consensus        67 ~nla~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           67 ANMSQCYLNIGDLHEAEETSSEVLKREET-NEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            55555555555555555555555554433 4455555555555555555555555555544

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.25  E-value=0.0001  Score=67.19  Aligned_cols=175  Identities=6%  Similarity=-0.046  Sum_probs=145.2

Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC----------HHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH----------VIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      ...++|++.++++....+.+..+|+.--.++...++          +++++..++++..       ..+.+..+|+.-..
T Consensus        43 ~~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~-------~~pK~y~aW~hR~w  115 (567)
T 1dce_A           43 ELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLR-------VNPKSYGTWHHRCW  115 (567)
T ss_dssp             CCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHH-------hCCCCHHHHHHHHH
Confidence            345688999999999999888999888888877777          8999999999887       55788899999999


Q ss_pred             HHHhcC--ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcC-ChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc--
Q 041804          151 GWFKMS--WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSG-KPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS--  225 (403)
Q Consensus       151 ~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~--  225 (403)
                      .+.+.+  +++++.+.++++.+.++. +..+|+.-..++.+.| .++++++.++++.+.. +-|...|+.....+.+.  
T Consensus       116 ~l~~l~~~~~~~el~~~~k~l~~d~~-N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~-p~n~saW~~r~~ll~~l~~  193 (567)
T 1dce_A          116 LLSRLPEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHP  193 (567)
T ss_dssp             HHHTCSSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSC
T ss_pred             HHHHcccccHHHHHHHHHHHHhhccc-cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC-CCCccHHHHHHHHHHhhcc
Confidence            999999  679999999999999888 8999999988888989 8999999999998875 44777888777766553  


Q ss_pred             ------------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHH
Q 041804          226 ------------EGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVRE  265 (403)
Q Consensus       226 ------------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  265 (403)
                                  +.++++.+.++.+....+. +...|+.+-..+.+.++.++
T Consensus       194 ~~~~~~~~~~~~~~~~eel~~~~~ai~~~P~-~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          194 QPDSGPQGRLPENVLLKELELVQNAFFTDPN-DQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             CCCSSSCCSSCHHHHHHHHHHHHHHHHHCSS-CSHHHHHHHHHHSCCCCCSC
T ss_pred             cccccccccccHHHHHHHHHHHHHHHhhCCC-CccHHHHHHHHHhcCCCccc
Confidence                        5578999999998887543 77788887777777666433

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=98.21  E-value=3e-06  Score=58.85  Aligned_cols=97  Identities=7%  Similarity=-0.157  Sum_probs=79.8

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCc------HH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKD------EV  102 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~------~~  102 (403)
                      ++...+..+...+...|++++|+..|++..+..  +.+...|..+..++...|++++|+..|++..+..+.+      ..
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~   79 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ--PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIRSK   79 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHHHH
Confidence            346778889999999999999999999998865  4578889999999999999999999999999988776      66


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHhcc
Q 041804          103 SYCNLVDALCEYKHVIEAQELCFGE  127 (403)
Q Consensus       103 ~~~~l~~~~~~~~~~~~a~~~~~~~  127 (403)
                      .+..+..++...|+.+.|...++++
T Consensus        80 ~~~~~~~~~~~~~~~~~a~~~~~~~  104 (111)
T 2l6j_A           80 LQYRLELAQGAVGSVQIPVVEVDEL  104 (111)
T ss_dssp             HHHHHHHHHHHHHCCCCCSSSSSSC
T ss_pred             HHHHHHHHHHHHHhHhhhHhHHHHh
Confidence            6777777777777766665555444

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.18  E-value=1.7e-05  Score=58.09  Aligned_cols=99  Identities=13%  Similarity=-0.037  Sum_probs=82.6

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCC-----CH-----HHHHHHHHHHHhcCChHHHHHHHHHHhhc-----
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIP-----NH-----ATFRIMFKRYVTAHLVNEAMGTFNKLDEF-----   96 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----   96 (403)
                      ..+......+.+.|++++|+..|++..+..+..|     +.     ..|..+..++.+.|++++|+..+++.++.     
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~   91 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG   91 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccc
Confidence            4456677788899999999999998887551111     22     38999999999999999999999999998     


Q ss_pred             --CCCcHHHH----HHHHHHHHhcCCHHHHHHHHhccccc
Q 041804           97 --GLKDEVSY----CNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus        97 --~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                        .+.+...|    .....++...|++++|+..|++....
T Consensus        92 e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel  131 (159)
T 2hr2_A           92 ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEM  131 (159)
T ss_dssp             CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhc
Confidence              87788899    99999999999999999999887653

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.14  E-value=5.3e-06  Score=70.65  Aligned_cols=149  Identities=9%  Similarity=-0.042  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHH
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYN  146 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  146 (403)
                      ...+..+...+.+.|++++|+..|++.....+.+.        .+...++..++...+                ...+|.
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~--------~~~~~~~~~~~~~~l----------------~~~~~~  234 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDF--------MFQLYGKYQDMALAV----------------KNPCHL  234 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHH--------HHTCCHHHHHHHHHH----------------HTHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccch--------hhhhcccHHHHHHHH----------------HHHHHH
Confidence            34577778888899999999999999887654332        112233333333221                113577


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHH-Hhhc
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRA-VGVS  225 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~-~~~~  225 (403)
                      .+..+|.+.|++++|...+++..+.... +...|..+..+|...|++++|...|++..+.. +-+...+..+... ....
T Consensus       235 nla~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~-p~~~~a~~~L~~l~~~~~  312 (338)
T 2if4_A          235 NIAACLIKLKRYDEAIGHCNIVLTEEEK-NPKALFRRGKAKAELGQMDSARDDFRKAQKYA-PDDKAIRRELRALAEQEK  312 (338)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHTTC---------------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHH
Confidence            7888888888888888888888776554 67788888888888888888888888876542 1233344444443 2334


Q ss_pred             CCHHHHHHHHHHHHHc
Q 041804          226 EGVDFAMRVYREMREM  241 (403)
Q Consensus       226 ~~~~~a~~~~~~~~~~  241 (403)
                      +..+.+..+|..+...
T Consensus       313 ~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          313 ALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             ----------------
T ss_pred             HHHHHHHHHHHHhhCC
Confidence            5667777778777654

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.12  E-value=7e-05  Score=66.69  Aligned_cols=63  Identities=6%  Similarity=-0.102  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHh-----CCCC-C-cHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          143 KIYNMILRGWFKMSWWGKCREFWEEMDK-----RGVV-K-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       143 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      .+++.|...|...|++++|+.++++..+     .|.. | ...+.+.+-.++...+.+++|..+|..+++
T Consensus       394 ~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          394 MAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555555554444322     1211 1 223344455555666666677766666654

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=98.09  E-value=2.4e-05  Score=54.66  Aligned_cols=77  Identities=13%  Similarity=-0.009  Sum_probs=40.0

Q ss_pred             HHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhccc
Q 041804           50 SWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGEN  128 (403)
Q Consensus        50 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  128 (403)
                      |+..|++..+..  +.+...+..+...|...|++++|+..|++..+..+.+...+..+..++...|++++|...+++..
T Consensus         4 a~~~~~~al~~~--p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            4 ITERLEAMLAQG--TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             HHHHHHHHHTTT--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC--CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            444455444433  23344555555555555555555555555555554455555555555555555555555554443

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.09  E-value=5.6e-05  Score=55.39  Aligned_cols=104  Identities=13%  Similarity=0.025  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-------cH-----HHHHHHHHHHHhcCCHHHHHHHHhccccccccc
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-------DE-----VSYCNLVDALCEYKHVIEAQELCFGENKNVGFS  134 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-------~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  134 (403)
                      ...+......+...|++++|+..|++..+..+.       +.     ..|..+..++.+.|++++|+..+++......-.
T Consensus        11 a~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~   90 (159)
T 2hr2_A           11 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   90 (159)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcc
Confidence            345667778888999999999999999887766       33     389999999999999999999877655410000


Q ss_pred             ccccCcchHHH----HHHHHHHHhcCChhHHHHHHHHHHh
Q 041804          135 GLVEMNKTKIY----NMILRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       135 ~~~~~~~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      ....+.+...|    .....++...|++++|+..|++..+
T Consensus        91 ~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           91 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            00023344445    5555555555555555555555443

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=98.07  E-value=4.2e-05  Score=50.64  Aligned_cols=84  Identities=13%  Similarity=0.087  Sum_probs=71.7

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      +...+..+...+...|++++|...|++..+..  +.+..++..+..++...|++++|+..|++..+..+.+...+..+..
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            45678888899999999999999999988865  3467888999999999999999999999999988778888888877


Q ss_pred             HHHhcC
Q 041804          110 ALCEYK  115 (403)
Q Consensus       110 ~~~~~~  115 (403)
                      ++...|
T Consensus        86 ~~~~~g   91 (91)
T 1na3_A           86 AKQKQG   91 (91)
T ss_dssp             HHHHHC
T ss_pred             HHHhcC
Confidence            776543

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=98.04  E-value=2.2e-05  Score=54.88  Aligned_cols=96  Identities=10%  Similarity=-0.069  Sum_probs=75.1

Q ss_pred             HHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHH
Q 041804           12 KRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFN   91 (403)
Q Consensus        12 ~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~   91 (403)
                      +.|++.|+....  ..+.+...+..+..++...|++++|+..|++..+..  +.+...|..+..+|...|++++|...|+
T Consensus         2 ~~a~~~~~~al~--~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~g~~~~A~~~~~   77 (115)
T 2kat_A            2 QAITERLEAMLA--QGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD--PTYSVAWKWLGKTLQGQGDRAGARQAWE   77 (115)
T ss_dssp             CCHHHHHHHHHT--TTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHH--hCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            357778877764  234568899999999999999999999999998865  3567889999999999999999999999


Q ss_pred             HHhhcCCC--cHHHHHHHHHHH
Q 041804           92 KLDEFGLK--DEVSYCNLVDAL  111 (403)
Q Consensus        92 ~~~~~~~~--~~~~~~~l~~~~  111 (403)
                      +..+..+.  +......+...+
T Consensus        78 ~al~~~~~~~~~~~~~~l~~~l   99 (115)
T 2kat_A           78 SGLAAAQSRGDQQVVKELQVFL   99 (115)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHhccccccHHHHHHHHHHH
Confidence            98876543  334444443333

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.98  E-value=3.3e-05  Score=53.37  Aligned_cols=95  Identities=13%  Similarity=0.028  Sum_probs=76.0

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcc---
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNK---  141 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---  141 (403)
                      ++...|..+...+...|++++|+..|++..+..+.+...+..+..++...|++++|...+++.....       +.+   
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-------p~~~~~   74 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYT-------STAEHV   74 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC-------SSTTSH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-------CCccHH
Confidence            4567888899999999999999999999999988899999999999999999999999999887642       223   


Q ss_pred             ---hHHHHHHHHHHHhcCChhHHHHHHH
Q 041804          142 ---TKIYNMILRGWFKMSWWGKCREFWE  166 (403)
Q Consensus       142 ---~~~~~~l~~~~~~~~~~~~a~~~~~  166 (403)
                         ..++..+..++...|+++.|.+.++
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~  102 (111)
T 2l6j_A           75 AIRSKLQYRLELAQGAVGSVQIPVVEVD  102 (111)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCCCCSSSSS
T ss_pred             HHHHHHHHHHHHHHHHHHhHhhhHhHHH
Confidence               4455566666666666655554443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.97  E-value=0.00011  Score=65.32  Aligned_cols=101  Identities=7%  Similarity=-0.131  Sum_probs=67.5

Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHHHHHh-----CC--CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc-----CC
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWEEMDK-----RG--VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-----GI  208 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~  208 (403)
                      ...+++.|...|...|++++|+.++++..+     .|  .+-...+++.|...|...|++++|..++++..+.     |.
T Consensus       350 ~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~  429 (490)
T 3n71_A          350 VLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGP  429 (490)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            445677777777777777777777666543     22  2223467888999999999999999999887643     21


Q ss_pred             -CCC-hhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          209 -KMD-VVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       209 -~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                       .|+ ..+...+-.++...+.+++|+.++..+++.
T Consensus       430 ~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          430 SHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             TSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             122 224455556666777778888887777653

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.90  E-value=9.7e-05  Score=48.77  Aligned_cols=82  Identities=16%  Similarity=0.077  Sum_probs=68.7

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHH
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      +...+..+...+...|++++|+..|++..+..+.+..++..+..++...|++++|...+++....       .+.+..++
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~-------~p~~~~~~   80 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL-------DPNNAEAK   80 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTCHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-------CCCCHHHH
Confidence            45678889999999999999999999999988778999999999999999999999999988763       34455666


Q ss_pred             HHHHHHHHh
Q 041804          146 NMILRGWFK  154 (403)
Q Consensus       146 ~~l~~~~~~  154 (403)
                      ..+...+.+
T Consensus        81 ~~l~~~~~~   89 (91)
T 1na3_A           81 QNLGNAKQK   89 (91)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            666665544

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.88  E-value=0.00061  Score=49.25  Aligned_cols=111  Identities=6%  Similarity=-0.076  Sum_probs=86.6

Q ss_pred             CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh----cCCHHHH
Q 041804          156 SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV----SEGVDFA  231 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a  231 (403)
                      +++++|.+.|++..+.|.. +.  .  |...|...+.+++|+++|++..+.|   +...+..|-..|..    .+++++|
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 KDLKKAIQYYVKACELNEM-FG--C--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHHHTTCT-TH--H--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCH-hh--h--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHH
Confidence            4578889999988887733 33  2  6666777777888999999888875   56677777777777    7889999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHHHHHHHHHhchhcC
Q 041804          232 MRVYREMREMGCQPSVVTCNTVIKLLCE----NGRVREAYAVLAEMPKKG  277 (403)
Q Consensus       232 ~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~  277 (403)
                      ..+|+...+.|   ++..+..|...|..    .++.++|...|++..+.|
T Consensus        81 ~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           81 AQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            99999988864   56777778888887    788888888888887765

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.86  E-value=6.9e-05  Score=50.81  Aligned_cols=62  Identities=13%  Similarity=0.038  Sum_probs=32.0

Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcc
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGE  127 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  127 (403)
                      +...+..+..+|...|++++|+..|++..+.++.+..+|..+..+|...|++++|...+++.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~a   67 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQG   67 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            34445555555555555555555555555555444445555555555555555555554443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.84  E-value=6.6e-05  Score=50.91  Aligned_cols=82  Identities=15%  Similarity=0.067  Sum_probs=65.0

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC--cHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK--DEVSYC  105 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~  105 (403)
                      +.++..+..+..++.+.|++++|+..|++..+..  +.+..+|..+..+|...|++++|++.|++..+..+.  +.....
T Consensus         4 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~   81 (100)
T 3ma5_A            4 PEDPFTRYALAQEHLKHDNASRALALFEELVETD--PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVAREEGTQKDLS   81 (100)
T ss_dssp             -CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCHHHHH
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhcCCchhHHH
Confidence            4467889999999999999999999999999876  345678999999999999999999999998875432  334333


Q ss_pred             HHHHHH
Q 041804          106 NLVDAL  111 (403)
Q Consensus       106 ~l~~~~  111 (403)
                      .+...+
T Consensus        82 ~l~~~l   87 (100)
T 3ma5_A           82 ELQDAK   87 (100)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            333333

>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=97.81  E-value=0.00045  Score=49.97  Aligned_cols=49  Identities=12%  Similarity=0.029  Sum_probs=21.8

Q ss_pred             cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHc
Q 041804          155 MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~  206 (403)
                      .+++++|.++|++..+.|   +...+..|...|..    .+++++|..+|++..+.
T Consensus        74 ~~d~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~  126 (138)
T 1klx_A           74 KKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRL  126 (138)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             CccHHHHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHC
Confidence            344444444444444432   23344444444444    44444444444444444

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.76  E-value=0.0037  Score=52.62  Aligned_cols=143  Identities=7%  Similarity=-0.110  Sum_probs=80.6

Q ss_pred             CCCHHHHHHHHHHHH--hcC---ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh---cC--C---HHHHHHHHhccccc
Q 041804           64 IPNHATFRIMFKRYV--TAH---LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE---YK--H---VIEAQELCFGENKN  130 (403)
Q Consensus        64 ~~~~~~~~~l~~~~~--~~~---~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~--~---~~~a~~~~~~~~~~  130 (403)
                      +.+..+|...+++..  ..+   +..+|+.+|++..+.+|.....+..+..+|..   .+  .   .......+......
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            356666776665544  333   34789999999999888877777766665541   00  0   00000011110000


Q ss_pred             ccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCC
Q 041804          131 VGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKM  210 (403)
Q Consensus       131 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  210 (403)
                      .     ..+.+..+|..+...+...|++++|...+++....+  |+...|..+...+.-.|++++|.+.|++....  .|
T Consensus       271 ~-----~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P  341 (372)
T 3ly7_A          271 P-----ELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RP  341 (372)
T ss_dssp             G-----GGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SC
T ss_pred             c-----cCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CC
Confidence            0     234455566666555555566666666666666654  45555656666666666666666666666654  34


Q ss_pred             ChhhH
Q 041804          211 DVVAY  215 (403)
Q Consensus       211 ~~~~~  215 (403)
                      ...+|
T Consensus       342 ~~~t~  346 (372)
T 3ly7_A          342 GANTL  346 (372)
T ss_dssp             SHHHH
T ss_pred             CcChH
Confidence            44444

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.74  E-value=7.8e-05  Score=54.54  Aligned_cols=88  Identities=10%  Similarity=0.015  Sum_probs=69.6

Q ss_pred             HhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC----------HHHHHHHHhcccccccccccccCcchHHHHH
Q 041804           78 VTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH----------VIEAQELCFGENKNVGFSGLVEMNKTKIYNM  147 (403)
Q Consensus        78 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (403)
                      .+.+.+++|++.++...+..+.+...|..+..++...++          +++|+..|++...       -.+.+..+|..
T Consensus        13 ~r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~-------ldP~~~~A~~~   85 (158)
T 1zu2_A           13 DRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL-------IDPKKDEAVWC   85 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHHHH
T ss_pred             HHHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHH-------hCcCcHHHHHH
Confidence            455677888888888888888888888888888887765          4589999988887       44667788999


Q ss_pred             HHHHHHhcC-----------ChhHHHHHHHHHHhCC
Q 041804          148 ILRGWFKMS-----------WWGKCREFWEEMDKRG  172 (403)
Q Consensus       148 l~~~~~~~~-----------~~~~a~~~~~~~~~~~  172 (403)
                      +..+|...|           ++++|.+.|++..+.+
T Consensus        86 LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~  121 (158)
T 1zu2_A           86 IGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQ  121 (158)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHhC
Confidence            999998775           7778888887777763

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.71  E-value=9.3e-05  Score=54.13  Aligned_cols=98  Identities=9%  Similarity=0.018  Sum_probs=72.7

Q ss_pred             ccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh----------HHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           43 KFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV----------NEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        43 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----------~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      +.+.+++|++.++...+..  +.+...|..+..++...+++          ++|+..|++..+.++.+..+|..+..+|.
T Consensus        14 r~~~feeA~~~~~~Ai~l~--P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~   91 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYT   91 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHH
Confidence            3456777777777777765  34667777777777776654          59999999999999888889999999998


Q ss_pred             hcC-----------CHHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804          113 EYK-----------HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus       113 ~~~-----------~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      ..|           ++++|.+.|++....        .|+...|...+.
T Consensus        92 ~lg~l~P~~~~a~g~~~eA~~~~~kAl~l--------~P~~~~y~~al~  132 (158)
T 1zu2_A           92 SFAFLTPDETEAKHNFDLATQFFQQAVDE--------QPDNTHYLKSLE  132 (158)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHHHHH--------CTTCHHHHHHHH
T ss_pred             HhcccCcchhhhhccHHHHHHHHHHHHHh--------CCCCHHHHHHHH
Confidence            764           899999999988764        455544544433

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.47  E-value=0.00064  Score=45.64  Aligned_cols=83  Identities=10%  Similarity=0.065  Sum_probs=63.8

Q ss_pred             HHHHHHccCChhHHHHHHHHhhhCCCCCCCHH-HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC
Q 041804           37 VIDILGKFFEFDLSWNLIHRMKDNPSSIPNHA-TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK  115 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  115 (403)
                      ....+.+.|++++|...|++..+..  +.+.. .|..+..+|...|++++|+..|++..+..+.+..++..        +
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~--------~   75 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE--PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDSPALQAR--------K   75 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC--SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHH--------H
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHH--------H
Confidence            4567788899999999999988865  34567 88889999999999999999999999988776665532        4


Q ss_pred             CHHHHHHHHhcccc
Q 041804          116 HVIEAQELCFGENK  129 (403)
Q Consensus       116 ~~~~a~~~~~~~~~  129 (403)
                      .+.++...+++...
T Consensus        76 ~~~~a~~~~~~~~~   89 (99)
T 2kc7_A           76 MVMDILNFYNKDMY   89 (99)
T ss_dssp             HHHHHHHHHCCTTH
T ss_pred             HHHHHHHHHHHHhc
Confidence            55666666655543

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.33  E-value=0.00075  Score=59.08  Aligned_cols=85  Identities=5%  Similarity=-0.138  Sum_probs=47.1

Q ss_pred             CChhHHHHHHHHhhh-----CCCCCCCH-HHHHHHHHHHHhcCChHHHHHHHHHHhh-----cCCC---cHHHHHHHHHH
Q 041804           45 FEFDLSWNLIHRMKD-----NPSSIPNH-ATFRIMFKRYVTAHLVNEAMGTFNKLDE-----FGLK---DEVSYCNLVDA  110 (403)
Q Consensus        45 ~~~~~a~~~~~~~~~-----~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~---~~~~~~~l~~~  110 (403)
                      |++++|+.++++..+     .|...|+. .+++.|..+|...|++++|+.++++..+     .|..   ...+++.|...
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            455555555554432     12122332 4566666666666666666666666542     2322   44456666666


Q ss_pred             HHhcCCHHHHHHHHhcccc
Q 041804          111 LCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~  129 (403)
                      |...|++++|+.++++...
T Consensus       392 ~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHH
Confidence            6666766666666665543

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.24  E-value=0.014  Score=49.28  Aligned_cols=143  Identities=9%  Similarity=-0.059  Sum_probs=84.3

Q ss_pred             CcchHHHHHHHHHHHh--cC---ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH---cC-Ch-hHHHH---HHHHHHH
Q 041804          139 MNKTKIYNMILRGWFK--MS---WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK---SG-KP-WKAVK---LYKEMKK  205 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~--~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~~-~~-~~a~~---~~~~~~~  205 (403)
                      +.+..+|...+++...  .+   +..+|..+|++..+..+. ....|..+.-+|..   .+ .. .....   .++....
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~-~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a  269 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPE-FTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVT  269 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHh
Confidence            4455566666655432  22   357788888888877554 44455544444431   11 11 11111   1111111


Q ss_pred             -cCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhh
Q 041804          206 -KGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVIT  284 (403)
Q Consensus       206 -~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~  284 (403)
                       ...+.+..++..+...+...|+++.|...++++...+  |+...|..+...+.-.|++++|.+.|++....  .|...+
T Consensus       270 ~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t  345 (372)
T 3ly7_A          270 LPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANT  345 (372)
T ss_dssp             CGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHH
T ss_pred             cccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcCh
Confidence             1124456677666666666788888888888888764  67667767777777888888888888877665  455555


Q ss_pred             HH
Q 041804          285 YH  286 (403)
Q Consensus       285 ~~  286 (403)
                      |.
T Consensus       346 ~~  347 (372)
T 3ly7_A          346 LY  347 (372)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.15  E-value=0.0033  Score=55.01  Aligned_cols=65  Identities=9%  Similarity=-0.026  Sum_probs=42.4

Q ss_pred             chHHHHHHHHHHHhcCChhHHHHHHHHHHh-----CCC-CC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          141 KTKIYNMILRGWFKMSWWGKCREFWEEMDK-----RGV-VK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~-~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      ...+++.+...|...|++++|+.++++..+     .|. .| ...+++.|...|...|++++|+.++++..+
T Consensus       339 ~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          339 MLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence            345566777777777777777776666543     121 12 235677777788888888888888777654

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.04  E-value=0.027  Score=54.07  Aligned_cols=128  Identities=9%  Similarity=0.022  Sum_probs=69.2

Q ss_pred             HHHccCChhHHHH-HHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHH
Q 041804           40 ILGKFFEFDLSWN-LIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVI  118 (403)
Q Consensus        40 ~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  118 (403)
                      .....+++++|.+ ++..+       |+......++..+.+.|..+.|+++.+.        +.   .-.......|+++
T Consensus       608 ~~~~~~~~~~a~~~~l~~i-------~~~~~~~~~~~~l~~~~~~~~a~~~~~~--------~~---~~f~~~l~~~~~~  669 (814)
T 3mkq_A          608 TLTLRGEIEEAIENVLPNV-------EGKDSLTKIARFLEGQEYYEEALNISPD--------QD---QKFELALKVGQLT  669 (814)
T ss_dssp             HHHHTTCHHHHHHHTGGGC-------CCHHHHHHHHHHHHHTTCHHHHHHHCCC--------HH---HHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHhcC-------CchHHHHHHHHHHHhCCChHHheecCCC--------cc---hheehhhhcCCHH
Confidence            3345677777765 44222       2122236666666777777777665521        10   1122345567777


Q ss_pred             HHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHH
Q 041804          119 EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVK  198 (403)
Q Consensus       119 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  198 (403)
                      .|.++.+.+            .+...|..+...+.+.++++.|++.|.++..         |..+...|...++.+...+
T Consensus       670 ~A~~~~~~~------------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~  728 (814)
T 3mkq_A          670 LARDLLTDE------------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVT  728 (814)
T ss_dssp             HHHHHHTTC------------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHhh------------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHH
Confidence            777765433            2345677777777777777777777776642         2233333444445444444


Q ss_pred             HHHHHHHc
Q 041804          199 LYKEMKKK  206 (403)
Q Consensus       199 ~~~~~~~~  206 (403)
                      +-+.....
T Consensus       729 ~~~~a~~~  736 (814)
T 3mkq_A          729 LAKDAETT  736 (814)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHc
Confidence            44444433

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=97.03  E-value=0.0054  Score=41.60  Aligned_cols=79  Identities=11%  Similarity=0.005  Sum_probs=63.8

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCC-----CCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP-----SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVS  103 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  103 (403)
                      .+...+..+...+.+.|++..|..+|+...+..     ...+....+..+..++.+.|+++.|+..+++..+..|.+..+
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~~~~~   82 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRA   82 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHH
Confidence            456677889999999999999999998876531     113456788999999999999999999999999988777666


Q ss_pred             HHHH
Q 041804          104 YCNL  107 (403)
Q Consensus       104 ~~~l  107 (403)
                      .+.+
T Consensus        83 ~~n~   86 (104)
T 2v5f_A           83 NGNL   86 (104)
T ss_dssp             HHHH
T ss_pred             HhhH
Confidence            5544

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.02  E-value=0.011  Score=38.92  Aligned_cols=68  Identities=6%  Similarity=-0.085  Sum_probs=52.3

Q ss_pred             CcchHHHHHHHHHHHhcCC---hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcC
Q 041804          139 MNKTKIYNMILRGWFKMSW---WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKG  207 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  207 (403)
                      +.+...+..+..++...++   .++|..++++..+.++. +..+...+...+.+.|++++|+..|+.+.+..
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~-~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPY-NEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            4566667777777755444   68888888888887766 77788888888888888888888888888763

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.99  E-value=0.011  Score=38.99  Aligned_cols=70  Identities=14%  Similarity=0.030  Sum_probs=50.2

Q ss_pred             cCCHHhHHHHHHHHHccCC---hhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC
Q 041804           28 THTTDTYNSVIDILGKFFE---FDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~   99 (403)
                      +.|+..+..+..++...++   .++|..++++..+.+  +.+..+...+...+...|++++|+..|+++.+..++
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~d--p~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~   75 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLE--PYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP   75 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHC--cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            4566677777776654443   678888888877765  355677777777888888888888888888777665

>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=96.95  E-value=0.0072  Score=52.93  Aligned_cols=99  Identities=6%  Similarity=-0.078  Sum_probs=70.4

Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccc-cccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC-----CC-CC-cHH
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNV-GFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR-----GV-VK-DLH  178 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~-~~-~~~  178 (403)
                      .+..+.+.|++++|+.++++..... ..-+...+....+++.+...|...|++++|+.++++....     |. .| ...
T Consensus       293 ~ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~  372 (429)
T 3qwp_A          293 KIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGV  372 (429)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHH
T ss_pred             HHHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHH
Confidence            3455667899999999988766432 1122233445667888999999999999999888876542     21 22 235


Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      +++.|...|...|++++|..++++..+
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            678888888888999888888887654

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.94  E-value=0.031  Score=41.51  Aligned_cols=130  Identities=8%  Similarity=0.023  Sum_probs=91.2

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV  117 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (403)
                      .......|+++.|.++.+.+       .+...|..|.......|+++-|+++|.+...        +..+.-.|...|+.
T Consensus        12 F~LAL~lg~l~~A~e~a~~l-------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D--------~~~L~~Ly~~tg~~   76 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKL-------NDSITWERLIQEALAQGNASLAEMIYQTQHS--------FDKLSFLYLVTGDV   76 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH-------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC--------HHHHHHHHHHHTCH
T ss_pred             HHHHHhcCCHHHHHHHHHHh-------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC--------HHHHHHHHHHhCCH
Confidence            45567789999999998776       3677999999999999999999999988876        66777777788888


Q ss_pred             HHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHH
Q 041804          118 IEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAV  197 (403)
Q Consensus       118 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  197 (403)
                      +...++-+.....      +      -++.....+...|+++++.++|.+.-+.   |-      -.-.....|..+.|.
T Consensus        77 e~L~kla~iA~~~------g------~~n~af~~~l~lGdv~~~i~lL~~~~r~---~e------A~~~A~t~g~~~~a~  135 (177)
T 3mkq_B           77 NKLSKMQNIAQTR------E------DFGSMLLNTFYNNSTKERSSIFAEGGSL---PL------AYAVAKANGDEAAAS  135 (177)
T ss_dssp             HHHHHHHHHHHHT------T------CHHHHHHHHHHHTCHHHHHHHHHHTTCH---HH------HHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHC------c------cHHHHHHHHHHcCCHHHHHHHHHHCCCh---HH------HHHHHHHcCcHHHHH
Confidence            8777664443322      1      1566667777889999998888654321   11      111112245566666


Q ss_pred             HHHHHH
Q 041804          198 KLYKEM  203 (403)
Q Consensus       198 ~~~~~~  203 (403)
                      ++.+.+
T Consensus       136 ~~~~~~  141 (177)
T 3mkq_B          136 AFLEQA  141 (177)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            666554

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.90  E-value=0.008  Score=40.05  Aligned_cols=58  Identities=9%  Similarity=0.019  Sum_probs=52.7

Q ss_pred             HHHHHHhcCChHHHHHHHHHHhhcCCCcHH-HHHHHHHHHHhcCCHHHHHHHHhccccc
Q 041804           73 MFKRYVTAHLVNEAMGTFNKLDEFGLKDEV-SYCNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus        73 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      ....+...|++++|+..|++..+..+.+.. .+..+..++...|++++|...|++....
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            456788899999999999999999888888 9999999999999999999999988764

>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=96.89  E-value=0.076  Score=42.99  Aligned_cols=91  Identities=11%  Similarity=0.026  Sum_probs=59.4

Q ss_pred             hHHHHHHHHHHHcCCCCC---hhhHHHHHHHHhh-----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc-CcHH
Q 041804          194 WKAVKLYKEMKKKGIKMD---VVAYNTVIRAVGV-----SEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCEN-GRVR  264 (403)
Q Consensus       194 ~~a~~~~~~~~~~~~~~~---~~~~~~ll~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~-g~~~  264 (403)
                      ..|...+++..+.  .|+   -..|..+...|.+     .|+.++|.+.|++..+.+..-+..++......+++. |+.+
T Consensus       180 ~~A~a~lerAleL--DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~  257 (301)
T 3u64_A          180 HAAVMMLERACDL--WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRA  257 (301)
T ss_dssp             HHHHHHHHHHHHH--CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHH
T ss_pred             HHHHHHHHHHHHh--CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHH
Confidence            3556666666655  344   3467777777776     378888888888887764433466666677777774 7788


Q ss_pred             HHHHHHHhchhcCCC--CChhhHH
Q 041804          265 EAYAVLAEMPKKGCV--PDVITYH  286 (403)
Q Consensus       265 ~a~~~~~~~~~~~~~--p~~~~~~  286 (403)
                      .+.+.+++.......  |+....+
T Consensus       258 ~a~~~L~kAL~a~p~~~P~~~lan  281 (301)
T 3u64_A          258 GFDEALDRALAIDPESVPHNKLLV  281 (301)
T ss_dssp             HHHHHHHHHHHCCGGGCSSCHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCChhHHH
Confidence            888888877766554  5544444

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.86  E-value=0.027  Score=39.25  Aligned_cols=140  Identities=14%  Similarity=0.000  Sum_probs=101.6

Q ss_pred             hhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHH
Q 041804          223 GVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLF  302 (403)
Q Consensus       223 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~  302 (403)
                      ...|.+++..++..+....   .+..-||.+|--....-+-+-..++++.+-.-   -|       +..|++.......+
T Consensus        18 ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGki---FD-------is~C~NlKrVi~C~   84 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FD-------LDKCQNLKSVVECG   84 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SC-------GGGCSCTHHHHHHH
T ss_pred             HHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhh---cC-------cHhhhcHHHHHHHH
Confidence            3467888888888877764   36666777776666666666666666655431   12       22345555555444


Q ss_pred             HHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 041804          303 DRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLS  381 (403)
Q Consensus       303 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~  381 (403)
                      -.+     ..+...++..+......|+-++-.+++..+... -+|++...-.+..||.+.|+..+|.+++.+.-++|++
T Consensus        85 ~~~-----n~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           85 VIN-----NTLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHT-----TCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHh-----cchHHHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            332     236677888899999999999999999996543 3789999999999999999999999999999999974

>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=96.83  E-value=0.0058  Score=53.54  Aligned_cols=97  Identities=5%  Similarity=-0.174  Sum_probs=73.7

Q ss_pred             HHHHHhcCChHHHHHHHHHHhhcC-----CC---cHHHHHHHHHHHHhcCCHHHHHHHHhccccccc-ccccccCcchHH
Q 041804           74 FKRYVTAHLVNEAMGTFNKLDEFG-----LK---DEVSYCNLVDALCEYKHVIEAQELCFGENKNVG-FSGLVEMNKTKI  144 (403)
Q Consensus        74 ~~~~~~~~~~~~a~~~~~~~~~~~-----~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~  144 (403)
                      +..+.+.|++++|+.++++..+..     ..   ...+++.+..+|...|++++|+.++++...... .-+...+....+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            455667899999999999887542     22   456788999999999999999999887654321 111133445567


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHh
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDK  170 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~  170 (403)
                      ++.|...|...|++++|+.++++..+
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            99999999999999999999988754

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.75  E-value=0.091  Score=39.02  Aligned_cols=99  Identities=8%  Similarity=0.077  Sum_probs=52.3

Q ss_pred             HHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhc
Q 041804           76 RYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKM  155 (403)
Q Consensus        76 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  155 (403)
                      .....|+++.|.++.+.+     .+...|..|.......|+++-|+..|.+...               +..+.-.|.-.
T Consensus        14 LAL~lg~l~~A~e~a~~l-----~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------------~~~L~~Ly~~t   73 (177)
T 3mkq_B           14 LALEYGNLDAALDEAKKL-----NDSITWERLIQEALAQGNASLAEMIYQTQHS---------------FDKLSFLYLVT   73 (177)
T ss_dssp             HHHHTTCHHHHHHHHHHH-----CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------------HHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHh-----CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------------HHHHHHHHHHh
Confidence            334556666666665543     3455666666666666666666666655443               34445555555


Q ss_pred             CChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHH
Q 041804          156 SWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLY  200 (403)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  200 (403)
                      |+.+...++-+.....|      -++....++...|+++++.++|
T Consensus        74 g~~e~L~kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL  112 (177)
T 3mkq_B           74 GDVNKLSKMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIF  112 (177)
T ss_dssp             TCHHHHHHHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHH
Confidence            55555444444333322      2334444445555555555555

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.67  E-value=0.022  Score=41.18  Aligned_cols=85  Identities=14%  Similarity=0.013  Sum_probs=59.7

Q ss_pred             HHHHHHHHHHHcCCCCchhhHHHHHHHHHhcC---CcchHHHHHHHHHhcCCCC--CHHHHHHHHHHHHhcCCHHHHHHH
Q 041804          297 EILGLFDRMIESGIRPKMDTYVMLLRKFGRWG---FLRPVFVVWKKMEELGCSP--DEFAYNALVDALIDKGMLDMARKY  371 (403)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~  371 (403)
                      .+.+-|.+..+.+. ++..+.-.+..++++.+   ++++++.++++..+.. .|  +...+-.+.-+|.+.|++++|.++
T Consensus        16 ~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~y   93 (152)
T 1pc2_A           16 KFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKY   93 (152)
T ss_dssp             HHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHHH
Confidence            44555555555554 57777777788888877   5668888888887764 24  345555666778889999999999


Q ss_pred             HHHHHHcCCCCChh
Q 041804          372 DEEMFAKGLSAKPR  385 (403)
Q Consensus       372 ~~~m~~~~~~p~~~  385 (403)
                      ++.+++  ++|+..
T Consensus        94 ~~~lL~--ieP~n~  105 (152)
T 1pc2_A           94 VRGLLQ--TEPQNN  105 (152)
T ss_dssp             HHHHHH--HCTTCH
T ss_pred             HHHHHh--cCCCCH
Confidence            988887  456543

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.66  E-value=0.065  Score=51.36  Aligned_cols=157  Identities=10%  Similarity=0.060  Sum_probs=109.9

Q ss_pred             HHHHhcCChHHHHH-HHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHH
Q 041804           75 KRYVTAHLVNEAMG-TFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWF  153 (403)
Q Consensus        75 ~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  153 (403)
                      ......+++++|.+ ++..+     ++......++..+.+.|..+.|.++.+.             +.     .-.....
T Consensus       607 ~~~~~~~~~~~a~~~~l~~i-----~~~~~~~~~~~~l~~~~~~~~a~~~~~~-------------~~-----~~f~~~l  663 (814)
T 3mkq_A          607 QTLTLRGEIEEAIENVLPNV-----EGKDSLTKIARFLEGQEYYEEALNISPD-------------QD-----QKFELAL  663 (814)
T ss_dssp             HHHHHTTCHHHHHHHTGGGC-----CCHHHHHHHHHHHHHTTCHHHHHHHCCC-------------HH-----HHHHHHH
T ss_pred             hHHHHhCCHHHHHHHHHhcC-----CchHHHHHHHHHHHhCCChHHheecCCC-------------cc-----hheehhh
Confidence            33446788888877 54221     1133347778888889999999876422             11     1134456


Q ss_pred             hcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHH
Q 041804          154 KMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMR  233 (403)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~  233 (403)
                      ..|+++.|.++.+.+      .+...|..+...+.+.++++.|.+.|..+..         |..+...+...++.+...+
T Consensus       664 ~~~~~~~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~  728 (814)
T 3mkq_A          664 KVGQLTLARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVT  728 (814)
T ss_dssp             HHTCHHHHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHH
T ss_pred             hcCCHHHHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHH
Confidence            789999999886544      2678999999999999999999999988753         3455566666788887777


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          234 VYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      +-+.....|-      ++....+|.+.|++++|.+++.++.+
T Consensus       729 ~~~~a~~~~~------~~~A~~~~~~~g~~~~a~~~~~~~~~  764 (814)
T 3mkq_A          729 LAKDAETTGK------FNLAFNAYWIAGDIQGAKDLLIKSQR  764 (814)
T ss_dssp             HHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCc------hHHHHHHHHHcCCHHHHHHHHHHcCC
Confidence            7777666542      13444557778888888888887764

>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=96.65  E-value=0.2  Score=40.61  Aligned_cols=113  Identities=9%  Similarity=-0.116  Sum_probs=81.5

Q ss_pred             cchHHHHHHHHH-HHh--cCC------hhHHHHHHHHHHhCCCCC-cHHHHHHHHHHHHHc-----CChhHHHHHHHHHH
Q 041804          140 NKTKIYNMILRG-WFK--MSW------WGKCREFWEEMDKRGVVK-DLHSYSIYMDIMCKS-----GKPWKAVKLYKEMK  204 (403)
Q Consensus       140 ~~~~~~~~l~~~-~~~--~~~------~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~  204 (403)
                      +....|..++.+ +..  .|+      ...|...+++..+.+..- +...|..+...|.+.     |+.++|.+.|++.+
T Consensus       152 ve~L~W~ai~~ss~a~~~~gg~~Al~~l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL  231 (301)
T 3u64_A          152 VGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLT  231 (301)
T ss_dssp             HHHHHHHHHHHHHHHTTSCTTSCCHHHHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhcCCCChHHHHhHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHH
Confidence            444556555543 333  233      466777888887764331 356899999999984     99999999999999


Q ss_pred             HcCCCCChhhHHHHHHHHhhc-CCHHHHHHHHHHHHHcCCC--CCHHHHHH
Q 041804          205 KKGIKMDVVAYNTVIRAVGVS-EGVDFAMRVYREMREMGCQ--PSVVTCNT  252 (403)
Q Consensus       205 ~~~~~~~~~~~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~--~~~~~~~~  252 (403)
                      +.+..-+..++......++.. ++.+.+.+.+++.......  |+....+.
T Consensus       232 ~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p~~~P~~~lan~  282 (301)
T 3u64_A          232 RYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVI  282 (301)
T ss_dssp             HHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCGGGCSSCHHHHH
T ss_pred             HhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCChhHHHH
Confidence            974322477788888888885 9999999999999998666  66544443

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.51  E-value=0.028  Score=40.65  Aligned_cols=81  Identities=9%  Similarity=0.024  Sum_probs=41.0

Q ss_pred             HHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC---CHHHHHHHHhcccccccccccccC-cchHHHHHHHHHHHhcCChhH
Q 041804           85 EAMGTFNKLDEFGLKDEVSYCNLVDALCEYK---HVIEAQELCFGENKNVGFSGLVEM-NKTKIYNMILRGWFKMSWWGK  160 (403)
Q Consensus        85 ~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~  160 (403)
                      .+.+-|.+..+.+.++..+...+..++++++   +.+++..++++....      ..+ .+...+-.+.-+|.+.|++++
T Consensus        16 ~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~------~~p~~~rd~lY~LAv~~~kl~~Y~~   89 (152)
T 1pc2_A           16 KFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPK------GSKEEQRDYVFYLAVGNYRLKEYEK   89 (152)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHH------SCHHHHHHHHHHHHHHHHHTSCHHH
T ss_pred             HHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc------CCccchHHHHHHHHHHHHHccCHHH
Confidence            3444444444444445555555555555555   344555555555442      101 123344445555566666666


Q ss_pred             HHHHHHHHHhC
Q 041804          161 CREFWEEMDKR  171 (403)
Q Consensus       161 a~~~~~~~~~~  171 (403)
                      |.+.++.+.+.
T Consensus        90 A~~y~~~lL~i  100 (152)
T 1pc2_A           90 ALKYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            66666666554

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.46  E-value=0.054  Score=38.70  Aligned_cols=103  Identities=15%  Similarity=0.175  Sum_probs=67.4

Q ss_pred             cHHHHHHHHHHHHHcCCh------hHHHHHHHHHHHcCCCCChh-hHHHHHH------HHhhcCCHHHHHHHHHHHHHcC
Q 041804          176 DLHSYSIYMDIMCKSGKP------WKAVKLYKEMKKKGIKMDVV-AYNTVIR------AVGVSEGVDFAMRVYREMREMG  242 (403)
Q Consensus       176 ~~~~~~~l~~~~~~~~~~------~~a~~~~~~~~~~~~~~~~~-~~~~ll~------~~~~~~~~~~a~~~~~~~~~~~  242 (403)
                      |..+|-..+...-+.|++      ++..++|++.... ++|+.. .|...+.      .+...++++.|.++|+.+.+.+
T Consensus        12 ~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~h   90 (161)
T 4h7y_A           12 NPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANC   90 (161)
T ss_dssp             SHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence            455666666666666666      6677777777665 455431 1111111      1123478889999999887764


Q ss_pred             CCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCC
Q 041804          243 CQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVP  280 (403)
Q Consensus       243 ~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p  280 (403)
                      -.. ...|-.....-.+.|++.+|.+++......+.+|
T Consensus        91 KkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~  127 (161)
T 4h7y_A           91 KKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP  127 (161)
T ss_dssp             TTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC
T ss_pred             HHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc
Confidence            343 6677777777788999999999998888765544

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.45  E-value=0.023  Score=38.35  Aligned_cols=74  Identities=4%  Similarity=-0.041  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCC
Q 041804          101 EVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVV  174 (403)
Q Consensus       101 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  174 (403)
                      ...+..+...+.+.+++..|...++..............+...++..+..++.+.|+++.|...+++..+..+.
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~   78 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPE   78 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCC
Confidence            34455666666677777777776666554321110012345677888888888899999999888888876444

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.36  E-value=0.15  Score=35.72  Aligned_cols=146  Identities=12%  Similarity=0.042  Sum_probs=73.7

Q ss_pred             HHHHHHH--HHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC-CcHHHHHHHHHH
Q 041804           34 YNSVIDI--LGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL-KDEVSYCNLVDA  110 (403)
Q Consensus        34 ~~~li~~--~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~l~~~  110 (403)
                      ...|+.+  +.-.|.+++..++..+....    .+..-+|.+|--....-+-+-..++++.+-+.-- .--.-...++.+
T Consensus         8 ~kkLmeAK~~ildG~v~qGveii~k~~~s----sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi~C   83 (172)
T 1wy6_A            8 IRKLMDAKKFLLDGYIDEGVKIVLEITKS----STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVEC   83 (172)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH----SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHcCC----CCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHHHH
Confidence            3344443  44567888888888777763    3555566666655555555555555544432110 011112233333


Q ss_pred             HHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Q 041804          111 LCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKS  190 (403)
Q Consensus       111 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  190 (403)
                      |.+.+..                        ....+..+......|.-+.-.+++..+.. +.+|++.....+..+|.+.
T Consensus        84 ~~~~n~~------------------------se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Kl  138 (172)
T 1wy6_A           84 GVINNTL------------------------NEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRV  138 (172)
T ss_dssp             HHHTTCC------------------------CHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHT
T ss_pred             HHHhcch------------------------HHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHh
Confidence            3332211                        12234444555555555555555555433 2234555555566666666


Q ss_pred             CChhHHHHHHHHHHHcCC
Q 041804          191 GKPWKAVKLYKEMKKKGI  208 (403)
Q Consensus       191 ~~~~~a~~~~~~~~~~~~  208 (403)
                      |+..++.+++.+.-+.|+
T Consensus       139 g~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A          139 GDERDATTLLIEACKKGE  156 (172)
T ss_dssp             TCHHHHHHHHHHHHHTTC
T ss_pred             cchhhHHHHHHHHHHhhh
Confidence            666666666666666554

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.10  E-value=0.66  Score=40.78  Aligned_cols=266  Identities=11%  Similarity=0.106  Sum_probs=156.7

Q ss_pred             cccHHHHHHhhhhhcc----cCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHH--HHHHHHHHHhcC
Q 041804            8 ANDWKRALEFFNWVET----DCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHAT--FRIMFKRYVTAH   81 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~----~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~   81 (403)
                      +++++.|++.+..+.+    ..+..-+......++..|...|+++...+.+..+....+..+...+  .+.++.......
T Consensus        29 ~~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai~~~V~~~~~~l~~~~  108 (445)
T 4b4t_P           29 QNDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSIQYMIQKVMEYLKSSK  108 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHHHHHHHHHHHHHHHHC
T ss_pred             cCCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCC
Confidence            4789999988766654    2333445778889999999999999998888776654422222222  223333333344


Q ss_pred             ChHH--HHHHHHHHhh--cC---CC--cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHH
Q 041804           82 LVNE--AMGTFNKLDE--FG---LK--DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        82 ~~~~--a~~~~~~~~~--~~---~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      ..+.  -+.+.+.+..  .|   +.  .......|...+...|++.+|..++..+..... ......--...+..-++.|
T Consensus       109 ~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~-~~~~~~~kve~~l~q~rl~  187 (445)
T 4b4t_P          109 SLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETY-GSMEMSEKIQFILEQMELS  187 (445)
T ss_dssp             TTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-SSSCHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHH-hcccHHHHHHHHHHHHHHH
Confidence            3332  2222222211  11   11  233456788889999999999999988764310 0001122345678888999


Q ss_pred             HhcCChhHHHHHHHHHHh----CCCCCc--HHHHHHHHHHHHHcCChhHHHHHHHHHHHc-CCCCChhhHHHHHH----H
Q 041804          153 FKMSWWGKCREFWEEMDK----RGVVKD--LHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-GIKMDVVAYNTVIR----A  221 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~----~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~ll~----~  221 (403)
                      ...+++..|..++.++..    ....|+  ...+..++..+...+++.+|...|.+.... ....|...+..++.    +
T Consensus       188 l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~  267 (445)
T 4b4t_P          188 ILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYF  267 (445)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHH
Confidence            999999999999988642    222232  245666777788899999998888777543 11123322222211    1


Q ss_pred             HhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc--CcHHHHHHHHHhch
Q 041804          222 VGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCEN--GRVREAYAVLAEMP  274 (403)
Q Consensus       222 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~--g~~~~a~~~~~~~~  274 (403)
                      ..-.+..+.-..++........-++...|..++.+|...  .+++.+...|....
T Consensus       268 ~iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L  322 (445)
T 4b4t_P          268 LVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVL  322 (445)
T ss_dssp             HHHSSCSSTTHHHHHSHHHHSSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSST
T ss_pred             HHhCCCCchHHHHHHHHhhcccccccHHHHHHHHHHHhchHhhhHHHHHHHHHHh
Confidence            111222122223333333332334677888888888764  45777777776544

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=95.81  E-value=0.23  Score=35.53  Aligned_cols=114  Identities=11%  Similarity=0.027  Sum_probs=79.4

Q ss_pred             CcchHHHHHHHHHHHhcCCh------hHHHHHHHHHHhCCCCCcH-HHHHHHHH------HHHHcCChhHHHHHHHHHHH
Q 041804          139 MNKTKIYNMILRGWFKMSWW------GKCREFWEEMDKRGVVKDL-HSYSIYMD------IMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       139 ~~~~~~~~~l~~~~~~~~~~------~~a~~~~~~~~~~~~~~~~-~~~~~l~~------~~~~~~~~~~a~~~~~~~~~  205 (403)
                      +.|..+|-..+...-+.|+.      +...++|++.... ++|+. ..|...+.      .+...+++++|.++|+.+++
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~   88 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARA   88 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            56777788888888878888      8888899888764 33332 11111111      12334899999999999987


Q ss_pred             cCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 041804          206 KGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIK  255 (403)
Q Consensus       206 ~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  255 (403)
                      ..-.. ...|....+.-.+.|+++.|.+++......+..|. ......++
T Consensus        89 ~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~-~~le~a~~  136 (161)
T 4h7y_A           89 NCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPL-EMLEIALR  136 (161)
T ss_dssp             HCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCH-HHHHHHHH
T ss_pred             HhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcH-HHHHHHHH
Confidence            64343 66777777777899999999999999999876643 33444443

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=95.45  E-value=0.0012  Score=57.18  Aligned_cols=316  Identities=7%  Similarity=-0.048  Sum_probs=168.9

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      |+..|..+|.+..+.|.+++-++++....+..   .++..=+.|+-+|++.++..+-++++.      .++..-...+.+
T Consensus        82 Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~---ke~~IDteLi~ayAk~~rL~elEefl~------~~N~A~iq~VGD  152 (624)
T 3lvg_A           82 DPSSYMEVVQAANTSGNWEELVKYLQMARKKA---RESYVETELIFALAKTNRLAELEEFIN------GPNNAHIQQVGD  152 (624)
T ss_dssp             CCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTC---CSTTTTHHHHHHHHTSCSSSTTTSTTS------CCSSSCTHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh---cccccHHHHHHHHHhhCcHHHHHHHHc------CCCcccHHHHHH
Confidence            45567777888888888888777777666543   333444577778888777665443321      124444556666


Q ss_pred             HHHhcCCHHHHHHHHhccccccc--------------ccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 041804          110 ALCEYKHVIEAQELCFGENKNVG--------------FSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK  175 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  175 (403)
                      -|...|.++.|.-+|..+..-..              +.......++.+|..+-.+|...+++.-|.-.--.+.-.   |
T Consensus       153 rcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvh---a  229 (624)
T 3lvg_A          153 RCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH---A  229 (624)
T ss_dssp             HHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC---S
T ss_pred             HHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhccc---H
Confidence            67777777777666655443221              111123456677888888888888877776554444322   1


Q ss_pred             cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc-CCC------CCHH
Q 041804          176 DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM-GCQ------PSVV  248 (403)
Q Consensus       176 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~------~~~~  248 (403)
                      |  -...++..|-..|.+++-+.+++..... -+.....|+-|.-.|++- ++++..+.++..-.+ +++      -...
T Consensus       230 d--eL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ah  305 (624)
T 3lvg_A          230 D--ELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAH  305 (624)
T ss_dssp             S--CCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTT
T ss_pred             H--HHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHh
Confidence            1  2334667778888888888888876643 234566777777777654 444444444432221 111      1234


Q ss_pred             HHHHHHHHHHhcCcHHHHHHHHHhchhc-CCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhc
Q 041804          249 TCNTVIKLLCENGRVREAYAVLAEMPKK-GCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRW  327 (403)
Q Consensus       249 ~~~~li~~~~~~g~~~~a~~~~~~~~~~-~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  327 (403)
                      .|.-++..|.+-.+++.|....   .++ ...-+...|--++....+.+--.+...-.++    -.+...+-|+.++...
T Consensus       306 LW~ElvfLY~~ydE~DnA~ltM---i~h~~~Aw~h~~Fkdii~KVaN~EiyYKAi~FYL~----e~P~lL~DLL~vL~pr  378 (624)
T 3lvg_A          306 LWAELVFLYDKYEEYDNAIITM---MNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLE----FKPLLLNDLLMVLSPR  378 (624)
T ss_dssp             CHHHHHHHHHHHTCHHHHHHTT---TSCHHHHCCGGGGTTTGGGCSCSHHHHHHHHHHTT----SCCTTSHHHHHHHCTT
T ss_pred             hHHHHHHHHhcchhHHHHHHHH---HhCChhhccHHHHHHHHHHcchHHHHHHHHHHHHH----hChHHHHHHHHhcccc
Confidence            5666777777777777654321   111 0000111111111111222111111111111    1222345555555555


Q ss_pred             CCcchHHHHHHHHHh----------cCCCCCHHHHHHHHHHHHhcCCHHHH
Q 041804          328 GFLRPVFVVWKKMEE----------LGCSPDEFAYNALVDALIDKGMLDMA  368 (403)
Q Consensus       328 g~~~~a~~~~~~~~~----------~~~~~~~~~~~~l~~~~~~~g~~~~a  368 (403)
                      =|..++.++|++.-.          ..-..+..+-.++-+.|....+++.-
T Consensus       379 lDh~RvV~~~~k~~~LpLIkpYL~~Vq~~N~~aVNeAln~L~IEEEDy~~L  429 (624)
T 3lvg_A          379 LDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQAL  429 (624)
T ss_dssp             CCSTTTHHHHHTTTCGGGGTGGGTSCCCSCCHHHHHHHHHHHHHTTCCHHH
T ss_pred             CChHHHHHHHHhcCCchhhHHHHHHHHHhhHHHHHHHHHHHHhhhhhHHHH
Confidence            555555555554321          01123455556777788888876643

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.43  E-value=0.29  Score=33.99  Aligned_cols=83  Identities=7%  Similarity=-0.015  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHH---HHHHHhcccccccccccccC-cchHHHHHHHHHHHhcCCh
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIE---AQELCFGENKNVGFSGLVEM-NKTKIYNMILRGWFKMSWW  158 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~  158 (403)
                      ...+.+-|......|.++..+-..+..++.+..+...   +..++..+...      ..+ ......-.|.-++.+.|++
T Consensus        17 l~~~~~~y~~e~~~~~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~------~~p~~~Rd~lY~LAvg~yklg~Y   90 (126)
T 1nzn_A           17 LLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPK------GSKEEQRDYVFYLAVGNYRLKEY   90 (126)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTT------SCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHhccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc------CCcchHHHHHHHHHHHHHHhhhH
Confidence            3344455554444454555555555555555554444   55555555443      111 2333444555566666666


Q ss_pred             hHHHHHHHHHHhC
Q 041804          159 GKCREFWEEMDKR  171 (403)
Q Consensus       159 ~~a~~~~~~~~~~  171 (403)
                      ++|.+.++.+.+.
T Consensus        91 ~~A~~~~~~lL~~  103 (126)
T 1nzn_A           91 EKALKYVRGLLQT  103 (126)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            6666666666554

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.23  E-value=2.3  Score=40.88  Aligned_cols=229  Identities=7%  Similarity=-0.155  Sum_probs=109.2

Q ss_pred             HHHHccCChhHHHHHHHHhhhCC-CCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC-----C-cH----HHHHHH
Q 041804           39 DILGKFFEFDLSWNLIHRMKDNP-SSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL-----K-DE----VSYCNL  107 (403)
Q Consensus        39 ~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~-~~----~~~~~l  107 (403)
                      -.....|+.++++.+++.....+ ...+....-..+.-+.+..|..+++..++.......-     . +.    .+...|
T Consensus       382 LGlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGL  461 (963)
T 4ady_A          382 LGVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGI  461 (963)
T ss_dssp             HHHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHH
T ss_pred             hhhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHH
Confidence            34556777777777777665421 0112233333444455556665566666666544321     0 01    111122


Q ss_pred             HHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHH
Q 041804          108 VDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIM  187 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  187 (403)
                      ..++.-.++ +++...+..+....     .......+--.+...+.-.|+.+....++..+.+.... +..-...+.-++
T Consensus       462 Gla~~GS~~-eev~e~L~~~L~dd-----~~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~~e-~vrR~aalgLGl  534 (963)
T 4ady_A          462 GLAAMGSAN-IEVYEALKEVLYND-----SATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQHG-NITRGLAVGLAL  534 (963)
T ss_dssp             HHHSTTCCC-HHHHHHHHHHHHTC-----CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCSCH-HHHHHHHHHHHH
T ss_pred             HHHhcCCCC-HHHHHHHHHHHhcC-----CHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccCcH-HHHHHHHHHHHh
Confidence            222223333 23333333333221     10001112223334455667766667777666553211 222222233334


Q ss_pred             HHcCChhHHHHHHHHHHHcCCCCChhh--HHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHH
Q 041804          188 CKSGKPWKAVKLYKEMKKKGIKMDVVA--YNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVRE  265 (403)
Q Consensus       188 ~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  265 (403)
                      ...|+.+.+..+++.+.... .|...-  ..++.-+|+..|+.....+++..+.+.. ..++.....+.-++...|+.+.
T Consensus       535 l~~g~~e~~~~li~~L~~~~-dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~d~-~d~VRraAViaLGlI~~g~~e~  612 (963)
T 4ady_A          535 INYGRQELADDLITKMLASD-ESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVSDS-NDDVRRAAVIALGFVLLRDYTT  612 (963)
T ss_dssp             HTTTCGGGGHHHHHHHHHCS-CHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHCS-CHHHHHHHHHHHHHHTSSSCSS
T ss_pred             hhCCChHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccCC-cHHHHHHHHHHHHhhccCCHHH
Confidence            46677777777777776541 222211  1233446677777777777777776541 2223333333334444666666


Q ss_pred             HHHHHHhchhc
Q 041804          266 AYAVLAEMPKK  276 (403)
Q Consensus       266 a~~~~~~~~~~  276 (403)
                      +.+++..+.+.
T Consensus       613 v~rlv~~L~~~  623 (963)
T 4ady_A          613 VPRIVQLLSKS  623 (963)
T ss_dssp             HHHHTTTGGGC
T ss_pred             HHHHHHHHHhc
Confidence            66666665553

>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=94.83  E-value=0.3  Score=42.08  Aligned_cols=78  Identities=10%  Similarity=-0.064  Sum_probs=62.6

Q ss_pred             hHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCCChhhHHHH
Q 041804          316 TYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA-----KGLSAKPREELGT  390 (403)
Q Consensus       316 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~~~~p~~~~~~~~  390 (403)
                      +...++..+...|++++|...+..+.... +-+...|..++.++.+.|+..+|.+.|++...     .|+.|.+.+.--.
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~  251 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALN  251 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            34556778888999999999988887764 56888999999999999999999999988765     3999998876555


Q ss_pred             HHHh
Q 041804          391 KLVQ  394 (403)
Q Consensus       391 ~~~~  394 (403)
                      ..+.
T Consensus       252 ~~il  255 (388)
T 2ff4_A          252 ERIL  255 (388)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=94.73  E-value=0.47  Score=32.93  Aligned_cols=84  Identities=13%  Similarity=0.003  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcch---HHHHHHHHHhcCCCC--CHHHHHHHHHHHHhcCCHHHHHHHH
Q 041804          298 ILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRP---VFVVWKKMEELGCSP--DEFAYNALVDALIDKGMLDMARKYD  372 (403)
Q Consensus       298 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~---a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~~  372 (403)
                      +.+-|......|. |+..+--.+.+++.+..+...   ++.+++.+.+.+ .|  .....-.|.-++.+.|++++|.+++
T Consensus        20 ~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~-~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~   97 (126)
T 1nzn_A           20 FEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALKYV   97 (126)
T ss_dssp             HHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            3344444444443 566666667777777776555   777888777653 23  2333345566788888888888888


Q ss_pred             HHHHHcCCCCChh
Q 041804          373 EEMFAKGLSAKPR  385 (403)
Q Consensus       373 ~~m~~~~~~p~~~  385 (403)
                      +.+++  +.|+..
T Consensus        98 ~~lL~--~eP~n~  108 (126)
T 1nzn_A           98 RGLLQ--TEPQNN  108 (126)
T ss_dssp             HHHHH--HCTTCH
T ss_pred             HHHHH--hCCCCH
Confidence            88887  445543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=94.29  E-value=0.53  Score=44.09  Aligned_cols=129  Identities=9%  Similarity=0.059  Sum_probs=82.5

Q ss_pred             HHHHHHHHHhcCC-hhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCC-hhHHHHHHHHHHHc------CCCCChh---
Q 041804          145 YNMILRGWFKMSW-WGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK-PWKAVKLYKEMKKK------GIKMDVV---  213 (403)
Q Consensus       145 ~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~------~~~~~~~---  213 (403)
                      ...++..+...++ ++.|..+|+++....+..+......++..+...++ --+|.+++.+..+.      ..++...   
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            3455566666666 58899999999887543233223333433333332 22455555554321      1222111   


Q ss_pred             --------hHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          214 --------AYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       214 --------~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                              ....=...+...|+++.|+.+-++....- +.+-.+|..|..+|...|+++.|+-.++.++
T Consensus       331 ~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          331 RLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             cccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                    11222344567899999999999998863 3357899999999999999999999999875

>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=93.97  E-value=0.32  Score=41.94  Aligned_cols=200  Identities=9%  Similarity=-0.048  Sum_probs=103.2

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh-cCChHHHHHHHHHHhhcC-------CC-c
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT-AHLVNEAMGTFNKLDEFG-------LK-D  100 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~-------~~-~  100 (403)
                      +...+..|.....+.|+.-...++.+.+-..........+....+.-+-+ .+.....-..+......|       .. |
T Consensus        32 ~~k~~~LL~~L~~~~g~~vsr~~L~~~lW~~~~~~~a~~~L~~~i~rLRk~L~~~~~~~~~i~~~~~~GY~l~~~~~~~D  111 (388)
T 2ff4_A           32 TPKQRAVLAMLVINRNRPVGVDALITALWEEWPPSGARASIHSYVSNLRKLLGGAGIDPRVVLAAAPPGYRLSIPDNTCD  111 (388)
T ss_dssp             SHHHHHHHHHHHHTTTSEEEHHHHHHHHHTTCCCTTHHHHHHHHHHHHHHHHGGGTSCHHHHEEECSSEEEECCCGGGBH
T ss_pred             ChHHHHHHHHHHhCCCCcccHHHHHHHhCCCCCChhHHHHHHHHHHHHHHhhcccCCCCceEEEEECCEEEEcCCCccch
Confidence            45556555555666677766777777776654111223344443332221 111100000111111111       11 5


Q ss_pred             HHHHHHHHHHHH---hcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChh-HHHHHHHHHHhCCCCCc
Q 041804          101 EVSYCNLVDALC---EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWG-KCREFWEEMDKRGVVKD  176 (403)
Q Consensus       101 ~~~~~~l~~~~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~a~~~~~~~~~~~~~~~  176 (403)
                      ...|..++....   ..|+.+.+...+.++.....-   ..-++..           ...|- ....-+++..       
T Consensus       112 ~~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG---~~L~~~~-----------~~~w~~~~r~~l~~~~-------  170 (388)
T 2ff4_A          112 LGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRG---PVLDDLR-----------DFQFVEPFATALVEDK-------  170 (388)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS---STTGGGT-----------TSTTHHHHHHHHHHHH-------
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCC---CCCCCCC-----------chhHHHHHHHHHHHHH-------
Confidence            555666554432   357888777777665543210   1111110           01111 1112222221       


Q ss_pred             HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHH-----cCCCCCHHHHH
Q 041804          177 LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMRE-----MGCQPSVVTCN  251 (403)
Q Consensus       177 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~  251 (403)
                      ..+...++..+...|+++++...+..+.... +.+...+..+|.++.+.|+..+|++.|+.+.+     .|+.|+..+-.
T Consensus       171 ~~a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          171 VLAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            1244556677777888888887777776653 55777888888888888888888888877653     47777776543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=93.44  E-value=0.77  Score=43.04  Aligned_cols=133  Identities=8%  Similarity=-0.055  Sum_probs=83.5

Q ss_pred             HHHHHHHHHhcCC-hHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcC-CHHHHHHHHhcccccc-----cccccc----
Q 041804           70 FRIMFKRYVTAHL-VNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYK-HVIEAQELCFGENKNV-----GFSGLV----  137 (403)
Q Consensus        70 ~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~-----~~~~~~----  137 (403)
                      ...++..+...++ .+.|..+|+++.+.++. +......++..+...+ +--+|.+++.+..+..     ......    
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            3445555555666 57899999999987766 3333333343333332 2234555554433210     000000    


Q ss_pred             --cCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHH
Q 041804          138 --EMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEM  203 (403)
Q Consensus       138 --~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  203 (403)
                        .+........-...+...|+++.|+++-++.....+. +-.+|..|..+|...|+++.|+-.++.+
T Consensus       331 ~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~aPs-eF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          331 RLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTELALD-SFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             cccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHhcCch-hhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence              0011122333356677889999999999999887555 6789999999999999999999988876

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.17  E-value=4.1  Score=35.73  Aligned_cols=196  Identities=8%  Similarity=0.025  Sum_probs=119.9

Q ss_pred             CChhHHHHHHHHhhhC----CCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH----hcCC
Q 041804           45 FEFDLSWNLIHRMKDN----PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC----EYKH  116 (403)
Q Consensus        45 ~~~~~a~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~----~~~~  116 (403)
                      |+++.|++.+-.+.+.    +...........++..|...++++...+.+..+.+...........+++.+.    ....
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            6788888877665532    2133456778889999999999999988887776554443333344444332    3333


Q ss_pred             HH--HHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhC--CCCCc---HHHHHHHHHHHHH
Q 041804          117 VI--EAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKR--GVVKD---LHSYSIYMDIMCK  189 (403)
Q Consensus       117 ~~--~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~---~~~~~~l~~~~~~  189 (403)
                      .+  .-..+.........-.-............|...|...|++.+|.+++..+...  +....   ...+...++.|..
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            22  22333333222110000000113445677888999999999999999987542  22111   3466777888889


Q ss_pred             cCChhHHHHHHHHHHHc----CCCCCh--hhHHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041804          190 SGKPWKAVKLYKEMKKK----GIKMDV--VAYNTVIRAVGVSEGVDFAMRVYREMRE  240 (403)
Q Consensus       190 ~~~~~~a~~~~~~~~~~----~~~~~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~  240 (403)
                      .+++..|..++......    ...|+.  ..+...+..+...+++..|.+.|.++.+
T Consensus       190 ~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          190 KGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            99999999888886432    112221  2445556666778888888877777654

>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=93.10  E-value=0.69  Score=30.35  Aligned_cols=44  Identities=11%  Similarity=0.084  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          196 AVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       196 a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      +.+-++.+...++.|+..+..+.+++|.+.+++..|.++|+-++
T Consensus        29 ~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK   72 (109)
T 1v54_E           29 LRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVK   72 (109)
T ss_dssp             HHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            33334444444444555555555555555555555555554444

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=92.82  E-value=3  Score=41.72  Aligned_cols=139  Identities=9%  Similarity=-0.054  Sum_probs=93.6

Q ss_pred             ccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCC---------------------CCC
Q 041804            7 YANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPS---------------------SIP   65 (403)
Q Consensus         7 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~---------------------~~~   65 (403)
                      ..+.++.|.++..|...      ++...-.+..++..+|++++|...|.+....-.                     ...
T Consensus       824 ~~~~~~~~~~l~~~~~~------~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~~~~~~~~~~  897 (1139)
T 4fhn_B          824 LFKQYNACMQLIGWLNS------DPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEIAEKYHHQNL  897 (1139)
T ss_dssp             HHSCTTHHHHHHHHSCC------CHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHHHHTTTSCCS
T ss_pred             HhhhHHHHHHHhhhccC------CcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhccccccccccccccc
Confidence            34666677777666652      344445667889999999999999987532100                     001


Q ss_pred             CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC-cH----HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCc
Q 041804           66 NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK-DE----VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMN  140 (403)
Q Consensus        66 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  140 (403)
                      -..-|..++..+.+.+.++.+.++-....+...+ +.    ..|..+.+.+...|++++|...+..+...        ..
T Consensus       898 l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~--------~~  969 (1139)
T 4fhn_B          898 LSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTT--------PL  969 (1139)
T ss_dssp             SHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHS--------SS
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCH--------HH
Confidence            1235778888999999999999888877665443 22    36888999999999999998887655432        22


Q ss_pred             chHHHHHHHHHHHhcCChh
Q 041804          141 KTKIYNMILRGWFKMSWWG  159 (403)
Q Consensus       141 ~~~~~~~l~~~~~~~~~~~  159 (403)
                      .......++...+..|..+
T Consensus       970 r~~cLr~LV~~lce~~~~~  988 (1139)
T 4fhn_B          970 KKSCLLDFVNQLTKQGKIN  988 (1139)
T ss_dssp             CHHHHHHHHHHHHHHCCHH
T ss_pred             HHHHHHHHHHHHHhCCChh
Confidence            3345566666666555543

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=92.75  E-value=1.7  Score=30.30  Aligned_cols=77  Identities=12%  Similarity=0.054  Sum_probs=51.1

Q ss_pred             CCCCchhhHHHHHHHHHhcCC---cchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChh
Q 041804          309 GIRPKMDTYVMLLRKFGRWGF---LRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPR  385 (403)
Q Consensus       309 ~~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~  385 (403)
                      +..|+..+--.+.+++.+..+   ..+++.+++.+.+.+..-....+-.|.-++.+.|++++|.++.+.+.+  +.|+..
T Consensus        35 ~~~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~--~eP~N~  112 (134)
T 3o48_A           35 GPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERNNK  112 (134)
T ss_dssp             GGGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHT--TCTTCH
T ss_pred             CCCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHh--hCCCCH
Confidence            445566665566667766654   456788888887654111344555666788889999999998888877  556554


Q ss_pred             hH
Q 041804          386 EE  387 (403)
Q Consensus       386 ~~  387 (403)
                      -.
T Consensus       113 QA  114 (134)
T 3o48_A          113 QV  114 (134)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=92.62  E-value=9.2  Score=38.31  Aligned_cols=150  Identities=11%  Similarity=-0.002  Sum_probs=84.8

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhccccccccccccc-------------
Q 041804           72 IMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVE-------------  138 (403)
Q Consensus        72 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------------  138 (403)
                      .++..+...+..+.+.++.....    .++...-.+..++...|++++|...|.+............             
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~~----~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~~~~~  892 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWLN----SDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEIAEKY  892 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHSC----CCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHHHHTT
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcc----CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcccccccccc
Confidence            35555666777776666543332    2555556677888999999999999988755331111000             


Q ss_pred             ---CcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCc----HHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCC
Q 041804          139 ---MNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKD----LHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMD  211 (403)
Q Consensus       139 ---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  211 (403)
                         ..-..-|..++..+-+.+.++.+.++-....+....-+    ...|..+.+.+...|++++|...+-.+.....  -
T Consensus       893 ~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~--r  970 (1139)
T 4fhn_B          893 HHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPL--K  970 (1139)
T ss_dssp             TSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSS--C
T ss_pred             cccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHH--H
Confidence               00112355666666666777666666555444321111    12466666777777777777766666554422  2


Q ss_pred             hhhHHHHHHHHhhcCC
Q 041804          212 VVAYNTVIRAVGVSEG  227 (403)
Q Consensus       212 ~~~~~~ll~~~~~~~~  227 (403)
                      ......|+...+..+.
T Consensus       971 ~~cLr~LV~~lce~~~  986 (1139)
T 4fhn_B          971 KSCLLDFVNQLTKQGK  986 (1139)
T ss_dssp             HHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHhCCC
Confidence            3344555555554444

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=92.10  E-value=9  Score=36.99  Aligned_cols=312  Identities=10%  Similarity=-0.096  Sum_probs=165.6

Q ss_pred             HHHHHHHHHccCChhHH-HHH-HHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCcHH--HHHHHH
Q 041804           34 YNSVIDILGKFFEFDLS-WNL-IHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFG-LKDEV--SYCNLV  108 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a-~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~--~~~~l~  108 (403)
                      -..+.+++..+|--.+. ... .+.+.+.   .+....-....-+....|+.++++.++......+ ..+..  .=..+.
T Consensus       342 A~~f~Naf~naG~~~D~~l~~~~~Wl~k~---~~~~k~sA~aSLGlIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAlla  418 (963)
T 4ady_A          342 AVSVANGFMHAGTTDNSFIKANLPWLGKA---QNWAKFTATASLGVIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYG  418 (963)
T ss_dssp             HHHHHHHHHTTTTCCCHHHHHCHHHHHHC---CTHHHHHHHHHHHHHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCcchhhhcchhhhhcc---chHHHHHHHHHhhhhccCchHHHHHHHHHhccccCCCcHHHHHHHHHH
Confidence            34667788888854333 221 2233332   2333333444556778899999999988876532 12222  223333


Q ss_pred             HHHHhcCCHHHHHHHHhccccccc-ccccccCcchHHHHHHHHHHHhcCC-hhHHHHHHHHHHhCCCCCcH--HHHHHHH
Q 041804          109 DALCEYKHVIEAQELCFGENKNVG-FSGLVEMNKTKIYNMILRGWFKMSW-WGKCREFWEEMDKRGVVKDL--HSYSIYM  184 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~~~~~~~~--~~~~~l~  184 (403)
                      -+....|...++..++........ ..+....+....-..+.-+.+-.|. -+++.+.+..+....-. ..  .+-..|.
T Consensus       419 LGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLGla~~GS~~eev~e~L~~~L~dd~~-~~~~~AalALG  497 (963)
T 4ady_A          419 LGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGLAAMGSANIEVYEALKEVLYNDSA-TSGEAAALGMG  497 (963)
T ss_dssp             HHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHTCCH-HHHHHHHHHHH
T ss_pred             HHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhcCCH-HHHHHHHHHHh
Confidence            344455555567776666554321 0000112333334444444444443 24556666665543211 11  1222334


Q ss_pred             HHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHH--hhcCCHHHHHHHHHHHHHcCCCCCHHHH--HHHHHHHHhc
Q 041804          185 DIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAV--GVSEGVDFAMRVYREMREMGCQPSVVTC--NTVIKLLCEN  260 (403)
Q Consensus       185 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~li~~~~~~  260 (403)
                      ..+.-.|+.+....++..+.+..   +..+...+..++  .-.|+.+.+..+++.+... ..|....-  .++.-+|+..
T Consensus       498 li~vGTgn~~ai~~LL~~~~e~~---~e~vrR~aalgLGll~~g~~e~~~~li~~L~~~-~dp~vRygaa~alglAyaGT  573 (963)
T 4ady_A          498 LCMLGTGKPEAIHDMFTYSQETQ---HGNITRGLAVGLALINYGRQELADDLITKMLAS-DESLLRYGGAFTIALAYAGT  573 (963)
T ss_dssp             HHHTTCCCHHHHHHHHHHHHHCS---CHHHHHHHHHHHHHHTTTCGGGGHHHHHHHHHC-SCHHHHHHHHHHHHHHTTTS
T ss_pred             hhhcccCCHHHHHHHHHHHhccC---cHHHHHHHHHHHHhhhCCChHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHhcCC
Confidence            44556678777788887776642   333444444444  4678989999998888764 12222222  2344567788


Q ss_pred             CcHHHHHHHHHhchhcCCCCChhhHHHHHH-----hhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCc-chHH
Q 041804          261 GRVREAYAVLAEMPKKGCVPDVITYHCFFR-----CLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFL-RPVF  334 (403)
Q Consensus       261 g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~-----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~-~~a~  334 (403)
                      |+.....+++..+.+.   ++...-...+.     .++..+.+..++..+.+.+ .|....-..+.-+....|.. .++.
T Consensus       574 Gn~~aIq~LL~~~~~d---~~d~VRraAViaLGlI~~g~~e~v~rlv~~L~~~~-d~~VR~gAalALGli~aGn~~~~ai  649 (963)
T 4ady_A          574 GNNSAVKRLLHVAVSD---SNDDVRRAAVIALGFVLLRDYTTVPRIVQLLSKSH-NAHVRCGTAFALGIACAGKGLQSAI  649 (963)
T ss_dssp             CCHHHHHHHHHHHHHC---SCHHHHHHHHHHHHHHTSSSCSSHHHHTTTGGGCS-CHHHHHHHHHHHHHHTSSSCCHHHH
T ss_pred             CCHHHHHHHHHHhccC---CcHHHHHHHHHHHHhhccCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHHhccCCCcHHHH
Confidence            9988887899888764   22222222222     2245555566665554443 45555444555555555654 5788


Q ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHH
Q 041804          335 VVWKKMEELGCSPDEFAYNALVDALI  360 (403)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~l~~~~~  360 (403)
                      +++..+..   .+|..+-...+.++.
T Consensus       650 d~L~~L~~---D~d~~Vrq~Ai~ALG  672 (963)
T 4ady_A          650 DVLDPLTK---DPVDFVRQAAMIALS  672 (963)
T ss_dssp             HHHHHHHT---CSSHHHHHHHHHHHH
T ss_pred             HHHHHHcc---CCCHHHHHHHHHHHH
Confidence            88888864   355555444444443

>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=91.94  E-value=1.5  Score=28.63  Aligned_cols=86  Identities=8%  Similarity=0.065  Sum_probs=62.2

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHH-hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTD-TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      ..+++|.-+-+|+..    .++.+ +--.-+..+...|++++|..+.+.+.     .||...|..|-.  .+.|..+++.
T Consensus        21 H~HqEA~tIAdwL~~----~~~~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c-----~pdlepw~ALce--~rlGl~s~le   89 (116)
T 2p58_C           21 HYHEEANCIAEWLHL----KGEEEAVQLIRLSSLMNRGDYASALQQGNKLA-----YPDLEPWLALCE--YRLGLGSALE   89 (116)
T ss_dssp             TCHHHHHHHHHHHHH----TTCHHHHHHHHHHHHHHTTCHHHHHHHHTTSC-----CGGGHHHHHHHH--HHHTCHHHHH
T ss_pred             hHHHHHHHHHHHHHh----CCcHHHHHHHHHHHHHcchhHHHHHHhcCCCC-----CchHHHHHHHHH--HhcccHHHHH
Confidence            468899999999985    23322 22233456778999999999887765     488888876654  6788888898


Q ss_pred             HHHHHHhhcCCCcHHHHH
Q 041804           88 GTFNKLDEFGLKDEVSYC  105 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~  105 (403)
                      ..+.++...|.+....|.
T Consensus        90 ~rL~~la~sg~p~~q~Fa  107 (116)
T 2p58_C           90 SRLNRLARSQDPRIQTFV  107 (116)
T ss_dssp             HHHHHHTTCCCHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHH
Confidence            888888887766444443

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=90.79  E-value=0.00051  Score=59.30  Aligned_cols=216  Identities=6%  Similarity=0.004  Sum_probs=147.7

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      .+.+|..|..+..+.+.+.+|++-|-+.       .|+..|..++.+..+.|.+++-++.+...++ ...++.+=+.|+-
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsyIkA-------~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk-~~ke~~IDteLi~  124 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMARK-KARESYVETELIF  124 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSSCCC-------SCCCSSSHHHHHTTTSSCCTTHHHHHHTTST-TCCSTTTTHHHHH
T ss_pred             CccHHHHHHHHHHccCchHHHHHHHHhC-------CChHHHHHHHHHHHhCCCHHHHHHHHHHHHH-HhcccccHHHHHH
Confidence            4668899999999999999987765322       3555688899999999999999988865554 3457777788999


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC-----------------
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG-----------------  172 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----------------  172 (403)
                      +|++.++..+.++.             -..||..-...+..-|...|.++.|.-+|..+....                 
T Consensus       125 ayAk~~rL~elEef-------------l~~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVd  191 (624)
T 3lvg_A          125 ALAKTNRLAELEEF-------------INGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVD  191 (624)
T ss_dssp             HHHTSCSSSTTTST-------------TSCCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTT
T ss_pred             HHHhhCcHHHHHHH-------------HcCCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHH
Confidence            99999987665443             223555555677788888888888877665542211                 


Q ss_pred             ---CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHH
Q 041804          173 ---VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVT  249 (403)
Q Consensus       173 ---~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  249 (403)
                         -.-++.||..+-.+|...+.+.-|.-.--.+.-.   ||  -...++..|-..|.+++.+.+++..... -......
T Consensus       192 aArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvh---ad--eL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGm  265 (624)
T 3lvg_A          192 GARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH---AD--ELEELINYYQDRGYFEELITMLEAALGL-ERAHMGM  265 (624)
T ss_dssp             TTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC---SS--CCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHH
T ss_pred             HHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhccc---HH--HHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHH
Confidence               1125668888888888888877665444333322   22  2234566777888888888888776632 2346777


Q ss_pred             HHHHHHHHHhcCcHHHHHHHHHhc
Q 041804          250 CNTVIKLLCENGRVREAYAVLAEM  273 (403)
Q Consensus       250 ~~~li~~~~~~g~~~~a~~~~~~~  273 (403)
                      |+-|.-.|++- ++++..+.++..
T Consensus       266 FTELaILYsKY-~PeKlmEHlklf  288 (624)
T 3lvg_A          266 FTELAILYSKF-KPQKMREHLELF  288 (624)
T ss_dssp             HHHHHHHHHSS-CTTHHHHHHTTS
T ss_pred             HHHHHHHHHhc-CHHHHHHHHHHH
Confidence            88888777764 455555555543

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=90.67  E-value=1.4  Score=28.73  Aligned_cols=86  Identities=12%  Similarity=0.066  Sum_probs=62.3

Q ss_pred             ccHHHHHHhhhhhcccCCCcCCHH-hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHH
Q 041804            9 NDWKRALEFFNWVETDCHFTHTTD-TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAM   87 (403)
Q Consensus         9 ~~~~~A~~~~~~~~~~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~   87 (403)
                      ..+++|.-+-+|+..    .++.+ +--.-+..+...|++++|..+.+.+.     .||...|..|-.  .+.|..+++.
T Consensus        20 H~HqEA~tIAdwL~~----~~~~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c-----~pdlepw~ALce--~rlGl~s~le   88 (115)
T 2uwj_G           20 HCHEEALCIAEWLER----LGQDEAARLIRISSLANQGRYQEALAFAHGNP-----WPALEPWFALCE--WHLGLGAALD   88 (115)
T ss_dssp             TCHHHHHHHHHHHHH----TTCHHHHHHHHHHHHHHTTCHHHHHGGGTTCC-----CGGGHHHHHHHH--HHTTCHHHHH
T ss_pred             hHHHHHHHHHHHHHh----CCcHHHHHHHHHHHHHcchhHHHHHHhcCCCC-----CchHHHHHHHHH--HhcccHHHHH
Confidence            478899999999985    23322 22233456778999999988877664     488888876654  6889999999


Q ss_pred             HHHHHHhhcCCCcHHHHH
Q 041804           88 GTFNKLDEFGLKDEVSYC  105 (403)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~  105 (403)
                      ..+.++...|.+....|.
T Consensus        89 ~rL~~la~sg~p~~q~Fa  106 (115)
T 2uwj_G           89 RRLAGLGGSSDPALADFA  106 (115)
T ss_dssp             HHHHHHHTCSSHHHHHHH
T ss_pred             HHHHHHHhCCCHHHHHHH
Confidence            988888887766444443

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=89.58  E-value=4.2  Score=28.83  Aligned_cols=74  Identities=11%  Similarity=0.027  Sum_probs=48.3

Q ss_pred             CCCchhhHHHHHHHHHhcCC---cchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChh
Q 041804          310 IRPKMDTYVMLLRKFGRWGF---LRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPR  385 (403)
Q Consensus       310 ~~~~~~~~~~li~~~~~~g~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~  385 (403)
                      ..|+..+--.+.+++.+..+   ..+++.+++.+.+.+-.-.....-.|.-++.+.|++++|.++.+.+++  +.|+..
T Consensus        35 ~~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~--~eP~n~  111 (144)
T 1y8m_A           35 PTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERNNK  111 (144)
T ss_dssp             TTSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH--TCCCCH
T ss_pred             CCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHh--cCCCcH
Confidence            34566665566667776664   456777888777653112233344555678888888888888888887  556554

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=89.47  E-value=3.2  Score=27.31  Aligned_cols=64  Identities=14%  Similarity=0.016  Sum_probs=51.6

Q ss_pred             ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHH
Q 041804          157 WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRA  221 (403)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~  221 (403)
                      +.=+..+-++.+...+..|++....+.+++|-+.+++..|.++|+-.+.. ..+...+|..+++-
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-~~~~~~iY~~~lqE   88 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQE   88 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCchhhHHHHHHH
Confidence            44567788888888999999999999999999999999999999988876 23344567666643

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=89.41  E-value=2.5  Score=34.04  Aligned_cols=246  Identities=15%  Similarity=0.090  Sum_probs=111.8

Q ss_pred             HHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH---HHHHHH
Q 041804          107 LVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL---HSYSIY  183 (403)
Q Consensus       107 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l  183 (403)
                      .+...++.|+.+....+++.-..-      ....+.. -.+.+...+..|+.+    +++.+.+.|..++.   ...+. 
T Consensus         8 ~L~~A~~~g~~~~v~~Ll~~g~~~------~~~~~~~-g~t~L~~A~~~g~~~----~v~~Ll~~g~~~~~~~~~g~t~-   75 (285)
T 1wdy_A            8 LLIKAVQNEDVDLVQQLLEGGANV------NFQEEEG-GWTPLHNAVQMSRED----IVELLLRHGADPVLRKKNGATP-   75 (285)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTTCCT------TCCCTTT-CCCHHHHHHHTTCHH----HHHHHHHTTCCTTCCCTTCCCH-
T ss_pred             HHHHHHHcCCHHHHHHHHHcCCCc------ccccCCC-CCcHHHHHHHcCCHH----HHHHHHHcCCCCcccCCCCCCH-
Confidence            344455667777766666542221      1010110 112344445566654    44444455544332   22222 


Q ss_pred             HHHHHHcCChhHHHHHHHHHHHcCCCCCh---hhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHH-----------
Q 041804          184 MDIMCKSGKPWKAVKLYKEMKKKGIKMDV---VAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVT-----------  249 (403)
Q Consensus       184 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-----------  249 (403)
                      +...+..|+.+    +++.+.+.|..++.   ..++.+. ..+..|+.+-    ++.+.+.|..++...           
T Consensus        76 L~~A~~~~~~~----~v~~Ll~~g~~~~~~~~~g~t~L~-~A~~~~~~~~----~~~Ll~~g~~~~~~~~~~~~~~~~~~  146 (285)
T 1wdy_A           76 FLLAAIAGSVK----LLKLFLSKGADVNECDFYGFTAFM-EAAVYGKVKA----LKFLYKRGANVNLRRKTKEDQERLRK  146 (285)
T ss_dssp             HHHHHHHTCHH----HHHHHHHTTCCTTCBCTTCCBHHH-HHHHTTCHHH----HHHHHHTTCCTTCCCCCCHHHHHTTC
T ss_pred             HHHHHHcCCHH----HHHHHHHcCCCCCccCcccCCHHH-HHHHhCCHHH----HHHHHHhCCCcccccccHHHHHhhcc
Confidence            33344556654    44444555554432   2223333 3345666544    444445554443210           


Q ss_pred             -HHHHHHHHHhcCcHHHHHHHHHhchhcCCCC---ChhhHHHHHHhh--CCHHHHHHHHHHHHHcCCCCchhh--HHHHH
Q 041804          250 -CNTVIKLLCENGRVREAYAVLAEMPKKGCVP---DVITYHCFFRCL--EKPREILGLFDRMIESGIRPKMDT--YVMLL  321 (403)
Q Consensus       250 -~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p---~~~~~~~l~~~~--~~~~~a~~~~~~~~~~~~~~~~~~--~~~li  321 (403)
                       -...+...+..|+.+-+..+++..   |..+   +....+.+..+.  +......++.+.+.+.|..++...  -.+.+
T Consensus       147 ~g~t~L~~A~~~~~~~~v~~Ll~~~---~~~~~~~~~~g~t~l~~a~~~~~~~~~~~i~~~Ll~~g~~~~~~~~~g~t~L  223 (285)
T 1wdy_A          147 GGATALMDAAEKGHVEVLKILLDEM---GADVNACDNMGRNALIHALLSSDDSDVEAITHLLLDHGADVNVRGERGKTPL  223 (285)
T ss_dssp             CCCCHHHHHHHHTCHHHHHHHHHTS---CCCTTCCCTTSCCHHHHHHHCSCTTTHHHHHHHHHHTTCCSSCCCTTSCCHH
T ss_pred             CCCcHHHHHHHcCCHHHHHHHHHhc---CCCCCccCCCCCCHHHHHHHccccchHHHHHHHHHHcCCCCCCcCCCCCcHH
Confidence             012333445667776666665542   2222   222223333332  344444667777777777665421  12334


Q ss_pred             HHHHhcCCcchHHHHHHHHHhcCCCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCh
Q 041804          322 RKFGRWGFLRPVFVVWKKMEELGCSPD---EFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKP  384 (403)
Q Consensus       322 ~~~~~~g~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~  384 (403)
                      ...++.|+.+-+..+++.   .|..++   ..-.+. +...++.|+.    ++.+-+.+.|..|+.
T Consensus       224 ~~A~~~~~~~~v~~Ll~~---~g~~~~~~~~~g~t~-l~~A~~~~~~----~i~~~Ll~~Ga~~~~  281 (285)
T 1wdy_A          224 ILAVEKKHLGLVQRLLEQ---EHIEINDTDSDGKTA-LLLAVELKLK----KIAELLCKRGASTDC  281 (285)
T ss_dssp             HHHHHTTCHHHHHHHHHS---SSCCTTCCCTTSCCH-HHHHHHTTCH----HHHHHHHHHSSCSCC
T ss_pred             HHHHHcCCHHHHHHHHhc---cCCCccccCCCCCcH-HHHHHHcCcH----HHHHHHHHcCCCCCc
Confidence            445566766544444331   333332   222223 3334455655    345555667776654

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=87.99  E-value=1.8  Score=34.51  Aligned_cols=48  Identities=15%  Similarity=0.143  Sum_probs=22.9

Q ss_pred             hcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhc
Q 041804           79 TAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFG  126 (403)
Q Consensus        79 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  126 (403)
                      +.|+++.|++....-.+..+.|...-..+++.+|-.|+++.|.+-++.
T Consensus         9 ~~g~L~~al~~~~~~VR~~P~da~~R~~LfqLLcv~G~w~RA~~QL~~   56 (273)
T 1zbp_A            9 SEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQ   56 (273)
T ss_dssp             TTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            344444444444444444444444444444444445555544444433

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=87.91  E-value=5.3  Score=29.17  Aligned_cols=99  Identities=8%  Similarity=-0.069  Sum_probs=67.7

Q ss_pred             HhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCH-------HHHHHHHHHHHhcCChHHHHHHHHHHhhcC-------
Q 041804           32 DTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNH-------ATFRIMFKRYVTAHLVNEAMGTFNKLDEFG-------   97 (403)
Q Consensus        32 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-------   97 (403)
                      .++-.-+..+...|.++.|+-+.+.+.......|+.       .++..+.+++...|++.+|...|++.....       
T Consensus        21 ~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~  100 (167)
T 3ffl_A           21 MNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTS  100 (167)
T ss_dssp             CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC----
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            345556777888899988888777654322112331       255667788889999999999998853211       


Q ss_pred             -----------------CC-cHHHHHHHHHHHHhcCCHHHHHHHHhccccc
Q 041804           98 -----------------LK-DEVSYCNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus        98 -----------------~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                                       .. +.+.---+..+|.+.+++++|+.+++.+...
T Consensus       101 s~~~~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k  151 (167)
T 3ffl_A          101 KVRPSTGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSR  151 (167)
T ss_dssp             ----------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGG
T ss_pred             CccccccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCch
Confidence                             01 2234455788899999999999999887654

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=87.68  E-value=5.5  Score=27.83  Aligned_cols=76  Identities=11%  Similarity=-0.084  Sum_probs=51.8

Q ss_pred             CCcCCHHhHHHHHHHHHccCC---hhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHH
Q 041804           26 HFTHTTDTYNSVIDILGKFFE---FDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEV  102 (403)
Q Consensus        26 ~~~~~~~~~~~li~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  102 (403)
                      +..|++.+--.+..++.+..+   ..+++.+++.+...+ ..-....+-.+.-++.+.|++++|.+..+.+.+..|.+..
T Consensus        35 ~~~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~-~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP~N~Q  113 (134)
T 3o48_A           35 GPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQ  113 (134)
T ss_dssp             GGGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCTTCHH
T ss_pred             CCCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-cchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCCHH
Confidence            445666666666667776654   446778888777754 1113455666777888888888888888888887766443

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.22  E-value=14  Score=32.12  Aligned_cols=98  Identities=3%  Similarity=-0.152  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCC--CCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc-CCCCChhhHHH---
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDKRG--VVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK-GIKMDVVAYNT---  217 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~---  217 (403)
                      +...+...|.+.|+++.|.+.+.++...-  ...-...+-.++..+...+++..+...+.+.... .-.++....+.   
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk~  212 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYKT  212 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHHH
Confidence            45678889999999999999999987642  2334567778888888999999999888887554 11122222111   


Q ss_pred             -HHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          218 -VIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       218 -ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                       -...+...+++..|.+.|-+....
T Consensus       213 ~~gl~~l~~r~f~~Aa~~f~e~~~t  237 (429)
T 4b4t_R          213 YYGIHCLAVRNFKEAAKLLVDSLAT  237 (429)
T ss_dssp             HHHHGGGGTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhChHHHHHHHHHHHhcc
Confidence             112234568888888888776654

>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=86.69  E-value=6.4  Score=27.53  Aligned_cols=45  Identities=13%  Similarity=0.077  Sum_probs=21.0

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      .+-++.+...+..|++......+++|-+.+++..|.++|+-.+.+
T Consensus        73 rrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K  117 (152)
T 2y69_E           73 RKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK  117 (152)
T ss_dssp             HHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            333444444444444444444444444444444444444444433

>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=85.80  E-value=7.2  Score=27.29  Aligned_cols=64  Identities=5%  Similarity=-0.000  Sum_probs=48.8

Q ss_pred             ChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           46 EFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        46 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      +.-+..+-++.+...+ ..|++......+++|-+.+++..|.++|+-++..-.....+|..+++-
T Consensus        68 D~wElrrglN~l~~~D-lVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~lqE  131 (152)
T 2y69_E           68 DAWELRKGMNTLVGYD-LVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQE  131 (152)
T ss_dssp             CHHHHHHHHHHHTTSS-BCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccc-cCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHHHH
Confidence            4446667777777776 679999999999999999999999999998877554445556666553

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=85.17  E-value=10  Score=33.10  Aligned_cols=98  Identities=11%  Similarity=-0.027  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHHHcCChhHHHHHHHHHHHcC--CCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc---CCCCCHHH--H
Q 041804          178 HSYSIYMDIMCKSGKPWKAVKLYKEMKKKG--IKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM---GCQPSVVT--C  250 (403)
Q Consensus       178 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~--~  250 (403)
                      .+...+...|.+.|+++.|.+.|.++...-  ..--...+-.+++.+...+++..+...+.++...   +..|+...  .
T Consensus       132 ~~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk  211 (429)
T 4b4t_R          132 QAWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYK  211 (429)
T ss_dssp             SCCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence            367789999999999999999999998763  2333457778889999999999999999988654   22222211  1


Q ss_pred             HHHHHHHHhcCcHHHHHHHHHhchh
Q 041804          251 NTVIKLLCENGRVREAYAVLAEMPK  275 (403)
Q Consensus       251 ~~li~~~~~~g~~~~a~~~~~~~~~  275 (403)
                      ..-...+...+++..|...|-+...
T Consensus       212 ~~~gl~~l~~r~f~~Aa~~f~e~~~  236 (429)
T 4b4t_R          212 TYYGIHCLAVRNFKEAAKLLVDSLA  236 (429)
T ss_dssp             HHHHHGGGGTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhChHHHHHHHHHHHhc
Confidence            1112233457889999888877654

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=84.87  E-value=13  Score=29.63  Aligned_cols=71  Identities=7%  Similarity=-0.103  Sum_probs=55.3

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC---cHHHHHHHHHH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK---DEVSYCNLVDA  110 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~l~~~  110 (403)
                      +..+.+.|++++++.....-.+..  +-|...-..++..++-.|++++|.+-++...+..+.   ....|..+|.+
T Consensus         4 ~~~ll~~g~L~~al~~~~~~VR~~--P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~~~~~a~~yr~lI~a   77 (273)
T 1zbp_A            4 WKNALSEGQLQQALELLIEAIKAS--PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKA   77 (273)
T ss_dssp             HHHHTTTTCHHHHHHHHHHHHHTC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhC--CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCchhhHHHHHHHHHHHH
Confidence            345678899999999887777765  467788888999999999999999999998888766   33355555555

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=83.17  E-value=11  Score=27.47  Aligned_cols=120  Identities=10%  Similarity=-0.007  Sum_probs=64.9

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCcH-------HHHHHHHHHHHHcCChhHHHHHHHHHHHcC-CCCCh-h
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDKRG-VVKDL-------HSYSIYMDIMCKSGKPWKAVKLYKEMKKKG-IKMDV-V  213 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~-~  213 (403)
                      ++..-+..+...+.++.|+-+.+.+.... ..|+.       .++..+.+++...+++..|...|++.++.. .-+.. .
T Consensus        22 ~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s  101 (167)
T 3ffl_A           22 NVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSK  101 (167)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC-----
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            34555677777888888877766654321 12221       245566677788888888888888865431 11111 1


Q ss_pred             hHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          214 AYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       214 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      +...+ .   .......         ......+...---+..+|.+.+++++|+.+++.+..+
T Consensus       102 ~~~~~-~---~~ss~p~---------s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k  151 (167)
T 3ffl_A          102 VRPST-G---NSASTPQ---------SQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSR  151 (167)
T ss_dssp             ----------------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGG
T ss_pred             ccccc-c---ccCCCcc---------cccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCch
Confidence            11111 0   0000000         0011223334344778899999999999999987654

>4a1g_A Mitotic checkpoint serine/threonine-protein kinas; cell cycle, transferase, spindle assembly checkpoint, mitosi repeat, KNL1, KMN network; 2.60A {Homo sapiens} PDB: 2lah_A

Probab=80.96  E-value=11  Score=27.10  Aligned_cols=53  Identities=13%  Similarity=0.103  Sum_probs=28.8

Q ss_pred             hHHHHHHHHHhcCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCh
Q 041804          332 PVFVVWKKMEELGCSP-DEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKP  384 (403)
Q Consensus       332 ~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~  384 (403)
                      .+.++|..|...|+-. -...|......+...|++++|.++|+.-++++-.|-.
T Consensus        83 dp~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~Gi~~~A~P~~  136 (152)
T 4a1g_A           83 DLHQFFEFLYNHGIGTLSSPLYIAWAGHLEAQGELQHASAVLQRGIQNQAEPRE  136 (152)
T ss_dssp             CHHHHHHHHHTTTTTTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBSHH
T ss_pred             CHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCccHH
Confidence            3555555555554332 2344555555555566666666666666665555543

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=80.21  E-value=8.5  Score=30.78  Aligned_cols=19  Identities=16%  Similarity=0.080  Sum_probs=10.7

Q ss_pred             HHHHHHccCChhHHHHHHH
Q 041804           37 VIDILGKFFEFDLSWNLIH   55 (403)
Q Consensus        37 li~~~~~~~~~~~a~~~~~   55 (403)
                      .+...++.|+++....+++
T Consensus         8 ~L~~A~~~g~~~~v~~Ll~   26 (285)
T 1wdy_A            8 LLIKAVQNEDVDLVQQLLE   26 (285)
T ss_dssp             HHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHH
Confidence            3445566677665555554

---

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	403
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.93
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.91
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.7
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.68
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.44
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.4
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.34
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.32
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.32
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.3
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.3
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.28
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.27
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.19
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.97
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.83
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.79
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.77
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.75
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.74
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.72
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.7
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.7
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.69
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.6
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.55
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.54
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.51
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.49
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.4
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.37
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.35
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.34
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.31
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.26
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.17
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	98.15
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.15
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.14
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.14
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.13
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.11
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.1
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.1
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.07
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.06
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.06
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.99
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.98
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.79
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.67
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.59
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.54
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.29
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.82
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.29
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	95.99
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	94.72
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	94.57
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.51
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	89.58
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	88.51

>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=99.93  E-value=5.5e-22  Score=171.80  Aligned_cols=361  Identities=12%  Similarity=0.025  Sum_probs=288.7

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      ...+.|++++|++.|+.+.+.  .+.++.++..+..++.+.|++++|...|++..+..  +.+..+|..+..+|.+.|++
T Consensus         8 ~~~~~G~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--p~~~~a~~~l~~~~~~~g~~   83 (388)
T d1w3ba_           8 REYQAGDFEAAERHCMQLWRQ--EPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN--PLLAEAYSNLGNVYKERGQL   83 (388)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHhhhhccc
Confidence            456789999999999998753  24468889999999999999999999999998865  34678899999999999999


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHH
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCRE  163 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  163 (403)
                      ++|+..+....+..+.+..............+....+.........       ...................+....+..
T Consensus        84 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (388)
T d1w3ba_          84 QEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQ-------YNPDLYCVRSDLGNLLKALGRLEEAKA  156 (388)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHH-------HCTTCTHHHHHHHHHHHTTSCHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccc-------cccccccccccccccccccchhhhhHH
Confidence            9999999999998887666666666666666666555555444433       334455556667777778888888888


Q ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          164 FWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      .+.......+. +...+..+...+...|++++|...++...+.. +-+..++..+...+...|++++|...++...+...
T Consensus       157 ~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~  234 (388)
T d1w3ba_         157 CYLKAIETQPN-FAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP  234 (388)
T ss_dssp             HHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT
T ss_pred             HHHHhhccCcc-hhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhh
Confidence            88888776555 67788888889999999999999999988763 33566888888999999999999999999888753


Q ss_pred             CCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCC-hhhHHHHHH---hhCCHHHHHHHHHHHHHcCCCCchhhHHH
Q 041804          244 QPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPD-VITYHCFFR---CLEKPREILGLFDRMIESGIRPKMDTYVM  319 (403)
Q Consensus       244 ~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (403)
                       .+...+..+...+.+.|++++|...|++..+.  .|+ ...+..+..   ..++.++|.+.++....... .+...+..
T Consensus       235 -~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~  310 (388)
T d1w3ba_         235 -NHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCP-THADSLNN  310 (388)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCT-TCHHHHHH
T ss_pred             -hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCC-ccchhhhH
Confidence             36677888889999999999999999998765  343 344444333   34888999999998887643 46778888


Q ss_pred             HHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCh
Q 041804          320 LLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKP  384 (403)
Q Consensus       320 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~  384 (403)
                      +...+...|++++|++.+++..+.. +.+..++..+..+|.+.|++++|...|++.++  +.|+.
T Consensus       311 l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--l~P~~  372 (388)
T d1w3ba_         311 LANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIR--ISPTF  372 (388)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHT--TCTTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCC
Confidence            8999999999999999999988753 44678889999999999999999999999887  44553

>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=99.91  E-value=2e-20  Score=161.83  Aligned_cols=346  Identities=11%  Similarity=0.020  Sum_probs=283.5

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      +.++...|++++|++.|+.+.+.  .+.+..++..+..++.+.|++++|+..+.......  +.+...+..........+
T Consensus        40 a~~~~~~~~~~~A~~~~~~al~~--~p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  115 (388)
T d1w3ba_          40 SSIHFQCRRLDRSAHFSTLAIKQ--NPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLK--PDFIDGYINLAAALVAAG  115 (388)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHhhhhccccccccccccccccc--cccccccccccccccccc
Confidence            45677889999999999998752  24457899999999999999999999999998865  456666777777777788


Q ss_pred             ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHH
Q 041804           82 LVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKC  161 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  161 (403)
                      ....+............................+....+...+.....       ..+.+...+..+...+...|++++|
T Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~A  188 (388)
T d1w3ba_         116 DMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIE-------TQPNFAVAWSNLGCVFNAQGEIWLA  188 (388)
T ss_dssp             CSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             cccccccccccccccccccccccccccccccccchhhhhHHHHHHhhc-------cCcchhHHHHhhcccccccCcHHHH
Confidence            888888888877777766777777777778888888888888777665       3455677888899999999999999


Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ...+++..+..+. +..+|..+...+...|++++|...++.....+ +.+...+..+...+.+.|++++|...|+++.+.
T Consensus       189 ~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  266 (388)
T d1w3ba_         189 IHHFEKAVTLDPN-FLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL  266 (388)
T ss_dssp             HHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCcc-cHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            9999999887655 77889999999999999999999999998874 446677888889999999999999999999886


Q ss_pred             CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHH---hhCCHHHHHHHHHHHHHcCCCCchhhHH
Q 041804          242 GCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFR---CLEKPREILGLFDRMIESGIRPKMDTYV  318 (403)
Q Consensus       242 ~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~  318 (403)
                      .. -+..++..+...+...|++++|...++...... +.+...+..+..   ..++.++|++.+++..+.... +..++.
T Consensus       267 ~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~  343 (388)
T d1w3ba_         267 QP-HFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPE-FAAAHS  343 (388)
T ss_dssp             CS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTT-CHHHHH
T ss_pred             CC-CCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-CccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHH
Confidence            43 357788899999999999999999999887652 223344444433   337899999999998875433 567888


Q ss_pred             HHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCC
Q 041804          319 MLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGM  364 (403)
Q Consensus       319 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  364 (403)
                      .+..++.+.|++++|.+.|++..+.. +-+...|..+..+|.+.||
T Consensus       344 ~la~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         344 NLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC
Confidence            89999999999999999999998753 3468889999999988875

>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=99.70  E-value=5.9e-15  Score=123.91  Aligned_cols=236  Identities=11%  Similarity=-0.038  Sum_probs=173.3

Q ss_pred             HHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC
Q 041804           36 SVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK  115 (403)
Q Consensus        36 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  115 (403)
                      .....+.+.|++++|+..|+++.+..  +.+..+|..+..++...|++++|+..|.+..+..+.+...+..+..++...|
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~  101 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQD--PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNES  101 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccc
Confidence            45667788888888888888888865  3457788888888888888888888888888887778888888888888888


Q ss_pred             CHHHHHHHHhcccccccccc--------cccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC-CCcHHHHHHHHHH
Q 041804          116 HVIEAQELCFGENKNVGFSG--------LVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGV-VKDLHSYSIYMDI  186 (403)
Q Consensus       116 ~~~~a~~~~~~~~~~~~~~~--------~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~  186 (403)
                      ++++|.+.+.+.....+...        .....+.......+..+...+.+.+|.+.|.+..+..+ .++...+..+...
T Consensus       102 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~  181 (323)
T d1fcha_         102 LQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVL  181 (323)
T ss_dssp             CHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHH
T ss_pred             cccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHH
Confidence            88888888776543321100        01112222333344455566777888888888766543 2356677888888


Q ss_pred             HHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHH
Q 041804          187 MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREA  266 (403)
Q Consensus       187 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  266 (403)
                      +...|++++|...|++..... +-+..+|..+..++...|++++|.+.|+.+.+... -+..++..+..+|.+.|++++|
T Consensus       182 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A  259 (323)
T d1fcha_         182 FNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQP-GYIRSRYNLGISCINLGAHREA  259 (323)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHHhh-ccHHHHHHHHHHHHHCCCHHHH
Confidence            889999999999999888763 33566788888888899999999999998887642 2567788888899999999999


Q ss_pred             HHHHHhchh
Q 041804          267 YAVLAEMPK  275 (403)
Q Consensus       267 ~~~~~~~~~  275 (403)
                      +..|++..+
T Consensus       260 ~~~~~~al~  268 (323)
T d1fcha_         260 VEHFLEALN  268 (323)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            998887654

>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=99.68  E-value=1.4e-14  Score=121.57  Aligned_cols=233  Identities=7%  Similarity=-0.052  Sum_probs=174.0

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|++++|++.|+.+.+.  .+.++.+|..+..++...|++++|...|++..+..  +-+...|..+..+|...|+
T Consensus        27 ~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          27 LRRLQEGDLPNAVLLFEAAVQQ--DPKHMEAWQYLGTTQAENEQELLAISALRRCLELK--PDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc--ccccccccccccccccccc
Confidence            3456789999999999998852  34468899999999999999999999999998865  3467889999999999999


Q ss_pred             hHHHHHHHHHHhhcCCCcHHHHHHHHHHHH--hcC----CH--HHHHHHHhcccccc--cccccccCcchHHHHHHHHHH
Q 041804           83 VNEAMGTFNKLDEFGLKDEVSYCNLVDALC--EYK----HV--IEAQELCFGENKNV--GFSGLVEMNKTKIYNMILRGW  152 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~--~~~----~~--~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~  152 (403)
                      +++|.+.++......+.....+........  ..+    ..  -.....+.+.....  .........+..++..+...+
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            999999999998877653322211111111  100    00  01111122211110  000001234567788889999


Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHH
Q 041804          153 FKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAM  232 (403)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~  232 (403)
                      ...|++++|...|++.....+. +..+|..+..+|...|++++|.+.|++..+.. +-+..++..+..+|.+.|++++|.
T Consensus       183 ~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~  260 (323)
T d1fcha_         183 NLSGEYDKAVDCFTAALSVRPN-DYLLWNKLGATLANGNQSEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAV  260 (323)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHhhhhcccccccccccc-cccchhhhhhcccccccchhHHHHHHHHHHHh-hccHHHHHHHHHHHHHCCCHHHHH
Confidence            9999999999999999887666 78899999999999999999999999998863 335678889999999999999999


Q ss_pred             HHHHHHHHc
Q 041804          233 RVYREMREM  241 (403)
Q Consensus       233 ~~~~~~~~~  241 (403)
                      ..|++..+.
T Consensus       261 ~~~~~al~l  269 (323)
T d1fcha_         261 EHFLEALNM  269 (323)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            999998875

>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=99.44  E-value=2.3e-11  Score=100.77  Aligned_cols=216  Identities=10%  Similarity=0.040  Sum_probs=172.8

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC-ChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH-LVNEAMGTFNKLDEFGLKDEVSYCNLVD  109 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~l~~  109 (403)
                      ..+++.+..++.+.+.+++|+.+++.+.+..  |-+..+|+....++...| ++++|+..+++..+..+.+..+|..+..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln--P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~  120 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhH
Confidence            5577788888889999999999999999976  456778999998888876 5899999999999999889999999999


Q ss_pred             HHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH
Q 041804          110 ALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK  189 (403)
Q Consensus       110 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  189 (403)
                      ++.+.|++++|+..+.++..       ..+.+..+|..+...+.+.|++++|.+.++++.+.++. +..+|+.+..++.+
T Consensus       121 ~~~~l~~~~eAl~~~~kal~-------~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~-n~~a~~~r~~~l~~  192 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILN-------QDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISN  192 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHhhccHHHHHHHHhhhhh-------hhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCc-cHHHHHHHHHHHHH
Confidence            99999999999999999887       55778899999999999999999999999999998777 77888888777777


Q ss_pred             cCC------hhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHH
Q 041804          190 SGK------PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQP-SVVTCNTVIKLLC  258 (403)
Q Consensus       190 ~~~------~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~li~~~~  258 (403)
                      .+.      +++|++.+....+.. +.+...|..+...+.. ...+++...++...+....+ +...+..++..|.
T Consensus       193 ~~~~~~~~~~~~ai~~~~~al~~~-P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~  266 (315)
T d2h6fa1         193 TTGYNDRAVLEREVQYTLEMIKLV-PHNESAWNYLKGILQD-RGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYE  266 (315)
T ss_dssp             TTCSCSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTT-TCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHH
T ss_pred             ccccchhhhhHHhHHHHHHHHHhC-CCchHHHHHHHHHHHh-cChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHH
Confidence            665      467888888887763 3466677666655543 44577778887777654332 3444555555553

>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=99.40  E-value=2.5e-10  Score=94.44  Aligned_cols=199  Identities=8%  Similarity=-0.017  Sum_probs=164.4

Q ss_pred             HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC-CHHHHHHHHhcccccccccccccCcchHHH
Q 041804           67 HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK-HVIEAQELCFGENKNVGFSGLVEMNKTKIY  145 (403)
Q Consensus        67 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  145 (403)
                      ..+++.+...+.+.+.+++|+++++++.+..|.+..+|+....++...| ++++|...+++...       ..+.+..+|
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~-------~~p~~~~a~  115 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIE-------EQPKNYQVW  115 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-------HCTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHH-------HHHhhhhHH
Confidence            4577788888889999999999999999999889999999999988876 58999999998877       557788999


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhc
Q 041804          146 NMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVS  225 (403)
Q Consensus       146 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~  225 (403)
                      +.+...+.+.|++++|++.++++.+..+. +..+|..+..++...|++++|++.++.+.+.+ +-+...|+.+...+.+.
T Consensus       116 ~~~~~~~~~l~~~~eAl~~~~kal~~dp~-n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~~  193 (315)
T d2h6fa1         116 HHRRVLVEWLRDPSQELEFIADILNQDAK-NYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNT  193 (315)
T ss_dssp             HHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHhHHHHhhccHHHHHHHHhhhhhhhhc-chHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHHc
Confidence            99999999999999999999999998777 88999999999999999999999999999985 33666777766666555


Q ss_pred             CC------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          226 EG------VDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       226 ~~------~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      +.      +++|...+..+.+..+ .+...|+.+...+... ..+++...++...+.
T Consensus       194 ~~~~~~~~~~~ai~~~~~al~~~P-~~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~l  248 (315)
T d2h6fa1         194 TGYNDRAVLEREVQYTLEMIKLVP-HNESAWNYLKGILQDR-GLSKYPNLLNQLLDL  248 (315)
T ss_dssp             TCSCSHHHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHTTT-CGGGCHHHHHHHHHH
T ss_pred             cccchhhhhHHhHHHHHHHHHhCC-CchHHHHHHHHHHHhc-ChHHHHHHHHHHHHh
Confidence            44      6788888888888743 3677777666655443 456677777766553

>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=99.34  E-value=2.5e-10  Score=94.35  Aligned_cols=187  Identities=12%  Similarity=0.017  Sum_probs=124.7

Q ss_pred             ChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhH
Q 041804           82 LVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGK  160 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  160 (403)
                      ..++|..+|++..+..++ +...|...+....+.|+.+.|..+++++...      .......+|...+....+.|+++.
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~------~~~~~~~~w~~~~~~~~~~~~~~~  152 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI------EDIDPTLVYIQYMKFARRAEGIKS  152 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS------SSSCTHHHHHHHHHHHHHHHCHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHH------hcCChHHHHHHHHHHHHHcCChHH
Confidence            346677777777765444 6666777777777777777777777776653      112223457777777777777777


Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHH-HHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHH
Q 041804          161 CREFWEEMDKRGVVKDLHSYSIYMDI-MCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMR  239 (403)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  239 (403)
                      |.++|++..+.++. +...|...... +...|+.+.|..+|+.+... .+.+...|...+..+.+.|+++.|+.+|++..
T Consensus       153 ar~i~~~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai  230 (308)
T d2onda1         153 GRMIFKKAREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVL  230 (308)
T ss_dssp             HHHHHHHHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            77777777766544 33344333332 23457778888888887776 34456677777777778888888888888877


Q ss_pred             HcCC-CC--CHHHHHHHHHHHHhcCcHHHHHHHHHhchhc
Q 041804          240 EMGC-QP--SVVTCNTVIKLLCENGRVREAYAVLAEMPKK  276 (403)
Q Consensus       240 ~~~~-~~--~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  276 (403)
                      +... .|  ....|...+..-...|+.+.+.++++++.+.
T Consensus       231 ~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~  270 (308)
T d2onda1         231 TSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             HSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             HhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            6532 22  2346777777777778888888888876553

>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=99.32  E-value=2.6e-09  Score=89.87  Aligned_cols=199  Identities=9%  Similarity=-0.056  Sum_probs=115.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHh----CCCC--C-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCC----CCCh
Q 041804          144 IYNMILRGWFKMSWWGKCREFWEEMDK----RGVV--K-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGI----KMDV  212 (403)
Q Consensus       144 ~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~  212 (403)
                      .+..+...+...|++..+...+.....    ....  + ....+..+...+...|+++.+...+........    ....
T Consensus        93 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  172 (366)
T d1hz4a_          93 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  172 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHH
Confidence            345555666666777777666665432    1111  1 123455566777788888888888877765421    1223


Q ss_pred             hhHHHHHHHHhhcCCHHHHHHHHHHHHHcC--CCC----CHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChh---
Q 041804          213 VAYNTVIRAVGVSEGVDFAMRVYREMREMG--CQP----SVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVI---  283 (403)
Q Consensus       213 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~---  283 (403)
                      .++......+...++...+...+.......  ...    ....+..+...+...|+++.|...+..........+..   
T Consensus       173 ~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  252 (366)
T d1hz4a_         173 QCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQG  252 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHH
Confidence            344555566677788888877777665431  111    12345556667778888888888888766442222211   


Q ss_pred             hHHH---HHHhhCCHHHHHHHHHHHHH----cCCCCc-hhhHHHHHHHHHhcCCcchHHHHHHHHHh
Q 041804          284 TYHC---FFRCLEKPREILGLFDRMIE----SGIRPK-MDTYVMLLRKFGRWGFLRPVFVVWKKMEE  342 (403)
Q Consensus       284 ~~~~---l~~~~~~~~~a~~~~~~~~~----~~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~  342 (403)
                      .+..   +....++.++|...++....    .+..|+ ..++..+...|...|++++|.+.+++..+
T Consensus       253 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         253 QWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            1111   12223666666666666552    233332 34566666777777888888877777765

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.32  E-value=4.1e-11  Score=96.52  Aligned_cols=155  Identities=11%  Similarity=-0.088  Sum_probs=102.0

Q ss_pred             cccHHHHHHhhhhhcccCCCcC--CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHH
Q 041804            8 ANDWKRALEFFNWVETDCHFTH--TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNE   85 (403)
Q Consensus         8 ~~~~~~A~~~~~~~~~~~~~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~   85 (403)
                      ..+.+.|+..++.+.......+  ...+|..+..+|.+.|++++|+..|++..+..  +-+..+|+.+..+|.+.|++++
T Consensus        12 ~~~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~--p~~~~a~~~lg~~~~~~g~~~~   89 (259)
T d1xnfa_          12 TLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR--PDMPEVFNYLGIYLTQAGNFDA   89 (259)
T ss_dssp             CHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHTTCHHH
T ss_pred             cHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC--CCCHHHHhhhchHHHHHHHHHH
Confidence            3456666666666654332222  23466677778888888888888888877754  3456778888888888888888


Q ss_pred             HHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHH
Q 041804           86 AMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFW  165 (403)
Q Consensus        86 a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  165 (403)
                      |+..|++..+..+.+..++..+..++...|++++|...+++....       .+.+......+...+.+.+..+.+..+.
T Consensus        90 A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~-------~p~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (259)
T d1xnfa_          90 AYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD-------DPNDPFRSLWLYLAEQKLDEKQAKEVLK  162 (259)
T ss_dssp             HHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             hhhhhhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhh-------ccccHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            888888888877777777888888888888888888887776653       2333333333444444555544444444


Q ss_pred             HHHHhC
Q 041804          166 EEMDKR  171 (403)
Q Consensus       166 ~~~~~~  171 (403)
                      ......
T Consensus       163 ~~~~~~  168 (259)
T d1xnfa_         163 QHFEKS  168 (259)
T ss_dssp             HHHHHS
T ss_pred             HHhhcc
Confidence            444443

>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=99.30  E-value=8.6e-10  Score=91.02  Aligned_cols=184  Identities=11%  Similarity=0.063  Sum_probs=121.8

Q ss_pred             CHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhH
Q 041804          116 HVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWK  195 (403)
Q Consensus       116 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  195 (403)
                      ..+++..++++....      ..+.+...|...+....+.|+++.|..+|+++.+.........|...+..+.+.|+++.
T Consensus        79 ~~~~a~~i~~ral~~------~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~  152 (308)
T d2onda1          79 FSDEAANIYERAIST------LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKS  152 (308)
T ss_dssp             HHHHHHHHHHHHHTT------TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHH
T ss_pred             chHHHHHHHHHHHHH------cCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHH
Confidence            346677777776653      23445566777777777888888888888887776544344567777888888888888


Q ss_pred             HHHHHHHHHHcCCCCChhhHHHHHHH-HhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          196 AVKLYKEMKKKGIKMDVVAYNTVIRA-VGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       196 a~~~~~~~~~~~~~~~~~~~~~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      |.++|+.+.+.+ +.+...|...... +...|+.+.|..+|+.+.+. .+.+...|...+..+.+.|+++.|..+|++..
T Consensus       153 ar~i~~~al~~~-~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai  230 (308)
T d2onda1         153 GRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVL  230 (308)
T ss_dssp             HHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            888888877663 2233344333332 33457788888888887776 23356777778888888888888888888876


Q ss_pred             hcC-CCCC--hhhHHHHH---HhhCCHHHHHHHHHHHHH
Q 041804          275 KKG-CVPD--VITYHCFF---RCLEKPREILGLFDRMIE  307 (403)
Q Consensus       275 ~~~-~~p~--~~~~~~l~---~~~~~~~~a~~~~~~~~~  307 (403)
                      ... ..|+  ...|...+   ..+|+.+.+.++++++.+
T Consensus       231 ~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         231 TSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             HSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            542 2332  23444443   345777778888777765

>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=99.30  E-value=4.9e-10  Score=94.46  Aligned_cols=269  Identities=11%  Similarity=-0.001  Sum_probs=141.1

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCC---HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC----HHHHHHHHHH
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHT---TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN----HATFRIMFKR   76 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~   76 (403)
                      +....|++++|+++++......+-.++   ..++..+..++...|++++|+..|++..+.....++    ..++..+...
T Consensus        21 ~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  100 (366)
T d1hz4a_          21 VAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEI  100 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHH
Confidence            344567777777777665531111111   234555666666777777777777665442101111    2344555566


Q ss_pred             HHhcCChHHHHHHHHHHhhc----CCC----cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           77 YVTAHLVNEAMGTFNKLDEF----GLK----DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        77 ~~~~~~~~~a~~~~~~~~~~----~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      +...|++..+...+......    +.+    ....+..+...+...|+++.+...+..........  +.......+...
T Consensus       101 ~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~~~~~~  178 (366)
T d1hz4a_         101 LFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSY--QPQQQLQCLAML  178 (366)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTS--CGGGGHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhh--hhhhHHHHHHHH
Confidence            66667777776666654431    111    22344455566666777777666665544332111  222334445555


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhC----CCCC--cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCC---ChhhHHHHH
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKR----GVVK--DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKM---DVVAYNTVI  219 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~----~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~ll  219 (403)
                      ...+...+++..+...+.+....    +..+  ....+..+...+...|++++|...++.........   ....+..+.
T Consensus       179 ~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la  258 (366)
T d1hz4a_         179 IQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIA  258 (366)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHH
Confidence            56666666666666666554331    1111  11234445555666677777776666554432111   122344455


Q ss_pred             HHHhhcCCHHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHhcCcHHHHHHHHHhch
Q 041804          220 RAVGVSEGVDFAMRVYREMREM----GCQPS-VVTCNTVIKLLCENGRVREAYAVLAEMP  274 (403)
Q Consensus       220 ~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~li~~~~~~g~~~~a~~~~~~~~  274 (403)
                      .++...|+++.|...++.+...    +..|+ ...+..+...|.+.|++++|.+.+++..
T Consensus       259 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         259 RAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            6666677777777766665432    22222 2345556666667777777776666543

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.28  E-value=2.4e-10  Score=91.95  Aligned_cols=221  Identities=8%  Similarity=-0.125  Sum_probs=152.5

Q ss_pred             hhHHHHHHHHhhhCCCCCC--CHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHH
Q 041804           47 FDLSWNLIHRMKDNPSSIP--NHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELC  124 (403)
Q Consensus        47 ~~~a~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  124 (403)
                      .+.++.-+++........+  ...+|..+..+|.+.|++++|+..|++..+..+.++.+|..+..++...|++++|...|
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~   94 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAF   94 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhh
Confidence            3455555566655431112  23477788899999999999999999999999889999999999999999999999999


Q ss_pred             hcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHH
Q 041804          125 FGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMK  204 (403)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  204 (403)
                      ++...       ..+.+..++..+..+|...|++++|.+.|+...+..+. +......+..++.+.+..+.+..+.....
T Consensus        95 ~~al~-------~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (259)
T d1xnfa_          95 DSVLE-------LDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPN-DPFRSLWLYLAEQKLDEKQAKEVLKQHFE  166 (259)
T ss_dssp             HHHHH-------HCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             hHHHH-------HHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhccc-cHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence            99887       34556778999999999999999999999999887654 45554445555556666555555555555


Q ss_pred             HcCCCCChhhHHHHHHHHhhcCC----HHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCC
Q 041804          205 KKGIKMDVVAYNTVIRAVGVSEG----VDFAMRVYREMREMGCQP-SVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCV  279 (403)
Q Consensus       205 ~~~~~~~~~~~~~ll~~~~~~~~----~~~a~~~~~~~~~~~~~~-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  279 (403)
                      ...  ++...+. ++..+.....    .+.+...+......  .| ...+|..+...|...|++++|...|+.....  .
T Consensus       167 ~~~--~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~  239 (259)
T d1xnfa_         167 KSD--KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSL--AEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--N  239 (259)
T ss_dssp             HSC--CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHH--HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C
T ss_pred             ccc--hhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhc--CcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--C
Confidence            442  2222222 2222222211    22222222222111  11 2346677889999999999999999998865  4


Q ss_pred             CCh
Q 041804          280 PDV  282 (403)
Q Consensus       280 p~~  282 (403)
                      |+.
T Consensus       240 p~~  242 (259)
T d1xnfa_         240 VHN  242 (259)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.27  E-value=1.5e-11  Score=103.15  Aligned_cols=276  Identities=9%  Similarity=0.038  Sum_probs=175.6

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHH----------HhcCChHHHHHHHHHHhhcCCCcH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRY----------VTAHLVNEAMGTFNKLDEFGLKDE  101 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~----------~~~~~~~~a~~~~~~~~~~~~~~~  101 (403)
                      ....++......+..++|+++++...+..   |+ ...|+..-..+          ...|.+++|+.+++...+..+.+.
T Consensus        31 ~~~~~~~~~~~~~~~~~al~~~~~~l~~~---P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~  107 (334)
T d1dcea1          31 ATQAVFQKRQAGELDESVLELTSQILGAN---PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSY  107 (334)
T ss_dssp             HHHHHHHHHHTTCCSHHHHHHHHHHHHHC---TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHhcccccHHHHHHHHHHHHHC---CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcH
Confidence            34444444444455689999999998865   54 44565433332          234457889999999998888888


Q ss_pred             HHHHHHHHHHHhcC--CHHHHHHHHhcccccccccccccCcchHHHHH-HHHHHHhcCChhHHHHHHHHHHhCCCCCcHH
Q 041804          102 VSYCNLVDALCEYK--HVIEAQELCFGENKNVGFSGLVEMNKTKIYNM-ILRGWFKMSWWGKCREFWEEMDKRGVVKDLH  178 (403)
Q Consensus       102 ~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  178 (403)
                      ..|..+..++...+  ++++|...+.+...       ..+++...+.. ....+...+.+++|...++.+.+.++. +..
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~a~~~~~~al~-------~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~-~~~  179 (334)
T d1dcea1         108 GTWHHRCWLLSRLPEPNWARELELCARFLE-------ADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYS  179 (334)
T ss_dssp             HHHHHHHHHHHTCSSCCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC-CHH
T ss_pred             HHHHHhhHHHHHhccccHHHHHHHHHHHHh-------hCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCC-CHH
Confidence            88888888877765  47888888888766       33555666544 446677788899999999988888776 788


Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLC  258 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~  258 (403)
                      +|+.+..++.+.|++++|...+......  .|+.   ..+...+...+..+.+...+........ ++...+..+...+.
T Consensus       180 a~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~---~~~~~~~~~l~~~~~a~~~~~~~l~~~~-~~~~~~~~l~~~~~  253 (334)
T d1dcea1         180 SWHYRSCLLPQLHPQPDSGPQGRLPENV--LLKE---LELVQNAFFTDPNDQSAWFYHRWLLGRA-EPLFRCELSVEKST  253 (334)
T ss_dssp             HHHHHHHHHHHHSCCCCSSSCCSSCHHH--HHHH---HHHHHHHHHHCSSCSHHHHHHHHHHSCC-CCSSSCCCCHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhHHh--HHHH---HHHHHHHHHhcchhHHHHHHHHHHHhCc-chhhHHHHHHHHHH
Confidence            8888888898988888776555443332  1111   1122233444555556666666555432 23334444555555


Q ss_pred             hcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHH
Q 041804          259 ENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWK  338 (403)
Q Consensus       259 ~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~  338 (403)
                      ..++.++|...+.+..+.                                .+ -+..++..+..++...|++++|.+.++
T Consensus       254 ~~~~~~~a~~~~~~~~~~--------------------------------~p-~~~~~~~~l~~~~~~~~~~~eA~~~~~  300 (334)
T d1dcea1         254 VLQSELESCKELQELEPE--------------------------------NK-WCLLTIILLMRALDPLLYEKETLQYFS  300 (334)
T ss_dssp             HHHHHHHHHHHHHHHCTT--------------------------------CH-HHHHHHHHHHHHHCTGGGHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHHhh--------------------------------Cc-hHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            556666666665554432                                11 134456666777777777888888887


Q ss_pred             HHHhcCCCC-CHHHHHHHHHHHH
Q 041804          339 KMEELGCSP-DEFAYNALVDALI  360 (403)
Q Consensus       339 ~~~~~~~~~-~~~~~~~l~~~~~  360 (403)
                      +..+.  .| +...|..+...+.
T Consensus       301 ~ai~l--dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         301 TLKAV--DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             HHHHH--CGGGHHHHHHHHHHHH
T ss_pred             HHHHH--CcccHHHHHHHHHHHh
Confidence            77765  34 3445555544443

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.19  E-value=5.1e-11  Score=99.93  Aligned_cols=260  Identities=7%  Similarity=-0.110  Sum_probs=183.6

Q ss_pred             hcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHH----------HHhcCChhHHHHHHHHHHhCCCCCcHHHHHH
Q 041804          113 EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG----------WFKMSWWGKCREFWEEMDKRGVVKDLHSYSI  182 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~----------~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  182 (403)
                      ..+..++|..++.++..       ..|.+..+|+..-..          +...|.+++|+.+++...+.+++ +...|..
T Consensus        41 ~~~~~~~al~~~~~~l~-------~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk-~~~~~~~  112 (334)
T d1dcea1          41 AGELDESVLELTSQILG-------ANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHH  112 (334)
T ss_dssp             TTCCSHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHH
T ss_pred             cccccHHHHHHHHHHHH-------HCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCC-cHHHHHH
Confidence            33445777777777765       224444445433322          23345578999999999888766 7778888


Q ss_pred             HHHHHHHcCC--hhHHHHHHHHHHHcCCCCChhhHH-HHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Q 041804          183 YMDIMCKSGK--PWKAVKLYKEMKKKGIKMDVVAYN-TVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCE  259 (403)
Q Consensus       183 l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~-~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~  259 (403)
                      +..++...++  +++|...+..+.+.. +++...+. .....+...+..+.|...++.+.+..+. +...|+.+...+.+
T Consensus       113 ~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~-~~~a~~~l~~~~~~  190 (334)
T d1dcea1         113 RCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQ  190 (334)
T ss_dssp             HHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCC-CHHHHHHHHHHHHH
T ss_pred             hhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHH
Confidence            8877777654  789999999998874 33555554 3446677789999999999998887543 78889999999999


Q ss_pred             cCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHH
Q 041804          260 NGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKK  339 (403)
Q Consensus       260 ~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  339 (403)
                      .|++++|...+....+.  .|....+.......+..+++...+........ ++...+..+...+...|++++|...+.+
T Consensus       191 ~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~  267 (334)
T d1dcea1         191 LHPQPDSGPQGRLPENV--LLKELELVQNAFFTDPNDQSAWFYHRWLLGRA-EPLFRCELSVEKSTVLQSELESCKELQE  267 (334)
T ss_dssp             HSCCCCSSSCCSSCHHH--HHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCC-CCSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHhHHh--HHHHHHHHHHHHHhcchhHHHHHHHHHHHhCc-chhhHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            99998887666655443  22222222222233556667777777766543 3455666777788888999999999998


Q ss_pred             HHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhhHH
Q 041804          340 MEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPREEL  388 (403)
Q Consensus       340 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  388 (403)
                      ..... +.+...|..+..+|.+.|+.++|.+.+++..+  +.|+...+.
T Consensus       268 ~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~--ldP~~~~y~  313 (334)
T d1dcea1         268 LEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKA--VDPMRAAYL  313 (334)
T ss_dssp             HCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHH--HCGGGHHHH
T ss_pred             HHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--HCcccHHHH
Confidence            87653 33567788889999999999999999999988  457555443

>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=98.97  E-value=3.5e-08  Score=74.66  Aligned_cols=137  Identities=12%  Similarity=-0.041  Sum_probs=103.6

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      .|+. ...+...|+++.|++.|+.+.     +|+..+|..+..+|...|++++|++.|++..+.++.....|..+..++.
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i~-----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~   81 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYY   81 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhcC-----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHH
Confidence            3443 566778899999999988753     3677888889999999999999999999999988888889999999999


Q ss_pred             hcCCHHHHHHHHhccccccccc--------ccccCc-chHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCC
Q 041804          113 EYKHVIEAQELCFGENKNVGFS--------GLVEMN-KTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVK  175 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~--------~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  175 (403)
                      +.|++++|.+.|++........        +..... ...++..+..++.+.|++++|.+.|....+..+.+
T Consensus        82 ~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~  153 (192)
T d1hh8a_          82 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  153 (192)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             hhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            9999999988887765321000        001111 23556677788888899999999888887765554

>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=98.83  E-value=6.9e-08  Score=73.00  Aligned_cols=121  Identities=12%  Similarity=-0.009  Sum_probs=103.0

Q ss_pred             ccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCC
Q 041804            3 TLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHL   82 (403)
Q Consensus         3 ~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~   82 (403)
                      ..+...|+++.|++.|+.+.     +|++.+|..+..++...|++++|++.|++..+.+  +.+..+|..+..+|.+.|+
T Consensus        13 ~~~~~~~d~~~Al~~~~~i~-----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld--p~~~~a~~~~g~~~~~~g~   85 (192)
T d1hh8a_          13 VLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD--KHLAVAYFQRGMLYYQTEK   85 (192)
T ss_dssp             HHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHCCCHHHHHHHHHhcC-----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh--hhhhhhHHHHHHHHHhhcc
Confidence            45567899999999999764     4678899999999999999999999999999976  4668899999999999999


Q ss_pred             hHHHHHHHHHHhhcCCC----------------cHHHHHHHHHHHHhcCCHHHHHHHHhccccc
Q 041804           83 VNEAMGTFNKLDEFGLK----------------DEVSYCNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus        83 ~~~a~~~~~~~~~~~~~----------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      +++|+..|++.......                ...++..+..++...|++++|.+.+......
T Consensus        86 ~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~  149 (192)
T d1hh8a_          86 YDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  149 (192)
T ss_dssp             HHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            99999999998654221                2356778888999999999999999877654

>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=98.79  E-value=1.2e-07  Score=65.09  Aligned_cols=90  Identities=13%  Similarity=-0.078  Sum_probs=42.6

Q ss_pred             HHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCH
Q 041804           38 IDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHV  117 (403)
Q Consensus        38 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  117 (403)
                      ...+.+.|++++|+..|++..+..  +.+...|..+..+|...|++++|+..++...+.++.++..|..+..++...|++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~--p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLD--PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcC--CcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCH
Confidence            334444455555555554444433  233444444444444555555555555554444444444444444444444444


Q ss_pred             HHHHHHHhcccc
Q 041804          118 IEAQELCFGENK  129 (403)
Q Consensus       118 ~~a~~~~~~~~~  129 (403)
                      ++|+..+++...
T Consensus        88 ~~A~~~~~~a~~   99 (117)
T d1elwa_          88 EEAKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHH
Confidence            444444444443

>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=98.77  E-value=1.6e-07  Score=64.47  Aligned_cols=103  Identities=10%  Similarity=-0.043  Sum_probs=90.2

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCCh
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLV   83 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~   83 (403)
                      .+...|++++|+..|+.+.+.  .+.++..|..+..++.+.|++++|+..++...+..  +.+...|..+..++...|++
T Consensus        12 ~~~~~g~~~eAi~~~~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~g~~~~~~~~~   87 (117)
T d1elwa_          12 KALSVGNIDDALQCYSEAIKL--DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK--PDWGKGYSRKAAALEFLNRF   87 (117)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHcCCHHHHHHHHHHHHhc--CCcchhhhhcccccccccccccccchhhhhHHHhc--cchhhHHHHHHHHHHHccCH
Confidence            355679999999999999852  35568899999999999999999999999999876  56788999999999999999


Q ss_pred             HHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 041804           84 NEAMGTFNKLDEFGLKDEVSYCNLVDA  110 (403)
Q Consensus        84 ~~a~~~~~~~~~~~~~~~~~~~~l~~~  110 (403)
                      ++|+..|++..+..+.++..+..+-++
T Consensus        88 ~~A~~~~~~a~~~~p~~~~~~~~l~~l  114 (117)
T d1elwa_          88 EEAKRTYEEGLKHEANNPQLKEGLQNM  114 (117)
T ss_dssp             HHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            999999999999988888877766554

>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=98.75  E-value=2e-07  Score=68.17  Aligned_cols=92  Identities=13%  Similarity=0.014  Sum_probs=51.6

Q ss_pred             HHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHH
Q 041804           74 FKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWF  153 (403)
Q Consensus        74 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  153 (403)
                      ...|.+.|++++|+..|++..+..+.+...|..+..+|...|++++|...|++..+       ..+.+..+|..+..++.
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~-------~~p~~~~a~~~~g~~~~   89 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIE-------LDKKYIKGYYRRAASNM   89 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHH-------HcccchHHHHHHHHHHH
Confidence            34455556666666666665555555555555555555555555555555555544       22444455555555555


Q ss_pred             hcCChhHHHHHHHHHHhCC
Q 041804          154 KMSWWGKCREFWEEMDKRG  172 (403)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~  172 (403)
                      ..|++++|.+.+++.....
T Consensus        90 ~~g~~~eA~~~~~~a~~~~  108 (159)
T d1a17a_          90 ALGKFRAALRDYETVVKVK  108 (159)
T ss_dssp             HTTCHHHHHHHHHHHHHHS
T ss_pred             HcCCHHHHHHHHHHHHHcC
Confidence            5555555555555555543

>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=98.74  E-value=2.3e-07  Score=75.39  Aligned_cols=172  Identities=9%  Similarity=-0.039  Sum_probs=108.6

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhC----CCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC------cHH
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDN----PSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK------DEV  102 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~------~~~  102 (403)
                      .|......|...|++++|.+.|.+..+.    +..+.-..+|+.+..+|.+.|++++|++.+++..+....      ...
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            4677788899999999999999887652    101112357889999999999999999999987653221      345


Q ss_pred             HHHHHHHHHHh-cCCHHHHHHHHhcccccccccccccC-cchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcH---
Q 041804          103 SYCNLVDALCE-YKHVIEAQELCFGENKNVGFSGLVEM-NKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDL---  177 (403)
Q Consensus       103 ~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---  177 (403)
                      ++..+...|.. .|++++|...+.+........  +.+ ....++..+...+...|++++|.+.|+++.........   
T Consensus       119 ~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~--~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~  196 (290)
T d1qqea_         119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQD--QSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQW  196 (290)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGG
T ss_pred             HHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhc--CchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhh
Confidence            56666666644 688999888887654321000  111 12344666677777777777777777776554322111   


Q ss_pred             ---HHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          178 ---HSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       178 ---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                         ..+..++.++...++++.|...++...+.
T Consensus       197 ~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~  228 (290)
T d1qqea_         197 SLKDYFLKKGLCQLAATDAVAAARTLQEGQSE  228 (290)
T ss_dssp             GHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC
T ss_pred             hHHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence               11233344555566666666666665544

>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=98.72  E-value=6.3e-07  Score=72.67  Aligned_cols=205  Identities=11%  Similarity=0.034  Sum_probs=126.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHhhcCC-----C-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchH
Q 041804           70 FRIMFKRYVTAHLVNEAMGTFNKLDEFGL-----K-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTK  143 (403)
Q Consensus        70 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  143 (403)
                      |......|...|++++|.+.|.+..+...     + -..+|..+..+|.+.|++++|...+++........+ .......
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~-~~~~~~~  118 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRG-QFRRGAN  118 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT-CHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcc-cchhHHH
Confidence            44456778899999999999998876421     1 346889999999999999999999887654321000 1112244


Q ss_pred             HHHHHHHHHHh-cCChhHHHHHHHHHHhC----CCCC-cHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCCh-----
Q 041804          144 IYNMILRGWFK-MSWWGKCREFWEEMDKR----GVVK-DLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDV-----  212 (403)
Q Consensus       144 ~~~~l~~~~~~-~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----  212 (403)
                      ++..+...|.. .|++++|.+.+++..+.    +..+ -..++..+...+...|++++|+..|++..........     
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            55666666644 58888888888776432    1111 1345677778888888888888888887765221111     


Q ss_pred             -hhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCC-CC---HHHHHHHHHHHHh--cCcHHHHHHHHHhchh
Q 041804          213 -VAYNTVIRAVGVSEGVDFAMRVYREMREMGCQ-PS---VVTCNTVIKLLCE--NGRVREAYAVLAEMPK  275 (403)
Q Consensus       213 -~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~---~~~~~~li~~~~~--~g~~~~a~~~~~~~~~  275 (403)
                       ..+...+..+...++++.|...++...+..+. ++   ......++.++-.  .+.+++|+..|+.+.+
T Consensus       199 ~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~~  268 (290)
T d1qqea_         199 KDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMR  268 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhh
Confidence             11233344555677888888777776654211 11   1233445555544  2346667766665543

>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=98.70  E-value=2.4e-07  Score=67.73  Aligned_cols=95  Identities=11%  Similarity=-0.030  Sum_probs=83.3

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      +......|.+.|++++|+..|++..+..  +.+...|..+..+|...|++++|+..|++..+..+.+..+|..+..++..
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~   90 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIELN--PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMA   90 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccccc--hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHH
Confidence            4455677889999999999999998876  45678899999999999999999999999999988899999999999999


Q ss_pred             cCCHHHHHHHHhccccc
Q 041804          114 YKHVIEAQELCFGENKN  130 (403)
Q Consensus       114 ~~~~~~a~~~~~~~~~~  130 (403)
                      .|++++|...+++....
T Consensus        91 ~g~~~eA~~~~~~a~~~  107 (159)
T d1a17a_          91 LGKFRAALRDYETVVKV  107 (159)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHc
Confidence            99999999999888763

>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=98.70  E-value=4.3e-08  Score=75.00  Aligned_cols=98  Identities=11%  Similarity=0.040  Sum_probs=49.8

Q ss_pred             CCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHH
Q 041804           65 PNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKI  144 (403)
Q Consensus        65 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  144 (403)
                      |+...+......|.+.|++++|+..|++..+..+.++.+|..+..+|.+.|++++|...|.+...       -.+-+..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~-------l~p~~~~a   74 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALE-------LDGQSVKA   74 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT-------SCTTCHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH-------hCCCcHHH
Confidence            44444444455555555555555555555555544555555555555555555555555555443       22333444


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHH
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMD  169 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~  169 (403)
                      |..+..+|...|++++|...|++..
T Consensus        75 ~~~lg~~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          75 HFFLGQCQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            5555555555555555555555443

>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=98.69  E-value=3.6e-08  Score=75.45  Aligned_cols=99  Identities=9%  Similarity=-0.108  Sum_probs=89.8

Q ss_pred             CCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 041804           29 HTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLV  108 (403)
Q Consensus        29 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~  108 (403)
                      |+...+......+.+.|++++|+..|++.....  +.+..+|..+..+|.+.|++++|+..|++..+..+.+..+|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~--p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHH
Confidence            777888888999999999999999999988865  467888999999999999999999999999999888999999999


Q ss_pred             HHHHhcCCHHHHHHHHhcccc
Q 041804          109 DALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       109 ~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      .+|...|++++|...|++...
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            999999999999999987654

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.60  E-value=3.6e-05  Score=61.00  Aligned_cols=224  Identities=10%  Similarity=-0.004  Sum_probs=129.8

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh----cCChHHHHHHHHHHhhcCCCcHHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT----AHLVNEAMGTFNKLDEFGLKDEVSYC  105 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~  105 (403)
                      |+..+..|...+.+.+++++|+++|++..+.+    +..++..|...|..    ..+...|...+......+.+  ....
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g----~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~--~a~~   74 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK----ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYS--NGCH   74 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT----CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH--HHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC----CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccccc--chhh
Confidence            45666777777777888888888888887754    45555566666665    55777788777777665433  3333


Q ss_pred             HHHHHHHh----cCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCcH
Q 041804          106 NLVDALCE----YKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFK----MSWWGKCREFWEEMDKRGVVKDL  177 (403)
Q Consensus       106 ~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~  177 (403)
                      .+...+..    ..+.+.|...+......      +   .......+...+..    ......+...+......   .+.
T Consensus        75 ~l~~~~~~~~~~~~~~~~a~~~~~~a~~~------g---~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~---~~~  142 (265)
T d1ouva_          75 LLGNLYYSGQGVSQNTNKALQYYSKACDL------K---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL---NDG  142 (265)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHT------T---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT---TCH
T ss_pred             ccccccccccccchhhHHHHHHHhhhhhh------h---hhhHHHhhcccccCCCcccchhHHHHHHhhhhhcc---ccc
Confidence            44333332    44666777766655442      1   11122222222222    23455555555555543   355


Q ss_pred             HHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh----cCCHHHHHHHHHHHHHcCCCCCHHH
Q 041804          178 HSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV----SEGVDFAMRVYREMREMGCQPSVVT  249 (403)
Q Consensus       178 ~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  249 (403)
                      ..+..+...|..    ..+...+...++...+.|   +......+...|..    ..+++.|..+|....+.|   ++..
T Consensus       143 ~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a  216 (265)
T d1ouva_         143 DGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGG  216 (265)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHH
T ss_pred             chhhhhhhhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHH
Confidence            566666666665    344556666666666554   44444444444433    456777777777777764   3445


Q ss_pred             HHHHHHHHHh----cCcHHHHHHHHHhchhcC
Q 041804          250 CNTVIKLLCE----NGRVREAYAVLAEMPKKG  277 (403)
Q Consensus       250 ~~~li~~~~~----~g~~~~a~~~~~~~~~~~  277 (403)
                      +..|...|.+    ..+.++|.+.|++..+.|
T Consensus       217 ~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g  248 (265)
T d1ouva_         217 CFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  248 (265)
T ss_dssp             HHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCccCHHHHHHHHHHHHHCc
Confidence            5556666654    235666777777666554

>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=98.55  E-value=3.3e-07  Score=62.31  Aligned_cols=92  Identities=9%  Similarity=-0.134  Sum_probs=83.2

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCE  113 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~  113 (403)
                      ...+...+.+.|++++|+..|++.....  +-+..+|..+..++.+.|++++|+..|++..+..+.+..++..+..+|..
T Consensus        19 ~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~   96 (112)
T d1hxia_          19 PMEEGLSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTN   96 (112)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHhhhcccc--cccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHH
Confidence            3456778889999999999999999876  34688999999999999999999999999999998899999999999999


Q ss_pred             cCCHHHHHHHHhcc
Q 041804          114 YKHVIEAQELCFGE  127 (403)
Q Consensus       114 ~~~~~~a~~~~~~~  127 (403)
                      .|+.++|.+.+++.
T Consensus        97 ~g~~~~A~~~l~~~  110 (112)
T d1hxia_          97 EHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999998764

>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=98.54  E-value=3.7e-07  Score=62.06  Aligned_cols=90  Identities=8%  Similarity=-0.146  Sum_probs=68.0

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHH
Q 041804           72 IMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRG  151 (403)
Q Consensus        72 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  151 (403)
                      .+...+.+.|++++|+..|++..+..+.+..+|..+..++.+.|++++|...+++...       ..|.+..++..+...
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~-------~~p~~~~a~~~la~~   93 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARM-------LDPKDIAVHAALAVS   93 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccc-------cccccccchHHHHHH
Confidence            3456677788888888888888887777788888888888888888888888777666       345566777777777


Q ss_pred             HHhcCChhHHHHHHHHH
Q 041804          152 WFKMSWWGKCREFWEEM  168 (403)
Q Consensus       152 ~~~~~~~~~a~~~~~~~  168 (403)
                      |...|++++|.+.|++.
T Consensus        94 y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          94 HTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHH
Confidence            77777777777777664

>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=98.51  E-value=9.7e-07  Score=60.70  Aligned_cols=97  Identities=7%  Similarity=0.015  Sum_probs=66.9

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCC---HHHHHHHHhcccccccccccccCcc-hHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKH---VIEAQELCFGENKNVGFSGLVEMNK-TKIYN  146 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~~~-~~~~~  146 (403)
                      ..+++.+...+++++|++.|++....++.++.++..+..++.+.++   .++|..+++++...      ...|+ ..++.
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~------~~~~~~~~~~~   76 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPK------GSKEEQRDYVF   76 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTT------SCHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhc------cCCchHHHHHH
Confidence            3566677777788888888888888777777788777777776444   34577777776653      21222 33566


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCC
Q 041804          147 MILRGWFKMSWWGKCREFWEEMDKRGV  173 (403)
Q Consensus       147 ~l~~~~~~~~~~~~a~~~~~~~~~~~~  173 (403)
                      .+..+|.+.|++++|.+.|+++.+..+
T Consensus        77 ~Lg~~y~~~g~~~~A~~~~~~aL~~~P  103 (122)
T d1nzna_          77 YLAVGNYRLKEYEKALKYVRGLLQTEP  103 (122)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHhCc
Confidence            777777777788888877777777643

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.49  E-value=1.9e-05  Score=62.71  Aligned_cols=218  Identities=9%  Similarity=0.001  Sum_probs=153.1

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHc----cCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGK----FFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRY   77 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~   77 (403)
                      +..+..++++++|++.|+.... .   -+..++..|...|..    ..++..|..++......+    +......+...+
T Consensus         9 G~~~~~~~d~~~A~~~~~kAa~-~---g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~----~~~a~~~l~~~~   80 (265)
T d1ouva_           9 GAKSYKEKDFTQAKKYFEKACD-L---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN----YSNGCHLLGNLY   80 (265)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH-T---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH-C---CCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc----ccchhhcccccc
Confidence            4556678999999999999874 3   356677777777776    668999999999988765    444455555555


Q ss_pred             Hh----cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH----hcCCHHHHHHHHhcccccccccccccCcchHHHHHHH
Q 041804           78 VT----AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC----EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMIL  149 (403)
Q Consensus        78 ~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  149 (403)
                      ..    ..+.+.|...++...+.|....  ...+...+.    .......+...+.....         ..+...+..+.
T Consensus        81 ~~~~~~~~~~~~a~~~~~~a~~~g~~~a--~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~---------~~~~~~~~~L~  149 (265)
T d1ouva_          81 YSGQGVSQNTNKALQYYSKACDLKYAEG--CASLGGIYHDGKVVTRDFKKAVEYFTKACD---------LNDGDGCTILG  149 (265)
T ss_dssp             HHTSSSCCCHHHHHHHHHHHHHTTCHHH--HHHHHHHHHHCSSSCCCHHHHHHHHHHHHH---------TTCHHHHHHHH
T ss_pred             ccccccchhhHHHHHHHhhhhhhhhhhH--HHhhcccccCCCcccchhHHHHHHhhhhhc---------ccccchhhhhh
Confidence            43    4677889999999888765433  233333333    24456666666655433         34566677788


Q ss_pred             HHHHh----cCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHH----cCChhHHHHHHHHHHHcCCCCChhhHHHHHHH
Q 041804          150 RGWFK----MSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCK----SGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRA  221 (403)
Q Consensus       150 ~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~  221 (403)
                      ..|..    ..+...+...++...+.|   +..+...+...|..    ..++++|..+|+...+.|   +...+..|...
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~  223 (265)
T d1ouva_         150 SLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAM  223 (265)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             hhhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHHH
Confidence            77775    456677788888887764   55666667666665    568999999999998887   45566666666


Q ss_pred             Hhh----cCCHHHHHHHHHHHHHcCCC
Q 041804          222 VGV----SEGVDFAMRVYREMREMGCQ  244 (403)
Q Consensus       222 ~~~----~~~~~~a~~~~~~~~~~~~~  244 (403)
                      |..    ..+.+.|.++|++..+.|..
T Consensus       224 y~~G~g~~~n~~~A~~~~~kAa~~g~~  250 (265)
T d1ouva_         224 QYNGEGVTRNEKQAIENFKKGCKLGAK  250 (265)
T ss_dssp             HHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             HHcCCCCccCHHHHHHHHHHHHHCcCH
Confidence            654    34788999999999887643

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.40  E-value=1.6e-06  Score=63.79  Aligned_cols=110  Identities=9%  Similarity=0.012  Sum_probs=83.5

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcC-------------CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHH
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTH-------------TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATF   70 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~-------------~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   70 (403)
                      .+..+|++++|++.|+......+..+             ...+|+.+..+|.+.|++++|+..++......  |.+..+|
T Consensus        22 ~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~--p~~~~a~   99 (170)
T d1p5qa1          22 VYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD--SNNEKGL   99 (170)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc--ccchhhh
Confidence            45678999999999987764211111             12456667788889999999999999888865  3578888


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK  115 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  115 (403)
                      ..+..+|...|++++|+..|+...+.+|.+..+...+..+..+.+
T Consensus       100 ~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~  144 (170)
T d1p5qa1         100 SRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIR  144 (170)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence            899999999999999999999999988777777766666554443

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.37  E-value=8.4e-06  Score=59.82  Aligned_cols=97  Identities=9%  Similarity=-0.091  Sum_probs=56.2

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCC-------------HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPN-------------HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~   99 (403)
                      .+......+.+.|++++|+..|.+........+.             ..+|+.+..+|.+.|++++|+..++...+.++.
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~   94 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN   94 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcccc
Confidence            4455566778888888888888777653211111             123444555555555666666655555555555


Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      ++.++..+..++...|++++|...|++...
T Consensus        95 ~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          95 NEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            555555555555555555555555555544

>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=98.35  E-value=2.4e-06  Score=58.61  Aligned_cols=94  Identities=10%  Similarity=0.014  Sum_probs=45.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCC---hhHHHHHHHHHHhCCCCCc-HHHHH
Q 041804          106 NLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSW---WGKCREFWEEMDKRGVVKD-LHSYS  181 (403)
Q Consensus       106 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~-~~~~~  181 (403)
                      .++..+...+++++|++.|++...       ..+.+..++..+..++.+.++   +++|.++|+++...+..|+ ..+|.
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~-------~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~   76 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKA-------AGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVF   76 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHH-------HSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHh-------hCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHH
Confidence            344444555555555555555544       224444555555555544332   2335555555554433322 12444


Q ss_pred             HHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          182 IYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       182 ~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      .+..+|.+.|++++|.+.|+++.+.
T Consensus        77 ~Lg~~y~~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          77 YLAVGNYRLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            4555555555555555555555553

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.34  E-value=0.00041  Score=56.18  Aligned_cols=285  Identities=11%  Similarity=0.025  Sum_probs=158.2

Q ss_pred             cCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 041804           28 THTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNL  107 (403)
Q Consensus        28 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l  107 (403)
                      .||..-...+...|.+.|.++.|..+|..+..          |..++..+.+.++++.|.+.+.+.     .+..+|..+
T Consensus        11 ~~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d----------~~rl~~~~v~l~~~~~avd~~~k~-----~~~~~~k~~   75 (336)
T d1b89a_          11 GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN----------FGRLASTLVHLGEYQAAVDGARKA-----NSTRTWKEV   75 (336)
T ss_dssp             CC----------------CTTTHHHHHHHTTC----------HHHHHHHHHTTTCHHHHHHHHHHH-----TCHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC----------HHHHHHHHHhhccHHHHHHHHHHc-----CCHHHHHHH
Confidence            35555666778888899999999999987754          567788888999999988877644     367788888


Q ss_pred             HHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHH
Q 041804          108 VDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIM  187 (403)
Q Consensus       108 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  187 (403)
                      ...|.+......+... . .         ...........++..|-..|.+++...+++...... .++...++.++..|
T Consensus        76 ~~~l~~~~e~~la~i~-~-~---------~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~ly  143 (336)
T d1b89a_          76 CFACVDGKEFRLAQMC-G-L---------HIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILY  143 (336)
T ss_dssp             HHHHHHTTCHHHHHHT-T-T---------TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHH
T ss_pred             HHHHHhCcHHHHHHHH-H-H---------HhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHH
Confidence            8888887776554332 1 1         222334445678888899999999999999876542 34777788888888


Q ss_pred             HHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHc--------CCCCCHHHHHHHHHHHHh
Q 041804          188 CKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREM--------GCQPSVVTCNTVIKLLCE  259 (403)
Q Consensus       188 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~~~~~~li~~~~~  259 (403)
                      ++.+ .++..+.   +...+..   .-...++..|-+.+-++++.-++..+.+.        ...++..-....+..+.+
T Consensus       144 ak~~-~~kl~e~---l~~~s~~---y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k  216 (336)
T d1b89a_         144 SKFK-PQKMREH---LELFWSR---VNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITK  216 (336)
T ss_dssp             HTTC-HHHHHHH---HHHHSTT---SCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHH
T ss_pred             HHhC-hHHHHHH---HHhcccc---CCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHc
Confidence            8753 3443333   3332111   11223344444444444444333332111        012233333344555555


Q ss_pred             cCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHH
Q 041804          260 NGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKK  339 (403)
Q Consensus       260 ~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~  339 (403)
                      ..+.+...++.....+.  .|  ...+.++...             .. .+  |   -.-++..+-+.+++......++.
T Consensus       217 ~~N~e~~~~~i~~yL~~--~p--~~i~~lL~~v-------------~~-~~--d---~~r~V~~~~k~~~l~li~p~Le~  273 (336)
T d1b89a_         217 VANVELYYRAIQFYLEF--KP--LLLNDLLMVL-------------SP-RL--D---HTRAVNYFSKVKQLPLVKPYLRS  273 (336)
T ss_dssp             CSSTHHHHHHHHHHHHH--CG--GGHHHHHHHH-------------GG-GC--C---HHHHHHHHHHTTCTTTTHHHHHH
T ss_pred             cCChHHHHHHHHHHHHc--CH--HHHHHHHHHh-------------cc-CC--C---HHHHHHHHHhcCCcHHHHHHHHH
Confidence            55555555544444332  12  1222222221             11 11  1   13345556677778888888877


Q ss_pred             HHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 041804          340 MEELGCSPDEFAYNALVDALIDKGMLDMARKYD  372 (403)
Q Consensus       340 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  372 (403)
                      ....+   +..+.+++.+.|...++++.-.+..
T Consensus       274 v~~~n---~~~vn~al~~lyie~~d~~~l~~~i  303 (336)
T d1b89a_         274 VQNHN---NKSVNESLNNLFITEEDYQALRTSI  303 (336)
T ss_dssp             HHTTC---CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHcC---hHHHHHHHHHHHhCcchhHHHHHHH
Confidence            66544   4578889999999999875544333

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.31  E-value=6.1e-06  Score=57.35  Aligned_cols=104  Identities=13%  Similarity=0.073  Sum_probs=72.4

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHH
Q 041804           69 TFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMI  148 (403)
Q Consensus        69 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l  148 (403)
                      .+..+...+.+.|++++|+..|++..+.++.+..++..+..+|.+.|++++|...+.++.............-..+|..+
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~l   85 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHH
Confidence            35566777888888888888888888888778888888888888888888888888776542100000001112456667


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCC
Q 041804          149 LRGWFKMSWWGKCREFWEEMDKRG  172 (403)
Q Consensus       149 ~~~~~~~~~~~~a~~~~~~~~~~~  172 (403)
                      ...+...+++++|.+.|++.....
T Consensus        86 g~~~~~~~~~~~A~~~~~kal~~~  109 (128)
T d1elra_          86 GNSYFKEEKYKDAIHFYNKSLAEH  109 (128)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcC
Confidence            777777888888888888776543

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.26  E-value=0.00065  Score=54.99  Aligned_cols=272  Identities=10%  Similarity=0.016  Sum_probs=170.3

Q ss_pred             cccccccccHHHHHHhhhhhcccCCCcCCHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcC
Q 041804            2 ETLSCYANDWKRALEFFNWVETDCHFTHTTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAH   81 (403)
Q Consensus         2 ~~l~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   81 (403)
                      +..|...|.++.|..+|..+..          |..++..+.+.++++.|.+++.+.       -+..+|..+...+....
T Consensus        21 ~~~c~~~~lye~A~~lY~~~~d----------~~rl~~~~v~l~~~~~avd~~~k~-------~~~~~~k~~~~~l~~~~   83 (336)
T d1b89a_          21 GDRCYDEKMYDAAKLLYNNVSN----------FGRLASTLVHLGEYQAAVDGARKA-------NSTRTWKEVCFACVDGK   83 (336)
T ss_dssp             --------CTTTHHHHHHHTTC----------HHHHHHHHHTTTCHHHHHHHHHHH-------TCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHCCCHHHHHHHHHhCCC----------HHHHHHHHHhhccHHHHHHHHHHc-------CCHHHHHHHHHHHHhCc
Confidence            3456678889999999987763          788889999999999998888755       35678999999998887


Q ss_pred             ChHHHHHHHHHHhhcCCC-cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhH
Q 041804           82 LVNEAMGTFNKLDEFGLK-DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGK  160 (403)
Q Consensus        82 ~~~~a~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  160 (403)
                      ....|.     +...... ++.....++..|-..|.+++...+++....       ....+...++.++..|++.+. ++
T Consensus        84 e~~la~-----i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~-------~~~~~~~~~~~L~~lyak~~~-~k  150 (336)
T d1b89a_          84 EFRLAQ-----MCGLHIVVHADELEELINYYQDRGYFEELITMLEAALG-------LERAHMGMFTELAILYSKFKP-QK  150 (336)
T ss_dssp             CHHHHH-----HTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT-------STTCCHHHHHHHHHHHHTTCH-HH
T ss_pred             HHHHHH-----HHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHc-------CCccchHHHHHHHHHHHHhCh-HH
Confidence            765542     2233333 667778899999999999999999987654       335677788999999998653 33


Q ss_pred             HHHHHHHHHhCCCCCcH----------HHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHH
Q 041804          161 CREFWEEMDKRGVVKDL----------HSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDF  230 (403)
Q Consensus       161 a~~~~~~~~~~~~~~~~----------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~  230 (403)
                         +.+.+...+...|.          ..|..++-.|.+.|.++.|..++   .+.  .++..-....+..+.+..+++.
T Consensus       151 ---l~e~l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~---i~~--~~~~~~~~~f~e~~~k~~N~e~  222 (336)
T d1b89a_         151 ---MREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITM---MNH--PTDAWKEGQFKDIITKVANVEL  222 (336)
T ss_dssp             ---HHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHH---HHS--TTTTCCHHHHHHHHHHCSSTHH
T ss_pred             ---HHHHHHhccccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHH---HHc--chhhhhHHHHHHHHHccCChHH
Confidence               33333331111111          12334444455555555544332   222  3344344556667777788877


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCC
Q 041804          231 AMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGI  310 (403)
Q Consensus       231 a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~  310 (403)
                      ..++.....+.    ++...+.++......-+..+..+.+++-                   ++..-....++.....+ 
T Consensus       223 ~~~~i~~yL~~----~p~~i~~lL~~v~~~~d~~r~V~~~~k~-------------------~~l~li~p~Le~v~~~n-  278 (336)
T d1b89a_         223 YYRAIQFYLEF----KPLLLNDLLMVLSPRLDHTRAVNYFSKV-------------------KQLPLVKPYLRSVQNHN-  278 (336)
T ss_dssp             HHHHHHHHHHH----CGGGHHHHHHHHGGGCCHHHHHHHHHHT-------------------TCTTTTHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHc----CHHHHHHHHHHhccCCCHHHHHHHHHhc-------------------CCcHHHHHHHHHHHHcC-
Confidence            77777766654    2344566666666666776666666432                   22333344555544444 


Q ss_pred             CCchhhHHHHHHHHHhcCCcchHHHHH
Q 041804          311 RPKMDTYVMLLRKFGRWGFLRPVFVVW  337 (403)
Q Consensus       311 ~~~~~~~~~li~~~~~~g~~~~a~~~~  337 (403)
                        +....+++...|...+|++.-.+..
T Consensus       279 --~~~vn~al~~lyie~~d~~~l~~~i  303 (336)
T d1b89a_         279 --NKSVNESLNNLFITEEDYQALRTSI  303 (336)
T ss_dssp             --CHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             --hHHHHHHHHHHHhCcchhHHHHHHH
Confidence              3457888888888888865544433

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.17  E-value=2.9e-05  Score=55.74  Aligned_cols=98  Identities=11%  Similarity=-0.071  Sum_probs=77.9

Q ss_pred             hHHHHHHHHHccCChhHHHHHHHHhhhCCCC---CCC-----------HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC
Q 041804           33 TYNSVIDILGKFFEFDLSWNLIHRMKDNPSS---IPN-----------HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGL   98 (403)
Q Consensus        33 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~   98 (403)
                      .+..-...+.+.|++++|+..|......-..   .++           ..+|+.+..+|.+.|++++|++.++...+.++
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~p   98 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDK   98 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhccccccc
Confidence            3455566777888888888888876643211   111           23567788889999999999999999999998


Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHhccccc
Q 041804           99 KDEVSYCNLVDALCEYKHVIEAQELCFGENKN  130 (403)
Q Consensus        99 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  130 (403)
                      .+..+|..+..++...|++++|...|++....
T Consensus        99 ~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l  130 (153)
T d2fbna1          99 NNVKALYKLGVANMYFGFLEEAKENLYKAASL  130 (153)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh
Confidence            89999999999999999999999999888763

>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=98.15  E-value=1.1e-05  Score=63.60  Aligned_cols=125  Identities=4%  Similarity=-0.169  Sum_probs=89.5

Q ss_pred             HHHccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHH
Q 041804           40 ILGKFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIE  119 (403)
Q Consensus        40 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  119 (403)
                      -..+.|++++|+..+++..+..  +.|...+..+...++..|++++|...|+...+..+.+...+..+...+...+..++
T Consensus         5 ~aL~~G~l~eAl~~l~~al~~~--P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~~~~~   82 (264)
T d1zbpa1           5 NALSEGQLQQALELLIEAIKAS--PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKD   82 (264)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHTC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHH
Confidence            3467799999999999988875  46778899999999999999999999999998887777777777666665555554


Q ss_pred             HHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 041804          120 AQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRG  172 (403)
Q Consensus       120 a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  172 (403)
                      +..-.......      ..+++...+......+...|+.++|.+.++++.+..
T Consensus        83 a~~~~~~~~~~------~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~  129 (264)
T d1zbpa1          83 FAQGAATAKVL------GENEELTKSLVSFNLSMVSQDYEQVSELALQIEELR  129 (264)
T ss_dssp             HTTSCCCEECC------CSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhhhhhcc------cCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence            43322211111      223444455555667777888888888888876653

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.15  E-value=1.3e-05  Score=57.67  Aligned_cols=105  Identities=7%  Similarity=-0.087  Sum_probs=84.2

Q ss_pred             ccccccHHHHHHhhhhhcccCCC---cCC-----------HHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHH
Q 041804            5 SCYANDWKRALEFFNWVETDCHF---THT-----------TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATF   70 (403)
Q Consensus         5 ~~~~~~~~~A~~~~~~~~~~~~~---~~~-----------~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   70 (403)
                      +...|++.+|+..|.........   .++           ..+|+.+..+|.+.|++++|+..++...+..  +.+..+|
T Consensus        27 ~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~--p~~~ka~  104 (153)
T d2fbna1          27 FFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID--KNNVKAL  104 (153)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--TTCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHhhhhHHHHHHhhHHHHHHHhcccchhhhhhhcccccc--chhhhhh
Confidence            44678999999999876641111   111           2356778889999999999999999998876  4678999


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDAL  111 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~  111 (403)
                      ..+..++...|++++|+..|++..+.+|.+..+...+-.+.
T Consensus       105 ~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~~~~~~l~~~~  145 (153)
T d2fbna1         105 YKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCV  145 (153)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHhHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999988877776655443

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.14  E-value=3.5e-06  Score=73.71  Aligned_cols=132  Identities=7%  Similarity=-0.079  Sum_probs=49.3

Q ss_pred             CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhH
Q 041804           81 HLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGK  160 (403)
Q Consensus        81 ~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  160 (403)
                      +.++.|+..+.......+++...+..+...+.+.|+.+.|...+......         ....++..+...+...|++++
T Consensus       100 ~~Y~~ai~~l~~~~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~---------~~~~~~~~LG~l~~~~~~~~~  170 (497)
T d1ya0a1         100 GFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSY---------ICQHCLVHLGDIARYRNQTSQ  170 (497)
T ss_dssp             HHHHHHHHHHTC-------------------------------CCHHHHH---------HHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHCCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCC---------CHHHHHHHHHHHHHHcccHHH
Confidence            33344444443333333334444555555555555555555443332211         112344445555555555555


Q ss_pred             HHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHh
Q 041804          161 CREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVG  223 (403)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~  223 (403)
                      |...|++..+..+. +..+|+.|...+...|+..+|...|.+..... +|-..++..|...+.
T Consensus       171 A~~~y~~A~~l~P~-~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~  231 (497)
T d1ya0a1         171 AESYYRHAAQLVPS-NGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALS  231 (497)
T ss_dssp             HHHHHHHHHHHCTT-BSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCC-chHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHH
Confidence            55555555555444 44555555555555555555555555555442 334445555544443

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.14  E-value=1.8e-05  Score=57.96  Aligned_cols=113  Identities=6%  Similarity=-0.108  Sum_probs=85.4

Q ss_pred             HHHHHHHHHccCChhHHHHHHHHhhhCC-------------CC-CCCHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC
Q 041804           34 YNSVIDILGKFFEFDLSWNLIHRMKDNP-------------SS-IPNHATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLK   99 (403)
Q Consensus        34 ~~~li~~~~~~~~~~~a~~~~~~~~~~~-------------~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~   99 (403)
                      +......+.+.|++++|+..|.+..+..             .. +.....|..+..++.+.|++++|+..+++..+..+.
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~  109 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPS  109 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhhhh
Confidence            4455666778889999888887664310             00 123446777888999999999999999999999888


Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHH
Q 041804          100 DEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWF  153 (403)
Q Consensus       100 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  153 (403)
                      +..+|..+..++...|++++|...|++....       .+.+..+...+..+..
T Consensus       110 ~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l-------~p~n~~~~~~l~~~~~  156 (169)
T d1ihga1         110 NTKALYRRAQGWQGLKEYDQALADLKKAQEI-------APEDKAIQAELLKVKQ  156 (169)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHH
T ss_pred             hhhHHHhHHHHHHHccCHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHH
Confidence            9999999999999999999999999988773       3455555555554443

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=5e-05  Score=52.50  Aligned_cols=96  Identities=10%  Similarity=0.079  Sum_probs=62.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCC-CC-----hhhHHHH
Q 041804          145 YNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIK-MD-----VVAYNTV  218 (403)
Q Consensus       145 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~-----~~~~~~l  218 (403)
                      +..+...+.+.|++++|.+.|.+..+.++. +..++..+..+|.+.|++++|+..++.+++.... +.     ..+|..+
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~l   85 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHH
Confidence            445566777777777777777777776655 6677777777777777777777777776654110 01     1244445


Q ss_pred             HHHHhhcCCHHHHHHHHHHHHHc
Q 041804          219 IRAVGVSEGVDFAMRVYREMREM  241 (403)
Q Consensus       219 l~~~~~~~~~~~a~~~~~~~~~~  241 (403)
                      ...+...++++.|...|+.....
T Consensus        86 g~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          86 GNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhc
Confidence            55556666777777777666554

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.11  E-value=1.4e-05  Score=58.42  Aligned_cols=110  Identities=9%  Similarity=0.016  Sum_probs=82.0

Q ss_pred             cccccccHHHHHHhhhhhcccCCCcC-------------CHHhHHHHHHHHHccCChhHHHHHHHHhhhCCCCCCCHHHH
Q 041804            4 LSCYANDWKRALEFFNWVETDCHFTH-------------TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNPSSIPNHATF   70 (403)
Q Consensus         4 l~~~~~~~~~A~~~~~~~~~~~~~~~-------------~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~   70 (403)
                      .+...|++++|++.|+....-....+             ...+|+.+..+|.+.|++++|+..++......  +.+..+|
T Consensus        24 ~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~--p~~~~a~  101 (168)
T d1kt1a1          24 VYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD--SANEKGL  101 (168)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc--cchHHHH
Confidence            45567899999999877654111111             12345567778888999999999999888865  4678888


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcC
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYK  115 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  115 (403)
                      ..+..++...|++++|+..|.+..+..|.+..+...+-.+....+
T Consensus       102 ~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~  146 (168)
T d1kt1a1         102 YRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQKKAK  146 (168)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence            889999999999999999999999888777777776665554444

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.10  E-value=5e-05  Score=55.41  Aligned_cols=99  Identities=9%  Similarity=-0.124  Sum_probs=58.3

Q ss_pred             HHhHHHHHHHHHccCChhHHHHHHHHhhhCCC--CCCC-----------HHHHHHHHHHHHhcCChHHHHHHHHHHhhcC
Q 041804           31 TDTYNSVIDILGKFFEFDLSWNLIHRMKDNPS--SIPN-----------HATFRIMFKRYVTAHLVNEAMGTFNKLDEFG   97 (403)
Q Consensus        31 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~--~~~~-----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~   97 (403)
                      ...+......+.+.|++++|...|......-.  ...+           ...|..+..+|.+.|++++|+..++...+.+
T Consensus        15 a~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~   94 (168)
T d1kt1a1          15 AAIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD   94 (168)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc
Confidence            34566677778888889888888876553110  0111           1123445555556666666666666666655


Q ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           98 LKDEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        98 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                      +.+..+|..+..++...|++++|...|.+...
T Consensus        95 p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~  126 (168)
T d1kt1a1          95 SANEKGLYRRGEAQLLMNEFESAKGDFEKVLE  126 (168)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            55556666666666666666666666555544

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.10  E-value=0.00015  Score=53.24  Aligned_cols=127  Identities=12%  Similarity=-0.011  Sum_probs=87.8

Q ss_pred             HHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHhcCCcchH
Q 041804          254 IKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLFDRMIESGIRPKMDTYVMLLRKFGRWGFLRPV  333 (403)
Q Consensus       254 i~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a  333 (403)
                      .......|++++|...|.+....  .+...     +..+....-+...-..+...    ....+..+..++...|++++|
T Consensus        18 g~~~~~~g~~e~A~~~~~~AL~l--~rG~~-----l~~~~~~~w~~~~r~~l~~~----~~~a~~~la~~~~~~g~~~~A   86 (179)
T d2ff4a2          18 GVHAAAAGRFEQASRHLSAALRE--WRGPV-----LDDLRDFQFVEPFATALVED----KVLAHTAKAEAEIACGRASAV   86 (179)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTT--CCSST-----TGGGTTSTTHHHHHHHHHHH----HHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhh--Ccccc-----cccCcchHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCchHH
Confidence            35667788999998888887653  11110     00011111111111111111    234677889999999999999


Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCCChhhHHHHHH
Q 041804          334 FVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA-----KGLSAKPREELGTKL  392 (403)
Q Consensus       334 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~~~~p~~~~~~~~~~  392 (403)
                      +..++++.+.. +-+...|..++.+|.+.|+.++|++.|+++..     .|+.|.+.+.--...
T Consensus        87 l~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~~l~~~  149 (179)
T d2ff4a2          87 IAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNER  149 (179)
T ss_dssp             HHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            99999999875 56899999999999999999999999999754     499999876544433

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.07  E-value=4e-05  Score=56.02  Aligned_cols=129  Identities=9%  Similarity=-0.034  Sum_probs=89.1

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHH
Q 041804           71 RIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILR  150 (403)
Q Consensus        71 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  150 (403)
                      ......+...|++++|+..|.+..+..           .............       .       ..+.....+..+..
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~~-----------~~~~~~~~~~~~~-------~-------~~~~~~~~~~nla~   85 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRYV-----------EGSRAAAEDADGA-------K-------LQPVALSCVLNIGA   85 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHH-----------HHHHHHSCHHHHG-------G-------GHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhh-----------hhhhhhhhhHHHH-------H-------hChhhHHHHHHHHH
Confidence            345666788999999999998876421           0001111111110       0       12345667788888


Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcC
Q 041804          151 GWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSE  226 (403)
Q Consensus       151 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~  226 (403)
                      ++.+.|++++|+..+++..+..+. +..+|..+..+|...|++++|+..|+...+.. +.+..+...+..+..+..
T Consensus        86 ~~~~~~~~~~Ai~~~~~al~~~p~-~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~-p~n~~~~~~l~~~~~~l~  159 (169)
T d1ihga1          86 CKLKMSDWQGAVDSCLEALEIDPS-NTKALYRRAQGWQGLKEYDQALADLKKAQEIA-PEDKAIQAELLKVKQKIK  159 (169)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHH
T ss_pred             HHHhhcccchhhhhhhhhhhhhhh-hhhHHHhHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHH
Confidence            999999999999999999888766 78889999999999999999999999988873 335555555555544333

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.06  E-value=5.9e-05  Score=55.47  Aligned_cols=70  Identities=10%  Similarity=-0.016  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH-----cCCCCChh
Q 041804          143 KIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK-----KGIKMDVV  213 (403)
Q Consensus       143 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~  213 (403)
                      ..+..+...+.+.|++++|...++++.+..+. +...|..++.+|...|++.+|++.|+++..     .|+.|+..
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~P~-~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~  142 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEHPY-REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPT  142 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHH
Confidence            34555566666666666666666666655544 556666666666666666666666665432     35555544

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.06  E-value=1.6e-05  Score=69.36  Aligned_cols=136  Identities=10%  Similarity=-0.093  Sum_probs=63.2

Q ss_pred             hcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCC
Q 041804          113 EYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK  192 (403)
Q Consensus       113 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  192 (403)
                      ..+.++.+...+.....       ..+++...+..+...+.+.|+.+.|...+.......   ...++..+...+...++
T Consensus        98 a~~~Y~~ai~~l~~~~~-------l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~---~~~~~~~LG~l~~~~~~  167 (497)
T d1ya0a1          98 ASGFYTQLLQELCTVFN-------VDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI---CQHCLVHLGDIARYRNQ  167 (497)
T ss_dssp             HHHHHHHHHHHHTC--------------------------------------CCHHHHHH---HHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHC-------CChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC---HHHHHHHHHHHHHHccc
Confidence            34556666665555443       224445556666666666777777666665544321   12355566667777777


Q ss_pred             hhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Q 041804          193 PWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCEN  260 (403)
Q Consensus       193 ~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~  260 (403)
                      +++|...|++..+.. +-+...|+.+...+...|+..+|...|.+..... +|-..++..|...+.+.
T Consensus       168 ~~~A~~~y~~A~~l~-P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~~~  233 (497)
T d1ya0a1         168 TSQAESYYRHAAQLV-PSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALSKA  233 (497)
T ss_dssp             HHHHHHHHHHHHHHC-TTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHh
Confidence            777777777766652 3344567777777777777777777777666543 34555566666555543

>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=97.99  E-value=7.6e-06  Score=64.53  Aligned_cols=123  Identities=10%  Similarity=-0.043  Sum_probs=80.4

Q ss_pred             HHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC
Q 041804           77 YVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS  156 (403)
Q Consensus        77 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  156 (403)
                      ..+.|++++|+..+++..+..+.+...+..+...++..|++++|.+.++.....       .+.+...+..+...+...+
T Consensus         6 aL~~G~l~eAl~~l~~al~~~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l-------~P~~~~~~~~l~~ll~a~~   78 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKL-------FPEYLPGASQLRHLVKAAQ   78 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-------CGGGHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-------CCCcHHHHHHHHHHHHhcc
Confidence            456789999999999999999889999999999999999999999999887763       2334444444444443333


Q ss_pred             ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHc
Q 041804          157 WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKK  206 (403)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  206 (403)
                      ..+++..-.......+..++...+......+...|+.++|.+.++++.+.
T Consensus        79 ~~~~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          79 ARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             HHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            22222111111111112223344444556677788888888888887765

>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=97.98  E-value=4.3e-05  Score=54.15  Aligned_cols=106  Identities=8%  Similarity=-0.067  Sum_probs=66.3

Q ss_pred             HHhcCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcC
Q 041804           77 YVTAHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMS  156 (403)
Q Consensus        77 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  156 (403)
                      |-+.+.+++|+..|+...+..|.+..++..+..++...+++..+..-                               .+
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~-------------------------------~~   55 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDA-------------------------------KQ   55 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHH-------------------------------HH
T ss_pred             HHHHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHH-------------------------------HH
Confidence            44566788888888888888877888888888888765554433221                               12


Q ss_pred             ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCC-----------hhHHHHHHHHHHHcCCCCChhhHH
Q 041804          157 WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGK-----------PWKAVKLYKEMKKKGIKMDVVAYN  216 (403)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----------~~~a~~~~~~~~~~~~~~~~~~~~  216 (403)
                      .+++|...|++..+.++. +..+|..+..+|...|+           +++|.+.|+...+.  .|+...+.
T Consensus        56 ~~~~Ai~~~~kAl~l~P~-~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l--~P~~~~~~  123 (145)
T d1zu2a1          56 MIQEAITKFEEALLIDPK-KDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYL  123 (145)
T ss_dssp             HHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHH
T ss_pred             HHHHHHHHHHHHHHhcch-hhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhccccc--CCCHHHHH
Confidence            245667777777666555 66667666666655432           34555555555543  34444443

>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=97.79  E-value=6.3e-05  Score=53.24  Aligned_cols=72  Identities=8%  Similarity=0.074  Sum_probs=48.8

Q ss_pred             ccCChhHHHHHHHHhhhCCCCCCCHHHHHHHHHHHHh----------cCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 041804           43 KFFEFDLSWNLIHRMKDNPSSIPNHATFRIMFKRYVT----------AHLVNEAMGTFNKLDEFGLKDEVSYCNLVDALC  112 (403)
Q Consensus        43 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----------~~~~~~a~~~~~~~~~~~~~~~~~~~~l~~~~~  112 (403)
                      +.+.+++|+..|+...+..  |.+..++..+..++..          .+.+++|+..|++..+.+|.+..+|..+..+|.
T Consensus         9 r~~~fe~A~~~~e~al~~~--P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~   86 (145)
T d1zu2a1           9 RILLFEQIRQDAENTYKSN--PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYT   86 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhhC--CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHH
Confidence            3445666666666666544  3445555555555543          244578999999999999889999999988887


Q ss_pred             hcCC
Q 041804          113 EYKH  116 (403)
Q Consensus       113 ~~~~  116 (403)
                      ..|.
T Consensus        87 ~~g~   90 (145)
T d1zu2a1          87 SFAF   90 (145)
T ss_dssp             HHHH
T ss_pred             Hccc
Confidence            7653

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.67  E-value=0.00014  Score=46.96  Aligned_cols=79  Identities=10%  Similarity=-0.036  Sum_probs=64.1

Q ss_pred             CHHhHHHHHHHHHccCChhHHHHHHHHhhhCC----CCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHHHH
Q 041804           30 TTDTYNSVIDILGKFFEFDLSWNLIHRMKDNP----SSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEVSY  104 (403)
Q Consensus        30 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  104 (403)
                      +...+-.+...+.+.|++++|+..|++..+..    ...++ ..+++.+..++.+.|++++|+..++++.+..|.+..++
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~~~~a~   83 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRAN   83 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcCCHHHH
Confidence            45566788999999999999999998876531    11222 56889999999999999999999999999998888877


Q ss_pred             HHHH
Q 041804          105 CNLV  108 (403)
Q Consensus       105 ~~l~  108 (403)
                      +.+.
T Consensus        84 ~Nl~   87 (95)
T d1tjca_          84 GNLK   87 (95)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7764

>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=97.59  E-value=0.00014  Score=52.12  Aligned_cols=99  Identities=12%  Similarity=-0.057  Sum_probs=74.4

Q ss_pred             HHhHHHH--HHHHHccCChhHHHHHHHHhhhCCCCCCC----------HHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-
Q 041804           31 TDTYNSV--IDILGKFFEFDLSWNLIHRMKDNPSSIPN----------HATFRIMFKRYVTAHLVNEAMGTFNKLDEFG-   97 (403)
Q Consensus        31 ~~~~~~l--i~~~~~~~~~~~a~~~~~~~~~~~~~~~~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-   97 (403)
                      ..+|..+  ...+.+.|++++|+..|++..+.....|+          ..+|+.+..+|...|++++|+..+++..+.. 
T Consensus         7 a~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~   86 (156)
T d2hr2a1           7 VGAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFN   86 (156)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhccc
Confidence            3456655  55677889999999999988763312222          3578899999999999999999998876532 


Q ss_pred             ------CC----cHHHHHHHHHHHHhcCCHHHHHHHHhcccc
Q 041804           98 ------LK----DEVSYCNLVDALCEYKHVIEAQELCFGENK  129 (403)
Q Consensus        98 ------~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  129 (403)
                            ..    ...++..+..+|...|++++|...|++...
T Consensus        87 ~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          87 RRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                  11    223577889999999999999999877654

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.54  E-value=0.00031  Score=45.34  Aligned_cols=81  Identities=4%  Similarity=-0.057  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHhcccccccccccccCcchHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCcHHHHH
Q 041804          102 VSYCNLVDALCEYKHVIEAQELCFGENKNVGFSGLVEMNKTKIYNMILRGWFKMSWWGKCREFWEEMDKRGVVKDLHSYS  181 (403)
Q Consensus       102 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  181 (403)
                      ..+..+...+.+.|++++|...|++.................+++.+..+|.+.|++++|.+.++++.+..+. +..+++
T Consensus         6 ddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~-~~~a~~   84 (95)
T d1tjca_           6 EDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPE-HQRANG   84 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcC-CHHHHH
Confidence            3445667777777777777777776654321111122334567888899999999999999999998887655 455554


Q ss_pred             HH
Q 041804          182 IY  183 (403)
Q Consensus       182 ~l  183 (403)
                      .+
T Consensus        85 Nl   86 (95)
T d1tjca_          85 NL   86 (95)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=97.29  E-value=0.0038  Score=44.32  Aligned_cols=62  Identities=5%  Similarity=-0.084  Sum_probs=34.8

Q ss_pred             HHHHH--HHHHHhcCChhHHHHHHHHHHhCCCC-C----------cHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          144 IYNMI--LRGWFKMSWWGKCREFWEEMDKRGVV-K----------DLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       144 ~~~~l--~~~~~~~~~~~~a~~~~~~~~~~~~~-~----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      +|..+  ...+...|++++|++.|++..+.... |          ...+|+.+..+|...|++++|...+++..+
T Consensus         9 a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~   83 (156)
T d2hr2a1           9 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH   83 (156)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhh
Confidence            44444  34455567777777777776542211 1          124555666666666666666666665543

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=96.82  E-value=0.026  Score=37.05  Aligned_cols=140  Identities=14%  Similarity=0.005  Sum_probs=99.3

Q ss_pred             hhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHhchhcCCCCChhhHHHHHHhhCCHHHHHHHH
Q 041804          223 GVSEGVDFAMRVYREMREMGCQPSVVTCNTVIKLLCENGRVREAYAVLAEMPKKGCVPDVITYHCFFRCLEKPREILGLF  302 (403)
Q Consensus       223 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~~~a~~~~  302 (403)
                      ...|.+++..+++.+....   .+..-||.+|--....-+-+-...+++.+-..   -|       +..|++.......+
T Consensus        13 ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~---FD-------ls~C~Nlk~vv~C~   79 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FD-------LDKCQNLKSVVECG   79 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SC-------GGGCSCTHHHHHHH
T ss_pred             HHhhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhh---cC-------chhhhcHHHHHHHH
Confidence            4567778888888777764   36666777776666666666666666655431   11       12234444433333


Q ss_pred             HHHHHcCCCCchhhHHHHHHHHHhcCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 041804          303 DRMIESGIRPKMDTYVMLLRKFGRWGFLRPVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFAKGLS  381 (403)
Q Consensus       303 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~  381 (403)
                      -.+     ..+...++..+....++|+-+.-.++++.+.+.+ +|++...-.+..||.+.|...++-+++.+.-++|++
T Consensus        80 ~~~-----n~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          80 VIN-----NTLNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHT-----TCCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHh-----cchHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            222     2355677888889999999999999999977755 789999999999999999999999999999999875

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=96.29  E-value=0.081  Score=35.82  Aligned_cols=110  Identities=6%  Similarity=-0.044  Sum_probs=66.4

Q ss_pred             ChhHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhh----cCCHHHHH
Q 041804          157 WWGKCREFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGV----SEGVDFAM  232 (403)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~----~~~~~~a~  232 (403)
                      |+++|.++|++..+.|..   ..+..|..  ....+.++|++++++..+.|   +......|-..|..    ..+.+.|.
T Consensus         8 d~~~A~~~~~kaa~~g~~---~a~~~l~~--~~~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~   79 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEM---FGCLSLVS--NSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCT---THHHHHHT--CTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCh---hhhhhhcc--ccccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHH
Confidence            567788888887776533   22333322  23456778888888877766   34444445444443    45677888


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHh----cCcHHHHHHHHHhchhcC
Q 041804          233 RVYREMREMGCQPSVVTCNTVIKLLCE----NGRVREAYAVLAEMPKKG  277 (403)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~  277 (403)
                      ++|+...+.|   ++.....|...|..    ..+.++|.++|+...+.|
T Consensus        80 ~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          80 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            8888877764   34444455555554    346667777777666554

>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=95.99  E-value=0.12  Score=34.97  Aligned_cols=81  Identities=15%  Similarity=-0.006  Sum_probs=50.1

Q ss_pred             CHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHh----cCCcchHHHHHHHHHhcCCCCCHHHHHHHHHHHHh----cCCH
Q 041804          294 KPREILGLFDRMIESGIRPKMDTYVMLLRKFGR----WGFLRPVFVVWKKMEELGCSPDEFAYNALVDALID----KGML  365 (403)
Q Consensus       294 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~  365 (403)
                      +.++|.+++++..+.|   ++.....|...|..    ..+.++|.+.|++..+.|   ++.....|...|..    ..+.
T Consensus        38 ~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~  111 (133)
T d1klxa_          38 NKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNE  111 (133)
T ss_dssp             CHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCH
T ss_pred             CHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHHHHHhhhhccC---cchHHHHHHHHHHcCCccCCCH
Confidence            3556666666666654   23333334444432    346778888888887765   34455556555554    4577


Q ss_pred             HHHHHHHHHHHHcCC
Q 041804          366 DMARKYDEEMFAKGL  380 (403)
Q Consensus       366 ~~a~~~~~~m~~~~~  380 (403)
                      ++|.++|++..+.|.
T Consensus       112 ~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_         112 KQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHCCC
Confidence            888888888877764

>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=94.72  E-value=0.25  Score=32.52  Aligned_cols=74  Identities=9%  Similarity=0.048  Sum_probs=49.0

Q ss_pred             CCchhhHHHHHHHHHhcC---CcchHHHHHHHHHhcCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCChhh
Q 041804          311 RPKMDTYVMLLRKFGRWG---FLRPVFVVWKKMEELGCSPDE-FAYNALVDALIDKGMLDMARKYDEEMFAKGLSAKPRE  386 (403)
Q Consensus       311 ~~~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~  386 (403)
                      .|...|--....++.+..   +.++++.+++++.+.+ +.+. ..+-.|.-+|.+.|++++|.++++.+++  +.|+..-
T Consensus        32 ~~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~--ieP~n~q  108 (124)
T d2pqrb1          32 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE--HERNNKQ  108 (124)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HCTTCHH
T ss_pred             CCCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc--cCCCcHH
Confidence            344445445556666554   4567888888887653 2233 4556677788889999999999988887  4455543


Q ss_pred             H
Q 041804          387 E  387 (403)
Q Consensus       387 ~  387 (403)
                      .
T Consensus       109 A  109 (124)
T d2pqrb1         109 V  109 (124)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=94.57  E-value=0.24  Score=32.58  Aligned_cols=75  Identities=11%  Similarity=-0.083  Sum_probs=54.7

Q ss_pred             CcCCHHhHHHHHHHHHccC---ChhHHHHHHHHhhhCCCCCCC-HHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCCcHH
Q 041804           27 FTHTTDTYNSVIDILGKFF---EFDLSWNLIHRMKDNPSSIPN-HATFRIMFKRYVTAHLVNEAMGTFNKLDEFGLKDEV  102 (403)
Q Consensus        27 ~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  102 (403)
                      ..+++.+--....++.+..   +.++++.+|+.+...+  +.+ ...+-.|.-+|.+.|++++|.+.++.+.+..|.+..
T Consensus        31 ~~~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~--p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~n~q  108 (124)
T d2pqrb1          31 PTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEA--ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQ  108 (124)
T ss_dssp             GGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHC--GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             CCCCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcC--chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCCcHH
Confidence            3456666556666676554   5678899999888754  223 356777888889999999999999999998877554


Q ss_pred             H
Q 041804          103 S  103 (403)
Q Consensus       103 ~  103 (403)
                      +
T Consensus       109 A  109 (124)
T d2pqrb1         109 V  109 (124)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=94.51  E-value=0.35  Score=31.70  Aligned_cols=64  Identities=17%  Similarity=0.122  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHcCChhHHHHHHHHHHHcCCCCChhhHHHHHHHHhhcCCHHHHHHHHHHHHHcCC
Q 041804          179 SYSIYMDIMCKSGKPWKAVKLYKEMKKKGIKMDVVAYNTVIRAVGVSEGVDFAMRVYREMREMGC  243 (403)
Q Consensus       179 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  243 (403)
                      .+...++.+..+|+-++-.++++.+.+.+ +|++...-.+..+|.+.|+..++..++.++-+.|+
T Consensus        88 ~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~  151 (161)
T d1wy6a1          88 HVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGE  151 (161)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhH
Confidence            44444555555555555555555544432 44555555555566666666666665555555543

>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=89.58  E-value=1.4  Score=27.17  Aligned_cols=46  Identities=11%  Similarity=-0.052  Sum_probs=21.9

Q ss_pred             hHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 041804          332 PVFVVWKKMEELGCSPDEFAYNALVDALIDKGMLDMARKYDEEMFA  377 (403)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  377 (403)
                      ++.+-++.+....+.|++.+..+.++||-+.+++..|+++++-.+.
T Consensus        24 e~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~   69 (105)
T d1v54e_          24 ELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKD   69 (105)
T ss_dssp             HHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3333344444444445555555555555555555555555554443

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=88.51  E-value=1.7  Score=26.78  Aligned_cols=44  Identities=11%  Similarity=0.055  Sum_probs=20.5

Q ss_pred             HHHHHHHHhCCCCCcHHHHHHHHHHHHHcCChhHHHHHHHHHHH
Q 041804          162 REFWEEMDKRGVVKDLHSYSIYMDIMCKSGKPWKAVKLYKEMKK  205 (403)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  205 (403)
                      .+-++.+...+..|++....+.+.+|-+.+++..|.++|+-.+.
T Consensus        26 rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~   69 (105)
T d1v54e_          26 RKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKD   69 (105)
T ss_dssp             HHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            33444444444444444444444444444444444444444443