Citrus Sinensis ID: 011102

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490---
Protein Sequence
MNCTLSYMSLHPVVLSNRIFPISKNNNITTTLMAHSNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDPIKADSVEEQEADNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRIGTI
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEcccccccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccHHcHHHHHHHHHccccHHHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccEEEEcEEccEEEccEEEEEccccccEEEEEEEccccccccccccccccccccccccccccccccEEEEEEccccccccccccccccccccccEEEcHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHEEEccccccHHHHHccccHHHHHHHHHHHcccccHHHHHHHHHHccccccccHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
mnctlsymslhpvvlsnrifpisknnnitTTLMahsnqrrrptttrhpklpknlqnprrtklppdfgvnlflkkpsdeydpikadsveeqeadndfIWESEELEAISSLFQgripqkpgrlyrerplplplphrlrplelptpkkrvclassrASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRelghmnlperALQTFCwaqkqphlfpddrlLASTVEVLARHhelkvpfklENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKdggrmldpSIYAKLILELGKNPDKYMLVMTLLDelgqrddlnlsqQDCTAIMKVGIRLQKFGVVESLFHWfthsgrdptvVMYTTLIHSRLSEKKCREALTVVWNMEasnclfdlpaYRVVIKLFVALNDISRAIRYFSKlkeagfcptydIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRIGTI
Flexible Loop (DISEMBL)
MNCTLSYMSLHPVVLSNRIFPISKNNNITTtlmahsnqrrrptttrhpklpknlqnprrtklppdFGVNLFLKKPSDEYDPIKADSVEEQEADNDFIWESEELEAISSLfqgripqkpgrlyrerplplplphrlrplelptpKKRVCLAssrasickqvyknPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAkgfvkggnlKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWfthsgrdptVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYfsklkeagfcpTYDIYRDMIRIFMASGRLAKCRDVCKEAEmagfkldkqtvvELLQiekesrigti
Low Complexity Region (SEG)
MNCTLSYMSLHPVVLSNRIFPISKNNNITTTLMAHSNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDPIKADSVEEQEADNDFIWESEELEAISSLFQGRIPQKPGrlyrerplplplphrlrplelptpKKRVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRIGTI
Disordered region (IsUnstruct)
***TLSYMSLHPVVLSNRIFPISKNNNITT**************************************NLF************************FIWES*ELEAISSLF**********************************KRVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI*********
Disordered Region (DISOPRED)
*****SYMSLHPVVLSNRIFPISKNNNITTTLM********************************FGVNLF**************************WESEELEAI****************************LR************************YKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRIGTI
Disordered Region (DISEMBL)
MNCTLSYMSLHPVVLSNRIFPISKNNNITTTLMA***********RHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDPIKADSVEEQEADNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRIGTI
Disordered Region (DISPRO)
MNCTLSYMSLHPVVLSNRIFPISKNNNITTTLMAHSNQ*RRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPS****************DNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESR****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNCTLSYMSLHPVVLSNRIFPISKNNNITTTLMAHSNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDPIKADSVEEQEADNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRIGTI
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	493	2.2.26 [Sep-21-2011]
Q5XET4	486	Pentatricopeptide repeat-	yes	no	0.959	0.973	0.607	1e-164
O80958	867	Pentatricopeptide repeat-	no	no	0.413	0.235	0.239	4e-09
Q9LW84	642	Pentatricopeptide repeat-	no	no	0.423	0.325	0.241	3e-08
Q9SS81	687	Pentatricopeptide repeat-	no	no	0.237	0.170	0.298	5e-07
Q5G1S8	1440	Pentatricopeptide repeat-	no	no	0.565	0.193	0.229	7e-07
Q9SV46	851	Pentatricopeptide repeat-	no	no	0.241	0.139	0.277	1e-06
Q9SIC9	918	Pentatricopeptide repeat-	no	no	0.572	0.307	0.201	1e-06
Q9LYT2	583	Pentatricopeptide repeat-	no	no	0.340	0.288	0.254	1e-06
P0C8A0	638	Pentatricopeptide repeat-	no	no	0.367	0.283	0.234	2e-06
Q0WMY5	952	Pentatricopeptide repeat-	no	no	0.389	0.201	0.257	5e-06

>sp|Q5XET4|PP142_ARATH Pentatricopeptide repeat-containing protein At2g01860 OS=Arabidopsis thaliana GN=EMB975 PE=2 SV=1

 Score =  577 bits (1488), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 297/489 (60%), Positives = 372/489 (76%), Gaps = 16/489 (3%)

Query: 8   MSLH-PVVLSNRIFPISKNNNITTTLMAHSNQRRRPTTTRH--PKLPKNLQNPRRTKLPP 64
           M LH PV LS     +S + N+ T+ + +    R   + R+   KL KNL+NPRRTKLPP
Sbjct: 1   MILHCPVSLS-----LSFHLNLRTSRIGNIGVTRVNASQRNHSKKLTKNLRNPRRTKLPP 55

Query: 65  DFGVNLFLKKPSDEYDPIKADSVEEQEADND----FIWESEELEAISSLFQGRIPQKPGR 120
           DFGVNLFL+KP  E   I  D  + QE+ ND     +WE EE+EAISSLFQ RIPQKP +
Sbjct: 56  DFGVNLFLRKPKIEPLVIDDDDEQVQESVNDDDDAVVWEPEEIEAISSLFQKRIPQKPDK 115

Query: 121 LYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVYKNPSFLISLARDIKGL-DS 179
             R RPLPLP PH+LRPL LPTPKK +  + + +S+ KQVYK+PSFLI LAR+IK L  S
Sbjct: 116 PSRVRPLPLPQPHKLRPLGLPTPKKNIIRSPALSSVSKQVYKDPSFLIGLAREIKSLPSS 175

Query: 180 HKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTV 239
             DV+ VL+K   FLRKGSLS T+RELGHM LPERALQT+ WA+K  HL PD+R+LAST+
Sbjct: 176 DADVSLVLNKWVSFLRKGSLSTTIRELGHMGLPERALQTYHWAEKHSHLVPDNRILASTI 235

Query: 240 EVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS 299
           +VLA+HHELK+  K +N  SLASK V+EA  KG ++GG L LA KL++++K   R+LD S
Sbjct: 236 QVLAKHHELKL-LKFDN--SLASKNVIEAMIKGCIEGGWLNLARKLILISKSNNRILDSS 292

Query: 300 IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFH 359
           +Y K+ILE+ KNPDKY LV+ LL+EL +R+DL LSQQDCT+IMK+ ++L +F +VESLF 
Sbjct: 293 VYVKMILEIAKNPDKYHLVVALLEELKKREDLKLSQQDCTSIMKICVKLGEFELVESLFD 352

Query: 360 WFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN 419
           WF  S R+P+VVMYTT+IHSR SE+K REA++VVW ME SNCL DLPAYRVVIKLFVAL+
Sbjct: 353 WFKASNREPSVVMYTTMIHSRYSEQKYREAMSVVWEMEESNCLLDLPAYRVVIKLFVALD 412

Query: 420 DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVV 479
           D+ RA+RY+SKLKEAGF PTYDIYRDMI ++ ASGRL KC+++CKE E AG +LDK T  
Sbjct: 413 DLGRAMRYYSKLKEAGFSPTYDIYRDMISVYTASGRLTKCKEICKEVEDAGLRLDKDTSF 472

Query: 480 ELLQIEKES 488
            LLQ+EK++
Sbjct: 473 RLLQLEKQT 481

Arabidopsis thaliana (taxid: 3702)

>sp|O80958|PP194_ARATH Pentatricopeptide repeat-containing protein At2g39230, mitochondrial OS=Arabidopsis thaliana GN=LOJ PE=1 SV=1

 Score = 63.2 bits (152), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 52/217 (23%), Positives = 92/217 (42%), Gaps = 13/217 (5%)

Query: 272 GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLI---LELGKNPDKYMLVMTLLDELGQR 328
           GF K  + + AW ++          +  IY  +I    ++G+      ++  L+ E  +R
Sbjct: 528 GFFKNKDEQNAWDVINQMNASNFEANEVIYNTIINGLCKVGQTSKAKEMLQNLIKE--KR 585

Query: 329 DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWF---THSGRDPTVVMYTTLIHSRLSEKK 385
             ++     CT+   +     K G  +S    +   + +G+ P VV +T+LI+      +
Sbjct: 586 YSMS-----CTSYNSIIDGFVKVGDTDSAVETYREMSENGKSPNVVTFTSLINGFCKSNR 640

Query: 386 CREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRD 445
              AL +   M++     DLPAY  +I  F   ND+  A   FS+L E G  P   +Y  
Sbjct: 641 MDLALEMTHEMKSMELKLDLPAYGALIDGFCKKNDMKTAYTLFSELPELGLMPNVSVYNS 700

Query: 446 MIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELL 482
           +I  F   G++    D+ K+    G   D  T   ++
Sbjct: 701 LISGFRNLGKMDAAIDLYKKMVNDGISCDLFTYTTMI 737

Involved in lateral organ development and boundary demarcation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LW84|PP236_ARATH Pentatricopeptide repeat-containing protein At3g16010 OS=Arabidopsis thaliana GN=At3g16010 PE=2 SV=1

 Score = 60.8 bits (146), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 51/211 (24%), Positives = 89/211 (42%), Gaps = 2/211 (0%)

Query: 272 GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDL 331
           G+ K   ++ A  LL    + G    P+ Y  LI  LGK   +Y     L  EL + +  
Sbjct: 418 GYCKTNRVEKALLLLEEMDEKGFPPCPAAYCSLINALGK-AKRYEAANELFKEL-KENFG 475

Query: 332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALT 391
           N+S +    ++K   +  K      LF+   + G  P V  Y  L+   +      EA +
Sbjct: 476 NVSSRVYAVMIKHFGKCGKLSEAVDLFNEMKNQGSGPDVYAYNALMSGMVKAGMINEANS 535

Query: 392 VVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFM 451
           ++  ME + C  D+ ++ +++  F       RAI  F  +K +G  P    Y  ++  F 
Sbjct: 536 LLRKMEENGCRADINSHNIILNGFARTGVPRRAIEMFETIKHSGIKPDGVTYNTLLGCFA 595

Query: 452 ASGRLAKCRDVCKEAEMAGFKLDKQTVVELL 482
            +G   +   + +E +  GF+ D  T   +L
Sbjct: 596 HAGMFEEAARMMREMKDKGFEYDAITYSSIL 626

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SS81|PP221_ARATH Pentatricopeptide repeat-containing protein At3g09060 OS=Arabidopsis thaliana GN=At3g09060 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 37/124 (29%), Positives = 61/124 (49%), Gaps = 7/124 (5%)

Query: 340 AIMKVGI-RLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEA 398
           +I+  G+ R +K  +   L+H F  SG +  V+M+  LIH   S  K  +A+TV+ NME 
Sbjct: 538 SILLCGLCRDRKIDLALELWHQFLQSGLETDVMMHNILIHGLCSVGKLDDAMTVMANMEH 597

Query: 399 SNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAK 458
            NC  +L  Y  +++ F  + D +RA   +  + + G  P    Y  +++       L  
Sbjct: 598 RNCTANLVTYNTLMEGFFKVGDSNRATVIWGYMYKMGLQPDIISYNTIMK------GLCM 651

Query: 459 CRDV 462
           CR V
Sbjct: 652 CRGV 655

Arabidopsis thaliana (taxid: 3702)

>sp|Q5G1S8|PP241_ARATH Pentatricopeptide repeat-containing protein At3g18110, chloroplastic OS=Arabidopsis thaliana GN=EMB1270 PE=2 SV=2

 Score = 55.8 bits (133), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 73/318 (22%), Positives = 125/318 (39%), Gaps = 39/318 (12%)

Query: 170 LARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLF 229
           L   I  L S++ VA++LD     +      F V+ +G  +  +RAL+ F W   +    
Sbjct: 130 LTDKILSLKSNQFVADILDARLVQMTPTDYCFVVKSVGQESW-QRALEVFEWLNLRHWHS 188

Query: 230 PDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVA 289
           P+ R++A+ + VL R           N  SLA    +E   +     G+    +  +M  
Sbjct: 189 PNARMVAAILGVLGRW----------NQESLA----VEIFTRAEPTVGDRVQVYNAMM-- 232

Query: 290 KDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRD---DLNLSQQDCTAIMKVGI 346
                     +Y++          K+     L+D + QR    DL        A +K G 
Sbjct: 233 ---------GVYSR--------SGKFSKAQELVDAMRQRGCVPDLISFNTLINARLKSGG 275

Query: 347 RLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLP 406
                 V   L     +SG  P  + Y TL+ +   +     A+ V  +MEA  C  DL 
Sbjct: 276 LTPNLAV--ELLDMVRNSGLRPDAITYNTLLSACSRDSNLDGAVKVFEDMEAHRCQPDLW 333

Query: 407 AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEA 466
            Y  +I ++      + A R F +L+  GF P    Y  ++  F       K ++V ++ 
Sbjct: 334 TYNAMISVYGRCGLAAEAERLFMELELKGFFPDAVTYNSLLYAFARERNTEKVKEVYQQM 393

Query: 467 EMAGFKLDKQTVVELLQI 484
           +  GF  D+ T   ++ +
Sbjct: 394 QKMGFGKDEMTYNTIIHM 411

May play a role in embryogenesis.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SV46|PP282_ARATH Pentatricopeptide repeat-containing protein At3g54980, mitochondrial OS=Arabidopsis thaliana GN=At3g54980 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 55/119 (46%)

Query: 364 SGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISR 423
           +G  P V+ YT+L++      +  +AL +   M+      D+PAY  +I  F   +++  
Sbjct: 613 NGISPNVITYTSLMNGLCKNNRMDQALEMRDEMKNKGVKLDIPAYGALIDGFCKRSNMES 672

Query: 424 AIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELL 482
           A   FS+L E G  P+  IY  +I  F   G +    D+ K+    G + D  T   L+
Sbjct: 673 ASALFSELLEEGLNPSQPIYNSLISGFRNLGNMVAALDLYKKMLKDGLRCDLGTYTTLI 731

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIC9|PP178_ARATH Pentatricopeptide repeat-containing protein At2g31400, chloroplastic OS=Arabidopsis thaliana GN=At2g31400 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/288 (20%), Positives = 115/288 (39%), Gaps = 6/288 (2%)

Query: 200 SFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLAST-VEVLARHHELKVPFKLENFV 258
           ++ +RELG+ N  ++A+  + +A K+     +   LAS  +  L R+ ++ +  ++    
Sbjct: 200 TYIIRELGNRNECDKAVGFYEFAVKRERRKNEQGKLASAMISTLGRYGKVTIAKRIFETA 259

Query: 259 SLASKG----VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDK 314
                G       A    + + G  + A  +    K+ G   +   Y  +I   GK   +
Sbjct: 260 FAGGYGNTVYAFSALISAYGRSGLHEEAISVFNSMKEYGLRPNLVTYNAVIDACGKGGME 319

Query: 315 YMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYT 374
           +  V    DE+ QR+ +   +    +++ V  R   +    +LF   T+   +  V  Y 
Sbjct: 320 FKQVAKFFDEM-QRNGVQPDRITFNSLLAVCSRGGLWEAARNLFDEMTNRRIEQDVFSYN 378

Query: 375 TLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEA 434
           TL+ +     +   A  ++  M     + ++ +Y  VI  F        A+  F +++  
Sbjct: 379 TLLDAICKGGQMDLAFEILAQMPVKRIMPNVVSYSTVIDGFAKAGRFDEALNLFGEMRYL 438

Query: 435 GFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELL 482
           G       Y  ++ I+   GR  +  D+ +E    G K D  T   LL
Sbjct: 439 GIALDRVSYNTLLSIYTKVGRSEEALDILREMASVGIKKDVVTYNALL 486

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LYT2|PP287_ARATH Pentatricopeptide repeat-containing protein At3g59040 OS=Arabidopsis thaliana GN=At3g59040 PE=2 SV=2

 Score = 54.7 bits (130), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 74/173 (42%), Gaps = 5/173 (2%)

Query: 310 KNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT 369
           K   K+ LV  +L+ L  ++  N S+ D   ++    +L  F   E +    +  G  P 
Sbjct: 114 KQLKKWNLVSEILEWLRYQNWWNFSEIDFLMLITAYGKLGNFNGAERVLSVLSKMGSTPN 173

Query: 370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFS 429
           V+ YT L+ S     KC  A  +   M++S        Y++++K FV  +    A   F 
Sbjct: 174 VISYTALMESYGRGGKCNNAEAIFRRMQSSGPEPSAITYQIILKTFVEGDKFKEAEEVFE 233

Query: 430 KL---KEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVV 479
            L   K++   P   +Y  MI ++  +G   K R V   + M G  + + TV 
Sbjct: 234 TLLDEKKSPLKPDQKMYHMMIYMYKKAGNYEKARKVF--SSMVGKGVPQSTVT 284

Arabidopsis thaliana (taxid: 3702)

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

 Score = 54.7 bits (130), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/188 (23%), Positives = 83/188 (44%), Gaps = 7/188 (3%)

Query: 272 GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELG---KNPDKYMLVMTLLDELGQR 328
           G+   G +  A+ L+   +  G   + + Y  LI  L    K  D+ M V   ++  G  
Sbjct: 280 GYAHAGKMADAYDLMNDMRKRGFEPNVNCYTVLIQALCRTEKRMDEAMRVFVEMERYGCE 339

Query: 329 DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCRE 388
            D+       +   K G+  + + V++ +       G  P+ V Y  ++ +   +++  E
Sbjct: 340 ADIVTYTALISGFCKWGMIDKGYSVLDDM----RKKGVMPSQVTYMQIMVAHEKKEQFEE 395

Query: 389 ALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR 448
            L ++  M+   C  DL  Y VVI+L   L ++  A+R +++++  G  P  D +  MI 
Sbjct: 396 CLELIEKMKRRGCHPDLLIYNVVIRLACKLGEVKEAVRLWNEMEANGLSPGVDTFVIMIN 455

Query: 449 IFMASGRL 456
            F + G L
Sbjct: 456 GFTSQGFL 463

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WMY5|PP365_ARATH Pentatricopeptide repeat-containing protein At5g04810, chloroplastic OS=Arabidopsis thaliana GN=PPR4 PE=1 SV=1

 Score = 53.1 bits (126), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 51/198 (25%), Positives = 83/198 (41%), Gaps = 6/198 (3%)

Query: 272 GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGK--NPDKYMLVMTLLDELGQRD 329
           GF K G+ + A      AK   + L+ SIY K+I    +  N ++   ++  ++E G   
Sbjct: 388 GFSKAGHAEAADYWFDEAKRIHKTLNASIYGKIIYAHCQTCNMERAEALVREMEEEGIDA 447

Query: 330 DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREA 389
            + +          V    +K G+V  +F      G  PTVV Y  LI+      K  +A
Sbjct: 448 PIAIYHTMMDGYTMVAD--EKKGLV--VFKRLKECGFTPTVVTYGCLINLYTKVGKISKA 503

Query: 390 LTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRI 449
           L V   M+      +L  Y ++I  FV L D + A   F  + + G  P   +Y ++I  
Sbjct: 504 LEVSRVMKEEGVKHNLKTYSMMINGFVKLKDWANAFAVFEDMVKEGMKPDVILYNNIISA 563

Query: 450 FMASGRLAKCRDVCKEAE 467
           F   G + +     KE +
Sbjct: 564 FCGMGNMDRAIQTVKEMQ 581

May play a role in the plastid ribosome biogenesis.

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	493
224086056	475	predicted protein [Populus trichocarpa]	0.904	0.938	0.656	1e-180
255539244	469	pentatricopeptide repeat-containing prot	0.922	0.970	0.686	1e-175
356519741	478	PREDICTED: pentatricopeptide repeat-cont	0.937	0.966	0.621	1e-171
147814819	514	hypothetical protein VITISV_012024 [Viti	0.943	0.904	0.625	1e-171
356577063	480	PREDICTED: pentatricopeptide repeat-cont	0.943	0.968	0.607	1e-166
225457564	514	PREDICTED: pentatricopeptide repeat-cont	0.941	0.902	0.630	1e-166
42568870	486	pentatricopeptide repeat-containing prot	0.959	0.973	0.607	1e-162
297814426	486	pentatricopeptide repeat-containing prot	0.880	0.893	0.638	1e-161
449516830	489	PREDICTED: LOW QUALITY PROTEIN: pentatri	0.904	0.912	0.609	1e-154
449443604	489	PREDICTED: pentatricopeptide repeat-cont	0.904	0.912	0.609	1e-153

>gi|224086056|ref|XP_002307797.1| predicted protein [Populus trichocarpa] gi|222857246|gb|EEE94793.1| predicted protein [Populus trichocarpa]

 Score =  636 bits (1641), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 311/474 (65%), Positives = 375/474 (79%), Gaps = 28/474 (5%)

Query: 33  MAHSNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDPIKADSVEEQEA 92
           MAHS+ R       + K+PKN++ PRR+KLPPDFGVNLFLKKP       + DSV++   
Sbjct: 1   MAHSSTR-----ICYRKIPKNIRYPRRSKLPPDFGVNLFLKKP-------QTDSVQDHSD 48

Query: 93  D--------------NDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPL 138
           D               + +WESEE+EAISSLF+GRIPQKPG+L RERPLPLP+P++LRPL
Sbjct: 49  DLTEEEEEEEIEVNNGEIVWESEEIEAISSLFRGRIPQKPGKLGRERPLPLPVPYKLRPL 108

Query: 139 ELPTPKKRVC--LASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRK 196
            LP PKK V   ++ SRASI  Q+YKNPSFLI LA++IK L   +DV+ VLD C R+L K
Sbjct: 109 GLPAPKKHVNKQVSLSRASISSQIYKNPSFLIGLAKEIKRLSPDQDVSVVLDNCSRYLHK 168

Query: 197 GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLEN 256
           GSLS T+RELGH+ LPERALQTFCW QKQP LFPDDR+LASTVEVLAR+H+LKVPF LE 
Sbjct: 169 GSLSLTIRELGHLGLPERALQTFCWVQKQPRLFPDDRVLASTVEVLARNHDLKVPFNLEK 228

Query: 257 FVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYM 316
           F +LAS+ V+EA  KG ++GG+LKL+WKL+ VAKDG RMLDPS+YAK+ILELGKNPDK++
Sbjct: 229 FTNLASRRVIEAMVKGLIRGGSLKLSWKLISVAKDGKRMLDPSVYAKIILELGKNPDKHV 288

Query: 317 LVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTL 376
           L   LLDEL +R+DLNLSQQDCTA+MKV I+L KF  VESLF+WF  SG +P+VVMYTTL
Sbjct: 289 LAEALLDELAEREDLNLSQQDCTAVMKVCIKLGKFEAVESLFNWFRQSGHEPSVVMYTTL 348

Query: 377 IHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGF 436
           IHSR SE K REAL VVW ME S+CLFDL AYRVVIKLFVALND+ RA+RYFSKLKEAG 
Sbjct: 349 IHSRYSESKYREALAVVWEMEGSDCLFDLTAYRVVIKLFVALNDLPRAVRYFSKLKEAGL 408

Query: 437 CPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRI 490
            PTYDIYR++I ++M SGRLAKC++V KEAEMAGFK  K+    LLQ+++E+R+
Sbjct: 409 SPTYDIYRNLITLYMVSGRLAKCKEVWKEAEMAGFKFSKEMAAGLLQLKRETRL 462

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539244|ref|XP_002510687.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223551388|gb|EEF52874.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  620 bits (1600), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 324/472 (68%), Positives = 376/472 (79%), Gaps = 17/472 (3%)

Query: 33  MAHSNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDPIKADSV----- 87
           M+HSN +    T    KLPKNLQ+PRR+KLPPDFGVNLFLKKP+   DP + DS      
Sbjct: 1   MSHSNTK----TYYRKKLPKNLQSPRRSKLPPDFGVNLFLKKPTTGVDPFQMDSFLVDDG 56

Query: 88  ------EEQEADNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELP 141
                 EE+E + D +WES+E+EAISSLFQGRIPQ+PG L RERPLPLPLPH+LRPL  P
Sbjct: 57  DGDLNQEEKEQNGDIVWESDEIEAISSLFQGRIPQRPGNLNRERPLPLPLPHKLRPLGPP 116

Query: 142 TPKK--RVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSL 199
           +PKK  R  + S R+ IC +VYKNPSFLISLA+ IK L+   DV+ VLD C RFLRKGSL
Sbjct: 117 SPKKHNRNVVVSLRSPICNKVYKNPSFLISLAKQIKCLNPDDDVSAVLDDCARFLRKGSL 176

Query: 200 SFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS 259
           S T+RELGHM  P+RALQTFCWAQKQP L+PDDR+LASTVE+LAR+ +LKVP   + F S
Sbjct: 177 SLTIRELGHMGFPDRALQTFCWAQKQPQLYPDDRILASTVEILARNQDLKVPIDWQKFTS 236

Query: 260 LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVM 319
           LAS+GV+EA  +GF+KGG LKLAWKLL VAK   RMLD S+YA+LILELGKNPDKYMLV 
Sbjct: 237 LASRGVIEAMIRGFLKGGRLKLAWKLLAVAKHDKRMLDASLYARLILELGKNPDKYMLVE 296

Query: 320 TLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHS 379
            LLDELG+R+DLNLS QDCTAIMKV IRLQKF  VE LF WF  SG +P+VVMYTTLIHS
Sbjct: 297 QLLDELGEREDLNLSHQDCTAIMKVCIRLQKFEFVECLFTWFKQSGHEPSVVMYTTLIHS 356

Query: 380 RLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPT 439
           R SEKK REAL  VW ME S+ LFDLPAYRVVIKLFVALND+ RA+RYFSKLKEAG  PT
Sbjct: 357 RYSEKKYREALAGVWEMEGSSFLFDLPAYRVVIKLFVALNDLPRAVRYFSKLKEAGLSPT 416

Query: 440 YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKESRIG 491
           YDIYR++I+I++ SGRLAKC+++ KEAEMAGFKLD+Q  ++LL  EKE R G
Sbjct: 417 YDIYRNLIKIYLVSGRLAKCKEIWKEAEMAGFKLDEQIKMDLLHQEKEIRSG 468

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356519741|ref|XP_003528528.1| PREDICTED: pentatricopeptide repeat-containing protein At2g01860-like [Glycine max]

 Score =  607 bits (1564), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 305/491 (62%), Positives = 375/491 (76%), Gaps = 29/491 (5%)

Query: 1   MNCTLSYMSLHPVVLSNRIFPISKN--NNITTTLMAHSNQRRRPTTTRHPKLPKNLQNPR 58
           M+CT+S+  +H V       P+ +   N    T++AHS +RR P   R+   PK      
Sbjct: 1   MDCTVSFPCVHFV-------PVGRTLCNYRRVTVVAHSKRRRPPKDNRYRPRPKQ----- 48

Query: 59  RTKLPPDFGVNLFLKKPSDEYDPIKAD------SVEEQEADNDFIWESEELEAISSLFQG 112
               PP+FGVNLFLKKPS    P   D      + EE++ +   +WES+ELEAISSLFQG
Sbjct: 49  ----PPEFGVNLFLKKPSTASKPTDDDMDSNEENDEEEDGNIGVVWESDELEAISSLFQG 104

Query: 113 RIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRV-----CLASSRASICKQVYKNPSFL 167
           RIPQKPG+L RERPLPLP+P +LRPL LPTPK +V      + SSRAS+ K+VYK+PSFL
Sbjct: 105 RIPQKPGKLDRERPLPLPVPFKLRPLRLPTPKTQVKLTAPAVVSSRASMAKKVYKSPSFL 164

Query: 168 ISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPH 227
           + LAR I  L    DV+++L K  +FLRKGSLS T+RELGHM  PERALQTF WAQ QPH
Sbjct: 165 VGLARQISRLGPDADVSKILGKWVQFLRKGSLSLTIRELGHMGFPERALQTFLWAQNQPH 224

Query: 228 LFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLM 287
           LFPDD +LASTVEVLAR+HEL++PF L  +  LAS+ VLEA  KGF+KGGNL+ AWK+L+
Sbjct: 225 LFPDDWILASTVEVLARNHELRIPFNLGQYTGLASRAVLEAMIKGFIKGGNLRFAWKVLI 284

Query: 288 VAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR 347
           VA+   RMLD SIYAKLILELGKNPD++  V+ LLDELG+RD+LNLSQQDCTAIMKV ++
Sbjct: 285 VARRDKRMLDSSIYAKLILELGKNPDRHRHVLPLLDELGERDELNLSQQDCTAIMKVCVK 344

Query: 348 LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPA 407
           + KF VVESLF WF  SG  P++VM+T++IHSR +EKK REAL VVW MEASNCLFDLPA
Sbjct: 345 MGKFEVVESLFSWFKQSGYQPSIVMFTSVIHSRYTEKKYREALAVVWEMEASNCLFDLPA 404

Query: 408 YRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE 467
           YRVVIKLFVALND+SRA RYFSKLKEAGF P++ +Y+DM++I+MASGR+AKC+++C+EAE
Sbjct: 405 YRVVIKLFVALNDLSRATRYFSKLKEAGFSPSFGLYKDMLQIYMASGRIAKCKELCREAE 464

Query: 468 MAGFKLDKQTV 478
           +AGFKLDK  V
Sbjct: 465 IAGFKLDKYLV 475

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147814819|emb|CAN74746.1| hypothetical protein VITISV_012024 [Vitis vinifera]

 Score =  606 bits (1563), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 307/491 (62%), Positives = 369/491 (75%), Gaps = 26/491 (5%)

Query: 20  FPISKNNNITTTLMAHSNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEY 79
           F +  +N     L    N R       H K  KNL +PRR KLPP+  ++ FLK  +   
Sbjct: 29  FVVEFSNKNEIKLGVQCNAR-----VNHRKPTKNLPHPRRAKLPPEPEISTFLKGGNSGT 83

Query: 80  DPIKADSVEEQEAD----------------NDFIWESEELEAISSLFQGRIPQKPGRLYR 123
           +  +  +V ++E D                 + +W+S+E+EAISSLF GRIPQKPG+L R
Sbjct: 84  EQSEMGTVLDKELDPNDDGFLVDGIEGRKEGEIVWDSDEIEAISSLFMGRIPQKPGKLNR 143

Query: 124 ERPLPLPLPHRLRPLELPTPKKRVCLASS-----RASICKQVYKNPSFLISLARDIKGLD 178
           ERPLPLPLP+++RP+ LPT K+ V  ASS     RAS+ KQVYKNP FLIS+AR+I+ L 
Sbjct: 144 ERPLPLPLPYKIRPMGLPTTKRHVRAASSMPYASRASLSKQVYKNPDFLISIAREIRNLP 203

Query: 179 SHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLAST 238
              DV+ VL+K  RFLRKGSLS T+RELGHM LPERALQTF WAQKQP LFPDDR+LAST
Sbjct: 204 LEDDVSPVLNKWVRFLRKGSLSLTIRELGHMGLPERALQTFFWAQKQPQLFPDDRILAST 263

Query: 239 VEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP 298
           VEVLAR H+LKVPF LE F  LA++ V+EA A+GF++ G+L LAWKLL+VAKD  RML P
Sbjct: 264 VEVLARTHKLKVPFSLEKFTGLATRSVIEALARGFIRRGSLSLAWKLLLVAKDSKRMLGP 323

Query: 299 SIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLF 358
           SIYAKLI ELGKNPDK+ LV  LLDELG+R+DL LS QDCTA+MKV IRL KF +VESLF
Sbjct: 324 SIYAKLIFELGKNPDKHSLVQALLDELGEREDLKLSHQDCTAVMKVCIRLGKFEIVESLF 383

Query: 359 HWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL 418
           +W+  S   P+VVMYTTLIHSR +EKK REAL VVW MEAS+CLFDLPAYRVVIKLF+AL
Sbjct: 384 NWYKQSENSPSVVMYTTLIHSRYTEKKYREALAVVWEMEASDCLFDLPAYRVVIKLFIAL 443

Query: 419 NDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTV 478
           ND+SR  RYFSKLKEAGF PTYDIYRDM++I+M   RLAKCR+VCKE EM+GFKLDK T+
Sbjct: 444 NDLSRTGRYFSKLKEAGFSPTYDIYRDMLKIYMVFRRLAKCREVCKELEMSGFKLDKGTL 503

Query: 479 VELLQIEKESR 489
            +LLQ+E+E+R
Sbjct: 504 SQLLQLERENR 514

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356577063|ref|XP_003556649.1| PREDICTED: pentatricopeptide repeat-containing protein At2g01860-like [Glycine max]

 Score =  592 bits (1527), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 300/494 (60%), Positives = 374/494 (75%), Gaps = 29/494 (5%)

Query: 1   MNCTLSYMSLHPVVLSNRIFPISKN--NNITTTLMAHSNQRRRPTTTRHPKLPKNLQNPR 58
           M+CT+S+  +H         P+ +   N    TL+AHS +R+     R+   PK      
Sbjct: 1   MDCTVSFPCVH-------FIPVGRTLCNYSRVTLVAHSKRRKPSKDNRYRPRPKQ----- 48

Query: 59  RTKLPPDFGVNLFLKKPSDEYDPIKAD------SVEEQEADNDFIWESEELEAISSLFQG 112
               PP+FGVNLFLKKPS    P + D      + EE++ +   +WES+ELEAISSLFQG
Sbjct: 49  ----PPEFGVNLFLKKPSTTSKPTEDDMDSNEENDEEEDGNIGVVWESDELEAISSLFQG 104

Query: 113 RIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRV-----CLASSRASICKQVYKNPSFL 167
           RIPQKPG+L RERPLPLP+P++LRPL LPTPK +V      + SSRAS+ K+VYK+P FL
Sbjct: 105 RIPQKPGKLDRERPLPLPVPYKLRPLGLPTPKTQVKLTAPAVVSSRASMAKKVYKSPRFL 164

Query: 168 ISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPH 227
           + LAR+I  L   +DV+++L K  +FLRKGSLS T+RELGHM  PERALQTF WAQ QPH
Sbjct: 165 VGLAREISRLGPDEDVSKILGKWVQFLRKGSLSLTIRELGHMGFPERALQTFLWAQNQPH 224

Query: 228 LFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLM 287
           LFPDD +LASTVEVLAR+HEL++PF L  +  LAS+ VLEA  KGF+KGGNL+LAWK+L+
Sbjct: 225 LFPDDWILASTVEVLARNHELRIPFNLNQYTGLASRVVLEAMIKGFIKGGNLRLAWKVLI 284

Query: 288 VAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR 347
           VA+   RMLD SIYAKLILELGKNPD++  V+ LLDEL +RD+LNLSQQDCTAIMKV ++
Sbjct: 285 VARRDKRMLDSSIYAKLILELGKNPDRHRHVLPLLDELAERDELNLSQQDCTAIMKVCVK 344

Query: 348 LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPA 407
           + KF VVE LF WF  SG   +VVM+T++IHSR +EKK REAL VVW ME+S+CLFDLPA
Sbjct: 345 MGKFEVVECLFSWFKQSGYHTSVVMFTSVIHSRYTEKKYREALAVVWEMESSSCLFDLPA 404

Query: 408 YRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE 467
           Y VVIKLFVALND+SRA RYFSKLKEAGF P++ +Y+DM+ I+MASGR+AKC+++CKEAE
Sbjct: 405 YCVVIKLFVALNDLSRATRYFSKLKEAGFSPSFGLYKDMLHIYMASGRIAKCKELCKEAE 464

Query: 468 MAGFKLDKQTVVEL 481
           M+GFKLDK  V +L
Sbjct: 465 MSGFKLDKYLVSQL 478

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457564|ref|XP_002272601.1| PREDICTED: pentatricopeptide repeat-containing protein At2g01860-like [Vitis vinifera]

 Score =  589 bits (1519), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/492 (63%), Positives = 369/492 (75%), Gaps = 28/492 (5%)

Query: 20  FPISKNNNITTTLMAHSNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLK------ 73
           F +  +N     L    N R       H K  KNL +PRR KLPP+  ++ FLK      
Sbjct: 29  FVVEFSNKNEIKLGVQCNAR-----VNHRKPTKNLPHPRRAKLPPEPEISTFLKGGNSGT 83

Query: 74  -----------KPSDEYDPIKADSVEEQEADNDFIWESEELEAISSLFQGRIPQKPGRLY 122
                      +P    D    D +E ++ + + +W+S+E+EAISSLF GRIPQKPG+L 
Sbjct: 84  EQSEMGTVLDKEPDANDDGFLVDGIEGRK-EGEIVWDSDEIEAISSLFMGRIPQKPGKLN 142

Query: 123 RERPLPLPLPHRLRPLELPTPKKRVCLASS-----RASICKQVYKNPSFLISLARDIKGL 177
           RERPLPLPLP++LRP+ LPT K+ V  ASS     RAS+ KQVYKNP FLIS+AR+I+ L
Sbjct: 143 RERPLPLPLPYKLRPMGLPTTKRHVRAASSMPYASRASLSKQVYKNPDFLISIAREIRKL 202

Query: 178 DSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLAS 237
               DV+ VL+K  RFLRKGSLS T+RELGHM LPERALQTF WAQKQP LFPDDR+LAS
Sbjct: 203 PLEDDVSPVLNKWVRFLRKGSLSLTIRELGHMGLPERALQTFFWAQKQPQLFPDDRILAS 262

Query: 238 TVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD 297
           TVEVLAR H+LKVPF LE F  LAS+ V+EA A+GF++ G+L LAWKLL+VAKD  RML 
Sbjct: 263 TVEVLARTHKLKVPFSLEKFTGLASRSVIEALARGFIRRGSLSLAWKLLLVAKDSKRMLG 322

Query: 298 PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL 357
           PSIYAKLI ELGKNPDK+ LV  LLDELG+R+DL LS QDCTA+MKV IRL KF +VESL
Sbjct: 323 PSIYAKLIFELGKNPDKHSLVQALLDELGEREDLKLSHQDCTAVMKVCIRLGKFEIVESL 382

Query: 358 FHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA 417
           F+W+  S   P+VVMYTTLIHSR +EKK REAL VVW MEAS+C+FDLPAYRVVIKLF+A
Sbjct: 383 FNWYKQSENSPSVVMYTTLIHSRYTEKKYREALAVVWEMEASDCVFDLPAYRVVIKLFIA 442

Query: 418 LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQT 477
           LND+SR  RYFSKLKEAGF PTYDIYRDM++I+M   RLAKCR+VCKE EM+GFKLDK T
Sbjct: 443 LNDLSRTGRYFSKLKEAGFSPTYDIYRDMLKIYMVFRRLAKCREVCKELEMSGFKLDKGT 502

Query: 478 VVELLQIEKESR 489
           + +LLQ+EKE+R
Sbjct: 503 LSQLLQLEKENR 514

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42568870|ref|NP_178295.2| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75110949|sp|Q5XET4.1|PP142_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At2g01860; AltName: Full=Protein EMBRYO DEFECTIVE 975 gi|53850483|gb|AAU95418.1| At2g01860 [Arabidopsis thaliana] gi|55733739|gb|AAV59266.1| At2g01860 [Arabidopsis thaliana] gi|110738080|dbj|BAF00974.1| hypothetical protein [Arabidopsis thaliana] gi|330250415|gb|AEC05509.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  577 bits (1488), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 297/489 (60%), Positives = 372/489 (76%), Gaps = 16/489 (3%)

Query: 8   MSLH-PVVLSNRIFPISKNNNITTTLMAHSNQRRRPTTTRH--PKLPKNLQNPRRTKLPP 64
           M LH PV LS     +S + N+ T+ + +    R   + R+   KL KNL+NPRRTKLPP
Sbjct: 1   MILHCPVSLS-----LSFHLNLRTSRIGNIGVTRVNASQRNHSKKLTKNLRNPRRTKLPP 55

Query: 65  DFGVNLFLKKPSDEYDPIKADSVEEQEADND----FIWESEELEAISSLFQGRIPQKPGR 120
           DFGVNLFL+KP  E   I  D  + QE+ ND     +WE EE+EAISSLFQ RIPQKP +
Sbjct: 56  DFGVNLFLRKPKIEPLVIDDDDEQVQESVNDDDDAVVWEPEEIEAISSLFQKRIPQKPDK 115

Query: 121 LYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVYKNPSFLISLARDIKGL-DS 179
             R RPLPLP PH+LRPL LPTPKK +  + + +S+ KQVYK+PSFLI LAR+IK L  S
Sbjct: 116 PSRVRPLPLPQPHKLRPLGLPTPKKNIIRSPALSSVSKQVYKDPSFLIGLAREIKSLPSS 175

Query: 180 HKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTV 239
             DV+ VL+K   FLRKGSLS T+RELGHM LPERALQT+ WA+K  HL PD+R+LAST+
Sbjct: 176 DADVSLVLNKWVSFLRKGSLSTTIRELGHMGLPERALQTYHWAEKHSHLVPDNRILASTI 235

Query: 240 EVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS 299
           +VLA+HHELK+  K +N  SLASK V+EA  KG ++GG L LA KL++++K   R+LD S
Sbjct: 236 QVLAKHHELKL-LKFDN--SLASKNVIEAMIKGCIEGGWLNLARKLILISKSNNRILDSS 292

Query: 300 IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFH 359
           +Y K+ILE+ KNPDKY LV+ LL+EL +R+DL LSQQDCT+IMK+ ++L +F +VESLF 
Sbjct: 293 VYVKMILEIAKNPDKYHLVVALLEELKKREDLKLSQQDCTSIMKICVKLGEFELVESLFD 352

Query: 360 WFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN 419
           WF  S R+P+VVMYTT+IHSR SE+K REA++VVW ME SNCL DLPAYRVVIKLFVAL+
Sbjct: 353 WFKASNREPSVVMYTTMIHSRYSEQKYREAMSVVWEMEESNCLLDLPAYRVVIKLFVALD 412

Query: 420 DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVV 479
           D+ RA+RY+SKLKEAGF PTYDIYRDMI ++ ASGRL KC+++CKE E AG +LDK T  
Sbjct: 413 DLGRAMRYYSKLKEAGFSPTYDIYRDMISVYTASGRLTKCKEICKEVEDAGLRLDKDTSF 472

Query: 480 ELLQIEKES 488
            LLQ+EK++
Sbjct: 473 RLLQLEKQT 481

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297814426|ref|XP_002875096.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297320934|gb|EFH51355.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  574 bits (1480), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 286/448 (63%), Positives = 356/448 (79%), Gaps = 14/448 (3%)

Query: 49  KLPKNLQNPRRTKLPPDFGVNLFLKKPS-----DEYDPIKADSVEEQEA--DNDFIWESE 101
           KL KNL+NPR TKLPPDFGVNLFL+KP      D+YD    + V++QE+  D+  +WE E
Sbjct: 40  KLTKNLRNPRLTKLPPDFGVNLFLRKPKIEPVVDDYD--ADNDVQDQESVDDDAVVWEPE 97

Query: 102 ELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVY 161
           E+EAISSLFQ RIPQKPG+  R RPLPLP PH+LRPL LPTPKK +  +++ +S+ KQVY
Sbjct: 98  EIEAISSLFQKRIPQKPGKPIRVRPLPLPQPHKLRPLGLPTPKKNI-RSAALSSVSKQVY 156

Query: 162 KNPSFLISLARDIKGL-DSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFC 220
           K+PSFLI LAR+IK L  S  DV+ VL+K   FLRKGSLS T+RELGHM LPERALQT+ 
Sbjct: 157 KDPSFLIGLAREIKSLPSSDADVSLVLNKWVSFLRKGSLSMTIRELGHMGLPERALQTYH 216

Query: 221 WAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLK 280
           WA+K  HL PD+R+LAST++VLA+HHELK+  K +N  SLASK V+EA  KG ++GG L 
Sbjct: 217 WAEKHSHLVPDNRILASTIQVLAKHHELKL-LKFDN--SLASKNVIEAMIKGCIEGGWLN 273

Query: 281 LAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTA 340
           LA KL++++K   R+LD S+Y K+ILE+ KNPDKY LV+TLL+EL +R+DL LSQQDCT 
Sbjct: 274 LARKLILISKSNNRILDSSVYVKMILEIAKNPDKYHLVVTLLEELKEREDLRLSQQDCTG 333

Query: 341 IMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN 400
           IMK+ ++L +F +VESLF WF  S R+P+VVMYTT+IHSR SE+K REA+ VVW ME SN
Sbjct: 334 IMKICVKLGEFELVESLFDWFKESNREPSVVMYTTMIHSRYSEQKYREAMNVVWEMEESN 393

Query: 401 CLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCR 460
           CL DLPAYRVVIKLFVAL+D+ RA+RY+SKLKEAGF PTYDIYRDMI ++ ASGRL KC+
Sbjct: 394 CLLDLPAYRVVIKLFVALDDLGRAMRYYSKLKEAGFLPTYDIYRDMINVYTASGRLTKCK 453

Query: 461 DVCKEAEMAGFKLDKQTVVELLQIEKES 488
           ++CKE E AG +LDK T   LLQ+EK++
Sbjct: 454 EICKEVEDAGLRLDKDTSFRLLQLEKQT 481

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449516830|ref|XP_004165449.1| PREDICTED: LOW QUALITY PROTEIN: pentatricopeptide repeat-containing protein At2g01860-like [Cucumis sativus]

 Score =  550 bits (1416), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 287/471 (60%), Positives = 353/471 (74%), Gaps = 25/471 (5%)

Query: 33  MAH--SNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDP--------- 81
           M H  +N RRRP        PKNL  PRR KLPP+  VN F    +    P         
Sbjct: 27  MVHFKANSRRRP--------PKNLLCPRRAKLPPNPAVNQFFNNKTSAPSPPFTDLISSK 78

Query: 82  IKADSVEEQEA-----DNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLR 136
           I  D  EE  A     D D +W+S+E+EAISSLFQGRIPQKPG+L RERPLPLPLPH+LR
Sbjct: 79  IFQDEHEEIHAHDYTKDTDVVWDSDEIEAISSLFQGRIPQKPGKLNRERPLPLPLPHKLR 138

Query: 137 PLELPTPKKR-VCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLR 195
           P  LP PK R   + SSRA + KQVYK P FLI LAR+I+ L   ++V++VL++ G FL+
Sbjct: 139 PPRLPNPKIRPTTVVSSRALLSKQVYKRPDFLIGLAREIRDLSPEENVSKVLNRWGPFLQ 198

Query: 196 KGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLE 255
           KGSLS T++ELGHM LP+RAL TFCWAQ+Q  LFPDDR+LASTVEVL+R+HELKVP  LE
Sbjct: 199 KGSLSLTIKELGHMGLPDRALNTFCWAQEQHRLFPDDRVLASTVEVLSRNHELKVPVNLE 258

Query: 256 NFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKY 315
            F  LAS+GVLEA  +GF++GG+L LAWKLL+ AK G RMLDPS+Y KLILELGKNPDK 
Sbjct: 259 EFTKLASRGVLEAMMRGFIRGGSLNLAWKLLVAAKKGKRMLDPSVYVKLILELGKNPDKN 318

Query: 316 MLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTT 375
           MLV+TLL+ELGQR+ L L+QQDCT I+KV  RL KF + E L+ W+  SG +P++V+YT 
Sbjct: 319 MLVLTLLEELGQREALKLNQQDCTTIVKVCTRLGKFEIAEKLYSWYVESGHEPSIVIYTA 378

Query: 376 LIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG 435
           L+HSR S++K REAL++VW ME+ NC FDLPAY VVIKLFVAL D+SRA+RYF+KLKEAG
Sbjct: 379 LVHSRYSDRKYREALSLVWEMESGNCPFDLPAYSVVIKLFVALGDLSRAVRYFAKLKEAG 438

Query: 436 FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEK 486
           F PTY++YR+MI I++ SGRLAKC+++ KEAE AGF +DKQ    LLQ ++
Sbjct: 439 FSPTYNVYRNMITIYLVSGRLAKCKEIYKEAENAGFMMDKQITSMLLQAKR 489

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443604|ref|XP_004139567.1| PREDICTED: pentatricopeptide repeat-containing protein At2g01860-like [Cucumis sativus]

 Score =  548 bits (1413), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 287/471 (60%), Positives = 352/471 (74%), Gaps = 25/471 (5%)

Query: 33  MAH--SNQRRRPTTTRHPKLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDP--------- 81
           M H  +N RRRP        PKNL  PRR KLPP+  VN F    +    P         
Sbjct: 27  MVHFKANSRRRP--------PKNLLCPRRAKLPPNPAVNQFFNNKTSAPSPPFTDLISSK 78

Query: 82  IKADSVEEQEA-----DNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLR 136
           I  D  EE  A     D D +W+S+E+EAISSLFQGRIPQKPG+L RERPLPLPLPH+LR
Sbjct: 79  IFQDEHEEIHAHDYTKDTDVVWDSDEIEAISSLFQGRIPQKPGKLNRERPLPLPLPHKLR 138

Query: 137 PLELPTPKKR-VCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLR 195
           P  LP PK R   + SSRA + KQVYK P FLI LAR+I+ L   ++V++VL++ G FL+
Sbjct: 139 PPRLPNPKIRPTTVVSSRALLSKQVYKRPDFLIGLAREIRDLSPEENVSKVLNRWGPFLQ 198

Query: 196 KGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLE 255
           KGSLS T++ELGHM LP+RAL TFCWAQ+Q  LFPDDR+LASTVEVL+R+HELKV   LE
Sbjct: 199 KGSLSLTIKELGHMGLPDRALNTFCWAQEQHRLFPDDRVLASTVEVLSRNHELKVAVNLE 258

Query: 256 NFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKY 315
            F  LAS+GVLEA  +GF++GG+L LAWKLL+ AK G RMLDPS+Y KLILELGKNPDK 
Sbjct: 259 EFTKLASRGVLEAMMRGFIRGGSLNLAWKLLVAAKKGKRMLDPSVYVKLILELGKNPDKN 318

Query: 316 MLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTT 375
           MLV+TLL+ELGQR+ L L+QQDCT I+KV  RL KF + E L+ W+  SG +P++VMYT 
Sbjct: 319 MLVLTLLEELGQREALKLNQQDCTTIVKVCTRLGKFEIAEKLYSWYVESGHEPSIVMYTA 378

Query: 376 LIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG 435
           L+HSR S++K REAL++VW ME+ NC FDLPAY VVIKLFVAL D+SRA+RYF+KLKEAG
Sbjct: 379 LVHSRYSDRKYREALSLVWEMESGNCPFDLPAYSVVIKLFVALGDLSRAVRYFAKLKEAG 438

Query: 436 FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEK 486
           F PTY++YR+MI I++ SGRLAKC+++ KEAE AGF +DKQ    LLQ ++
Sbjct: 439 FSPTYNVYRNMITIYLVSGRLAKCKEIYKEAENAGFMMDKQITSMLLQAKR 489

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	493
TAIR|locus:2059733	486	EMB975 "AT2G01860" [Arabidopsi	0.959	0.973	0.574	4.6e-137
TAIR|locus:2056078	867	LOJ "LATERAL ORGAN JUNCTION" [	0.436	0.247	0.246	1.1e-07
TAIR|locus:2093472	642	AT3G16010 [Arabidopsis thalian	0.423	0.325	0.241	3.4e-07
TAIR|locus:2096099	599	AT3G62470 "AT3G62470" [Arabido	0.649	0.534	0.2	1.3e-06
TAIR|locus:2178037	678	AT5G39980 [Arabidopsis thalian	0.415	0.302	0.270	2.1e-06
TAIR|locus:2185455	598	AT5G14820 "AT5G14820" [Arabido	0.665	0.548	0.202	2.2e-06
TAIR|locus:2206385	836	EMB2217 "embryo defective 2217	0.657	0.387	0.217	2.7e-06
TAIR|locus:2095309	687	AT3G09060 "AT3G09060" [Arabido	0.427	0.307	0.273	3.5e-06
TAIR|locus:2096074	599	AT3G62540 "AT3G62540" [Arabido	0.665	0.547	0.199	1.7e-05
TAIR|locus:2027166	862	PTAC2 "plastid transcriptional	0.667	0.381	0.210	2.1e-05

TAIR|locus:2059733 EMB975 "AT2G01860" [Arabidopsis thaliana (taxid:3702)]

 Score = 1342 (477.5 bits), Expect = 4.6e-137, P = 4.6e-137
 Identities = 281/489 (57%), Positives = 354/489 (72%)

Query:     8 MSLH-PVVLSNRIFPISKNNNITTTLMAHSNQRRRPTTTRH--PKLPKNLQNPRRTKLPP 64
             M LH PV LS     +S + N+ T+ + +    R   + R+   KL KNL+NPRRTKLPP
Sbjct:     1 MILHCPVSLS-----LSFHLNLRTSRIGNIGVTRVNASQRNHSKKLTKNLRNPRRTKLPP 55

Query:    65 DFGVNLFLKKPSDEYDPIKADSVEEQEADND----FIWESEELEAISSLFQGRIPQKXXX 120
             DFGVNLFL+KP  E   I  D  + QE+ ND     +WE EE+EAISSLFQ RIPQK   
Sbjct:    56 DFGVNLFLRKPKIEPLVIDDDDEQVQESVNDDDDAVVWEPEEIEAISSLFQKRIPQKPDK 115

Query:   121 XXXXXXXXXXXXXXXXXXXXXTPKKRVCLASSRASICKQVYKNPSFLISLARDIKGL-DS 179
                                  TPKK +  + + +S+ KQVYK+PSFLI LAR+IK L  S
Sbjct:   116 PSRVRPLPLPQPHKLRPLGLPTPKKNIIRSPALSSVSKQVYKDPSFLIGLAREIKSLPSS 175

Query:   180 HKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTV 239
               DV+ VL+K   FLRKGSLS T+RELGHM LPERALQT+ WA+K  HL PD+R+LAST+
Sbjct:   176 DADVSLVLNKWVSFLRKGSLSTTIRELGHMGLPERALQTYHWAEKHSHLVPDNRILASTI 235

Query:   240 EVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS 299
             +VLA+HHELK+  K +N  SLASK V+EA  KG ++GG L LA KL++++K   R+LD S
Sbjct:   236 QVLAKHHELKL-LKFDN--SLASKNVIEAMIKGCIEGGWLNLARKLILISKSNNRILDSS 292

Query:   300 IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFH 359
             +Y K+ILE+ KNPDKY LV+ LL+EL +R+DL LSQQDCT+IMK+ ++L +F +VESLF 
Sbjct:   293 VYVKMILEIAKNPDKYHLVVALLEELKKREDLKLSQQDCTSIMKICVKLGEFELVESLFD 352

Query:   360 WFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN 419
             WF  S R+P+VVMYTT+IHSR SE+K REA++VVW ME SNCL DLPAYRVVIKLFVAL+
Sbjct:   353 WFKASNREPSVVMYTTMIHSRYSEQKYREAMSVVWEMEESNCLLDLPAYRVVIKLFVALD 412

Query:   420 DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVV 479
             D+ RA+RY+SKLKEAGF PTYDIYRDMI ++ ASGRL KC+++CKE E AG +LDK T  
Sbjct:   413 DLGRAMRYYSKLKEAGFSPTYDIYRDMISVYTASGRLTKCKEICKEVEDAGLRLDKDTSF 472

Query:   480 ELLQIEKES 488
              LLQ+EK++
Sbjct:   473 RLLQLEKQT 481

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2056078 LOJ "LATERAL ORGAN JUNCTION" [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 1.1e-07, P = 1.1e-07
 Identities = 55/223 (24%), Positives = 93/223 (41%)

Query:   272 GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDL 331
             GF K  + + AW ++          +  IY  +I  L K   +      +L  L +    
Sbjct:   528 GFFKNKDEQNAWDVINQMNASNFEANEVIYNTIINGLCK-VGQTSKAKEMLQNLIKEKRY 586

Query:   332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWF---THSGRDPTVVMYTTLIHSRLSEKKCRE 388
             ++S   CT+   +     K G  +S    +   + +G+ P VV +T+LI+      +   
Sbjct:   587 SMS---CTSYNSIIDGFVKVGDTDSAVETYREMSENGKSPNVVTFTSLINGFCKSNRMDL 643

Query:   389 ALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR 448
             AL +   M++     DLPAY  +I  F   ND+  A   FS+L E G  P   +Y  +I 
Sbjct:   644 ALEMTHEMKSMELKLDLPAYGALIDGFCKKNDMKTAYTLFSELPELGLMPNVSVYNSLIS 703

Query:   449 IFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ-IEKESRI 490
              F   G++    D+ K+    G   D  T   ++  + K+  I
Sbjct:   704 GFRNLGKMDAAIDLYKKMVNDGISCDLFTYTTMIDGLLKDGNI 746

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2093472 AT3G16010 [Arabidopsis thaliana (taxid:3702)]

 Score = 158 (60.7 bits), Expect = 3.4e-07, Sum P(3) = 3.4e-07
 Identities = 51/211 (24%), Positives = 88/211 (41%)

Query:   272 GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDL 331
             G+ K   ++ A  LL    + G    P+ Y  LI  LGK   +Y     L  EL +    
Sbjct:   418 GYCKTNRVEKALLLLEEMDEKGFPPCPAAYCSLINALGK-AKRYEAANELFKELKENFG- 475

Query:   332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALT 391
             N+S +    ++K   +  K      LF+   + G  P V  Y  L+   +      EA +
Sbjct:   476 NVSSRVYAVMIKHFGKCGKLSEAVDLFNEMKNQGSGPDVYAYNALMSGMVKAGMINEANS 535

Query:   392 VVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFM 451
             ++  ME + C  D+ ++ +++  F       RAI  F  +K +G  P    Y  ++  F 
Sbjct:   536 LLRKMEENGCRADINSHNIILNGFARTGVPRRAIEMFETIKHSGIKPDGVTYNTLLGCFA 595

Query:   452 ASGRLAKCRDVCKEAEMAGFKLDKQTVVELL 482
              +G   +   + +E +  GF+ D  T   +L
Sbjct:   596 HAGMFEEAARMMREMKDKGFEYDAITYSSIL 626

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2096099 AT3G62470 "AT3G62470" [Arabidopsis thaliana (taxid:3702)]

 Score = 144 (55.7 bits), Expect = 1.3e-06, P = 1.3e-06
 Identities = 67/335 (20%), Positives = 136/335 (40%)

Query:   157 CKQVYKNPSFLISLARDIKGLDS-HKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERA 215
             C +   NP  +  + + I  L +  +++  VLD+    L    +   +    H   P  A
Sbjct:   121 CVESSTNPEEVERVCKVIDELFALDRNMEAVLDEMKLDLSHDLIVEVLERFRHARKP--A 178

Query:   216 LQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATA----- 270
              + FCWA ++     D R   S + +LA+  + +    +     + +KG+L         
Sbjct:   179 FRFFCWAAERQGFAHDSRTYNSMMSILAKTRQFETMVSV--LEEMGTKGLLTMETFTIAM 236

Query:   271 KGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNP-DKYMLVMTLLDELGQRD 329
             K F      K A  +  + K     +       L+  LG+    K   V  L D+L +R 
Sbjct:   237 KAFAAAKERKKAVGIFELMKKYKFKIGVETINCLLDSLGRAKLGKEAQV--LFDKLKERF 294

Query:   330 DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREA 389
               N+     T ++    R++       +++     G  P +V +  ++   L  +K  +A
Sbjct:   295 TPNMMTY--TVLLNGWCRVRNLIEAARIWNDMIDQGLKPDIVAHNVMLEGLLRSRKKSDA 352

Query:   390 LTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRI 449
             + +   M++     ++ +Y ++I+ F   + +  AI YF  + ++G  P   +Y  +I  
Sbjct:   353 IKLFHVMKSKGPCPNVRSYTIMIRDFCKQSSMETAIEYFDDMVDSGLQPDAAVYTCLITG 412

Query:   450 FMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI 484
             F    +L    ++ KE +  G   D +T   L+++
Sbjct:   413 FGTQKKLDTVYELLKEMQEKGHPPDGKTYNALIKL 447

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2178037 AT5G39980 [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 2.1e-06, P = 2.1e-06
 Identities = 57/211 (27%), Positives = 90/211 (42%)

Query:   278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQD 337
             N K  + LL   KD  R L  SI  + ++ L    + +   + LLD + +      S   
Sbjct:   104 NEKELFSLLSTYKD--RQL--SI--RFMVSLLSRENDWQRSLALLDWVHEEAKYTPSVFA 157

Query:   338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME 397
                +++  +R ++F +   LF         P    Y+TLI S   E     AL+ +  ME
Sbjct:   158 YNVVLRNVLRAKQFDIAHGLFDEMRQRALAPDRYTYSTLITSFGKEGMFDSALSWLQKME 217

Query:   398 ASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLA 457
                   DL  Y  +I+L   L D S+AI  FS+LK +G  P    Y  MI ++  +    
Sbjct:   218 QDRVSGDLVLYSNLIELSRRLCDYSKAISIFSRLKRSGITPDLVAYNSMINVYGKAKLFR 277

Query:   458 KCRDVCKEAEMAGFKLDKQTVVELLQIEKES 488
             + R + KE   AG   +  +   LL +  E+
Sbjct:   278 EARLLIKEMNEAGVLPNTVSYSTLLSVYVEN 308

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2185455 AT5G14820 "AT5G14820" [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 2.2e-06, P = 2.2e-06
 Identities = 70/346 (20%), Positives = 140/346 (40%)

Query:   157 CKQVYKNPSFLISLARDIKGLDS-HKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERA 215
             C +   NP  +  + + I  L +  +++  VLD+    L    +   +    H   P  A
Sbjct:   120 CVESSTNPEEVERVCKVIDELFALDRNMEAVLDEMKLDLSHDLIVEVLERFRHARKP--A 177

Query:   216 LQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATA----- 270
              + FCWA ++     D R   S + +LA+  + +    +     + +KG+L         
Sbjct:   178 FRFFCWAAERQGFAHDSRTYNSMMSILAKTRQFETMVSV--LEEMGTKGLLTMETFTIAM 235

Query:   271 KGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNP-DKYMLVMTLLDELGQRD 329
             K F      K A  +  + K     +       L+  LG+    K   V  L D+L +R 
Sbjct:   236 KAFAAAKERKKAVGIFELMKKYKFKIGVETINCLLDSLGRAKLGKEAQV--LFDKLKERF 293

Query:   330 DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREA 389
               N+     T ++    R++       +++     G  P +V +  ++   L   K  +A
Sbjct:   294 TPNMMTY--TVLLNGWCRVRNLIEAARIWNDMIDHGLKPDIVAHNVMLEGLLRSMKKSDA 351

Query:   390 LTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRI 449
             + +   M++     ++ +Y ++I+ F   + +  AI YF  + ++G  P   +Y  +I  
Sbjct:   352 IKLFHVMKSKGPCPNVRSYTIMIRDFCKQSSMETAIEYFDDMVDSGLQPDAAVYTCLITG 411

Query:   450 FMASGRLAKCRDVCKEAEMAGFKLDKQT---VVELLQIEKESRIGT 492
             F    +L    ++ KE +  G   D +T   +++L+  +K    GT
Sbjct:   412 FGTQKKLDTVYELLKEMQEKGHPPDGKTYNALIKLMANQKMPEHGT 457

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2206385 EMB2217 "embryo defective 2217" [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 2.7e-06, P = 2.7e-06
 Identities = 74/340 (21%), Positives = 137/340 (40%)

Query:   158 KQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQ 217
             K+ Y N S +  +   ++      ++   LDK  +F+   ++    + L  +   + AL 
Sbjct:   134 KKPYMNASSVAKIVEVVQRWKWGPELETQLDKL-QFVP--NMVHITQSLKIVKEVDAALS 190

Query:   218 TFCWAQKQPHLFPDDRLLASTVEVLARHHE-LKVPFKLENFVS-LASKGVLEATAKGFV- 274
              F WA+KQP   P D       + L +  + + +    E  V   +S G L   A   V 
Sbjct:   191 LFRWAKKQPWYLPSDECYVVLFDGLNQGRDFVGIQSLFEEMVQDSSSHGDLSFNAYNQVI 250

Query:   275 ----KGGNLKLAWKLLMVAKDGGRMLDPSIYAKLI-LELGKN-PDKYMLVMTLLDELGQR 328
                 K   L++A+     A++ G  +D   Y  L+ L L K  P K   +   +++    
Sbjct:   251 QYLAKAEKLEVAFCCFKKAQESGCKIDTQTYNNLMMLFLNKGLPYKAFEIYESMEKTDSL 310

Query:   329 DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCRE 388
              D +  +    ++ K G RL        LF         P+  ++++L+ S     +   
Sbjct:   311 LDGSTYELIIPSLAKSG-RLD---AAFKLFQQMKERKLRPSFSVFSSLVDSMGKAGRLDT 366

Query:   389 ALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR 448
             ++ V   M+          +  +I  +     +  A+R + ++K++GF P + +Y  +I 
Sbjct:   367 SMKVYMEMQGFGHRPSATMFVSLIDSYAKAGKLDTALRLWDEMKKSGFRPNFGLYTMIIE 426

Query:   449 IFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKES 488
                 SG+L     V K+ E AGF     T   LL++   S
Sbjct:   427 SHAKSGKLEVAMTVFKDMEKAGFLPTPSTYSCLLEMHAGS 466

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0009793 "embryo development ending in seed dormancy" evidence=NAS

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

TAIR|locus:2095309 AT3G09060 "AT3G09060" [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 3.5e-06, P = 3.5e-06
 Identities = 63/230 (27%), Positives = 105/230 (45%)

Query:   236 ASTVEVLARHHELKVPFKL-----ENFVSLASKGVLEATAKGFVKGGNL-KLAWKLLMVA 289
             AS ++ L +   L+    L     ++ V L S  V  A   G ++   L + ++ L  + 
Sbjct:   433 ASIIDCLCKKKRLEEASNLVKEMSKHGVELNSH-VCNALIGGLIRDSRLGEASFFLREMG 491

Query:   290 KDGGRMLDPSIYAKLILEL---GKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGI 346
             K+G R    S Y  LI  L   GK  +    V  +L+  G + DL        +I+  G+
Sbjct:   492 KNGCRPTVVS-YNILICGLCKAGKFGEASAFVKEMLEN-GWKPDLKTY-----SILLCGL 544

Query:   347 -RLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL 405
              R +K  +   L+H F  SG +  V+M+  LIH   S  K  +A+TV+ NME  NC  +L
Sbjct:   545 CRDRKIDLALELWHQFLQSGLETDVMMHNILIHGLCSVGKLDDAMTVMANMEHRNCTANL 604

Query:   406 PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR-IFMASG 454
               Y  +++ F  + D +RA   +  + + G  P    Y  +++ + M  G
Sbjct:   605 VTYNTLMEGFFKVGDSNRATVIWGYMYKMGLQPDIISYNTIMKGLCMCRG 654

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2096074 AT3G62540 "AT3G62540" [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 1.7e-05, P = 1.7e-05
 Identities = 69/346 (19%), Positives = 139/346 (40%)

Query:   157 CKQVYKNPSFLISLARDIKGLDS-HKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERA 215
             C +   NP  +  + + I  L +  +++  VLD+    L    +   +    H   P  A
Sbjct:   121 CVESSTNPEEVERVCKVIDELFALDRNMEAVLDEMKLDLSHDLIVEVLERFRHARKP--A 178

Query:   216 LQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATA----- 270
              + FCWA ++       R   S + +LA+  + +    +     + +KG+L         
Sbjct:   179 FRFFCWAAERQGFAHASRTYNSMMSILAKTRQFETMVSV--LEEMGTKGLLTMETFTIAM 236

Query:   271 KGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNP-DKYMLVMTLLDELGQRD 329
             K F      K A  +  + K     +       L+  LG+    K   V  L D+L +R 
Sbjct:   237 KAFAAAKERKKAVGIFELMKKYKFKIGVETINCLLDSLGRAKLGKEAQV--LFDKLKERF 294

Query:   330 DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREA 389
               N+     T ++    R++       +++     G  P +V +  ++   L   K  +A
Sbjct:   295 TPNMMTY--TVLLNGWCRVRNLIEAARIWNDMIDHGLKPDIVAHNVMLEGLLRSMKKSDA 352

Query:   390 LTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRI 449
             + +   M++     ++ +Y ++I+ F   + +  AI YF  + ++G  P   +Y  +I  
Sbjct:   353 IKLFHVMKSKGPCPNVRSYTIMIRDFCKQSSMETAIEYFDDMVDSGLQPDAAVYTCLITG 412

Query:   450 FMASGRLAKCRDVCKEAEMAGFKLDKQT---VVELLQIEKESRIGT 492
             F    +L    ++ KE +  G   D +T   +++L+  +K    GT
Sbjct:   413 FGTQKKLDTVYELLKEMQEKGHPPDGKTYNALIKLMANQKMPEHGT 458

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2027166 PTAC2 "plastid transcriptionally active 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 2.1e-05, P = 2.1e-05
 Identities = 74/352 (21%), Positives = 140/352 (39%)

Query:   145 KRVCLASSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTVR 204
             K + L +   S+ K  Y     + SL   +  L     +A  LD     L     +   +
Sbjct:    56 KDLVLGNPSVSVEKGKYSYD--VESLINKLSSLPPRGSIARCLDIFKNKLSLNDFALVFK 113

Query:   205 ELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKG 264
             E       +R+L+ F + Q+Q    P++ +    + +L R   L     LE F  + S+G
Sbjct:   114 EFAGRGDWQRSLRLFKYMQRQIWCKPNEHIYTIMISLLGREGLLDKC--LEVFDEMPSQG 171

Query:   265 VLEA----TAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSI--YAKLILELGKNPDKYMLV 318
             V  +    TA     G N +    L ++ +     + PSI  Y  +I    +    +  +
Sbjct:   172 VSRSVFSYTALINAYGRNGRYETSLELLDRMKNEKISPSILTYNTVINACARGGLDWEGL 231

Query:   319 MTLLDEL---GQRDDL---NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVM 372
             + L  E+   G + D+   N     C AI  +G         E +F      G  P +  
Sbjct:   232 LGLFAEMRHEGIQPDIVTYNTLLSAC-AIRGLGDE------AEMVFRTMNDGGIVPDLTT 284

Query:   373 YTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK 432
             Y+ L+ +    ++  +   ++  M +   L D+ +Y V+++ +     I  A+  F +++
Sbjct:   285 YSHLVETFGKLRRLEKVCDLLGEMASGGSLPDITSYNVLLEAYAKSGSIKEAMGVFHQMQ 344

Query:   433 EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI 484
              AG  P  + Y  ++ +F  SGR    R +  E + +    D  T   L+++
Sbjct:   345 AAGCTPNANTYSVLLNLFGQSGRYDDVRQLFLEMKSSNTDPDAATYNILIEV 396

GO:0009507 "chloroplast" evidence=IDA

GO:0009295 "nucleoid" evidence=IDA

GO:0009508 "plastid chromosome" evidence=IDA

GO:0042793 "transcription from plastid promoter" evidence=RCA;IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP

GO:0006364 "rRNA processing" evidence=RCA

GO:0006399 "tRNA metabolic process" evidence=RCA

GO:0009658 "chloroplast organization" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010207 "photosystem II assembly" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

GO:0045036 "protein targeting to chloroplast" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5XET4	PP142_ARATH	No assigned EC number	0.6073	0.9594	0.9732	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	493
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
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.84
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.78
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.77
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.77
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.61
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.56
PF13041	50	PPR_2: PPR repeat family	99.51
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.47
PF13041	50	PPR_2: PPR repeat family	99.46
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.45
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.25
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.24
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.23
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.22
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.2
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.2
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.2
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.19
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.17
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.14
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.14
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.1
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.1
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.09
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.01
PRK14574	822	hmsH outer membrane protein; Provisional	98.98
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.96
PF12854	34	PPR_1: PPR repeat	98.96
KOG1126	638	consensus DNA-binding cell division cycle control	98.94
PF12854	34	PPR_1: PPR repeat	98.93
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	98.91
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	98.91
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	98.9
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	98.87
PRK14574	822	hmsH outer membrane protein; Provisional	98.86
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	98.83
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.83
KOG2003	840	consensus TPR repeat-containing protein [General f	98.81
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.74
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.74
PRK12370	553	invasion protein regulator; Provisional	98.69
KOG1126	638	consensus DNA-binding cell division cycle control	98.67
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.64
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	98.56
PRK12370	553	invasion protein regulator; Provisional	98.54
KOG2076	895	consensus RNA polymerase III transcription factor	98.49
KOG2076	895	consensus RNA polymerase III transcription factor	98.49
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.41
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.39
PRK11189	296	lipoprotein NlpI; Provisional	98.38
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.36
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.32
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.28
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.27
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.25
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.25
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.2
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.18
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.17
PRK11189	296	lipoprotein NlpI; Provisional	98.17
KOG2003	840	consensus TPR repeat-containing protein [General f	98.15
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.13
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	98.1
KOG1129	478	consensus TPR repeat-containing protein [General f	98.08
KOG1129	478	consensus TPR repeat-containing protein [General f	98.05
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.05
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.03
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	98.02
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.01
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.98
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	97.96
KOG1915	677	consensus Cell cycle control protein (crooked neck	97.96
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.94
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.91
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	97.89
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	97.89
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.88
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.85
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.82
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.8
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.73
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.72
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	97.72
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.71
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	97.7
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	97.68
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.68
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.64
KOG0547	606	consensus Translocase of outer mitochondrial membr	97.61
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.56
PRK15359	144	type III secretion system chaperone protein SscB;	97.53
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	97.51
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.5
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.48
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.46
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.45
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.45
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.44
PRK04841	903	transcriptional regulator MalT; Provisional	97.44
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.44
KOG1128	777	consensus Uncharacterized conserved protein, conta	97.42
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.4
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.39
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.38
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	97.38
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.35
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.32
KOG0495	913	consensus HAT repeat protein [RNA processing and m	97.3
KOG0547	606	consensus Translocase of outer mitochondrial membr	97.3
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.27
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.25
PRK15359	144	type III secretion system chaperone protein SscB;	97.24
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.24
PRK04841	903	transcriptional regulator MalT; Provisional	97.23
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.21
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.17
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.13
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.11
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.09
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.06
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.02
KOG4340	459	consensus Uncharacterized conserved protein [Funct	96.99
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	96.97
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.97
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	96.97
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	96.96
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	96.95
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	96.93
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	96.9
PLN02789	320	farnesyltranstransferase	96.89
KOG2376	652	consensus Signal recognition particle, subunit Srp	96.83
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.81
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	96.81
PLN02789	320	farnesyltranstransferase	96.79
COG4783	484	Putative Zn-dependent protease, contains TPR repea	96.75
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.74
KOG3941	406	consensus Intermediate in Toll signal transduction	96.68
KOG1125	579	consensus TPR repeat-containing protein [General f	96.66
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.61
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.55
KOG3941	406	consensus Intermediate in Toll signal transduction	96.49
KOG2376	652	consensus Signal recognition particle, subunit Srp	96.48
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	96.48
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	96.46
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	96.45
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	96.42
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.35
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	96.19
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.18
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.14
KOG3060	289	consensus Uncharacterized conserved protein [Funct	96.1
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.1
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	96.08
KOG1915	677	consensus Cell cycle control protein (crooked neck	96.0
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	95.98
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	95.97
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	95.95
KOG1125	579	consensus TPR repeat-containing protein [General f	95.94
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	95.88
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	95.8
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	95.78
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	95.77
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	95.69
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.66
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.63
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	95.62
PF12688	120	TPR_5: Tetratrico peptide repeat	95.6
PF12688	120	TPR_5: Tetratrico peptide repeat	95.4
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.14
KOG3060	289	consensus Uncharacterized conserved protein [Funct	95.11
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	95.09
KOG2796	366	consensus Uncharacterized conserved protein [Funct	95.04
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.04
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	95.03
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.86
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	94.85
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.83
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	94.71
KOG2041	1189	consensus WD40 repeat protein [General function pr	94.63
PRK10803	263	tol-pal system protein YbgF; Provisional	94.62
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.35
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.32
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	94.23
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.21
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.1
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	94.02
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	93.9
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	93.84
PRK10803	263	tol-pal system protein YbgF; Provisional	93.74
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.73
KOG2796	366	consensus Uncharacterized conserved protein [Funct	93.68
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	93.38
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	93.33
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	93.33
PF13371	73	TPR_9: Tetratricopeptide repeat	93.27
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.2
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	93.2
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	93.18
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.16
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	93.09
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	92.86
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	92.32
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	92.19
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	92.11
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	91.91
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	91.78
COG4700	251	Uncharacterized protein conserved in bacteria cont	91.68
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	91.61
KOG0553	304	consensus TPR repeat-containing protein [General f	91.58
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	91.51
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	91.34
PF13371	73	TPR_9: Tetratricopeptide repeat	91.33
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	91.16
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	91.0
KOG2297	412	consensus Predicted translation factor, contains W	91.0
COG3629	280	DnrI DNA-binding transcriptional activator of the	90.71
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	90.09
KOG2041	1189	consensus WD40 repeat protein [General function pr	90.01
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	89.99
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	89.8
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	89.69
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	89.61
KOG0553	304	consensus TPR repeat-containing protein [General f	89.6
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	89.6
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	89.3
KOG4570	418	consensus Uncharacterized conserved protein [Funct	89.2
PF13762	145	MNE1: Mitochondrial splicing apparatus component	89.11
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	89.08
COG3898	531	Uncharacterized membrane-bound protein [Function u	88.65
PF13762	145	MNE1: Mitochondrial splicing apparatus component	88.4
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	88.23
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	87.89
PF13929	292	mRNA_stabil: mRNA stabilisation	87.59
KOG4570	418	consensus Uncharacterized conserved protein [Funct	87.59
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	87.19
COG3629	280	DnrI DNA-binding transcriptional activator of the	87.17
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	87.0
COG0457	291	NrfG FOG: TPR repeat [General function prediction	86.64
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	86.2
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	86.16
PF13929	292	mRNA_stabil: mRNA stabilisation	85.85
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	85.76
COG4700	251	Uncharacterized protein conserved in bacteria cont	85.23
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	84.87
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	84.79
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	84.69
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	84.62
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	84.56
KOG2610	491	consensus Uncharacterized conserved protein [Funct	84.49
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	84.47
COG3118	304	Thioredoxin domain-containing protein [Posttransla	84.24
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	84.04
PF13512	142	TPR_18: Tetratricopeptide repeat	83.95
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	83.66
PRK15331	165	chaperone protein SicA; Provisional	83.14
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	82.27
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	82.21
PF13512	142	TPR_18: Tetratricopeptide repeat	82.19
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	81.86
KOG4555	175	consensus TPR repeat-containing protein [Function	81.43
KOG2297	412	consensus Predicted translation factor, contains W	80.53
KOG1585	308	consensus Protein required for fusion of vesicles	80.46

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.8e-57  Score=497.79  Aligned_cols=364  Identities=11%  Similarity=0.152  Sum_probs=336.5

Q ss_pred             cchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh------hhhhhhhhhccCCchhHHHHHH
Q 011102           99 ESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA------SSRASICKQVYKNPSFLISLAR  172 (493)
Q Consensus        99 ~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a------~~~~~~~~~~~~~~~~l~~l~~  172 (493)
                      ..|.+++|..+|..|   +.||.++|+.++          .+|+..+.++.|      |...|..|+...+..++     
T Consensus       418 ~~g~~~eAl~lf~~M---~~pd~~Tyn~LL----------~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI-----  479 (1060)
T PLN03218        418 KQRAVKEAFRFAKLI---RNPTLSTFNMLM----------SVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLI-----  479 (1060)
T ss_pred             HCCCHHHHHHHHHHc---CCCCHHHHHHHH----------HHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHH-----
Confidence            356777888888887   348999999999          999988888777      66777777766555444     


Q ss_pred             HHhhccCCCCHHHHHHHHhhhcccC------cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC
Q 011102          173 DIKGLDSHKDVAEVLDKCGRFLRKG------SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHH  246 (493)
Q Consensus       173 ~l~~~~~~~~~~~a~~~~~~m~~~~------~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g  246 (493)
                        ..|++.|++++|.++|++|...+      +||++|.+|++.|++++|+++|++|.+. |+.||..||+++|.+|++.|
T Consensus       480 --~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~-Gv~PD~vTYnsLI~a~~k~G  556 (1060)
T PLN03218        480 --STCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSK-NVKPDRVVFNALISACGQSG  556 (1060)
T ss_pred             --HHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHCC
Confidence              55667899999999999998654      9999999999999999999999999987 99999999999999999999


Q ss_pred             CCchhhhHHHhhc--------cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHH
Q 011102          247 ELKVPFKLENFVS--------LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLV  318 (493)
Q Consensus       247 ~~~~~~~l~~~~~--------~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a  318 (493)
                      +++.+..+  |.+        .+|..+|++||.+|++.|++++|.++|++|.+.|+.|+..+||++|.+|++. |++++|
T Consensus       557 ~~deA~~l--f~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~-G~~deA  633 (1060)
T PLN03218        557 AVDRAFDV--LAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQK-GDWDFA  633 (1060)
T ss_pred             CHHHHHHH--HHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhc-CCHHHH
Confidence            96665554  433        3578899999999999999999999999999999999999999999999999 999999


Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          319 MTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       319 ~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      .++|++|.+. |+.||..+|+++|++|++.|++++|.++|++|.+.|+.||..+||+||.+|++.|++++|.++|++|.+
T Consensus       634 l~lf~eM~~~-Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~  712 (1060)
T PLN03218        634 LSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKS  712 (1060)
T ss_pred             HHHHHHHHHc-CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            9999999998 999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHH
Q 011102          399 SNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTV  478 (493)
Q Consensus       399 ~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~  478 (493)
                      .|+.||..+||+||.+|++.|++++|.++|++|.+.|+.||..||++||.+|++.|++++|.++|++|.+.|+.||..+|
T Consensus       713 ~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~ty  792 (1060)
T PLN03218        713 IKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMC  792 (1060)
T ss_pred             cCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhh
Q 011102          479 VELLQIEKE  487 (493)
Q Consensus       479 ~~Ll~~~~~  487 (493)
                      ++|+.+|+.
T Consensus       793 nsLIglc~~  801 (1060)
T PLN03218        793 RCITGLCLR  801 (1060)
T ss_pred             HHHHHHHHH
Confidence            999998763

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=8.1e-56  Score=484.80  Aligned_cols=369  Identities=11%  Similarity=0.094  Sum_probs=333.2

Q ss_pred             cccchhHHHHHhhhcCC-CCCC-CCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhhhh--hhhhhhhccCCchhHHHHHH
Q 011102           97 IWESEELEAISSLFQGR-IPQK-PGRLYRERPLPLPLPHRLRPLELPTPKKRVCLASS--RASICKQVYKNPSFLISLAR  172 (493)
Q Consensus        97 ~~~~~~~~~a~~lf~~m-~~g~-~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a~~--~~~~~~~~~~~~~~l~~l~~  172 (493)
                      +++.|++++|.++|++| ..|. +|+..+++.++          .+|+..+.+..|+.  +....|+..+++       .
T Consensus       380 l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li----------~~~~~~g~~~eAl~lf~~M~~pd~~Tyn-------~  442 (1060)
T PLN03218        380 LLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFF----------KACKKQRAVKEAFRFAKLIRNPTLSTFN-------M  442 (1060)
T ss_pred             HHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHH----------HHHHHCCCHHHHHHHHHHcCCCCHHHHH-------H
Confidence            55679999999999999 6553 56666677777          77777777777722  111123433333       3


Q ss_pred             HHhhccCCCCHHHHHHHHhhhcccC------cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC
Q 011102          173 DIKGLDSHKDVAEVLDKCGRFLRKG------SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHH  246 (493)
Q Consensus       173 ~l~~~~~~~~~~~a~~~~~~m~~~~------~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g  246 (493)
                      .+..+++.+++++|.++|+.|.+.+      +||++|.+|++.|++++|.++|++|.+. |+.||..||+++|.+|++.|
T Consensus       443 LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~-Gv~PdvvTynaLI~gy~k~G  521 (1060)
T PLN03218        443 LMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNA-GVEANVHTFGALIDGCARAG  521 (1060)
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHCc
Confidence            4566778899999999999998765      9999999999999999999999999997 99999999999999999999


Q ss_pred             CCchhhhHHHhhcc------CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--CCCCCCHHHHHHHHHHHhcCCCCHHHH
Q 011102          247 ELKVPFKLENFVSL------ASKGVLEATAKGFVKGGNLKLAWKLLMVAKD--GGRMLDPSIYAKLILELGKNPDKYMLV  318 (493)
Q Consensus       247 ~~~~~~~l~~~~~~------~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~--~g~~pd~~t~~~li~~~~~~~~~~~~a  318 (493)
                      +++  +++..|..|      +|..+||+||.+|++.|++++|.++|++|.+  .|+.||.+||+++|.+|++. |++++|
T Consensus       522 ~~e--eAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~-G~ldeA  598 (1060)
T PLN03218        522 QVA--KAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANA-GQVDRA  598 (1060)
T ss_pred             CHH--HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHC-CCHHHH
Confidence            955  444556555      6889999999999999999999999999986  68999999999999999999 999999


Q ss_pred             HHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          319 MTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       319 ~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      .++|++|.+. |+.|+..+||++|.+|++.|++++|.++|++|.+.|+.||.++|++||++|++.|++++|.++|++|.+
T Consensus       599 ~elf~~M~e~-gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k  677 (1060)
T PLN03218        599 KEVYQMIHEY-NIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK  677 (1060)
T ss_pred             HHHHHHHHHc-CCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            9999999998 999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHH
Q 011102          399 SNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTV  478 (493)
Q Consensus       399 ~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~  478 (493)
                      .|+.||..+|++||.+|++.|++++|.++|++|.+.|+.||..+||+||.+|++.|++++|.++|++|.+.|+.||..||
T Consensus       678 ~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty  757 (1060)
T PLN03218        678 QGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITY  757 (1060)
T ss_pred             cCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhh
Q 011102          479 VELLQIEKE  487 (493)
Q Consensus       479 ~~Ll~~~~~  487 (493)
                      ++||..|..
T Consensus       758 ~sLL~a~~k  766 (1060)
T PLN03218        758 SILLVASER  766 (1060)
T ss_pred             HHHHHHHHH
Confidence            999996543

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

Probab=100.00  E-value=1.8e-54  Score=468.92  Aligned_cols=363  Identities=12%  Similarity=0.065  Sum_probs=324.1

Q ss_pred             cccchhHHHHHhhhcCC-CC-CCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh------hhhhhhhhhccCCchhHH
Q 011102           97 IWESEELEAISSLFQGR-IP-QKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA------SSRASICKQVYKNPSFLI  168 (493)
Q Consensus        97 ~~~~~~~~~a~~lf~~m-~~-g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a------~~~~~~~~~~~~~~~~l~  168 (493)
                      +...|++++|..+|+.| .. +..||..+|+.++          .+++..+..+.|      |...|+.|+...++.   
T Consensus        97 l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll----------~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~---  163 (697)
T PLN03081         97 LVACGRHREALELFEILEAGCPFTLPASTYDALV----------EACIALKSIRCVKAVYWHVESSGFEPDQYMMNR---  163 (697)
T ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHH----------HHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHH---
Confidence            45579999999999999 44 3689999999999          888776665544      666777766554443   


Q ss_pred             HHHHHHhhccCCCCHHHHHHHHhhhcccC--cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHH-----------
Q 011102          169 SLARDIKGLDSHKDVAEVLDKCGRFLRKG--SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLL-----------  235 (493)
Q Consensus       169 ~l~~~l~~~~~~~~~~~a~~~~~~m~~~~--~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~-----------  235 (493)
                          .+..|++.|++++|.++|++|..++  +||++|.+|++.|++++|+++|++|.+. |+.||..||           
T Consensus       164 ----Li~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~-g~~p~~~t~~~ll~a~~~~~  238 (697)
T PLN03081        164 ----VLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWED-GSDAEPRTFVVMLRASAGLG  238 (697)
T ss_pred             ----HHHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHh-CCCCChhhHHHHHHHHhcCC
Confidence                3467788899999999999999877  9999999999999999999999999876 666665554           


Q ss_pred             ------------------------HHHHHHHHHcCCCchhhhHHHhhcc--CcHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 011102          236 ------------------------ASTVEVLARHHELKVPFKLENFVSL--ASKGVLEATAKGFVKGGNLKLAWKLLMVA  289 (493)
Q Consensus       236 ------------------------~~li~~~~~~g~~~~~~~l~~~~~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m  289 (493)
                                              +++|++|++.|+++.+.  ..|..|  +|..+||+||.+|++.|++++|+++|++|
T Consensus       239 ~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~--~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M  316 (697)
T PLN03081        239 SARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDAR--CVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEM  316 (697)
T ss_pred             cHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHH--HHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence                                    66677777778754444  446555  47889999999999999999999999999


Q ss_pred             HhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC
Q 011102          290 KDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT  369 (493)
Q Consensus       290 ~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~  369 (493)
                      .+.|+.||..||+++|.+|++. |.+++|.+++.+|.+. |+.||..+||+||++|+++|++++|.++|++|.    .||
T Consensus       317 ~~~g~~pd~~t~~~ll~a~~~~-g~~~~a~~i~~~m~~~-g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~~d  390 (697)
T PLN03081        317 RDSGVSIDQFTFSIMIRIFSRL-ALLEHAKQAHAGLIRT-GFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKN  390 (697)
T ss_pred             HHcCCCCCHHHHHHHHHHHHhc-cchHHHHHHHHHHHHh-CCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----CCC
Confidence            9999999999999999999999 9999999999999998 999999999999999999999999999999998    789


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIR  448 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~  448 (493)
                      +++||+||.+|++.|+.++|+++|++|.+.|+.||.+||+++|.+|++.|++++|.++|+.|. +.|+.|+..+|++||+
T Consensus       391 ~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~  470 (697)
T PLN03081        391 LISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIE  470 (697)
T ss_pred             eeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHH
Confidence            999999999999999999999999999999999999999999999999999999999999998 4799999999999999


Q ss_pred             HHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHhhhhc
Q 011102          449 IFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKES  488 (493)
Q Consensus       449 ~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~~~~~  488 (493)
                      +|++.|++++|.+++++|   ++.||..+|++|+..|...
T Consensus       471 ~l~r~G~~~eA~~~~~~~---~~~p~~~~~~~Ll~a~~~~  507 (697)
T PLN03081        471 LLGREGLLDEAYAMIRRA---PFKPTVNMWAALLTACRIH  507 (697)
T ss_pred             HHHhcCCHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHc
Confidence            999999999999998876   5899999999999988653

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=4.2e-54  Score=476.54  Aligned_cols=372  Identities=14%  Similarity=0.097  Sum_probs=308.1

Q ss_pred             cccchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh------hhhhhhhhhccCCchhHHHH
Q 011102           97 IWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA------SSRASICKQVYKNPSFLISL  170 (493)
Q Consensus        97 ~~~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a------~~~~~~~~~~~~~~~~l~~l  170 (493)
                      ..+.|+++.|+.+|++|   +.||+++||+++          .+|+..|..++|      |...|+.|+..+++.++..+
T Consensus       131 ~~~~g~~~~A~~~f~~m---~~~d~~~~n~li----------~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~  197 (857)
T PLN03077        131 FVRFGELVHAWYVFGKM---PERDLFSWNVLV----------GGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTC  197 (857)
T ss_pred             HHhCCChHHHHHHHhcC---CCCCeeEHHHHH----------HHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHh
Confidence            35678999999999999   778999999999          999988888777      66778888888887766543


Q ss_pred             ----------------------------HHHHhhccCCCCHHHHHHHHhhhcccC--cHHHHHHHHHhCCChHHHHHHHH
Q 011102          171 ----------------------------ARDIKGLDSHKDVAEVLDKCGRFLRKG--SLSFTVRELGHMNLPERALQTFC  220 (493)
Q Consensus       171 ----------------------------~~~l~~~~~~~~~~~a~~~~~~m~~~~--~~~~li~~~~~~g~~~~A~~l~~  220 (493)
                                                  ...+..|++.|++++|.++|++|+.++  +||++|.+|++.|++++|+++|+
T Consensus       198 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~  277 (857)
T PLN03077        198 GGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFF  277 (857)
T ss_pred             CCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHH
Confidence                                        234688999999999999999998877  99999999999999999999999


Q ss_pred             HHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhH---------------------------------HHhhcc--CcHHH
Q 011102          221 WAQKQPHLFPDDRLLASTVEVLARHHELKVPFKL---------------------------------ENFVSL--ASKGV  265 (493)
Q Consensus       221 ~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l---------------------------------~~~~~~--~~~~~  265 (493)
                      +|.+. |+.||..||+++|.+|++.|+++.++.+                                 ..|.+|  +|..+
T Consensus       278 ~M~~~-g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s  356 (857)
T PLN03077        278 TMREL-SVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVS  356 (857)
T ss_pred             HHHHc-CCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeee
Confidence            99987 8888888888887777776665544333                                 223333  36678


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Q 011102          266 LEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVG  345 (493)
Q Consensus       266 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~  345 (493)
                      ||++|.+|++.|++++|+++|++|.+.|+.||..||+++|.+|++. |++++|.++++.|.+. |+.|+..+||+||++|
T Consensus       357 ~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~-g~~~~a~~l~~~~~~~-g~~~~~~~~n~Li~~y  434 (857)
T PLN03077        357 WTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACL-GDLDVGVKLHELAERK-GLISYVVVANALIEMY  434 (857)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhcc-chHHHHHHHHHHHHHh-CCCcchHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999998 8999999999999887 8888888888888888


Q ss_pred             HHcCCHHHHHHHHHHHHHcC------------------------------C-----------------------------
Q 011102          346 IRLQKFGVVESLFHWFTHSG------------------------------R-----------------------------  366 (493)
Q Consensus       346 ~~~g~~~~A~~l~~~m~~~g------------------------------~-----------------------------  366 (493)
                      +++|++++|.++|++|.+.+                              +                             
T Consensus       435 ~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~  514 (857)
T PLN03077        435 SKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAH  514 (857)
T ss_pred             HHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHH
Confidence            88888888888887775321                              1                             


Q ss_pred             ------------------------------------CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q 011102          367 ------------------------------------DPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRV  410 (493)
Q Consensus       367 ------------------------------------~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~  410 (493)
                                                          .||+++||+||.+|++.|+.++|+++|++|.+.|+.||.+||++
T Consensus       515 ~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~  594 (857)
T PLN03077        515 VLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFIS  594 (857)
T ss_pred             HHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHH
Confidence                                                45666777778888888888888888888888888888888888


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHhhhh
Q 011102          411 VIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKE  487 (493)
Q Consensus       411 li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~~~~  487 (493)
                      +|.+|++.|++++|.++|++|. +.|+.|+..+|++|+++|++.|++++|.+++++|.   ++||..+|++||..|+.
T Consensus       595 ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~---~~pd~~~~~aLl~ac~~  669 (857)
T PLN03077        595 LLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMP---ITPDPAVWGALLNACRI  669 (857)
T ss_pred             HHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCC---CCCCHHHHHHHHHHHHH
Confidence            8888888888888888888887 67888888888888888888888888888888874   78888888888887754

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2e-50  Score=447.26  Aligned_cols=366  Identities=13%  Similarity=0.097  Sum_probs=307.5

Q ss_pred             CccccchhHHHHHhhhcCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh------hhhhhhhhhccCCchhH
Q 011102           95 DFIWESEELEAISSLFQGR-IPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA------SSRASICKQVYKNPSFL  167 (493)
Q Consensus        95 ~~~~~~~~~~~a~~lf~~m-~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a------~~~~~~~~~~~~~~~~l  167 (493)
                      ..++..|++++|..+|+.| ..|.+|+..+|..++          .++...+.+..|      +...+..++..      
T Consensus        59 ~~l~~~g~~~~A~~l~~~m~~~g~~~~~~~~~~ll----------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------  122 (857)
T PLN03077         59 RALCSHGQLEQALKLLESMQELRVPVDEDAYVALF----------RLCEWKRAVEEGSRVCSRALSSHPSLGVR------  122 (857)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhcCCCCChhHHHHHH----------HHHhhCCCHHHHHHHHHHHHHcCCCCCch------
Confidence            3577789999999999999 888999999999998          766655554444      22233322221      


Q ss_pred             HHHHHHHhhccCCCCHHHHHHHHhhhcccC--cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHH----
Q 011102          168 ISLARDIKGLDSHKDVAEVLDKCGRFLRKG--SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEV----  241 (493)
Q Consensus       168 ~~l~~~l~~~~~~~~~~~a~~~~~~m~~~~--~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~----  241 (493)
                       .....+..|++.|+++.|+++|++|..++  +||++|.+|++.|++++|+++|++|... |+.||.+||+++|++    
T Consensus       123 -~~n~li~~~~~~g~~~~A~~~f~~m~~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~-g~~Pd~~t~~~ll~~~~~~  200 (857)
T PLN03077        123 -LGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWA-GVRPDVYTFPCVLRTCGGI  200 (857)
T ss_pred             -HHHHHHHHHHhCCChHHHHHHHhcCCCCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHc-CCCCChhHHHHHHHHhCCc
Confidence             12234577889999999999999998887  9999999999999999999999999987 999988887655555    


Q ss_pred             -------------------------------HHHcCCCchhhhHHHhhccC--cHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011102          242 -------------------------------LARHHELKVPFKLENFVSLA--SKGVLEATAKGFVKGGNLKLAWKLLMV  288 (493)
Q Consensus       242 -------------------------------~~~~g~~~~~~~l~~~~~~~--~~~~~~~li~~~~~~g~~~~A~~l~~~  288 (493)
                                                     |++.|+++.  +...|.+|+  |..+||+||.+|++.|++++|+++|++
T Consensus       201 ~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~--A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~  278 (857)
T PLN03077        201 PDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVS--ARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFT  278 (857)
T ss_pred             cchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHH--HHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHH
Confidence                                           455555333  334465554  778999999999999999999999999


Q ss_pred             HHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC
Q 011102          289 AKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP  368 (493)
Q Consensus       289 m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  368 (493)
                      |.+.|+.||..||+++|.+|++. |+++.|.+++..|.+. |+.||..+||+||++|+++|++++|.++|++|.    .|
T Consensus       279 M~~~g~~Pd~~ty~~ll~a~~~~-g~~~~a~~l~~~~~~~-g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~  352 (857)
T PLN03077        279 MRELSVDPDLMTITSVISACELL-GDERLGREMHGYVVKT-GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME----TK  352 (857)
T ss_pred             HHHcCCCCChhHHHHHHHHHHhc-CChHHHHHHHHHHHHh-CCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC----CC
Confidence            99999999999999999999999 9999999999999998 899999999999999999999999999999997    78


Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR  448 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~  448 (493)
                      |.++||+||.+|++.|++++|+++|++|.+.|+.||..||+++|.+|++.|++++|.++++.|.+.|+.|+..+||+||+
T Consensus       353 d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~  432 (857)
T PLN03077        353 DAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIE  432 (857)
T ss_pred             CeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999988888888888888888888888888888888


Q ss_pred             HHHHcCCHHHHHHHHHHHHH------------------------------CCCccCHHHHHHHHHhhh
Q 011102          449 IFMASGRLAKCRDVCKEAEM------------------------------AGFKLDKQTVVELLQIEK  486 (493)
Q Consensus       449 ~~~~~g~~~~A~~l~~~m~~------------------------------~g~~pd~~t~~~Ll~~~~  486 (493)
                      +|++.|++++|.++|++|.+                              .++.||..||+++|..|.
T Consensus       433 ~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~  500 (857)
T PLN03077        433 MYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACA  500 (857)
T ss_pred             HHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHh
Confidence            88888877777777766643                              256788888888887653

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

Probab=100.00  E-value=2.1e-49  Score=429.37  Aligned_cols=352  Identities=12%  Similarity=0.045  Sum_probs=318.9

Q ss_pred             ccccchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh------hhhhhhhhhccCCchhHHH
Q 011102           96 FIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA------SSRASICKQVYKNPSFLIS  169 (493)
Q Consensus        96 ~~~~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a------~~~~~~~~~~~~~~~~l~~  169 (493)
                      ...+.|+++.|..+|++|   +.||.++||+++          .+|+..|..++|      |...|..|+..++..++..
T Consensus       167 ~y~k~g~~~~A~~lf~~m---~~~~~~t~n~li----------~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a  233 (697)
T PLN03081        167 MHVKCGMLIDARRLFDEM---PERNLASWGTII----------GGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRA  233 (697)
T ss_pred             HHhcCCCHHHHHHHHhcC---CCCCeeeHHHHH----------HHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHH
Confidence            355689999999999999   679999999999          999999988887      6677777777666555433


Q ss_pred             HH----------------------------HHHhhccCCCCHHHHHHHHhhhcccC--cHHHHHHHHHhCCChHHHHHHH
Q 011102          170 LA----------------------------RDIKGLDSHKDVAEVLDKCGRFLRKG--SLSFTVRELGHMNLPERALQTF  219 (493)
Q Consensus       170 l~----------------------------~~l~~~~~~~~~~~a~~~~~~m~~~~--~~~~li~~~~~~g~~~~A~~l~  219 (493)
                      ++                            ..+..|+++|++++|.++|++|..++  +||++|.+|++.|++++|+++|
T Consensus       234 ~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf  313 (697)
T PLN03081        234 SAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLY  313 (697)
T ss_pred             HhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHH
Confidence            22                            24688999999999999999998887  9999999999999999999999


Q ss_pred             HHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC
Q 011102          220 CWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRM  295 (493)
Q Consensus       220 ~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  295 (493)
                      ++|.+. |+.||..||+++|.+|++.|+++.++.++....    .++..+||+||++|+++|++++|.++|++|.+    
T Consensus       314 ~~M~~~-g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----  388 (697)
T PLN03081        314 YEMRDS-GVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----  388 (697)
T ss_pred             HHHHHc-CCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----
Confidence            999987 999999999999999999999887777644322    45778999999999999999999999999975    


Q ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-cCCCCCHHHHH
Q 011102          296 LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTH-SGRDPTVVMYT  374 (493)
Q Consensus       296 pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~-~g~~p~~~ty~  374 (493)
                      ||.++||+||.+|++. |+.++|.++|++|.+. |+.||..||+++|++|++.|++++|.++|+.|.+ .|+.|+..+|+
T Consensus       389 ~d~~t~n~lI~~y~~~-G~~~~A~~lf~~M~~~-g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~  466 (697)
T PLN03081        389 KNLISWNALIAGYGNH-GRGTKAVEMFERMIAE-GVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYA  466 (697)
T ss_pred             CCeeeHHHHHHHHHHc-CCHHHHHHHHHHHHHh-CCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchH
Confidence            8999999999999999 9999999999999998 9999999999999999999999999999999975 69999999999


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHc
Q 011102          375 TLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCP-TYDIYRDMIRIFMAS  453 (493)
Q Consensus       375 ~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~li~~~~~~  453 (493)
                      +||++|++.|++++|.+++++|   ++.||..+|++||.+|++.|+++.|..+++++.+  +.| +..+|+.|++.|++.
T Consensus       467 ~li~~l~r~G~~~eA~~~~~~~---~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~--~~p~~~~~y~~L~~~y~~~  541 (697)
T PLN03081        467 CMIELLGREGLLDEAYAMIRRA---PFKPTVNMWAALLTACRIHKNLELGRLAAEKLYG--MGPEKLNNYVVLLNLYNSS  541 (697)
T ss_pred             hHHHHHHhcCCHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhC--CCCCCCcchHHHHHHHHhC
Confidence            9999999999999999999876   6789999999999999999999999999999864  445 467999999999999


Q ss_pred             CCHHHHHHHHHHHHHCCCc
Q 011102          454 GRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       454 g~~~~A~~l~~~m~~~g~~  472 (493)
                      |++++|.+++++|.+.|+.
T Consensus       542 G~~~~A~~v~~~m~~~g~~  560 (697)
T PLN03081        542 GRQAEAAKVVETLKRKGLS  560 (697)
T ss_pred             CCHHHHHHHHHHHHHcCCc
Confidence            9999999999999999975

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.84  E-value=4.3e-18  Score=172.51  Aligned_cols=289  Identities=9%  Similarity=0.012  Sum_probs=236.9

Q ss_pred             cCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCC---HHHHHHHHHHHHHcCCCc
Q 011102          178 DSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPD---DRLLASTVEVLARHHELK  249 (493)
Q Consensus       178 ~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd---~~t~~~li~~~~~~g~~~  249 (493)
                      ...++.++|+..|.++...+     .+..+...+.+.|++++|..+++.+... +..++   ..++..+...+.+.|+++
T Consensus        46 ~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~-~~~~~~~~~~~~~~La~~~~~~g~~~  124 (389)
T PRK11788         46 LLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSR-PDLTREQRLLALQELGQDYLKAGLLD  124 (389)
T ss_pred             HhcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHHHHHHHCCCHH
Confidence            45688999999999887654     6778888999999999999999999875 32222   246788899999999855


Q ss_pred             hhhhHHHhhcc-----CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHHHhcCCCCHHHHHH
Q 011102          250 VPFKLENFVSL-----ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP----SIYAKLILELGKNPDKYMLVMT  320 (493)
Q Consensus       250 ~~~~l~~~~~~-----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~----~t~~~li~~~~~~~~~~~~a~~  320 (493)
                      .+.  ..|..+     .+..+++.++..|.+.|++++|.+.++.+.+.+-.++.    ..|..+...+.+. |++++|..
T Consensus       125 ~A~--~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~-~~~~~A~~  201 (389)
T PRK11788        125 RAE--ELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALAR-GDLDAARA  201 (389)
T ss_pred             HHH--HHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhC-CCHHHHHH
Confidence            544  334433     35668999999999999999999999999986643322    2345666778888 99999999


Q ss_pred             HHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          321 LLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       321 l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      .|+++.+.  ...+...+..+...|.+.|++++|.++|+++.+.+......+++.++.+|++.|+.++|.+.++++.+. 
T Consensus       202 ~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~-  278 (389)
T PRK11788        202 LLKKALAA--DPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE-  278 (389)
T ss_pred             HHHHHHhH--CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-
Confidence            99999765  223466788888999999999999999999987643333567899999999999999999999999876 


Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---cCCHHHHHHHHHHHHHCCCccCHH
Q 011102          401 CLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA---SGRLAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       401 i~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~---~g~~~~A~~l~~~m~~~g~~pd~~  476 (493)
                       .|+...+..+...+.+.|++++|..+|+++.+.  .|+..+++.++..+..   .|+.+++..++++|.+.++.|+..
T Consensus       279 -~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        279 -YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             -CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCC
Confidence             477777899999999999999999999998865  5999999999998885   569999999999999988887765

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

Probab=99.78  E-value=4.4e-16  Score=173.84  Aligned_cols=295  Identities=10%  Similarity=0.005  Sum_probs=217.5

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+...|+.++|+..+..+....     .|..+...|.+.|++++|++.|+.+.+. . ..+...+..+..++.+.|+++
T Consensus       575 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~-~~~~~~~~~l~~~~~~~~~~~  652 (899)
T TIGR02917       575 QYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLAL-Q-PDSALALLLLADAYAVMKNYA  652 (899)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-C-CCChHHHHHHHHHHHHcCCHH
Confidence            44556677777777777665432     6777777777888888888888777653 1 224556777777777777744


Q ss_pred             hhhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHH
Q 011102          250 VPFKLENFVS-----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDE  324 (493)
Q Consensus       250 ~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~  324 (493)
                      .+.  ..+..     ..+..+|..+...+.+.|++++|.++++.+.+.+ ..+...+..+...+.+. |++++|.+.|+.
T Consensus       653 ~A~--~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-g~~~~A~~~~~~  728 (899)
T TIGR02917       653 KAI--TSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQ-KDYPAAIQAYRK  728 (899)
T ss_pred             HHH--HHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHC-CCHHHHHHHHHH
Confidence            333  33322     1245677888888888888888888888887765 34566777777778888 888888888888


Q ss_pred             HhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC
Q 011102          325 LGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD  404 (493)
Q Consensus       325 m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd  404 (493)
                      +...   .|+..++..+..++.+.|++++|.+.++.+.+.. +.+...++.+...|.+.|++++|.+.|+++.+.. ..+
T Consensus       729 ~~~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~  803 (899)
T TIGR02917       729 ALKR---APSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDN  803 (899)
T ss_pred             HHhh---CCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCC
Confidence            7664   3555677778888888888888888888877643 4567888888888888899999999888887764 356


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          405 LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       405 ~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      ...++.+...+.+.|+ ++|..++++..+... -+..++..+...+...|++++|.++++++.+.+.. |..++..+..
T Consensus       804 ~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~l~~  879 (899)
T TIGR02917       804 AVVLNNLAWLYLELKD-PRALEYAEKALKLAP-NIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYHLAL  879 (899)
T ss_pred             HHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCC-CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHHHHH
Confidence            7788888888888888 778888888875432 25566778888889999999999999999987654 7777766665

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=99.77  E-value=7.5e-16  Score=171.95  Aligned_cols=295  Identities=8%  Similarity=-0.036  Sum_probs=207.1

Q ss_pred             hccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCch
Q 011102          176 GLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKV  250 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~  250 (493)
                      .+...|+.++|.+.+.++....     .+..+...+.+.|+.++|..+|+.+...  ...+...+..+...+.+.|+++.
T Consensus       508 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~  585 (899)
T TIGR02917       508 IDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAEL--NPQEIEPALALAQYYLGKGQLKK  585 (899)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CccchhHHHHHHHHHHHCCCHHH
Confidence            3455677788887777665432     5666777777788888888888777653  22345566777777777777443


Q ss_pred             hhhHHHhhcc-----CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Q 011102          251 PFKLENFVSL-----ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDEL  325 (493)
Q Consensus       251 ~~~l~~~~~~-----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m  325 (493)
                      +  +..+..+     .+..+|..+...|.+.|++++|...|+++.+.. +.+...+..+...+.+. |++++|...++.+
T Consensus       586 A--~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~~  661 (899)
T TIGR02917       586 A--LAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVM-KNYAKAITSLKRA  661 (899)
T ss_pred             H--HHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHc-CCHHHHHHHHHHH
Confidence            3  3333322     245677888888888888888888888877643 23455677777777777 8888888888877


Q ss_pred             hhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH
Q 011102          326 GQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL  405 (493)
Q Consensus       326 ~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~  405 (493)
                      ...  ...+..++..+...+.+.|++++|.++++.+.+.+ ..+...+..+...+.+.|++++|.+.|+.+.+.+  |+.
T Consensus       662 ~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~  736 (899)
T TIGR02917       662 LEL--KPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSS  736 (899)
T ss_pred             Hhc--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCc
Confidence            654  23456777788888888888888888888887654 4466677777788888888888888888877653  444


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      .++..+..++.+.|++++|.+.++.+.+.. ..+...+..+...|.+.|++++|.++|+++.+.. +.+..++..+..
T Consensus       737 ~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~  812 (899)
T TIGR02917       737 QNAIKLHRALLASGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA-PDNAVVLNNLAW  812 (899)
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            667777788888888888888888877543 3467777778888888888888888888887653 345555555544

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=99.77  E-value=9.1e-16  Score=155.50  Aligned_cols=267  Identities=13%  Similarity=0.150  Sum_probs=218.1

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCchhhhHHHhhcc---C------cHHHHHHHHHHHH
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELKVPFKLENFVSL---A------SKGVLEATAKGFV  274 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~~~~~l~~~~~~---~------~~~~~~~li~~~~  274 (493)
                      .+...|++++|++.|..+.+.   .| +..++..+...+.+.|+++.+...  +..+   +      ...++..+...|.
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~la~~~~~~g~~~~A~~~--~~~~l~~~~~~~~~~~~~~~~La~~~~  118 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKV---DPETVELHLALGNLFRRRGEVDRAIRI--HQNLLSRPDLTREQRLLALQELGQDYL  118 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhc---CcccHHHHHHHHHHHHHcCcHHHHHHH--HHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence            456789999999999999864   34 455788899999999986544433  3322   1      1246889999999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC----HHHHHHHHHHHHHcCC
Q 011102          275 KGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS----QQDCTAIMKVGIRLQK  350 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~----~~~~~~li~~~~~~g~  350 (493)
                      +.|++++|.++|+++.+.. ..+..+++.+...+.+. |++++|.+.++.+.+. +-.++    ...|..+...+.+.|+
T Consensus       119 ~~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~-g~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~la~~~~~~~~  195 (389)
T PRK11788        119 KAGLLDRAEELFLQLVDEG-DFAEGALQQLLEIYQQE-KDWQKAIDVAERLEKL-GGDSLRVEIAHFYCELAQQALARGD  195 (389)
T ss_pred             HCCCHHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHh-chHHHHHHHHHHHHHh-cCCcchHHHHHHHHHHHHHHHhCCC
Confidence            9999999999999998753 34677899999999999 9999999999999876 32222    2245667788899999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          351 FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSK  430 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~  430 (493)
                      +++|...|+++.+.. +.+...+..+...|.+.|++++|.++|+++.+.+......+++.+..+|++.|++++|...+++
T Consensus       196 ~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~  274 (389)
T PRK11788        196 LDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRR  274 (389)
T ss_pred             HHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            999999999998653 3356788889999999999999999999998764333356789999999999999999999999


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          431 LKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       431 m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      +.+.  .|+...+..+...+.+.|++++|.++++++.+.  .|+..++..++..
T Consensus       275 ~~~~--~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~  324 (389)
T PRK11788        275 ALEE--YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDY  324 (389)
T ss_pred             HHHh--CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHH
Confidence            9875  477777899999999999999999999998875  7999999988763

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.61  E-value=1.8e-12  Score=123.88  Aligned_cols=288  Identities=12%  Similarity=0.074  Sum_probs=206.6

Q ss_pred             CCCHHHHHHHHhhhcccC-cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhh
Q 011102          180 HKDVAEVLDKCGRFLRKG-SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFV  258 (493)
Q Consensus       180 ~~~~~~a~~~~~~m~~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~  258 (493)
                      .|++.+  -.|+..++.+ +|+++|.++|+--..+.|.+++++.... ..+.+..+||.+|.+-+-...-+....+....
T Consensus       192 ~G~vAd--L~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~-k~kv~~~aFN~lI~~~S~~~~K~Lv~EMisqk  268 (625)
T KOG4422|consen  192 SGAVAD--LLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAA-KGKVYREAFNGLIGASSYSVGKKLVAEMISQK  268 (625)
T ss_pred             cccHHH--HHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHh-hheeeHHhhhhhhhHHHhhccHHHHHHHHHhh
Confidence            466655  3455555444 9999999999999999999999999886 78889999999998876554423333333334


Q ss_pred             ccCcHHHHHHHHHHHHhcCCHHH----HHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc-C--CC
Q 011102          259 SLASKGVLEATAKGFVKGGNLKL----AWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQR-D--DL  331 (493)
Q Consensus       259 ~~~~~~~~~~li~~~~~~g~~~~----A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~-~--g~  331 (493)
                      --||..|||+++...++.|+++.    |.+++.+|++.|+.|...+|..+|.-+++.++....|..++.++... .  .+
T Consensus       269 m~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~f  348 (625)
T KOG4422|consen  269 MTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTF  348 (625)
T ss_pred             cCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcc
Confidence            45799999999999999998765    57889999999999999999999999999944445555555555432 0  22


Q ss_pred             CC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc----CCCCCH---HHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          332 NL----SQQDCTAIMKVGIRLQKFGVVESLFHWFTHS----GRDPTV---VMYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       332 ~p----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~~---~ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      +|    |...|...|+.|.+..+.+.|.++-.-+...    -+.|+.   +-|.-+....|+....+.-++.++.|.-.-
T Consensus       349 kp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~  428 (625)
T KOG4422|consen  349 KPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSA  428 (625)
T ss_pred             cCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccce
Confidence            32    4556778888888888888888876655421    122332   235566677777777777777777777666


Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-------------------CCC-----------------------
Q 011102          401 CLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG-------------------FCP-----------------------  438 (493)
Q Consensus       401 i~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g-------------------~~p-----------------------  438 (493)
                      .-|+..+...++++.--.|.++-.-++|.+|+..|                   ..|                       
T Consensus       429 y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~  508 (625)
T KOG4422|consen  429 YFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAY  508 (625)
T ss_pred             ecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHH
Confidence            66777777777777777777776666666665444                   112                       


Q ss_pred             ------------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          439 ------------TYDIYRDMIRIFMASGRLAKCRDVCKEAEMAG  470 (493)
Q Consensus       439 ------------~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g  470 (493)
                                  .....+.+.-.+.|.|+.++|.++|....+++
T Consensus       509 e~~~~R~r~~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~  552 (625)
T KOG4422|consen  509 ESQPIRQRAQDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKH  552 (625)
T ss_pred             HhhHHHHHhccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcC
Confidence                        22235556666788899999999988885544

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.56  E-value=2.9e-12  Score=122.53  Aligned_cols=216  Identities=14%  Similarity=0.183  Sum_probs=157.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      ...+|.+||.|+||-...+.|.+++++-.....+.+..+||.+|.+-+-..|     .+++.+|... .+.||..|+|++
T Consensus       206 T~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~-----K~Lv~EMisq-km~Pnl~TfNal  279 (625)
T KOG4422|consen  206 TDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG-----KKLVAEMISQ-KMTPNLFTFNAL  279 (625)
T ss_pred             CchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc-----HHHHHHHHHh-hcCCchHhHHHH
Confidence            4568999999999999999999999999998899999999999987655522     6888999988 899999999999


Q ss_pred             HHHHHHcCCHHH----HHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHH-HHHHHHHHHH----CCCCC----CHHHH
Q 011102          342 MKVGIRLQKFGV----VESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCRE-ALTVVWNMEA----SNCLF----DLPAY  408 (493)
Q Consensus       342 i~~~~~~g~~~~----A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~-A~~l~~~M~~----~gi~p----d~~ty  408 (493)
                      +++..+.|+++.    |.+++.+|++-|+.|...+|.-+|.-+++.++..+ |..++.++..    +.++|    |..-|
T Consensus       280 L~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF  359 (625)
T KOG4422|consen  280 LSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFF  359 (625)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHH
Confidence            999999998765    56888999999999999999999999999988644 5555555443    22333    33445


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHC---C-CCCCH---HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHH
Q 011102          409 RVVIKLFVALNDISRAIRYFSKLKEA---G-FCPTY---DIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVEL  481 (493)
Q Consensus       409 ~~li~~~~~~g~~~~A~~~~~~m~~~---g-~~p~~---~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~L  481 (493)
                      ...+..|.+..+.+.|.++-.-+...   . +.|+.   .-|.-+....|.....+.-...++.|.-+-+-|+..+...+
T Consensus       360 ~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~  439 (625)
T KOG4422|consen  360 QSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHL  439 (625)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHH
Confidence            66666677777777776665544411   1 11221   12445555555655666666666666555555555555555


Q ss_pred             HH
Q 011102          482 LQ  483 (493)
Q Consensus       482 l~  483 (493)
                      ++
T Consensus       440 lr  441 (625)
T KOG4422|consen  440 LR  441 (625)
T ss_pred             HH
Confidence            55

>PF13041 PPR_2: PPR repeat family

Probab=99.51  E-value=3.4e-14  Score=98.54  Aligned_cols=49  Identities=31%  Similarity=0.372  Sum_probs=26.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          368 PTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       368 p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      ||+++||+||++|++.|++++|+++|++|++.|+.||..||+++|++||
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

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.47  E-value=4.9e-10  Score=120.59  Aligned_cols=282  Identities=10%  Similarity=0.003  Sum_probs=210.0

Q ss_pred             hccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCc
Q 011102          176 GLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELK  249 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~  249 (493)
                      .....|+.++|...+++.....     .|..+-..+.+.|++++|++.|+.+...   .| +...+..+..++...|+.+
T Consensus        85 ~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l---~P~~~~a~~~la~~l~~~g~~~  161 (656)
T PRK15174         85 SPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLKSKQYATVADLAEQAWLA---FSGNSQIFALHLRTLVLMDKEL  161 (656)
T ss_pred             hHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHCCChH
Confidence            3445899999999998776543     6777778889999999999999998753   34 4556788888888989866


Q ss_pred             hhhhHHH-h-hccC-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHh
Q 011102          250 VPFKLEN-F-VSLA-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELG  326 (493)
Q Consensus       250 ~~~~l~~-~-~~~~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~  326 (493)
                      .+..... . ...+ +...+..+ ..+.+.|++++|..+++.+.+..-.++...+..+...+.+. |++++|...++...
T Consensus       162 eA~~~~~~~~~~~P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~-g~~~eA~~~~~~al  239 (656)
T PRK15174        162 QAISLARTQAQEVPPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAV-GKYQEAIQTGESAL  239 (656)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHC-CCHHHHHHHHHHHH
Confidence            5444321 1 1122 23334333 34788899999999999887764334455555566778888 99999999999987


Q ss_pred             hcCCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 011102          327 QRDDLNLSQQDCTAIMKVGIRLQKFGV----VESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL  402 (493)
Q Consensus       327 ~~~g~~p~~~~~~~li~~~~~~g~~~~----A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~  402 (493)
                      ..  -.-+...+..+-..|.+.|++++    |...|++..+.. +.+...+..+...+.+.|++++|...+++..+..  
T Consensus       240 ~~--~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~--  314 (656)
T PRK15174        240 AR--GLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATH--  314 (656)
T ss_pred             hc--CCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--
Confidence            65  23456777888889999999886    789998887542 3356788999999999999999999999987653  


Q ss_pred             CC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          403 FD-LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDI-YRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       403 pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~t-y~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      |+ ...+..+-..+.+.|++++|...|+.+.+..  |+... +..+..++...|+.++|.+.|++..+.
T Consensus       315 P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~--P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~  381 (656)
T PRK15174        315 PDLPYVRAMYARALRQVGQYTAASDEFVQLAREK--GVTSKWNRYAAAALLQAGKTSEAESVFEHYIQA  381 (656)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--ccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            44 4566777888999999999999999888643  55433 334566788999999999999998764

>PF13041 PPR_2: PPR repeat family

Probab=99.46  E-value=1.7e-13  Score=95.07  Aligned_cols=50  Identities=18%  Similarity=0.208  Sum_probs=46.6

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 011102          333 LSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS  382 (493)
Q Consensus       333 p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~  382 (493)
                      ||+++||++|++|++.|++++|.++|++|.+.|+.||..||++||++||+
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            78999999999999999999999999999999999999999999999985

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.45  E-value=8.3e-10  Score=118.80  Aligned_cols=243  Identities=11%  Similarity=-0.044  Sum_probs=109.2

Q ss_pred             cCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhh
Q 011102          178 DSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPF  252 (493)
Q Consensus       178 ~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~  252 (493)
                      ...|+.++|+..+.+.....     .+..+...+...|++++|...++.+... .-. +...+..+ ..+.+.|+++.+ 
T Consensus       121 ~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~-~P~-~~~a~~~~-~~l~~~g~~~eA-  196 (656)
T PRK15174        121 LKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQE-VPP-RGDMIATC-LSFLNKSRLPED-  196 (656)
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHh-CCC-CHHHHHHH-HHHHHcCCHHHH-
Confidence            34455555555555443321     4444555555555555555555544432 111 11112111 224444443222 


Q ss_pred             hHHHhhc------cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHH----HHHHH
Q 011102          253 KLENFVS------LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYML----VMTLL  322 (493)
Q Consensus       253 ~l~~~~~------~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~----a~~l~  322 (493)
                       +..+..      ..+...+..+...+.+.|++++|...|++..+.. .-+...+..+-..+.+. |++++    |...|
T Consensus       197 -~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~-G~~~eA~~~A~~~~  273 (656)
T PRK15174        197 -HDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQS-GRSREAKLQAAEHW  273 (656)
T ss_pred             -HHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHc-CCchhhHHHHHHHH
Confidence             222221      1112223333445555555555555555555432 12233444444455555 55543    45555


Q ss_pred             HHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 011102          323 DELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL  402 (493)
Q Consensus       323 ~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~  402 (493)
                      ++....  -.-+...+..+...+.+.|++++|...+++..+.. +-+...+..+...|.+.|++++|.+.++++.+.  .
T Consensus       274 ~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~--~  348 (656)
T PRK15174        274 RHALQF--NSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDEFVQLARE--K  348 (656)
T ss_pred             HHHHhh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--C
Confidence            554432  11233455555555555555555555555554331 112334444555555555555555555555443  2


Q ss_pred             CCHHH-HHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          403 FDLPA-YRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       403 pd~~t-y~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      |+... +..+..++...|+.++|...|+...
T Consensus       349 P~~~~~~~~~a~al~~~G~~deA~~~l~~al  379 (656)
T PRK15174        349 GVTSKWNRYAAAALLQAGKTSEAESVFEHYI  379 (656)
T ss_pred             ccchHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            33222 2223344555555555555555554

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

Probab=99.25  E-value=6.8e-11  Score=114.23  Aligned_cols=254  Identities=15%  Similarity=0.066  Sum_probs=111.7

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHH-HHHHcCCCchhhhHHHhhccC-----cHHHHHHHHHHHHhc
Q 011102          203 VRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVE-VLARHHELKVPFKLENFVSLA-----SKGVLEATAKGFVKG  276 (493)
Q Consensus       203 i~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~-~~~~~g~~~~~~~l~~~~~~~-----~~~~~~~li~~~~~~  276 (493)
                      -..+.+.|++++|++++...... ...|+...|-.++. ..-..++++.+.  ..+..+.     +...+..++.. ...
T Consensus        15 A~~~~~~~~~~~Al~~L~~~~~~-~~~~~~~~~~~~~a~La~~~~~~~~A~--~ay~~l~~~~~~~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   15 ARLLYQRGDYEKALEVLKKAAQK-IAPPDDPEYWRLLADLAWSLGDYDEAI--EAYEKLLASDKANPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccc-ccccccccccccccccccccccccccc--ccccccccccccccccccccccc-ccc
Confidence            34566778888888888544322 21344444433333 333345433333  3333322     33356667776 688


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          277 GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVES  356 (493)
Q Consensus       277 g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~  356 (493)
                      +++++|.+++++..+..  +++..+...+..+.+. ++++++.++++..........+...|..+...+.+.|+.++|++
T Consensus        91 ~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~  167 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERD--GDPRYLLSALQLYYRL-GDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALR  167 (280)
T ss_dssp             -----------------------------H-HHHT-T-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHH
T ss_pred             ccccccccccccccccc--cccchhhHHHHHHHHH-hHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            99999999998776543  6777788888889898 99999999999987654566788889999999999999999999


Q ss_pred             HHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          357 LFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       357 l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      .|++..+.  .| |....+.++..+...|+.+++.+++....+.. ..|...+..+-.+|...|+.++|..+|++.....
T Consensus       168 ~~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~  244 (280)
T PF13429_consen  168 DYRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN  244 (280)
T ss_dssp             HHHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc
Confidence            99998765  56 47788999999999999999999998877653 4455667888999999999999999999988643


Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          436 FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       436 ~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                       +.|......+.+++...|+.++|.++..+..
T Consensus       245 -p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  245 -PDDPLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             -TT-HHHHHHHHHHHT----------------
T ss_pred             -ccccccccccccccccccccccccccccccc
Confidence             2377778899999999999999999887654

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

Probab=99.24  E-value=7.9e-10  Score=110.49  Aligned_cols=346  Identities=14%  Similarity=0.068  Sum_probs=248.5

Q ss_pred             ccccchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh----hhhhhhhhhccCCchhHHHHH
Q 011102           96 FIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA----SSRASICKQVYKNPSFLISLA  171 (493)
Q Consensus        96 ~~~~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a----~~~~~~~~~~~~~~~~l~~l~  171 (493)
                      +.-+.|++++|..++..+..-.+.++..|.-+.          .++...+....|    ...-...|+.....+.+-.+.
T Consensus       125 ~~kerg~~~~al~~y~~aiel~p~fida~inla----------~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnLl  194 (966)
T KOG4626|consen  125 ILKERGQLQDALALYRAAIELKPKFIDAYINLA----------AALVTQGDLELAVQCFFEALQLNPDLYCARSDLGNLL  194 (966)
T ss_pred             HHHHhchHHHHHHHHHHHHhcCchhhHHHhhHH----------HHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhHHH
Confidence            455589999999999998444555666776666          555555555544    111122232222222222222


Q ss_pred             HHHhhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHH-HHHHHHHHHHHc
Q 011102          172 RDIKGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDR-LLASTVEVLARH  245 (493)
Q Consensus       172 ~~l~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~-t~~~li~~~~~~  245 (493)
                            ...|++.+|...+.+.....     .|+.|=..+-..|+.-.|++-|++..+-   .|+-- .|-.|=..|...
T Consensus       195 ------ka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl---dP~f~dAYiNLGnV~ke~  265 (966)
T KOG4626|consen  195 ------KAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL---DPNFLDAYINLGNVYKEA  265 (966)
T ss_pred             ------HhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcC---CCcchHHHhhHHHHHHHH
Confidence                  23578888888877655543     7888888889999999999999988743   44322 455566666666


Q ss_pred             CCCchhhhHHHhhc----cC-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHH
Q 011102          246 HELKVPFKLENFVS----LA-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVM  319 (493)
Q Consensus       246 g~~~~~~~l~~~~~----~~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~  319 (493)
                      +.++.+  +..|..    -+ ..++|..|...|-..|.+|.|+..+++..+.  .|+ +..|+.|-.++-.. |++.+|.
T Consensus       266 ~~~d~A--vs~Y~rAl~lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~--~P~F~~Ay~NlanALkd~-G~V~ea~  340 (966)
T KOG4626|consen  266 RIFDRA--VSCYLRALNLRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL--QPNFPDAYNNLANALKDK-GSVTEAV  340 (966)
T ss_pred             hcchHH--HHHHHHHHhcCCcchhhccceEEEEeccccHHHHHHHHHHHHhc--CCCchHHHhHHHHHHHhc-cchHHHH
Confidence            665443  333322    22 4456777778888999999999999988874  355 56899999999999 9999999


Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          320 TLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       320 ~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      +.+.....-  ..--....+.|-+.|...|++++|..+|..-.+-  .|. ...+|.|-..|-+.|++++|+.-+++..+
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            999987764  2223457788899999999999999999876642  444 46688999999999999999999998765


Q ss_pred             CCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCH
Q 011102          399 SNCLFDL-PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDK  475 (493)
Q Consensus       399 ~gi~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~  475 (493)
                        |+|+. ..|+.+=..|-..|+++.|.+.+.+....  .|. ...++.|-..|-.+|++.+|..-+++..+  ++||.
T Consensus       417 --I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~--nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPDf  489 (966)
T KOG4626|consen  417 --IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQI--NPTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPDF  489 (966)
T ss_pred             --cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhc--CcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCCC
Confidence              67775 57888888888999999999998887653  344 35678888899999999999999988775  56664

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.23  E-value=5.6e-08  Score=98.62  Aligned_cols=272  Identities=10%  Similarity=0.025  Sum_probs=205.2

Q ss_pred             CCCHHHHHHHHhhhcccC---cHHHHH--HHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHH--HHHHHHHHcCCCchhh
Q 011102          180 HKDVAEVLDKCGRFLRKG---SLSFTV--RELGHMNLPERALQTFCWAQKQPHLFPDDRLLA--STVEVLARHHELKVPF  252 (493)
Q Consensus       180 ~~~~~~a~~~~~~m~~~~---~~~~li--~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~--~li~~~~~~g~~~~~~  252 (493)
                      .|++..|.+......+..   ..+.++  .+..+.|+++.|.+.|..+.+.   .||...+.  .....+...|+.+.+.
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~---~~~~~~~~~l~~a~l~l~~g~~~~Al  173 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAEL---ADNDQLPVEITRVRIQLARNENHAAR  173 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CCcchHHHHHHHHHHHHHCCCHHHHH
Confidence            589999998888765542   333333  3447899999999999999754   55654333  3355677778855444


Q ss_pred             hHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-------HHHHHHHHHHhcCCCCHHHHHH
Q 011102          253 KLENFVS-----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP-------SIYAKLILELGKNPDKYMLVMT  320 (493)
Q Consensus       253 ~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~-------~t~~~li~~~~~~~~~~~~a~~  320 (493)
                      .  .+..     ..+......+...|.+.|++++|.+++..+.+.+..++.       .+|..++...... .+.+...+
T Consensus       174 ~--~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~-~~~~~l~~  250 (398)
T PRK10747        174 H--GVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMAD-QGSEGLKR  250 (398)
T ss_pred             H--HHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHh-cCHHHHHH
Confidence            3  3332     235678899999999999999999999999998765333       1334444444455 55677777


Q ss_pred             HHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          321 LLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       321 l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      +++.+-+.  ...+......+...+.+.|+.++|.+++++..+.  .||..  -.++.+....++.+++++..+...+. 
T Consensus       251 ~w~~lp~~--~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~--l~~l~~~l~~~~~~~al~~~e~~lk~-  323 (398)
T PRK10747        251 WWKNQSRK--TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER--LVLLIPRLKTNNPEQLEKVLRQQIKQ-  323 (398)
T ss_pred             HHHhCCHH--HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH--HHHHHhhccCCChHHHHHHHHHHHhh-
Confidence            77777543  4457888899999999999999999999998764  45542  23455666779999999999998765 


Q ss_pred             CCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          401 CLFDL-PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       401 i~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                       .||. ..+.++=..|.+.|++++|.+.|+...+.  .|+..+|..+...+.+.|+.++|.+++++-.
T Consensus       324 -~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        324 -HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             -CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence             3544 45778888899999999999999999864  5999999999999999999999999998764

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.22  E-value=1.8e-08  Score=115.81  Aligned_cols=346  Identities=13%  Similarity=0.014  Sum_probs=215.4

Q ss_pred             ccccchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh---hhhhh-hhhhccCCc---hhHH
Q 011102           96 FIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA---SSRAS-ICKQVYKNP---SFLI  168 (493)
Q Consensus        96 ~~~~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a---~~~~~-~~~~~~~~~---~~l~  168 (493)
                      .....|+++.|...|+......+.+...+..+.          ..+...++.++|   +.+.- ..|+.....   .++.
T Consensus       278 ~~~~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg----------~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~  347 (1157)
T PRK11447        278 AAVDSGQGGKAIPELQQAVRANPKDSEALGALG----------QAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLK  347 (1157)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHH----------HHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHH
Confidence            345678999999999887222222333343444          444444555555   11111 112111000   0110


Q ss_pred             -----HHHHHHhhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHH
Q 011102          169 -----SLARDIKGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFP-DDRLLAS  237 (493)
Q Consensus       169 -----~l~~~l~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~  237 (493)
                           .....-..+.+.+++++|+..+.+.....     .+..+-..+...|++++|++.|+...+.   .| +...+..
T Consensus       348 ~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~---~p~~~~a~~~  424 (1157)
T PRK11447        348 VNRYWLLIQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRM---DPGNTNAVRG  424 (1157)
T ss_pred             hhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHH
Confidence                 00111134557899999999999776543     5566777899999999999999999854   23 3445555


Q ss_pred             HHHHHHHcCCCchhhhHHHhhccCc--------------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHH
Q 011102          238 TVEVLARHHELKVPFKLENFVSLAS--------------KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYA  302 (493)
Q Consensus       238 li~~~~~~g~~~~~~~l~~~~~~~~--------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~  302 (493)
                      +...+.. ++  ..+++..+...+.              ...+..+...+...|++++|.+.|++..+..  |+ ...+.
T Consensus       425 L~~l~~~-~~--~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~--P~~~~~~~  499 (1157)
T PRK11447        425 LANLYRQ-QS--PEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD--PGSVWLTY  499 (1157)
T ss_pred             HHHHHHh-cC--HHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHH
Confidence            5555533 33  2333332322211              1134455566777788888888887777643  43 34455


Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHH-------------------------------------------
Q 011102          303 KLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCT-------------------------------------------  339 (493)
Q Consensus       303 ~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~-------------------------------------------  339 (493)
                      .+-..|.+. |++++|...++++.+...  -+...+.                                           
T Consensus       500 ~LA~~~~~~-G~~~~A~~~l~~al~~~P--~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~  576 (1157)
T PRK11447        500 RLAQDLRQA-GQRSQADALMRRLAQQKP--NDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQV  576 (1157)
T ss_pred             HHHHHHHHc-CCHHHHHHHHHHHHHcCC--CCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHH
Confidence            566667777 777777777777654311  1111111                                           


Q ss_pred             -HHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          340 -AIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL  418 (493)
Q Consensus       340 -~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~  418 (493)
                       .+...+...|+.++|.++++.     .+.+...+..+-..+.+.|+.++|++.|++..+.. .-+...+..+...|...
T Consensus       577 l~~a~~l~~~G~~~eA~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~-P~~~~a~~~la~~~~~~  650 (1157)
T PRK11447        577 LETANRLRDSGKEAEAEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTRE-PGNADARLGLIEVDIAQ  650 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHC
Confidence             123345555666666666551     24455667778888999999999999999987753 23567888899999999


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          419 NDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       419 g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      |+.++|.+.++...+.. ..+..++..+..++...|++++|.++++.+...
T Consensus       651 g~~~eA~~~l~~ll~~~-p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        651 GDLAAARAQLAKLPATA-NDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             CCHHHHHHHHHHHhccC-CCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            99999999999876432 124556677788888999999999999998764

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.20  E-value=3.1e-08  Score=91.74  Aligned_cols=200  Identities=13%  Similarity=0.004  Sum_probs=164.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      ...+..+...|...|++++|.+.+++..+.. +.+...+..+...+... |++++|.+.+++..+.  ...+...+..+.
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~-~~~~~A~~~~~~al~~--~~~~~~~~~~~~  106 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQL-GELEKAEDSFRRALTL--NPNNGDVLNNYG  106 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhh--CCCCHHHHHHHH
Confidence            4567888899999999999999999988754 23456777788888888 9999999999998765  234566788888


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRD-PTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      ..|...|++++|.+.|++....... .....+..+...+...|+.++|.+.+.+..+..- .+...+..+...+...|++
T Consensus       107 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~  185 (234)
T TIGR02521       107 TFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDP-QRPESLLELAELYYLRGQY  185 (234)
T ss_pred             HHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CChHHHHHHHHHHHHcCCH
Confidence            9999999999999999998764322 2445677788899999999999999999876532 2456788888999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          422 SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       422 ~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ++|..++++..+. ...+...+..+...+...|+.++|..+++.+..
T Consensus       186 ~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       186 KDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            9999999998866 345677778888999999999999999888764

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.

>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=99.20  E-value=3.7e-08  Score=105.95  Aligned_cols=252  Identities=12%  Similarity=-0.049  Sum_probs=191.9

Q ss_pred             CChHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHHcCCCchhhhHHHhhc----cC-cHHHHHHHHHHHHhcCCHHHHH
Q 011102          210 NLPERALQTFCWAQKQPHLFPD-DRLLASTVEVLARHHELKVPFKLENFVS----LA-SKGVLEATAKGFVKGGNLKLAW  283 (493)
Q Consensus       210 g~~~~A~~l~~~m~~~~g~~pd-~~t~~~li~~~~~~g~~~~~~~l~~~~~----~~-~~~~~~~li~~~~~~g~~~~A~  283 (493)
                      +++++|++.|+.........|+ ...|..+-..+...|+++.  ++..+..    -+ ....|..+...+...|++++|.
T Consensus       308 ~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~e--A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~  385 (615)
T TIGR00990       308 ESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLE--ALADLSKSIELDPRVTQSYIKRASMNLELGDPDKAE  385 (615)
T ss_pred             hhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHH--HHHHHHHHHHcCCCcHHHHHHHHHHHHHCCCHHHHH
Confidence            6788999999999875223443 3457777777778888544  4443433    22 3457888889999999999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          284 KLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTH  363 (493)
Q Consensus       284 ~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  363 (493)
                      ..|++..+.. +-+..+|..+-..+... |++++|...|++....  ...+...+..+...+.+.|++++|+..|++..+
T Consensus       386 ~~~~~al~~~-p~~~~~~~~lg~~~~~~-g~~~~A~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~  461 (615)
T TIGR00990       386 EDFDKALKLN-SEDPDIYYHRAQLHFIK-GEFAQAGKDYQKSIDL--DPDFIFSHIQLGVTQYKEGSIASSMATFRRCKK  461 (615)
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHc--CccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            9999988753 23467888888888898 9999999999998765  223566777888899999999999999999875


Q ss_pred             cCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-----CH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC
Q 011102          364 SGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-----DL-PAYRVVIKLFVALNDISRAIRYFSKLKEAGFC  437 (493)
Q Consensus       364 ~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-----d~-~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~  437 (493)
                      . .+-+...|+.+-..+...|++++|.+.|++..+..-..     +. ..++..+..+...|++++|.+++++...... 
T Consensus       462 ~-~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p-  539 (615)
T TIGR00990       462 N-FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDP-  539 (615)
T ss_pred             h-CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCC-
Confidence            4 23457889999999999999999999999977642211     11 1122223334457999999999999876542 


Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          438 PTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       438 p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      -+...+..+...+.+.|++++|.+.|++..+.
T Consensus       540 ~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       540 ECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            34567899999999999999999999998764

>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=99.20  E-value=1.1e-07  Score=102.44  Aligned_cols=282  Identities=9%  Similarity=-0.070  Sum_probs=202.3

Q ss_pred             hccCCCCHHHHHHHHhhhccc----CcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCch
Q 011102          176 GLDSHKDVAEVLDKCGRFLRK----GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELKV  250 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~----~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~~  250 (493)
                      .+-+.+++++|+..|.+....    ..|..+-.+|.+.|++++|++.+......   .| +...|..+-.++...|+++.
T Consensus       136 ~~~~~~~~~~Ai~~y~~al~~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l---~p~~~~a~~~~a~a~~~lg~~~e  212 (615)
T TIGR00990       136 KAYRNKDFNKAIKLYSKAIECKPDPVYYSNRAACHNALGDWEKVVEDTTAALEL---DPDYSKALNRRANAYDGLGKYAD  212 (615)
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHHHcCCHHH
Confidence            345567777777777754432    25666666777778888888888777643   33 34466666677777776443


Q ss_pred             hhhHHHhhc----------------------------------cC-cHHHHHHH--------------------------
Q 011102          251 PFKLENFVS----------------------------------LA-SKGVLEAT--------------------------  269 (493)
Q Consensus       251 ~~~l~~~~~----------------------------------~~-~~~~~~~l--------------------------  269 (493)
                      +.  ..+..                                  .+ +...+..+                          
T Consensus       213 A~--~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  290 (615)
T TIGR00990       213 AL--LDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEET  290 (615)
T ss_pred             HH--HHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhccccccccc
Confidence            32  11100                                  00 00000000                          


Q ss_pred             ----HHHH------HhcCCHHHHHHHHHHHHhCC-CCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-HH
Q 011102          270 ----AKGF------VKGGNLKLAWKLLMVAKDGG-RMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-QQ  336 (493)
Q Consensus       270 ----i~~~------~~~g~~~~A~~l~~~m~~~g-~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-~~  336 (493)
                          +..+      ...+++++|.+.|++..+.+ ..|+ ...|+.+-..+... |++++|+..++.....   .|+ ..
T Consensus       291 ~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~-g~~~eA~~~~~kal~l---~P~~~~  366 (615)
T TIGR00990       291 GNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLK-GKHLEALADLSKSIEL---DPRVTQ  366 (615)
T ss_pred             ccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHc---CCCcHH
Confidence                0000      12367899999999998865 3343 44677777777888 9999999999998764   344 55


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .|..+...+...|++++|...|++..+.. +-+...|..+...|...|++++|...|++..+..- .+...+..+-..+.
T Consensus       367 ~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P-~~~~~~~~la~~~~  444 (615)
T TIGR00990       367 SYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDP-DFIFSHIQLGVTQY  444 (615)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCc-cCHHHHHHHHHHHH
Confidence            78888889999999999999999987652 34578899999999999999999999999876531 24567777888899


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          417 ALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      +.|++++|...|++..+.. .-+...|+.+-..+...|++++|.+.|++..+.
T Consensus       445 ~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l  496 (615)
T TIGR00990       445 KEGSIASSMATFRRCKKNF-PEAPDVYNYYGELLLDQNKFDEAIEKFDTAIEL  496 (615)
T ss_pred             HCCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            9999999999999987542 235778899999999999999999999998764

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.19  E-value=4.3e-08  Score=107.75  Aligned_cols=292  Identities=10%  Similarity=-0.017  Sum_probs=171.0

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~  249 (493)
                      ..+...++.++|+..+++.....    .+..+-..+...|+.++|+..++.+.+.   .| +...+..+..++...+..+
T Consensus        91 ~~l~~~g~~~eA~~~l~~~l~~~P~~~~~~~la~~l~~~g~~~~Al~~l~~al~~---~P~~~~~~~~la~~l~~~~~~e  167 (765)
T PRK10049         91 LTLADAGQYDEALVKAKQLVSGAPDKANLLALAYVYKRAGRHWDELRAMTQALPR---APQTQQYPTEYVQALRNNRLSA  167 (765)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHCCChH
Confidence            34566799999999888765432    2666677888999999999999999854   34 3334455555555555432


Q ss_pred             hhh--------------------------------------------hHHHhhccC-------cH-HHH----HHHHHHH
Q 011102          250 VPF--------------------------------------------KLENFVSLA-------SK-GVL----EATAKGF  273 (493)
Q Consensus       250 ~~~--------------------------------------------~l~~~~~~~-------~~-~~~----~~li~~~  273 (493)
                      .+.                                            ++..+..+.       +. ..+    ...+..+
T Consensus       168 ~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~L  247 (765)
T PRK10049        168 PALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGAL  247 (765)
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHH
Confidence            111                                            111111100       00 000    0112234


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCC--CCHHHHHHHHHHHHHcCC
Q 011102          274 VKGGNLKLAWKLLMVAKDGGRM-LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLN--LSQQDCTAIMKVGIRLQK  350 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~~~g~~-pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~--p~~~~~~~li~~~~~~g~  350 (493)
                      ...|+.++|...|+.+.+.+-. |+-.- ..+-..|... |++++|+..|+++.......  ........+..++.+.|+
T Consensus       248 l~~g~~~eA~~~~~~ll~~~~~~P~~a~-~~la~~yl~~-g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~  325 (765)
T PRK10049        248 LARDRYKDVISEYQRLKAEGQIIPPWAQ-RWVASAYLKL-HQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESEN  325 (765)
T ss_pred             HHhhhHHHHHHHHHHhhccCCCCCHHHH-HHHHHHHHhc-CCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhccc
Confidence            4557777777777777766521 32211 1134456666 77777777777765431111  112345555566777777


Q ss_pred             HHHHHHHHHHHHHcC-----------CCCC---HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          351 FGVVESLFHWFTHSG-----------RDPT---VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g-----------~~p~---~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      +++|.++++.+.+..           -.|+   ...+..+...+...|+.++|+++++++.... .-+...+..+...+.
T Consensus       326 ~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~  404 (765)
T PRK10049        326 YPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQ  404 (765)
T ss_pred             HHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            777777777776431           1122   2244556667777777777777777766542 223456666667777


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHH
Q 011102          417 ALNDISRAIRYFSKLKEAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~  476 (493)
                      ..|+.++|++.+++..+..  || ...+-.+...+.+.|++++|+.+++++.+  ..|+..
T Consensus       405 ~~g~~~~A~~~l~~al~l~--Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~--~~Pd~~  461 (765)
T PRK10049        405 ARGWPRAAENELKKAEVLE--PRNINLEVEQAWTALDLQEWRQMDVLTDDVVA--REPQDP  461 (765)
T ss_pred             hcCCHHHHHHHHHHHHhhC--CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHH--hCCCCH
Confidence            7777777777777766533  43 44555555667777777777777777765  344443

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

Probab=99.17  E-value=2.8e-09  Score=110.59  Aligned_cols=245  Identities=13%  Similarity=0.081  Sum_probs=154.4

Q ss_pred             hhcccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHH
Q 011102          192 RFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAK  271 (493)
Q Consensus       192 ~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~  271 (493)
                      ..+.+.+|..+|..||..|+.+.|- +|..|+-+ ....+...|+.++.+-...++.+-++       .+...||+.|..
T Consensus        21 i~PnRvtyqsLiarYc~~gdieaat-if~fm~~k-sLpv~e~vf~~lv~sh~~And~Enpk-------ep~aDtyt~Ll~   91 (1088)
T KOG4318|consen   21 ILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIK-SLPVREGVFRGLVASHKEANDAENPK-------EPLADTYTNLLK   91 (1088)
T ss_pred             CCCchhhHHHHHHHHcccCCCcccc-chhhhhcc-cccccchhHHHHHhcccccccccCCC-------CCchhHHHHHHH
Confidence            3444557888888888888888777 88877765 56667777888887777777755444       455668888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHh-------CCCCCCHHHH--------------HHHHHHHhcCCCCHHHHHHHHHHHhhcCC
Q 011102          272 GFVKGGNLKLAWKLLMVAKD-------GGRMLDPSIY--------------AKLILELGKNPDKYMLVMTLLDELGQRDD  330 (493)
Q Consensus       272 ~~~~~g~~~~A~~l~~~m~~-------~g~~pd~~t~--------------~~li~~~~~~~~~~~~a~~l~~~m~~~~g  330 (493)
                      +|...|++..-..+=+.|..       .|+.--..-+              ...|.-..-. |.|+.+++++..+-....
T Consensus        92 ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~e-glwaqllkll~~~Pvsa~  170 (1088)
T KOG4318|consen   92 AYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLE-GLWAQLLKLLAKVPVSAW  170 (1088)
T ss_pred             HHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHH-HHHHHHHHHHhhCCcccc
Confidence            88888887552222111221       2211111111              1122222223 445555555544432212


Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q 011102          331 LNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRV  410 (493)
Q Consensus       331 ~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~  410 (493)
                      ..|..+    +|.-+...  ..-.+++.+..+...-.|+..+|.++++.-.-+|+++.|..++.+|++.|+..+..-|-.
T Consensus       171 ~~p~~v----fLrqnv~~--ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyFwp  244 (1088)
T KOG4318|consen  171 NAPFQV----FLRQNVVD--NTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYFWP  244 (1088)
T ss_pred             cchHHH----HHHHhccC--CchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccchh
Confidence            222222    12222222  223334443333221258888888888888888888889999888988888888887888


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          411 VIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGR  455 (493)
Q Consensus       411 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~  455 (493)
                      ||-+   .++...+..++..|.+.|+.|+..||...+-.+..+|.
T Consensus       245 Ll~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  245 LLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             hhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            8777   78888888888888888888888888888877777665

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.14  E-value=1.4e-07  Score=108.43  Aligned_cols=282  Identities=10%  Similarity=-0.033  Sum_probs=186.1

Q ss_pred             ccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHH------------H
Q 011102          177 LDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLAST------------V  239 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~l------------i  239 (493)
                      +...|++++|+..|++.....     .+..+-..|.+.|++++|++.|+...+...-.++...|..+            -
T Consensus       279 ~~~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g  358 (1157)
T PRK11447        279 AVDSGQGGKAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQG  358 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHH
Confidence            345789999999998765543     66777789999999999999999988642222222222222            2


Q ss_pred             HHHHHcCCCchhhhHHHhhcc-----CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHH--------
Q 011102          240 EVLARHHELKVPFKLENFVSL-----ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLI--------  305 (493)
Q Consensus       240 ~~~~~~g~~~~~~~l~~~~~~-----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li--------  305 (493)
                      ..+.+.|+++  +++..|.+.     .+...+..+-..+.+.|++++|++.|++..+..  |+ ...+..+.        
T Consensus       359 ~~~~~~g~~~--eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~--p~~~~a~~~L~~l~~~~~~  434 (1157)
T PRK11447        359 DAALKANNLA--QAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD--PGNTNAVRGLANLYRQQSP  434 (1157)
T ss_pred             HHHHHCCCHH--HHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHhcCH
Confidence            3455667644  444434332     245577788899999999999999999988743  33 22332222        


Q ss_pred             ----------------------------------HHHhcCCCCHHHHHHHHHHHhhcCCCCC-CHHHHHHHHHHHHHcCC
Q 011102          306 ----------------------------------LELGKNPDKYMLVMTLLDELGQRDDLNL-SQQDCTAIMKVGIRLQK  350 (493)
Q Consensus       306 ----------------------------------~~~~~~~~~~~~a~~l~~~m~~~~g~~p-~~~~~~~li~~~~~~g~  350 (493)
                                                        ..+... |++++|.+.|++..+.   .| +...+..+...|.+.|+
T Consensus       435 ~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~-g~~~eA~~~~~~Al~~---~P~~~~~~~~LA~~~~~~G~  510 (1157)
T PRK11447        435 EKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQ-GKWAQAAELQRQRLAL---DPGSVWLTYRLAQDLRQAGQ  510 (1157)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHC-CCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCC
Confidence                                              223455 7888888888887664   24 45566778888899999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-------------------------------
Q 011102          351 FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS-------------------------------  399 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-------------------------------  399 (493)
                      +++|...|++..+.. +-+...+..+...+...|+.++|+..++.+...                               
T Consensus       511 ~~~A~~~l~~al~~~-P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~  589 (1157)
T PRK11447        511 RSQADALMRRLAQQK-PNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKE  589 (1157)
T ss_pred             HHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCH
Confidence            999999999876532 112332322222333444444444444332111                               


Q ss_pred             --------CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          400 --------NCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       400 --------gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                              ....+...+..+-..+.+.|+.++|...|++..+..- .+...+..+...|...|++++|.+.++...+
T Consensus       590 ~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P-~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~  665 (1157)
T PRK11447        590 AEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREP-GNADARLGLIEVDIAQGDLAAARAQLAKLPA  665 (1157)
T ss_pred             HHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence                    0123344556677778889999999999998886542 3677888899999999999999999997765

>TIGR00540 hemY_coli hemY protein

Probab=99.14  E-value=2e-07  Score=94.99  Aligned_cols=279  Identities=11%  Similarity=0.010  Sum_probs=192.1

Q ss_pred             CCCCHHHHHHHHhhhcccC---cHHHHH--HHHHhCCChHHHHHHHHHHHhCCCCCCCHH--HHHHHHHHHHHcCCCchh
Q 011102          179 SHKDVAEVLDKCGRFLRKG---SLSFTV--RELGHMNLPERALQTFCWAQKQPHLFPDDR--LLASTVEVLARHHELKVP  251 (493)
Q Consensus       179 ~~~~~~~a~~~~~~m~~~~---~~~~li--~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~--t~~~li~~~~~~g~~~~~  251 (493)
                      ..|++..|.+.+.+..+..   ..+.++  .+..+.|+.+.|.+.|....+.   .|+..  ..-.....+...|+++.+
T Consensus        96 ~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~---~p~~~l~~~~~~a~l~l~~~~~~~A  172 (409)
T TIGR00540        96 AEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAEL---AGNDNILVEIARTRILLAQNELHAA  172 (409)
T ss_pred             hCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCcCchHHHHHHHHHHHHCCCHHHH
Confidence            4699999999888665542   334443  4677789999999999998754   24432  333346667778885544


Q ss_pred             hhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH---hcCCCCHHHHHHHHH
Q 011102          252 FKLENFVS-----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILEL---GKNPDKYMLVMTLLD  323 (493)
Q Consensus       252 ~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~---~~~~~~~~~a~~l~~  323 (493)
                      .  ..+..     ..+..++..+...|.+.|++++|.+++..+.+.+..++......-..++   ... +..+++.+.+.
T Consensus       173 l--~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~-~~~~~~~~~L~  249 (409)
T TIGR00540       173 R--HGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDE-AMADEGIDGLL  249 (409)
T ss_pred             H--HHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH-HHHhcCHHHHH
Confidence            4  33333     2356688899999999999999999999999987543332211111111   211 12222223333


Q ss_pred             HHhhcC--CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHH---HHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          324 ELGQRD--DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVM---YTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       324 ~m~~~~--g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t---y~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      .+....  ....+...+..+...+...|+.++|.+++++..+.  .||...   .....-.....++.+++.+.++...+
T Consensus       250 ~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk  327 (409)
T TIGR00540       250 NWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAK  327 (409)
T ss_pred             HHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHH
Confidence            333320  12247888999999999999999999999998865  344432   12222333445788889999988665


Q ss_pred             CCCCCCHH---HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          399 SNCLFDLP---AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       399 ~gi~pd~~---ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      .  .|+..   ...++=..|.+.|++++|.+.|+........||...+..+...+.+.|+.++|.+++++-.
T Consensus       328 ~--~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l  397 (409)
T TIGR00540       328 N--VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSL  397 (409)
T ss_pred             h--CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4  45544   3446667789999999999999965555567999999999999999999999999999753

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.

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

Probab=99.10  E-value=3.3e-08  Score=99.12  Aligned_cols=280  Identities=13%  Similarity=0.022  Sum_probs=170.4

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH-cCCC
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLAR-HHEL  248 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~-~g~~  248 (493)
                      +.+...|++++|+..++.+.+..     .|..+-.+|...|+.+.|.+.|.+..   .+.|+.+...+-+.-+-+ .|++
T Consensus       124 N~~kerg~~~~al~~y~~aiel~p~fida~inla~al~~~~~~~~a~~~~~~al---qlnP~l~ca~s~lgnLlka~Grl  200 (966)
T KOG4626|consen  124 NILKERGQLQDALALYRAAIELKPKFIDAYINLAAALVTQGDLELAVQCFFEAL---QLNPDLYCARSDLGNLLKAEGRL  200 (966)
T ss_pred             HHHHHhchHHHHHHHHHHHHhcCchhhHHHhhHHHHHHhcCCCcccHHHHHHHH---hcCcchhhhhcchhHHHHhhccc
Confidence            45666799999999999877654     78888999999999999999999887   457777665443333333 4554


Q ss_pred             chhhhHHHh--hccC-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHhcC-------------
Q 011102          249 KVPFKLENF--VSLA-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP-SIYAKLILELGKN-------------  311 (493)
Q Consensus       249 ~~~~~l~~~--~~~~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~-~t~~~li~~~~~~-------------  311 (493)
                      +.+.+-..-  ..-+ =...|+.|-..+-..|+...|+.-|++..+.  .|+- ..|-.|-..|...             
T Consensus       201 ~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl--dP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rA  278 (966)
T KOG4626|consen  201 EEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL--DPNFLDAYINLGNVYKEARIFDRAVSCYLRA  278 (966)
T ss_pred             chhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcC--CCcchHHHhhHHHHHHHHhcchHHHHHHHHH
Confidence            444432111  1111 1234666666666677777777777666553  2331 2333333333333             


Q ss_pred             --------------------CCCHHHHHHHHHHHhhcCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC-C
Q 011102          312 --------------------PDKYMLVMTLLDELGQRDDLNLS-QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP-T  369 (493)
Q Consensus       312 --------------------~~~~~~a~~l~~~m~~~~g~~p~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~  369 (493)
                                          .|.++.|+..+++....   .|+ ...|+.|-+++-..|++.+|++.|++-...  .| -
T Consensus       279 l~lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~---~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l--~p~h  353 (966)
T KOG4626|consen  279 LNLRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL---QPNFPDAYNNLANALKDKGSVTEAVDCYNKALRL--CPNH  353 (966)
T ss_pred             HhcCCcchhhccceEEEEeccccHHHHHHHHHHHHhc---CCCchHHHhHHHHHHHhccchHHHHHHHHHHHHh--CCcc
Confidence                                05555555555554332   233 345666666666667777777777665533  23 2


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCH-HHHHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL-PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTY-DIYRDMI  447 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~-~ty~~li  447 (493)
                      ..+.|.|-..|...|++++|..+|....+  +.|.. ..+|.|-..|-++|++++|...+++...  |.|+. ..|+.+=
T Consensus       354 adam~NLgni~~E~~~~e~A~~ly~~al~--v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr--I~P~fAda~~NmG  429 (966)
T KOG4626|consen  354 ADAMNNLGNIYREQGKIEEATRLYLKALE--VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALR--IKPTFADALSNMG  429 (966)
T ss_pred             HHHHHHHHHHHHHhccchHHHHHHHHHHh--hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHh--cCchHHHHHHhcc
Confidence            34566666677777777777777666544  23432 3566666677777777777777766653  44543 4566666


Q ss_pred             HHHHHcCCHHHHHHHHHHHHH
Q 011102          448 RIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       448 ~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ..|-..|+++.|...+.+...
T Consensus       430 nt~ke~g~v~~A~q~y~rAI~  450 (966)
T KOG4626|consen  430 NTYKEMGDVSAAIQCYTRAIQ  450 (966)
T ss_pred             hHHHHhhhHHHHHHHHHHHHh
Confidence            667777777777776666554

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.10  E-value=6.9e-07  Score=98.31  Aligned_cols=292  Identities=13%  Similarity=0.013  Sum_probs=196.5

Q ss_pred             hhccCCCCHHHHHHHHhhhccc-----CcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRK-----GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~-----~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+...+++.+|...|.+....     ..+..+...+...|+.++|+..++...+.  ...+.. +..+..++...|+. 
T Consensus        57 ~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~--~P~~~~-~~~la~~l~~~g~~-  132 (765)
T PRK10049         57 VAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGLILTLADAGQYDEALVKAKQLVSG--APDKAN-LLALAYVYKRAGRH-  132 (765)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHH-HHHHHHHHHHCCCH-
Confidence            3456679999999999975433     25667778899999999999999999864  222444 77777788888884 


Q ss_pred             hhhhHHHhhc----cC-cHHHHHHHHHHHHhcCCHHHHH-----------------------------------------
Q 011102          250 VPFKLENFVS----LA-SKGVLEATAKGFVKGGNLKLAW-----------------------------------------  283 (493)
Q Consensus       250 ~~~~l~~~~~----~~-~~~~~~~li~~~~~~g~~~~A~-----------------------------------------  283 (493)
                       .+++..+..    -| +...+..+...+.+.|..++|+                                         
T Consensus       133 -~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~  211 (765)
T PRK10049        133 -WDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAI  211 (765)
T ss_pred             -HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHH
Confidence             444443432    22 3344445555555555555444                                         


Q ss_pred             -----HHHHHHHhC-CCCCCHH-HHH----HHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          284 -----KLLMVAKDG-GRMLDPS-IYA----KLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFG  352 (493)
Q Consensus       284 -----~l~~~m~~~-g~~pd~~-t~~----~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~  352 (493)
                           +.++.+.+. ...|+.. .+.    ..+..+... |++++|...|+.+.+.+.-.|+... -.+...|...|+++
T Consensus       212 ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~-g~~~eA~~~~~~ll~~~~~~P~~a~-~~la~~yl~~g~~e  289 (765)
T PRK10049        212 ADRALAQYDALEALWHDNPDATADYQRARIDRLGALLAR-DRYKDVISEYQRLKAEGQIIPPWAQ-RWVASAYLKLHQPE  289 (765)
T ss_pred             HHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHh-hhHHHHHHHHHHhhccCCCCCHHHH-HHHHHHHHhcCCcH
Confidence                 444444432 1122221 111    113345666 8899999999998876222243221 22466889999999


Q ss_pred             HHHHHHHHHHHcCCCC---CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC-----------CCCCH---HHHHHHHHHH
Q 011102          353 VVESLFHWFTHSGRDP---TVVMYTTLIHSRLSEKKCREALTVVWNMEASN-----------CLFDL---PAYRVVIKLF  415 (493)
Q Consensus       353 ~A~~l~~~m~~~g~~p---~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g-----------i~pd~---~ty~~li~~~  415 (493)
                      +|+.+|+++.+..-..   ....+..|..++...|++++|.++++.+.+..           -.|+.   ..+..+...+
T Consensus       290 ~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l  369 (765)
T PRK10049        290 KAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVA  369 (765)
T ss_pred             HHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHH
Confidence            9999999886542111   13456677778899999999999999987642           11332   3455667788


Q ss_pred             HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHH
Q 011102          416 VALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~  476 (493)
                      ...|++++|.++++++.... +-+...+..+...+...|++++|++.+++..+  +.||..
T Consensus       370 ~~~g~~~eA~~~l~~al~~~-P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~--l~Pd~~  427 (765)
T PRK10049        370 KYSNDLPQAEMRARELAYNA-PGNQGLRIDYASVLQARGWPRAAENELKKAEV--LEPRNI  427 (765)
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--hCCCCh
Confidence            89999999999999987543 34577788889999999999999999998876  457653

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

Probab=99.09  E-value=1.1e-06  Score=84.54  Aligned_cols=283  Identities=11%  Similarity=0.086  Sum_probs=218.5

Q ss_pred             CCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhh-h
Q 011102          180 HKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPF-K  253 (493)
Q Consensus       180 ~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~-~  253 (493)
                      .|++..|.+...+-.+.+     .|-.-..+--+.|+.+.|-+.+.+.-+. .-.++...+-+........|+...+. .
T Consensus        97 eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~-~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAEL-AGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhcc-CCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            689999988887644433     4444556778889999999999998765 33455566777777788888765443 2


Q ss_pred             HHHhhcc--CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-------HHHHHHHHHhcCCCCHHHHHHHHHH
Q 011102          254 LENFVSL--ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS-------IYAKLILELGKNPDKYMLVMTLLDE  324 (493)
Q Consensus       254 l~~~~~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~-------t~~~li~~~~~~~~~~~~a~~l~~~  324 (493)
                      +....+|  ....+.......|.+.|++.....++..|.+.|+--|+.       +|+.++.-.... +..+.-...|+.
T Consensus       176 v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~-~~~~gL~~~W~~  254 (400)
T COG3071         176 VDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDD-NGSEGLKTWWKN  254 (400)
T ss_pred             HHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhcc-ccchHHHHHHHh
Confidence            3334443  366788999999999999999999999999999776653       688888888888 777777777877


Q ss_pred             HhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH-HHCCCCC
Q 011102          325 LGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNM-EASNCLF  403 (493)
Q Consensus       325 m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M-~~~gi~p  403 (493)
                      .-.+  .+-++..-.+++.-+.++|+.++|.++..+-.+++..|+..    ..-.+.+-++...-.+..+.- ...+-.|
T Consensus       255 ~pr~--lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~~~~l~~~d~~~l~k~~e~~l~~h~~~p  328 (400)
T COG3071         255 QPRK--LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RLIPRLRPGDPEPLIKAAEKWLKQHPEDP  328 (400)
T ss_pred             ccHH--hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HHHhhcCCCCchHHHHHHHHHHHhCCCCh
Confidence            7664  55667777888999999999999999999998888888732    234556677777777777663 4556666


Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccC
Q 011102          404 DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLD  474 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd  474 (493)
                        -.+.+|=..|.+.+.|.+|...|+.-.+  ..|+..+|+.+-++|.+.|+.++|.++.++-...-.+|+
T Consensus       329 --~L~~tLG~L~~k~~~w~kA~~~leaAl~--~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~~~~~~~  395 (400)
T COG3071         329 --LLLSTLGRLALKNKLWGKASEALEAALK--LRPSASDYAELADALDQLGEPEEAEQVRREALLLTRQPN  395 (400)
T ss_pred             --hHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCChhhHHHHHHHHHHcCChHHHHHHHHHHHHHhcCCC
Confidence              5577777889999999999999996554  459999999999999999999999999988764434443

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

Probab=99.01  E-value=5.2e-09  Score=108.60  Aligned_cols=306  Identities=12%  Similarity=-0.005  Sum_probs=180.6

Q ss_pred             hhhhhhhhhccCCchhHHHHHHHHhhccCCCCHHHHHHHHhhhccc------CcHHHHHHHHHhCCChHHHHHHHHHHHh
Q 011102          151 SSRASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRK------GSLSFTVRELGHMNLPERALQTFCWAQK  224 (493)
Q Consensus       151 ~~~~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~a~~~~~~m~~~------~~~~~li~~~~~~g~~~~A~~l~~~m~~  224 (493)
                      +...|+.|+..+|.+++       .+|+..|+++.|- .|.-|.-+      +.|+.++.+..+.++.+.+.        
T Consensus        16 ~e~~gi~PnRvtyqsLi-------arYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk--------   79 (1088)
T KOG4318|consen   16 HEISGILPNRVTYQSLI-------ARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK--------   79 (1088)
T ss_pred             HHHhcCCCchhhHHHHH-------HHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC--------
Confidence            44556666555444333       4455556666665 55543322      36677777666666654443        


Q ss_pred             CCCCCCCHHHHHHHHHHHHHcCCCchhhhHHH----hhcc--C----cHH---------------HHHHHHHHHHhcCCH
Q 011102          225 QPHLFPDDRLLASTVEVLARHHELKVPFKLEN----FVSL--A----SKG---------------VLEATAKGFVKGGNL  279 (493)
Q Consensus       225 ~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~----~~~~--~----~~~---------------~~~~li~~~~~~g~~  279 (493)
                          .|-..||..+..+|...|++..-+..+.    ....  +    ...               --...|.-..-.|.+
T Consensus        80 ----ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglw  155 (1088)
T KOG4318|consen   80 ----EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLW  155 (1088)
T ss_pred             ----CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHH
Confidence                4556677777777777776533221111    0000  0    000               012333444445666


Q ss_pred             HHHHHHHHHHHhCCCC-CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          280 KLAWKLLMVAKDGGRM-LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLF  358 (493)
Q Consensus       280 ~~A~~l~~~m~~~g~~-pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~  358 (493)
                      +.+++++..|...... |..+    .|.-+...   +.-..++....+.-.+ .|+..+|.++++.-.-+|+++.|..++
T Consensus       156 aqllkll~~~Pvsa~~~p~~v----fLrqnv~~---ntpvekLl~~cksl~e-~~~s~~l~a~l~~alaag~~d~Ak~ll  227 (1088)
T KOG4318|consen  156 AQLLKLLAKVPVSAWNAPFQV----FLRQNVVD---NTPVEKLLNMCKSLVE-APTSETLHAVLKRALAAGDVDGAKNLL  227 (1088)
T ss_pred             HHHHHHHhhCCcccccchHHH----HHHHhccC---CchHHHHHHHHHHhhc-CCChHHHHHHHHHHHhcCchhhHHHHH
Confidence            6666666555432211 2111    24444443   2334444444433323 699999999999999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC
Q 011102          359 HWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCP  438 (493)
Q Consensus       359 ~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p  438 (493)
                      .+|++.|+..+.+-|-.||-|   .++..-+..++..|++.|+.|+..|+..-+..+.++|....+....+.  +.|  .
T Consensus       228 ~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t~~~~e~sq~--~hg--~  300 (1088)
T KOG4318|consen  228 YEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQTKYGEEGSQL--AHG--F  300 (1088)
T ss_pred             HHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhhhhcccccch--hhh--h
Confidence            999999999999988888887   888999999999999999999999999999888887664333222110  111  1


Q ss_pred             CHHHHHHHHHHHHHcCCHHH-----HHHHHHHHHHCCCccCHHHHHHHHHhhhhccCC
Q 011102          439 TYDIYRDMIRIFMASGRLAK-----CRDVCKEAEMAGFKLDKQTVVELLQIEKESRIG  491 (493)
Q Consensus       439 ~~~ty~~li~~~~~~g~~~~-----A~~l~~~m~~~g~~pd~~t~~~Ll~~~~~~r~g  491 (493)
                      +...+..+..+.....+.+.     ....+.+..-.|+.-...+|...+++-.+++.|
T Consensus       301 tAavrsaa~rg~~a~k~l~~nl~~~v~~s~k~~fLlg~d~~~aiws~c~~l~hQgk~e  358 (1088)
T KOG4318|consen  301 TAAVRSAACRGLLANKRLRQNLRKSVIGSTKKLFLLGTDILEAIWSMCEKLRHQGKGE  358 (1088)
T ss_pred             hHHHHHHHhcccHhHHHHHHHHHHHHHHHhhHHHHhccccchHHHHHHHHHHHcCCCc
Confidence            22233444443222222221     222233333346666667788777766566655

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.98  E-value=4.1e-06  Score=91.37  Aligned_cols=291  Identities=12%  Similarity=0.034  Sum_probs=189.0

Q ss_pred             hccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCch
Q 011102          176 GLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKV  250 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~  250 (493)
                      .+...++.++|+++++++....     .+..++..+...++.++|++.++.+...   .|+...+..  .++...+..+.
T Consensus       111 ly~~~gdyd~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~---dp~~~~~l~--layL~~~~~~~  185 (822)
T PRK14574        111 AYRNEKRWDQALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAER---DPTVQNYMT--LSYLNRATDRN  185 (822)
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc---CcchHHHHH--HHHHHHhcchH
Confidence            4556688889999988776654     5666777888889999999998888744   455555533  34444333233


Q ss_pred             hhhHHHhhcc----C-cHHHHHHHHHHHHhcCCHHHHHHHHH--------------------------------------
Q 011102          251 PFKLENFVSL----A-SKGVLEATAKGFVKGGNLKLAWKLLM--------------------------------------  287 (493)
Q Consensus       251 ~~~l~~~~~~----~-~~~~~~~li~~~~~~g~~~~A~~l~~--------------------------------------  287 (493)
                      .+++..+.++    | +...+.-++....+.|-...|+++..                                      
T Consensus       186 ~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~  265 (822)
T PRK14574        186 YDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFD  265 (822)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHH
Confidence            3466555543    2 34455555555555555444443333                                      


Q ss_pred             ----------HHHh-CCCCCCH-HHH-H---HHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          288 ----------VAKD-GGRMLDP-SIY-A---KLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKF  351 (493)
Q Consensus       288 ----------~m~~-~g~~pd~-~t~-~---~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~  351 (493)
                                .+.. .+-.|.. .-| .   =.+-++.+. +++.++++.++.+... +......+--++.++|...+++
T Consensus       266 ~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r-~r~~~vi~~y~~l~~~-~~~~P~y~~~a~adayl~~~~P  343 (822)
T PRK14574        266 IADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVR-HQTADLIKEYEAMEAE-GYKMPDYARRWAASAYIDRRLP  343 (822)
T ss_pred             HHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHh-hhHHHHHHHHHHhhhc-CCCCCHHHHHHHHHHHHhcCCc
Confidence                      2221 1111221 111 1   233455666 7888888888888876 5554556777888888888899


Q ss_pred             HHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-------------CCCHH-HHHHHH
Q 011102          352 GVVESLFHWFTHSG-----RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNC-------------LFDLP-AYRVVI  412 (493)
Q Consensus       352 ~~A~~l~~~m~~~g-----~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi-------------~pd~~-ty~~li  412 (493)
                      ++|+.+|+......     ..++......|..+|...+++++|..+++.+.+.--             .||-. .+..++
T Consensus       344 ~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a  423 (822)
T PRK14574        344 EKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLV  423 (822)
T ss_pred             HHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHH
Confidence            99999988875432     233455567888888889999999999988876311             12222 234456


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHH
Q 011102          413 KLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       413 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~  476 (493)
                      ..+...|++.+|++.++++.... +-|......+-+.+...|...+|++.++....  +.|+..
T Consensus       424 ~~~~~~gdl~~Ae~~le~l~~~a-P~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~--l~P~~~  484 (822)
T PRK14574        424 QSLVALNDLPTAQKKLEDLSSTA-PANQNLRIALASIYLARDLPRKAEQELKAVES--LAPRSL  484 (822)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhh--hCCccH
Confidence            66788888999999998886443 34777788888888888888888888866554  356543

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.96  E-value=1e-05  Score=90.08  Aligned_cols=279  Identities=14%  Similarity=0.090  Sum_probs=146.5

Q ss_pred             CCCCHHHHHHHHhhhccc--CcHHHH---HHHHHhCCChHHHHHHHHHHHh-CCCCCCCHHHHHHHHHHHHHcCCCchhh
Q 011102          179 SHKDVAEVLDKCGRFLRK--GSLSFT---VRELGHMNLPERALQTFCWAQK-QPHLFPDDRLLASTVEVLARHHELKVPF  252 (493)
Q Consensus       179 ~~~~~~~a~~~~~~m~~~--~~~~~l---i~~~~~~g~~~~A~~l~~~m~~-~~g~~pd~~t~~~li~~~~~~g~~~~~~  252 (493)
                      ..+...++...+..|...  +.-..+   --...+.|+.++|.++|+.... ...-.++.....-++..+.+.+.+....
T Consensus       354 ~~~~~~~~~~~~~~~y~~~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~  433 (987)
T PRK09782        354 ATRNKAEALRLARLLYQQEPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPA  433 (987)
T ss_pred             ccCchhHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchH
Confidence            335555555556555544  222222   2244678888899998887765 2223334445557777777765532211


Q ss_pred             hHHH------------------------------hhccC---cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH
Q 011102          253 KLEN------------------------------FVSLA---SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS  299 (493)
Q Consensus       253 ~l~~------------------------------~~~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~  299 (493)
                      .+..                              ...++   +...|..+-..+.. ++.++|...|.+.....  |+..
T Consensus       434 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~  510 (987)
T PRK09782        434 KVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAW  510 (987)
T ss_pred             HHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchH
Confidence            1100                              00111   23345555555554 56666777665555432  5533


Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011102          300 IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHS  379 (493)
Q Consensus       300 t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~  379 (493)
                      ....+...+... |++++|...|+.+...   .|+...+..+...+.+.|+.++|...|++..+.. ..+...+..+...
T Consensus       511 ~~L~lA~al~~~-Gr~eeAi~~~rka~~~---~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~-P~~~~l~~~La~~  585 (987)
T PRK09782        511 QHRAVAYQAYQV-EDYATALAAWQKISLH---DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG-LGDNALYWWLHAQ  585 (987)
T ss_pred             HHHHHHHHHHHC-CCHHHHHHHHHHHhcc---CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CccHHHHHHHHHH
Confidence            322222333455 6777777777665432   2333344455555666666666666666665442 1222222233333


Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          380 RLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKC  459 (493)
Q Consensus       380 ~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A  459 (493)
                      +.+.|++++|...+++..+.  .|+...|..+-..+.+.|+.++|...|++..+..- -+...++.+-..+...|++++|
T Consensus       586 l~~~Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~P-d~~~a~~nLG~aL~~~G~~eeA  662 (987)
T PRK09782        586 RYIPGQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALELEP-NNSNYQAALGYALWDSGDIAQS  662 (987)
T ss_pred             HHhCCCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHH
Confidence            34446666666666665543  34555566666666666666666666666554331 1344455555566666666666


Q ss_pred             HHHHHHHHH
Q 011102          460 RDVCKEAEM  468 (493)
Q Consensus       460 ~~l~~~m~~  468 (493)
                      .+.+++..+
T Consensus       663 i~~l~~AL~  671 (987)
T PRK09782        663 REMLERAHK  671 (987)
T ss_pred             HHHHHHHHH
Confidence            666666554

>PF12854 PPR_1: PPR repeat

Probab=98.96  E-value=8.3e-10  Score=69.17  Aligned_cols=32  Identities=34%  Similarity=0.505  Sum_probs=14.2

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          365 GRDPTVVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       365 g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      |+.||.+|||+||++||+.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            34444444444444444444444444444444

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

Probab=98.94  E-value=3.8e-07  Score=92.72  Aligned_cols=280  Identities=14%  Similarity=0.024  Sum_probs=207.0

Q ss_pred             CCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCC-CCCCHHHHHHHHHHHHHcCCCc-hhhh
Q 011102          181 KDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPH-LFPDDRLLASTVEVLARHHELK-VPFK  253 (493)
Q Consensus       181 ~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g-~~pd~~t~~~li~~~~~~g~~~-~~~~  253 (493)
                      -...+|+..|.+.+...     ...-+=.+|...++.++|.++|+...+... ..-+..+|.+++--+-+.-.+. .++ 
T Consensus       333 y~~~~A~~~~~klp~h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq-  411 (638)
T KOG1126|consen  333 YNCREALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQ-  411 (638)
T ss_pred             HHHHHHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHH-
Confidence            45678888888744332     223445588899999999999999986533 2336678888886654432211 111 


Q ss_pred             HHHhhccC-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCC
Q 011102          254 LENFVSLA-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDL  331 (493)
Q Consensus       254 l~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~  331 (493)
                       ......+ ...+|.++-+.|.-.++.+.|++.|++..+.  .| ...+|+-+=+.+... ..+|.|...|....     
T Consensus       412 -~Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~-ee~d~a~~~fr~Al-----  482 (638)
T KOG1126|consen  412 -DLIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIAT-EEFDKAMKSFRKAL-----  482 (638)
T ss_pred             -HHHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhh-HHHHhHHHHHHhhh-----
Confidence             1133333 5679999999999999999999999999884  35 567888887888888 89999999998764     


Q ss_pred             CCCHHHHHHH---HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHH
Q 011102          332 NLSQQDCTAI---MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAY  408 (493)
Q Consensus       332 ~p~~~~~~~l---i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty  408 (493)
                      ..|...||++   --.|.|.++++.|+-.|++..+-+ +-+.+....+...+-+.|+.++|++++++.....-+ |...-
T Consensus       483 ~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~IN-P~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l~~  560 (638)
T KOG1126|consen  483 GVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEIN-PSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPLCK  560 (638)
T ss_pred             cCCchhhHHHHhhhhheeccchhhHHHHHHHhhhcCC-ccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-CchhH
Confidence            4577777765   568899999999999999877432 336677778888899999999999999998765432 22222


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccC
Q 011102          409 RVVIKLFVALNDISRAIRYFSKLKEAGFCP-TYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLD  474 (493)
Q Consensus       409 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd  474 (493)
                      ---...+...++.++|+..++++++.  .| +...|-.+-..|-+.|+.+.|+.-|--|.+..-++.
T Consensus       561 ~~~~~il~~~~~~~eal~~LEeLk~~--vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~  625 (638)
T KOG1126|consen  561 YHRASILFSLGRYVEALQELEELKEL--VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGA  625 (638)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHHh--CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccc
Confidence            23344556678999999999999864  35 456678888999999999999998888876543333

>PF12854 PPR_1: PPR repeat

Probab=98.93  E-value=1.2e-09  Score=68.39  Aligned_cols=32  Identities=19%  Similarity=0.454  Sum_probs=17.1

Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          400 NCLFDLPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       400 gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      |+.||.+|||+||++||+.|++++|.++|++|
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            45555555555555555555555555555554

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

Probab=98.91  E-value=1e-08  Score=99.02  Aligned_cols=247  Identities=9%  Similarity=0.002  Sum_probs=109.9

Q ss_pred             ccCCCCHHHHHHHHhhh-ccc-----C-cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          177 LDSHKDVAEVLDKCGRF-LRK-----G-SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m-~~~-----~-~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      +-+.|++++|++++.+. ...     . .|..+-...-..++.+.|++.++.+... +-. +...+..++.. ...++.+
T Consensus        18 ~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~-~~~-~~~~~~~l~~l-~~~~~~~   94 (280)
T PF13429_consen   18 LYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLAS-DKA-NPQDYERLIQL-LQDGDPE   94 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccc-ccccccccccc-ccccccc
Confidence            44568889999988532 111     1 3444444555678899999999999865 322 34456666666 5666655


Q ss_pred             hhhhH--HHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHh
Q 011102          250 VPFKL--ENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGG-RMLDPSIYAKLILELGKNPDKYMLVMTLLDELG  326 (493)
Q Consensus       250 ~~~~l--~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~  326 (493)
                      .+..+  ..+....+...+..++..+.+.++++++.++++...... ...+...|..+-..+.+. |+.++|.+.+++..
T Consensus        95 ~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~-G~~~~A~~~~~~al  173 (280)
T PF13429_consen   95 EALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQL-GDPDKALRDYRKAL  173 (280)
T ss_dssp             -----------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHC-CHHHHHHHHHHHHH
T ss_pred             ccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHH
Confidence            44432  234445566678889999999999999999999987643 346777788888888898 99999999999988


Q ss_pred             hcCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH
Q 011102          327 QRDDLNL-SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL  405 (493)
Q Consensus       327 ~~~g~~p-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~  405 (493)
                      +.   .| |....+.++..+...|+.+++.++++...+.. ..|...|..+..+|...|+.++|+..|++..+.. +-|.
T Consensus       174 ~~---~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~  248 (280)
T PF13429_consen  174 EL---DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDP  248 (280)
T ss_dssp             HH----TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-H
T ss_pred             Hc---CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhcccccccccccccccccccc-cccc
Confidence            75   35 47788899999999999999999998887654 4455568899999999999999999999977632 2367


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      .....+.+++...|+.++|.++..+..
T Consensus       249 ~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  249 LWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             HHHHHHHHHHT----------------
T ss_pred             ccccccccccccccccccccccccccc
Confidence            778888899999999999999887654

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=98.91  E-value=7.5e-06  Score=91.16  Aligned_cols=189  Identities=6%  Similarity=-0.129  Sum_probs=129.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcC
Q 011102          270 AKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQ  349 (493)
Q Consensus       270 i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g  349 (493)
                      ...+.+.|++++|...|+++...  .|+...+..+...+.+. |+.++|.+.++...+. . ..+...+..+...+.+.|
T Consensus       516 A~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~-Gd~~eA~~~l~qAL~l-~-P~~~~l~~~La~~l~~~G  590 (987)
T PRK09782        516 AYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAA-GNGAARDRWLQQAEQR-G-LGDNALYWWLHAQRYIPG  590 (987)
T ss_pred             HHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHC-CCHHHHHHHHHHHHhc-C-CccHHHHHHHHHHHHhCC
Confidence            33445778888888888876553  34444555555666777 7888888888877654 2 122222333333444558


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          350 KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVVIKLFVALNDISRAIRYF  428 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~~~~g~~~~A~~~~  428 (493)
                      ++++|...|++..+.  .|+...|..+-..+.+.|+.++|++.+++..+.  .|+ ...++.+-..+...|+.++|...|
T Consensus       591 r~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l--~Pd~~~a~~nLG~aL~~~G~~eeAi~~l  666 (987)
T PRK09782        591 QPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALEL--EPNNSNYQAALGYALWDSGDIAQSREML  666 (987)
T ss_pred             CHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            888888888877654  466777888888888888888888888887664  343 445566666788888888888888


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          429 SKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       429 ~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +...+..- -+...+..+-.++...|++++|+..+++..+
T Consensus       667 ~~AL~l~P-~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~  705 (987)
T PRK09782        667 ERAHKGLP-DDPALIRQLAYVNQRLDDMAATQHYARLVID  705 (987)
T ss_pred             HHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            87775432 2556677788888888888888888888765

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=98.90  E-value=3.8e-06  Score=85.30  Aligned_cols=273  Identities=8%  Similarity=-0.015  Sum_probs=192.6

Q ss_pred             cHHHHHHHHHh--CCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc----cCcHHHHH--HH
Q 011102          198 SLSFTVRELGH--MNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS----LASKGVLE--AT  269 (493)
Q Consensus       198 ~~~~li~~~~~--~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~----~~~~~~~~--~l  269 (493)
                      .+..+..++..  .|+++.|.+.+....+. .-.| ...|.....+..+.|+.+.+...  +..    .++...+-  ..
T Consensus        84 ~~~~~~~gl~a~~eGd~~~A~k~l~~~~~~-~~~p-~l~~llaA~aA~~~g~~~~A~~~--l~~A~~~~~~~~~~~~l~~  159 (398)
T PRK10747         84 ARKQTEQALLKLAEGDYQQVEKLMTRNADH-AEQP-VVNYLLAAEAAQQRGDEARANQH--LERAAELADNDQLPVEITR  159 (398)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHhc-ccch-HHHHHHHHHHHHHCCCHHHHHHH--HHHHHhcCCcchHHHHHHH
Confidence            34444444433  59999999888876543 1112 22343334444677775544433  332    23333322  33


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH------HHHHHHHH
Q 011102          270 AKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ------QDCTAIMK  343 (493)
Q Consensus       270 i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~------~~~~~li~  343 (493)
                      ...+...|+++.|.+.++++.+.. +-++..+..+...|.+. |+|++|.+++..+.+.....+..      ..|..++.
T Consensus       160 a~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~-gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~  237 (398)
T PRK10747        160 VRIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRT-GAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMD  237 (398)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHH-HhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            678889999999999999998866 23566778889999999 99999999999999873332221      23444455


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~  423 (493)
                      ...+..+.+...++++.+.+. .+.+......+..++...|+.++|.+++++..+.  .||..  -.++.+....++.++
T Consensus       238 ~~~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~--l~~l~~~l~~~~~~~  312 (398)
T PRK10747        238 QAMADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDER--LVLLIPRLKTNNPEQ  312 (398)
T ss_pred             HHHHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHH--HHHHHhhccCCChHH
Confidence            555556667777777776432 2457788899999999999999999999998774  44542  234555567799999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          424 AIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       424 A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      +.+..+...+..- -|...+.++-..+.+.|++++|.+.|+...+  ..|+..+|..|-.+
T Consensus       313 al~~~e~~lk~~P-~~~~l~l~lgrl~~~~~~~~~A~~~le~al~--~~P~~~~~~~La~~  370 (398)
T PRK10747        313 LEKVLRQQIKQHG-DTPLLWSTLGQLLMKHGEWQEASLAFRAALK--QRPDAYDYAWLADA  370 (398)
T ss_pred             HHHHHHHHHhhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh--cCCCHHHHHHHHHH
Confidence            9999999886542 3556678899999999999999999999987  57999987777664

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=98.87  E-value=2.1e-06  Score=79.42  Aligned_cols=199  Identities=14%  Similarity=0.011  Sum_probs=150.5

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcC
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGG  277 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g  277 (493)
                      .+..+...|...|++++|.+.|+...+.   .|+                              +...+..+...|...|
T Consensus        33 ~~~~la~~~~~~~~~~~A~~~~~~~l~~---~p~------------------------------~~~~~~~la~~~~~~~   79 (234)
T TIGR02521        33 IRVQLALGYLEQGDLEVAKENLDKALEH---DPD------------------------------DYLAYLALALYYQQLG   79 (234)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh---Ccc------------------------------cHHHHHHHHHHHHHcC
Confidence            5666677788888888888888877643   122                              1234455667777888


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      ++++|.+.+++..+.. ..+...+..+...+... |++++|.+.+++.............+..+...+.+.|++++|...
T Consensus        80 ~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~~~-g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  157 (234)
T TIGR02521        80 ELEKAEDSFRRALTLN-PNNGDVLNNYGTFLCQQ-GKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKY  157 (234)
T ss_pred             CHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHc-ccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHH
Confidence            8999999998887754 23456677777788888 899999999999876522233455677778888999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          358 FHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       358 ~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      |++..+.. +.+...+..+...+...|++++|.+.+++..+. ...+...+..+...+...|+.++|..+++.+..
T Consensus       158 ~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       158 LTRALQID-PQRPESLLELAELYYLRGQYKDARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHhC-cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            99887643 234667888889999999999999999998776 334567777788888899999999998887764

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.

>PRK14574 hmsH outer membrane protein; Provisional

Probab=98.86  E-value=7.6e-06  Score=89.31  Aligned_cols=285  Identities=12%  Similarity=-0.001  Sum_probs=181.5

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC---cHHHH--HHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG---SLSFT--VRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~---~~~~l--i~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+...|+.++|+..+++...+.   .+..+  ...|...|++++|+++|+.+.+...-  |...+..++..+...++  
T Consensus        76 ~l~~~~G~~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~dP~--n~~~l~gLa~~y~~~~q--  151 (822)
T PRK14574         76 QIAGWAGRDQEVIDVYERYQSSMNISSRGLASAARAYRNEKRWDQALALWQSSLKKDPT--NPDLISGMIMTQADAGR--  151 (822)
T ss_pred             HHHHHcCCcHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC--CHHHHHHHHHHHhhcCC--
Confidence            33445588888888888766543   22223  34667778888888888888764211  33445566667777776  


Q ss_pred             hhhhHHHhhc----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHH
Q 011102          250 VPFKLENFVS----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDE  324 (493)
Q Consensus       250 ~~~~l~~~~~----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~  324 (493)
                      ..+++..+..    .++...+-.++..+...++..+|++.++++.+..  | +...+..++.++.+. |-...|.++..+
T Consensus       152 ~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~--P~n~e~~~~~~~~l~~~-~~~~~a~~l~~~  228 (822)
T PRK14574        152 GGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEAVRLA--PTSEEVLKNHLEILQRN-RIVEPALRLAKE  228 (822)
T ss_pred             HHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHc-CCcHHHHHHHHh
Confidence            4444444433    2233344444444444555656888888888764  5 455667777788888 777777766655


Q ss_pred             HhhcCCCCCCHHHH------HHHHHHH-----HHcCC---HHHHHHHHHHHHH-cCCCCCH-----HHHHHHHHHHHcCC
Q 011102          325 LGQRDDLNLSQQDC------TAIMKVG-----IRLQK---FGVVESLFHWFTH-SGRDPTV-----VMYTTLIHSRLSEK  384 (493)
Q Consensus       325 m~~~~g~~p~~~~~------~~li~~~-----~~~g~---~~~A~~l~~~m~~-~g~~p~~-----~ty~~li~~~~~~g  384 (493)
                      -..-  +.+...-+      ..+|..-     ....+   .+.|+.-++.+.. .+-.|..     ...-=.+-++...|
T Consensus       229 ~p~~--f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~  306 (822)
T PRK14574        229 NPNL--VSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRH  306 (822)
T ss_pred             Cccc--cCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhh
Confidence            3221  22221111      1111100     01122   3445555555443 2233432     22234556788899


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG-----FCPTYDIYRDMIRIFMASGRLAKC  459 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g-----~~p~~~ty~~li~~~~~~g~~~~A  459 (493)
                      ++.++.+.++.|...|...-..+--++-++|...++.++|..+|+.+....     ..++......|.-+|...+++++|
T Consensus       307 r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A  386 (822)
T PRK14574        307 QTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKA  386 (822)
T ss_pred             hHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHH
Confidence            999999999999998865444577889999999999999999999987432     233555568899999999999999


Q ss_pred             HHHHHHHHH
Q 011102          460 RDVCKEAEM  468 (493)
Q Consensus       460 ~~l~~~m~~  468 (493)
                      ..+++++.+
T Consensus       387 ~~~l~~~~~  395 (822)
T PRK14574        387 YQFAVNYSE  395 (822)
T ss_pred             HHHHHHHHh
Confidence            999999987

>TIGR00540 hemY_coli hemY protein

Probab=98.83  E-value=8.4e-06  Score=83.13  Aligned_cols=274  Identities=10%  Similarity=0.011  Sum_probs=185.9

Q ss_pred             cHHHHHHHHH--hCCChHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHHcCCCchhhhHHHhhc----cCcHH--HHHH
Q 011102          198 SLSFTVRELG--HMNLPERALQTFCWAQKQPHLFPDD-RLLASTVEVLARHHELKVPFKLENFVS----LASKG--VLEA  268 (493)
Q Consensus       198 ~~~~li~~~~--~~g~~~~A~~l~~~m~~~~g~~pd~-~t~~~li~~~~~~g~~~~~~~l~~~~~----~~~~~--~~~~  268 (493)
                      .+..+..++.  ..|+++.|.+.+....+.   .|+. ..+-....+....|+.+.+...  +..    .++..  +.-+
T Consensus        84 ~~~~~~~glla~~~g~~~~A~~~l~~~~~~---~~~~~~~~llaA~aa~~~g~~~~A~~~--l~~a~~~~p~~~l~~~~~  158 (409)
T TIGR00540        84 AQKQTEEALLKLAEGDYAKAEKLIAKNADH---AAEPVLNLIKAAEAAQQRGDEARANQH--LEEAAELAGNDNILVEIA  158 (409)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHhhc---CCCCHHHHHHHHHHHHHCCCHHHHHHH--HHHHHHhCCcCchHHHHH
Confidence            4555666553  479999999999887654   3443 3334445566677875444433  322    23332  3334


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHH-HHHHHH--
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCT-AIMKVG--  345 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~-~li~~~--  345 (493)
                      ....+...|+++.|.+.++.+.+.. +-+...+..+...+.+. |++++|.+++..+.+. ++. +...+. .-..++  
T Consensus       159 ~a~l~l~~~~~~~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~-~d~~~a~~~l~~l~k~-~~~-~~~~~~~l~~~a~~~  234 (409)
T TIGR00540       159 RTRILLAQNELHAARHGVDKLLEMA-PRHKEVLKLAEEAYIRS-GAWQALDDIIDNMAKA-GLF-DDEEFADLEQKAEIG  234 (409)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHc-CCC-CHHHHHHHHHHHHHH
Confidence            5778888999999999999999976 22556788888999999 9999999999999987 443 333332 112222  


Q ss_pred             -HHcCCHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHH---HHHHHHHHHHc
Q 011102          346 -IRLQKFGVVESLFHWFTHSGR---DPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPA---YRVVIKLFVAL  418 (493)
Q Consensus       346 -~~~g~~~~A~~l~~~m~~~g~---~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~t---y~~li~~~~~~  418 (493)
                       ...+..+++.+.+..+.+..-   +.+...+..+...+...|+.++|.+++++..+.  .||...   ...........
T Consensus       235 ~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~  312 (409)
T TIGR00540       235 LLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKP  312 (409)
T ss_pred             HHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCC
Confidence             233333333445555554321   137888999999999999999999999998875  344432   12222223445


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          419 NDISRAIRYFSKLKEAGFCPTY---DIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       419 g~~~~A~~~~~~m~~~g~~p~~---~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      ++.+.+.+.++...+.  .|+.   ....++-..+.+.|++++|.+.|+........||..++..+-.+
T Consensus       313 ~~~~~~~~~~e~~lk~--~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~l  379 (409)
T TIGR00540       313 EDNEKLEKLIEKQAKN--VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADA  379 (409)
T ss_pred             CChHHHHHHHHHHHHh--CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHH
Confidence            7888888888877643  2443   45568888899999999999999965555568999888777664

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

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

Probab=98.83  E-value=2.3e-05  Score=73.54  Aligned_cols=278  Identities=14%  Similarity=0.088  Sum_probs=127.0

Q ss_pred             CCHHHHHHHHhhhcccC--cHH---HHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHH--HHHHHHHHHcCCCchhhh
Q 011102          181 KDVAEVLDKCGRFLRKG--SLS---FTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLL--ASTVEVLARHHELKVPFK  253 (493)
Q Consensus       181 ~~~~~a~~~~~~m~~~~--~~~---~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~--~~li~~~~~~g~~~~~~~  253 (493)
                      .+.+.|.+.|-+|.+.+  +|.   +|=+.|-+.|.+|.|+++-+...+.++..-+...+  --|-.-|-+.|-+|.++.
T Consensus        49 ~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~  128 (389)
T COG2956          49 NQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAED  128 (389)
T ss_pred             cCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHH
Confidence            44456666666665544  332   33345556666666666666666553333332221  123333445555555444


Q ss_pred             HHHhhccCc-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH----HHHHHHHHhcCCCCHHHHHHHHHH
Q 011102          254 LENFVSLAS-----KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSI----YAKLILELGKNPDKYMLVMTLLDE  324 (493)
Q Consensus       254 l~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t----~~~li~~~~~~~~~~~~a~~l~~~  324 (493)
                      +  |....+     ....-.|+..|-+..+|++|.++-+++.+.|-.+..+-    |--+-..+... .+++.|..++.+
T Consensus       129 ~--f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~-~~~d~A~~~l~k  205 (389)
T COG2956         129 I--FNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALAS-SDVDRARELLKK  205 (389)
T ss_pred             H--HHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhh-hhHHHHHHHHHH
Confidence            4  322222     22345555666666666666666655555442222211    11111122222 455555555555


Q ss_pred             HhhcCCCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC
Q 011102          325 LGQRDDLNLSQQDCT-AIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF  403 (493)
Q Consensus       325 m~~~~g~~p~~~~~~-~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p  403 (493)
                      ..+.   .|+.+--+ .+-+.+...|+++.|.+.++...+....--..+-..|..+|...|+.++....+.++.+..-.+
T Consensus       206 Alqa---~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~  282 (389)
T COG2956         206 ALQA---DKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGA  282 (389)
T ss_pred             HHhh---CccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCc
Confidence            4433   12222222 2234555556666666666665554333333444555566666666666666665555442222


Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---cCCHHHHHHHHHHHHH
Q 011102          404 DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA---SGRLAKCRDVCKEAEM  468 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~---~g~~~~A~~l~~~m~~  468 (493)
                      +.  -..+-.--....-.+.|..++.+-...  +|+...+.-+|+.-..   .|+..+-+.+++.|..
T Consensus       283 ~~--~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvg  346 (389)
T COG2956         283 DA--ELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVG  346 (389)
T ss_pred             cH--HHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHHH
Confidence            22  122222222222234444443333322  2566666666555432   2334444555555543

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

Probab=98.81  E-value=3.6e-06  Score=81.80  Aligned_cols=268  Identities=15%  Similarity=0.068  Sum_probs=182.3

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH----HcCCCchhhhHHHhhccCcHHHHHHHH-----HHHHh
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLA----RHHELKVPFKLENFVSLASKGVLEATA-----KGFVK  275 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~----~~g~~~~~~~l~~~~~~~~~~~~~~li-----~~~~~  275 (493)
                      .|.++|+++.|++++.-..++     |..|-++...-+|    -.|.-+.+.+-.--..-.+..-||.-.     +.-..
T Consensus       428 ~~lk~~d~~~aieilkv~~~k-----dnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~  502 (840)
T KOG2003|consen  428 ELLKNGDIEGAIEILKVFEKK-----DNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFA  502 (840)
T ss_pred             HHHhccCHHHHHHHHHHHHhc-----cchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeee
Confidence            578899999999999988876     3333332222222    112212222221111112222233221     11234


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          276 GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       276 ~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~  355 (493)
                      +|++++|.+.|++.....-.-....||+=+. +-.. |++++|++.|-.+..-  +.-+..+.-.+-+.|--..+...|.
T Consensus       503 ngd~dka~~~ykeal~ndasc~ealfniglt-~e~~-~~ldeald~f~klh~i--l~nn~evl~qianiye~led~aqai  578 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDASCTEALFNIGLT-AEAL-GNLDEALDCFLKLHAI--LLNNAEVLVQIANIYELLEDPAQAI  578 (840)
T ss_pred             cCcHHHHHHHHHHHHcCchHHHHHHHHhccc-HHHh-cCHHHHHHHHHHHHHH--HHhhHHHHHHHHHHHHHhhCHHHHH
Confidence            6899999999999887543223333443332 3344 8899999999877543  3345667777788888888899999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          356 SLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       356 ~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      +++-+.. .-++-|....+-|-.-|-+.|+-..|.+.+-+--. -+.-|..|...|-.-|....-+++|..+|++..  =
T Consensus       579 e~~~q~~-slip~dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~ayyidtqf~ekai~y~ekaa--l  654 (840)
T KOG2003|consen  579 ELLMQAN-SLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--L  654 (840)
T ss_pred             HHHHHhc-ccCCCCHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--h
Confidence            8886544 22345678888899999999999999887765332 245577888888888888889999999998764  3


Q ss_pred             CCCCHHHHHHHHHHHH-HcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHhhh
Q 011102          436 FCPTYDIYRDMIRIFM-ASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEK  486 (493)
Q Consensus       436 ~~p~~~ty~~li~~~~-~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~~~  486 (493)
                      ++|+..-|..||..|. +.|++.+|++++++..++ +.-|.....-|+++|.
T Consensus       655 iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrk-fpedldclkflvri~~  705 (840)
T KOG2003|consen  655 IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRK-FPEDLDCLKFLVRIAG  705 (840)
T ss_pred             cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-CccchHHHHHHHHHhc
Confidence            5799999999988876 679999999999998654 7778888888888753

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

Probab=98.74  E-value=3.9e-05  Score=72.04  Aligned_cols=265  Identities=9%  Similarity=0.085  Sum_probs=187.2

Q ss_pred             CCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHH-hhccCcH------HHHHHHHHHHHhcCCHHH
Q 011102          209 MNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLEN-FVSLASK------GVLEATAKGFVKGGNLKL  281 (493)
Q Consensus       209 ~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~-~~~~~~~------~~~~~li~~~~~~g~~~~  281 (493)
                      +.+.++|.++|-+|.+.  -.-+..+--+|=+.|-+.|..|.+..++. ....||.      ...-.|-.-|...|-+|.
T Consensus        48 s~Q~dKAvdlF~e~l~~--d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DR  125 (389)
T COG2956          48 SNQPDKAVDLFLEMLQE--DPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDR  125 (389)
T ss_pred             hcCcchHHHHHHHHHhc--CchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhH
Confidence            46789999999999864  11122234556677888888665555543 2222321      234567777889999999


Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH----HHHHHHHHHHHHcCCHHHHHHH
Q 011102          282 AWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ----QDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       282 A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~----~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      |+.+|..+.+.|. --......|+.-|-+. .+|++|+++-+++.+. +-++..    ..|--+-..+.-..+++.|..+
T Consensus       126 AE~~f~~L~de~e-fa~~AlqqLl~IYQ~t-reW~KAId~A~~L~k~-~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~  202 (389)
T COG2956         126 AEDIFNQLVDEGE-FAEGALQQLLNIYQAT-REWEKAIDVAERLVKL-GGQTYRVEIAQFYCELAQQALASSDVDRAREL  202 (389)
T ss_pred             HHHHHHHHhcchh-hhHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHc-CCccchhHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            9999999988542 2334567889999999 9999999999988776 333332    2566777778888899999999


Q ss_pred             HHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 011102          358 FHWFTHSGRDPTV-VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGF  436 (493)
Q Consensus       358 ~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~  436 (493)
                      +.+-.+.  .|+. ..--.+-+.+...|++..|.+.++...+.+..--..+...|..+|.+.|+.++...++.++.+...
T Consensus       203 l~kAlqa--~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~  280 (389)
T COG2956         203 LKKALQA--DKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNT  280 (389)
T ss_pred             HHHHHhh--CccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccC
Confidence            9987654  3433 333345577889999999999999998886555566788999999999999999999999886543


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          437 CPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       437 ~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      .++..  ..|-+.-....-.+.|..++.+-..  -+|+...+..||..
T Consensus       281 g~~~~--l~l~~lie~~~G~~~Aq~~l~~Ql~--r~Pt~~gf~rl~~~  324 (389)
T COG2956         281 GADAE--LMLADLIELQEGIDAAQAYLTRQLR--RKPTMRGFHRLMDY  324 (389)
T ss_pred             CccHH--HHHHHHHHHhhChHHHHHHHHHHHh--hCCcHHHHHHHHHh
Confidence            33332  3333333333334455554444333  48999999999874

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

Probab=98.74  E-value=1.9e-05  Score=77.37  Aligned_cols=297  Identities=12%  Similarity=0.004  Sum_probs=212.5

Q ss_pred             CCHHHHHHHHhhhcccC-----cHHHHHH-HHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCc-hhh
Q 011102          181 KDVAEVLDKCGRFLRKG-----SLSFTVR-ELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELK-VPF  252 (493)
Q Consensus       181 ~~~~~a~~~~~~m~~~~-----~~~~li~-~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~-~~~  252 (493)
                      ...++++.......+.|     -+-+.+. +.-...+++.|+.+|++..+...... |..+|+.++-.--...++. .++
T Consensus       241 ~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~  320 (559)
T KOG1155|consen  241 HQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQ  320 (559)
T ss_pred             HHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHH
Confidence            34555555555444444     1122222 34456789999999999998633333 6668888775443322211 122


Q ss_pred             hHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCC
Q 011102          253 KLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDL  331 (493)
Q Consensus       253 ~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~  331 (493)
                      .+...+. -...|+.++-+.|+-.++.++|...|+...+.+  |. ...|+-+-+.|... .....|.+-+....+.  .
T Consensus       321 ~v~~idK-yR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN--p~~~~aWTLmGHEyvEm-KNt~AAi~sYRrAvdi--~  394 (559)
T KOG1155|consen  321 NVSNIDK-YRPETCCIIANYYSLRSEHEKAVMYFKRALKLN--PKYLSAWTLMGHEYVEM-KNTHAAIESYRRAVDI--N  394 (559)
T ss_pred             HHHHhcc-CCccceeeehhHHHHHHhHHHHHHHHHHHHhcC--cchhHHHHHhhHHHHHh-cccHHHHHHHHHHHhc--C
Confidence            1111111 133578888899999999999999999998865  43 45677777889999 8899999999988764  3


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 011102          332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVV  411 (493)
Q Consensus       332 ~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~l  411 (493)
                      +.|-..|=.|-.+|.-.+...-|+-.|++-.+-. +-|...|.+|-+.|.+.++.++|.+-|......|= .+...|..|
T Consensus       395 p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~k-PnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d-te~~~l~~L  472 (559)
T KOG1155|consen  395 PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELK-PNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD-TEGSALVRL  472 (559)
T ss_pred             chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc-cchHHHHHH
Confidence            4577788899999999999999999999876432 44889999999999999999999999999887653 366889999


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHH----CCCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHhh
Q 011102          412 IKLFVALNDISRAIRYFSKLKE----AGFCPTY--DIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIE  485 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~~----~g~~p~~--~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~~  485 (493)
                      -+.|-+-++..+|...|+.-.+    .|..-+.  ..---|..-+.+.+++++|......... | .+...--..|++-+
T Consensus       473 akLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~-~-~~e~eeak~LlRei  550 (559)
T KOG1155|consen  473 AKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLVLK-G-ETECEEAKALLREI  550 (559)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHHhc-C-CchHHHHHHHHHHH
Confidence            9999999999999999887653    3443231  2222355567789999999887655543 3 66666777777755


Q ss_pred             hh
Q 011102          486 KE  487 (493)
Q Consensus       486 ~~  487 (493)
                      +.
T Consensus       551 r~  552 (559)
T KOG1155|consen  551 RK  552 (559)
T ss_pred             HH
Confidence            44

>PRK12370 invasion protein regulator; Provisional

Probab=98.69  E-value=1.4e-05  Score=84.86  Aligned_cols=257  Identities=8%  Similarity=-0.064  Sum_probs=158.8

Q ss_pred             cHHHHHHHHHh-----CCChHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHHc---CCC----chhhhHHHhhc-----
Q 011102          198 SLSFTVRELGH-----MNLPERALQTFCWAQKQPHLFPDD-RLLASTVEVLARH---HEL----KVPFKLENFVS-----  259 (493)
Q Consensus       198 ~~~~li~~~~~-----~g~~~~A~~l~~~m~~~~g~~pd~-~t~~~li~~~~~~---g~~----~~~~~l~~~~~-----  259 (493)
                      .|...+.+-..     .+..++|+++|++..+.   .|+. ..|..+..++...   |..    +..+++..+..     
T Consensus       258 a~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~l---dP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ld  334 (553)
T PRK12370        258 STMVYLRGKHELNQYTPYSLQQALKLLTQCVNM---SPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELD  334 (553)
T ss_pred             HHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhc---CCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcC
Confidence            44455555322     23467999999988753   4543 3454444433322   211    12333333332     


Q ss_pred             cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH-HH
Q 011102          260 LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ-QD  337 (493)
Q Consensus       260 ~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~-~~  337 (493)
                      ..+...|..+-..+...|++++|...|++..+..  |+ ...|..+-..+... |++++|...+++..+.   .|+. ..
T Consensus       335 P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~-G~~~eAi~~~~~Al~l---~P~~~~~  408 (553)
T PRK12370        335 HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS--PISADIKYYYGWNLFMA-GQLEEALQTINECLKL---DPTRAAA  408 (553)
T ss_pred             CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHhc---CCCChhh
Confidence            2255677778788888899999999999888764  54 45666777778888 8999999999988764   2432 22


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHH-HHHHHHHHH
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPA-YRVVIKLFV  416 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~t-y~~li~~~~  416 (493)
                      +..+...+...|++++|...+++..+..-+-+...+..+-..|...|+.++|.+.+.++...  .|+..+ .+.+-..|+
T Consensus       409 ~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~~  486 (553)
T PRK12370        409 GITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEYC  486 (553)
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHHh
Confidence            33344456678889999999888765432224455677778888899999999998886543  344333 344445566


Q ss_pred             HcCCHHHHHHHHHHHHH-CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          417 ALNDISRAIRYFSKLKE-AGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAG  470 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~-~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g  470 (493)
                      ..|  +.|...++.+.+ .+-.+....+..++  |.-.|+-+.+..+ +++.+.|
T Consensus       487 ~~g--~~a~~~l~~ll~~~~~~~~~~~~~~~~--~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        487 QNS--ERALPTIREFLESEQRIDNNPGLLPLV--LVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             ccH--HHHHHHHHHHHHHhhHhhcCchHHHHH--HHHHhhhHHHHHH-HHhhccc
Confidence            666  477777777662 22333333344444  3444555555444 7776553

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

Probab=98.67  E-value=3.9e-06  Score=85.58  Aligned_cols=259  Identities=14%  Similarity=0.027  Sum_probs=186.0

Q ss_pred             ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc------cCcHHHHHHHHHHHHhcCCHHHHHH
Q 011102          211 LPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS------LASKGVLEATAKGFVKGGNLKLAWK  284 (493)
Q Consensus       211 ~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~------~~~~~~~~~li~~~~~~g~~~~A~~  284 (493)
                      +.++|+..|.....+  +.-+..+..-+-.+|-..++.+.+++++....      ..+..+|.+.+-.+-+.    -++.
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 NCREALNLFEKLPSH--HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDE----VALS  407 (638)
T ss_pred             HHHHHHHHHHhhHHh--cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhh----HHHH
Confidence            467899999885533  22233555666777777777666666533222      23566888888765432    2233


Q ss_pred             HHH-HHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          285 LLM-VAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNL-SQQDCTAIMKVGIRLQKFGVVESLFHWFT  362 (493)
Q Consensus       285 l~~-~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p-~~~~~~~li~~~~~~g~~~~A~~l~~~m~  362 (493)
                      .+. ++.+ --+-.+.||-++-++|.-. ++++.|++.|++..+-   .| ...+|+.+-+-+.....+|.|...|+.-.
T Consensus       408 ~Laq~Li~-~~~~sPesWca~GNcfSLQ-kdh~~Aik~f~RAiQl---dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al  482 (638)
T KOG1126|consen  408 YLAQDLID-TDPNSPESWCALGNCFSLQ-KDHDTAIKCFKRAIQL---DPRFAYAYTLLGHESIATEEFDKAMKSFRKAL  482 (638)
T ss_pred             HHHHHHHh-hCCCCcHHHHHhcchhhhh-hHHHHHHHHHHHhhcc---CCccchhhhhcCChhhhhHHHHhHHHHHHhhh
Confidence            332 2222 1234788999999999999 9999999999998763   45 67888988888899999999999999877


Q ss_pred             HcCCCCCHHHHHH---HHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC
Q 011102          363 HSGRDPTVVMYTT---LIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPT  439 (493)
Q Consensus       363 ~~g~~p~~~ty~~---li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~  439 (493)
                          ..|...||+   |--.|.+.++++.|+--|+...+-+- -+.+....+-..+-+.|+.|+|+++|++.....-+ |
T Consensus       483 ----~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP-~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n  556 (638)
T KOG1126|consen  483 ----GVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINP-SNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-N  556 (638)
T ss_pred             ----cCCchhhHHHHhhhhheeccchhhHHHHHHHhhhcCCc-cchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-C
Confidence                667766665   56789999999999999998776432 24555666667788999999999999998865544 3


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHH-Hhhhhc
Q 011102          440 YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELL-QIEKES  488 (493)
Q Consensus       440 ~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll-~~~~~~  488 (493)
                      ..+---....+...+++++|+..++++++  +.|+..+--.|+ +.|++-
T Consensus       557 ~l~~~~~~~il~~~~~~~eal~~LEeLk~--~vP~es~v~~llgki~k~~  604 (638)
T KOG1126|consen  557 PLCKYHRASILFSLGRYVEALQELEELKE--LVPQESSVFALLGKIYKRL  604 (638)
T ss_pred             chhHHHHHHHHHhhcchHHHHHHHHHHHH--hCcchHHHHHHHHHHHHHH
Confidence            33333355667788999999999999987  677766655444 566553

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.64  E-value=9.3e-06  Score=83.13  Aligned_cols=232  Identities=15%  Similarity=0.035  Sum_probs=128.6

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhC----CC-CCCCHHH-HHHHHHHHHHcCCCchhhhHHHhhccC----------
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQ----PH-LFPDDRL-LASTVEVLARHHELKVPFKLENFVSLA----------  261 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~----~g-~~pd~~t-~~~li~~~~~~g~~~~~~~l~~~~~~~----------  261 (493)
                      +...+-..|...|+++.|..++.+..+.    .| ..|+..+ .+.+-..|...++++.  ++..|.+..          
T Consensus       201 ~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~e--Av~ly~~AL~i~e~~~G~~  278 (508)
T KOG1840|consen  201 TLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDE--AVNLYEEALTIREEVFGED  278 (508)
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHH--HHHHHHHHHHHHHHhcCCC
Confidence            3344666777777777777777665532    12 1233322 2224445555565333  333233221          


Q ss_pred             ---cHHHHHHHHHHHHhcCCHHHHHHHHHHHHh-----CCCC-CCHHH-HHHHHHHHhcCCCCHHHHHHHHHHHhhcC--
Q 011102          262 ---SKGVLEATAKGFVKGGNLKLAWKLLMVAKD-----GGRM-LDPSI-YAKLILELGKNPDKYMLVMTLLDELGQRD--  329 (493)
Q Consensus       262 ---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~-----~g~~-pd~~t-~~~li~~~~~~~~~~~~a~~l~~~m~~~~--  329 (493)
                         -..+++.|-..|.+.|++++|...++...+     .|.. |.+.+ ++.+...|+.. +++++|..+++...+..  
T Consensus       279 h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~-~~~Eea~~l~q~al~i~~~  357 (508)
T KOG1840|consen  279 HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSM-NEYEEAKKLLQKALKIYLD  357 (508)
T ss_pred             CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHh-cchhHHHHHHHHHHHHHHh
Confidence               123577788888888888888777765533     2221 22222 44555566666 88888888877543320  


Q ss_pred             CCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-----C-CCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          330 DLNLS----QQDCTAIMKVGIRLQKFGVVESLFHWFTHS-----G-RDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       330 g~~p~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g-~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      -+.++    ..+|+.|-..|-+.|++++|+++|++....     | ..+ .-..+|-|-..|.+.++.++|.++|.+-..
T Consensus       358 ~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~  437 (508)
T KOG1840|consen  358 APGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKD  437 (508)
T ss_pred             hccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHH
Confidence            12222    236777777777788888887777765431     1 112 234566666677777777777777665322


Q ss_pred             ----CCC-CCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          399 ----SNC-LFDL-PAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       399 ----~gi-~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                          .|. .||+ .+|..|...|...|++++|.++.+...
T Consensus       438 i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  438 IMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence                221 1222 456666666666666666666655443

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=98.56  E-value=2e-05  Score=80.71  Aligned_cols=245  Identities=13%  Similarity=0.058  Sum_probs=169.9

Q ss_pred             HHHHHHHcCCCchhhhHHHhh----------ccCcHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhC-----C-CCCC-HH
Q 011102          238 TVEVLARHHELKVPFKLENFV----------SLASKG-VLEATAKGFVKGGNLKLAWKLLMVAKDG-----G-RMLD-PS  299 (493)
Q Consensus       238 li~~~~~~g~~~~~~~l~~~~----------~~~~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g-~~pd-~~  299 (493)
                      +...|...|+++.+..+....          ..+... ..+.+-..|...+++++|..+|+++..-     | ..|. ..
T Consensus       205 La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~  284 (508)
T KOG1840|consen  205 LAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAA  284 (508)
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHH
Confidence            777888888877766553211          111222 3456777889999999999999998752     2 1122 23


Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHhh----cCCCC-CCHH-HHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCC-
Q 011102          300 IYAKLILELGKNPDKYMLVMTLLDELGQ----RDDLN-LSQQ-DCTAIMKVGIRLQKFGVVESLFHWFTH---SGRDPT-  369 (493)
Q Consensus       300 t~~~li~~~~~~~~~~~~a~~l~~~m~~----~~g~~-p~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~---~g~~p~-  369 (493)
                      +++.|=..|++. |++++|...+++..+    ..|.. |.+. -++.+...|+..+++++|..+++.-.+   .-..++ 
T Consensus       285 ~l~nLa~ly~~~-GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g~~~  363 (508)
T KOG1840|consen  285 TLNNLAVLYYKQ-GKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPGEDN  363 (508)
T ss_pred             HHHHHHHHHhcc-CChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhccccc
Confidence            566666689999 999999888876532    11222 2222 456778888999999999999986542   112222 


Q ss_pred             ---HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CC--CCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHH----HCC
Q 011102          370 ---VVMYTTLIHSRLSEKKCREALTVVWNMEAS----NC--LFD-LPAYRVVIKLFVALNDISRAIRYFSKLK----EAG  435 (493)
Q Consensus       370 ---~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi--~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~----~~g  435 (493)
                         .-+|+.|-..|...|++++|.+++++..+.    +-  .+. -..++-|-..|.+.++.++|.++|.+-.    ..|
T Consensus       364 ~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g  443 (508)
T KOG1840|consen  364 VNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCG  443 (508)
T ss_pred             hHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhC
Confidence               357999999999999999999999987542    11  222 3567778888999999999999998654    333


Q ss_pred             CC-CC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH------CCCccCHHHHHHHHH
Q 011102          436 FC-PT-YDIYRDMIRIFMASGRLAKCRDVCKEAEM------AGFKLDKQTVVELLQ  483 (493)
Q Consensus       436 ~~-p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~------~g~~pd~~t~~~Ll~  483 (493)
                      .. |+ ..+|..|...|.+.|++++|.++.+....      ....|+.........
T Consensus       444 ~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  499 (508)
T KOG1840|consen  444 PDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLNAREQRLGTASPTVEDEKLRLA  499 (508)
T ss_pred             CCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcCCCCCcchhHHHHhhh
Confidence            21 23 46789999999999999999999887752      235566555554443

>PRK12370 invasion protein regulator; Provisional

Probab=98.54  E-value=3.7e-05  Score=81.54  Aligned_cols=180  Identities=10%  Similarity=-0.037  Sum_probs=135.2

Q ss_pred             cCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC-CHHHHHHHHHHHHHcCCHHH
Q 011102          276 GGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNL-SQQDCTAIMKVGIRLQKFGV  353 (493)
Q Consensus       276 ~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p-~~~~~~~li~~~~~~g~~~~  353 (493)
                      .+++++|...+++..+..  | +...+..+-..+... |++++|...|++..+.   .| +...+..+-..|...|++++
T Consensus       317 ~~~~~~A~~~~~~Al~ld--P~~~~a~~~lg~~~~~~-g~~~~A~~~~~~Al~l---~P~~~~a~~~lg~~l~~~G~~~e  390 (553)
T PRK12370        317 QNAMIKAKEHAIKATELD--HNNPQALGLLGLINTIH-SEYIVGSLLFKQANLL---SPISADIKYYYGWNLFMAGQLEE  390 (553)
T ss_pred             chHHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHc-cCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHCCCHHH
Confidence            355899999999998864  4 556676766677788 9999999999998765   34 45677888889999999999


Q ss_pred             HHHHHHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          354 VESLFHWFTHSGRDPTV-VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       354 A~~l~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      |...|++..+.  .|+. ..+..+...+...|++++|.+.+++..+.. .|+ ...+..+-..+...|+.++|...+.++
T Consensus       391 Ai~~~~~Al~l--~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~  467 (553)
T PRK12370        391 ALQTINECLKL--DPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEI  467 (553)
T ss_pred             HHHHHHHHHhc--CCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHh
Confidence            99999998765  3432 233445556777899999999999987653 243 445667777888999999999999987


Q ss_pred             HHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          432 KEAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       432 ~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ...  .|+ ....+.+...|+..|  ++|...++.+.+
T Consensus       468 ~~~--~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~  501 (553)
T PRK12370        468 STQ--EITGLIAVNLLYAEYCQNS--ERALPTIREFLE  501 (553)
T ss_pred             hhc--cchhHHHHHHHHHHHhccH--HHHHHHHHHHHH
Confidence            643  233 344556666777777  578887777754

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

Probab=98.49  E-value=6.3e-05  Score=79.33  Aligned_cols=347  Identities=14%  Similarity=0.112  Sum_probs=235.5

Q ss_pred             ccchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhh----hhhhhhhhhccCCchhHHHHHHH
Q 011102           98 WESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLA----SSRASICKQVYKNPSFLISLARD  173 (493)
Q Consensus        98 ~~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a----~~~~~~~~~~~~~~~~l~~l~~~  173 (493)
                      +-.|+++.|..++.+...+.+.+...|-.|.          ..|...|+..++    +..+...|..+   .+   +.+.
T Consensus       150 farg~~eeA~~i~~EvIkqdp~~~~ay~tL~----------~IyEqrGd~eK~l~~~llAAHL~p~d~---e~---W~~l  213 (895)
T KOG2076|consen  150 FARGDLEEAEEILMEVIKQDPRNPIAYYTLG----------EIYEQRGDIEKALNFWLLAAHLNPKDY---EL---WKRL  213 (895)
T ss_pred             HHhCCHHHHHHHHHHHHHhCccchhhHHHHH----------HHHHHcccHHHHHHHHHHHHhcCCCCh---HH---HHHH
Confidence            3359999999999999777777888888888          778888887777    44455554433   22   2222


Q ss_pred             HhhccCCCCHHHHHHHHhhhcccC--cHHHH---HHHHHhCCChHHHHHHHHHHHhCCCCCCCHH-HHHH----HHHHHH
Q 011102          174 IKGLDSHKDVAEVLDKCGRFLRKG--SLSFT---VRELGHMNLPERALQTFCWAQKQPHLFPDDR-LLAS----TVEVLA  243 (493)
Q Consensus       174 l~~~~~~~~~~~a~~~~~~m~~~~--~~~~l---i~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~-t~~~----li~~~~  243 (493)
                      -....+.|.+..|.-.|.+.+...  .|-.+   +..|-+.|+...|.+-|.++....+  |+.. -+-.    +++.+-
T Consensus       214 adls~~~~~i~qA~~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p--~~d~er~~d~i~~~~~~~~  291 (895)
T KOG2076|consen  214 ADLSEQLGNINQARYCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDP--PVDIERIEDLIRRVAHYFI  291 (895)
T ss_pred             HHHHHhcccHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCC--chhHHHHHHHHHHHHHHHH
Confidence            233455688888888888766543  34333   5578889999999999999975422  2222 2222    334444


Q ss_pred             HcCCCchhhhHHHhhc-------cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH---------------
Q 011102          244 RHHELKVPFKLENFVS-------LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIY---------------  301 (493)
Q Consensus       244 ~~g~~~~~~~l~~~~~-------~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~---------------  301 (493)
                      ..++  ...++..+..       ..+...+|+++..|.+...++.|......+......+|..-|               
T Consensus       292 ~~~~--~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~  369 (895)
T KOG2076|consen  292 THNE--RERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCE  369 (895)
T ss_pred             HhhH--HHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhcccccccccc
Confidence            4444  2333333222       123346899999999999999999999888874444444333               


Q ss_pred             -------H----HHHHHHhcCCCCHHHHHHHHHHHhhcCC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC
Q 011102          302 -------A----KLILELGKNPDKYMLVMTLLDELGQRDD--LNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP  368 (493)
Q Consensus       302 -------~----~li~~~~~~~~~~~~a~~l~~~m~~~~g--~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  368 (493)
                             .    -++-++... +..+....+....... .  +.-++..|.-+-.+|...|++.+|.++|..+...-.--
T Consensus       370 ~~~~~s~~l~v~rl~icL~~L-~~~e~~e~ll~~l~~~-n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~  447 (895)
T KOG2076|consen  370 VGKELSYDLRVIRLMICLVHL-KERELLEALLHFLVED-NVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQ  447 (895)
T ss_pred             CCCCCCccchhHhHhhhhhcc-cccchHHHHHHHHHHh-cCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCcccc
Confidence                   1    122333343 4444555555555444 4  33455678889999999999999999999998776666


Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHH--------HCCCCCC
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL-PAYRVVIKLFVALNDISRAIRYFSKLK--------EAGFCPT  439 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~--------~~g~~p~  439 (493)
                      +...|--+-..|...|..++|.+.++.....  .||. -.-.+|-..+-+.|+.++|.+.++.|.        ..+..|+
T Consensus       448 ~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~--~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e  525 (895)
T KOG2076|consen  448 NAFVWYKLARCYMELGEYEEAIEFYEKVLIL--APDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPE  525 (895)
T ss_pred             chhhhHHHHHHHHHHhhHHHHHHHHHHHHhc--CCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHH
Confidence            7888999999999999999999999987764  3443 233345556788999999999999865        2334556


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          440 YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       440 ~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ...---..+.|...|+.++=..+-.+|..
T Consensus       526 ~ri~~~r~d~l~~~gk~E~fi~t~~~Lv~  554 (895)
T KOG2076|consen  526 RRILAHRCDILFQVGKREEFINTASTLVD  554 (895)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            66666677788889998886666666653

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

Probab=98.49  E-value=0.00054  Score=72.53  Aligned_cols=181  Identities=11%  Similarity=0.034  Sum_probs=106.6

Q ss_pred             hccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCc
Q 011102          176 GLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELK  249 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~  249 (493)
                      .+++ |++++|.+++.+..+.+     .|-+|-..|-+.|+.++|+..+-..-   .+.| |...|..+-......|.++
T Consensus       149 lfar-g~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAA---HL~p~d~e~W~~ladls~~~~~i~  224 (895)
T KOG2076|consen  149 LFAR-GDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAA---HLNPKDYELWKRLADLSEQLGNIN  224 (895)
T ss_pred             HHHh-CCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHH---hcCCCChHHHHHHHHHHHhcccHH
Confidence            4444 99999999999888776     78889999999999999988865554   3333 5556777777777777644


Q ss_pred             hhhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHH----HHHHHHHhcCCCCHHHHHH
Q 011102          250 VPFKLENFVS-----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIY----AKLILELGKNPDKYMLVMT  320 (493)
Q Consensus       250 ~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~----~~li~~~~~~~~~~~~a~~  320 (493)
                      .  +...|.+     ..+...+--=+..|-+.|+...|+.-|.++.+..-..|..-+    -.++..+... ++.+.|.+
T Consensus       225 q--A~~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~-~~~e~a~~  301 (895)
T KOG2076|consen  225 Q--ARYCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITH-NERERAAK  301 (895)
T ss_pred             H--HHHHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHh-hHHHHHHH
Confidence            3  3332322     112222223344566667777777777666664321111111    1233444444 44466666


Q ss_pred             HHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          321 LLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTH  363 (493)
Q Consensus       321 l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  363 (493)
                      .++......+-..+..+++++...|.+...++.|......+..
T Consensus       302 ~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~  344 (895)
T KOG2076|consen  302 ALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRN  344 (895)
T ss_pred             HHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhc
Confidence            5555444323334444556666666666666666666655554

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.41  E-value=3.4e-07  Score=57.67  Aligned_cols=33  Identities=27%  Similarity=0.257  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC
Q 011102          372 MYTTLIHSRLSEKKCREALTVVWNMEASNCLFD  404 (493)
Q Consensus       372 ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd  404 (493)
                      +||+||.+|++.|++++|.++|++|.+.|+.||
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.

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

Probab=98.39  E-value=0.00053  Score=71.13  Aligned_cols=282  Identities=16%  Similarity=0.098  Sum_probs=185.6

Q ss_pred             ccCCCCHHHHHHHHhhhcc----cC-cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHH-HHHHHHHcCCC--
Q 011102          177 LDSHKDVAEVLDKCGRFLR----KG-SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLAS-TVEVLARHHEL--  248 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~----~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~-li~~~~~~g~~--  248 (493)
                      +...|+.++|++.+..-..    +. .....-..|.+.|+.++|..+|..+.++   .||...|-. +..+++-...+  
T Consensus        14 l~e~g~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~r---NPdn~~Yy~~L~~~~g~~~~~~~   90 (517)
T PF12569_consen   14 LEEAGDYEEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDR---NPDNYDYYRGLEEALGLQLQLSD   90 (517)
T ss_pred             HHHCCCHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---CCCcHHHHHHHHHHHhhhccccc
Confidence            3456999999999875332    22 4456677889999999999999999865   567776554 44444333221  


Q ss_pred             -chhhhHHHhhccCcHH----HHHHHHHHHHhcCCH-HHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHH
Q 011102          249 -KVPFKLENFVSLASKG----VLEATAKGFVKGGNL-KLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLL  322 (493)
Q Consensus       249 -~~~~~l~~~~~~~~~~----~~~~li~~~~~~g~~-~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~  322 (493)
                       +.......|.+.....    ..-.+.-.+.....+ ..+...+..+...|++   .+|+.|-.-|... .+..-..+++
T Consensus        91 ~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP---slF~~lk~Ly~d~-~K~~~i~~l~  166 (517)
T PF12569_consen   91 EDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP---SLFSNLKPLYKDP-EKAAIIESLV  166 (517)
T ss_pred             ccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc---hHHHHHHHHHcCh-hHHHHHHHHH
Confidence             1222223333322111    111111111121222 3455666777888854   3455555556555 6666666666


Q ss_pred             HHHhhc----CC---------CCCCHHHH--HHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCH
Q 011102          323 DELGQR----DD---------LNLSQQDC--TAIMKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYTTLIHSRLSEKKC  386 (493)
Q Consensus       323 ~~m~~~----~g---------~~p~~~~~--~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~~~~~~g~~  386 (493)
                      ......    +.         -.|+...|  .-+-..|-..|++++|++..++-.+.  .|+ +.-|.+--..|-+.|++
T Consensus       167 ~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh~G~~  244 (517)
T PF12569_consen  167 EEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKHAGDL  244 (517)
T ss_pred             HHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHCCCH
Confidence            665432    11         13444444  45566788999999999999988765  676 56788888999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHH------HH--HHHHHHHHHcCCHHH
Q 011102          387 REALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYD------IY--RDMIRIFMASGRLAK  458 (493)
Q Consensus       387 ~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~------ty--~~li~~~~~~g~~~~  458 (493)
                      .+|.+.+++.++... -|...=+-....+.++|++++|.+++......+..|-..      .|  .-.-.+|.+.|++..
T Consensus       245 ~~Aa~~~~~Ar~LD~-~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~  323 (517)
T PF12569_consen  245 KEAAEAMDEARELDL-ADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGL  323 (517)
T ss_pred             HHHHHHHHHHHhCCh-hhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence            999999999988654 466676778888999999999999999988666543322      22  345567889999999


Q ss_pred             HHHHHHHHHH
Q 011102          459 CRDVCKEAEM  468 (493)
Q Consensus       459 A~~l~~~m~~  468 (493)
                      |++-|....+
T Consensus       324 ALk~~~~v~k  333 (517)
T PF12569_consen  324 ALKRFHAVLK  333 (517)
T ss_pred             HHHHHHHHHH
Confidence            9887666543

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 [], [].

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.38  E-value=0.00026  Score=68.82  Aligned_cols=208  Identities=12%  Similarity=0.004  Sum_probs=133.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC-CHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNL-SQQDCTAIMK  343 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p-~~~~~~~li~  343 (493)
                      .|..+-..|.+.|+.++|...|++..+.. +-+...|+.+-..+... |++++|.+.|+...+.   .| +...|..+..
T Consensus        66 ~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~-g~~~~A~~~~~~Al~l---~P~~~~a~~~lg~  140 (296)
T PRK11189         66 LHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQA-GNFDAAYEAFDSVLEL---DPTYNYAYLNRGI  140 (296)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHh---CCCCHHHHHHHHH
Confidence            35556667788888899988888887754 23467788888888888 8999999988888753   34 3566777778


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~  423 (493)
                      ++...|++++|.+.|+...+.  .|+-.........+...++.++|.+.|.+.... ..|+...+ .+.  ....|++++
T Consensus       141 ~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~-~~~~~~~~-~~~--~~~lg~~~~  214 (296)
T PRK11189        141 ALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRYEK-LDKEQWGW-NIV--EFYLGKISE  214 (296)
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhh-CCccccHH-HHH--HHHccCCCH
Confidence            888889999999999887754  343221222222234567889999888765432 22332221 222  223455544


Q ss_pred             HHHHHHHHHHC-CCC----C-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHH-HHHhh
Q 011102          424 AIRYFSKLKEA-GFC----P-TYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVE-LLQIE  485 (493)
Q Consensus       424 A~~~~~~m~~~-g~~----p-~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~-Ll~~~  485 (493)
                      + +.++.+.+. ...    | ....|..+-..+.+.|++++|...|++..+.+ .||.+-+.. ++.+.
T Consensus       215 ~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~-~~~~~e~~~~~~e~~  281 (296)
T PRK11189        215 E-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANN-VYNFVEHRYALLELA  281 (296)
T ss_pred             H-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CchHHHHHHHHHHHH
Confidence            4 344444421 111    1 23568888888889999999999999888654 335555443 44443

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.36  E-value=5.8e-07  Score=56.57  Aligned_cols=33  Identities=24%  Similarity=0.400  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccC
Q 011102          442 IYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLD  474 (493)
Q Consensus       442 ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd  474 (493)
                      +||++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            577777777777777777777777777777776

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.

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

Probab=98.32  E-value=0.00057  Score=70.89  Aligned_cols=258  Identities=12%  Similarity=0.080  Sum_probs=178.5

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhCCCCCCCHH-HHHHHHHHHHHcCCCchhhhH--HHhhccCcHHH-HHHHHHHHHhc--
Q 011102          203 VRELGHMNLPERALQTFCWAQKQPHLFPDDR-LLASTVEVLARHHELKVPFKL--ENFVSLASKGV-LEATAKGFVKG--  276 (493)
Q Consensus       203 i~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~-t~~~li~~~~~~g~~~~~~~l--~~~~~~~~~~~-~~~li~~~~~~--  276 (493)
                      ...+...|++++|++.++.-.   ...+|.. .+......+.+.|+.+.++..  ..+..-|+... |..+..+..-.  
T Consensus        11 ~~il~e~g~~~~AL~~L~~~~---~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~   87 (517)
T PF12569_consen   11 NSILEEAGDYEEALEHLEKNE---KQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQ   87 (517)
T ss_pred             HHHHHHCCCHHHHHHHHHhhh---hhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcc
Confidence            345678899999999998755   3345554 456677778888886665544  22344555554 44444444222  


Q ss_pred             ---CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHH-HHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          277 ---GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYM-LVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFG  352 (493)
Q Consensus       277 ---g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~-~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~  352 (493)
                         ...+...++|+++...-  |.......+.-.+... ..+. .+...+..+..+ |+.   .+|+.|-.-|....+.+
T Consensus        88 ~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g-~~F~~~~~~yl~~~l~K-gvP---slF~~lk~Ly~d~~K~~  160 (517)
T PF12569_consen   88 LSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEG-DEFKERLDEYLRPQLRK-GVP---SLFSNLKPLYKDPEKAA  160 (517)
T ss_pred             cccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCH-HHHHHHHHHHHHHHHhc-CCc---hHHHHHHHHHcChhHHH
Confidence               25677788888876643  5444444443333332 2332 334445555555 652   36777777777666677


Q ss_pred             HHHHHHHHHHHc----C----------CCCCH--HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH
Q 011102          353 VVESLFHWFTHS----G----------RDPTV--VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVVIKLF  415 (493)
Q Consensus       353 ~A~~l~~~m~~~----g----------~~p~~--~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~  415 (493)
                      -..+++..+...    |          -.|+.  ++|.-+-+.|-..|+.++|++.+++..++  .|+ +..|.+--..+
T Consensus       161 ~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~Karil  238 (517)
T PF12569_consen  161 IIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARIL  238 (517)
T ss_pred             HHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHH
Confidence            777777766532    1          23444  45577788899999999999999998876  466 45777888889


Q ss_pred             HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCcc
Q 011102          416 VALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKL  473 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  473 (493)
                      -+.|++++|.+.++...+.... |...=+-.+..+.++|++++|.+++....+.+..|
T Consensus       239 Kh~G~~~~Aa~~~~~Ar~LD~~-DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~  295 (517)
T PF12569_consen  239 KHAGDLKEAAEAMDEARELDLA-DRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDP  295 (517)
T ss_pred             HHCCCHHHHHHHHHHHHhCChh-hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCc
Confidence            9999999999999999877765 88888889999999999999999999988777544

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 [], [].

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.28  E-value=1e-06  Score=55.12  Aligned_cols=32  Identities=16%  Similarity=0.145  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC
Q 011102          372 MYTTLIHSRLSEKKCREALTVVWNMEASNCLF  403 (493)
Q Consensus       372 ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p  403 (493)
                      +||++|.+|++.|+++.|.++|++|++.|++|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            34444444444444444444444444444433

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.27  E-value=1.2e-06  Score=54.86  Aligned_cols=33  Identities=18%  Similarity=0.303  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCcc
Q 011102          441 DIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKL  473 (493)
Q Consensus       441 ~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  473 (493)
                      .||+++|++|++.|+++.|.++|++|.+.|++|
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            356666666666666666666666666666655

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

Probab=98.25  E-value=0.0002  Score=76.22  Aligned_cols=277  Identities=12%  Similarity=0.041  Sum_probs=184.0

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCC--CCCCCHH-------HHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQP--HLFPDDR-------LLASTVEVLARHHELKVPFKLENFVSLASKGVLEA  268 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~--g~~pd~~-------t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~  268 (493)
                      ..|.+-......|.+++|...|.......  ...+|..       -||. -..+-..++.+.++.+  |....  .-+-.
T Consensus       454 ~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNl-arl~E~l~~~~~A~e~--Yk~Il--kehp~  528 (1018)
T KOG2002|consen  454 VLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNL-ARLLEELHDTEVAEEM--YKSIL--KEHPG  528 (1018)
T ss_pred             HHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHH-HHHHHhhhhhhHHHHH--HHHHH--HHCch
Confidence            56777777788888888888888876431  1233331       1221 1111122233333332  22110  01223


Q ss_pred             HHHHHHhc-------CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          269 TAKGFVKG-------GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       269 li~~~~~~-------g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      .|++|.+.       +...+|...+.+..+.. .-++..++-+=.-+.+. ..|..|..-|..........+|..+.-+|
T Consensus       529 YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d-~~np~arsl~G~~~l~k-~~~~~a~k~f~~i~~~~~~~~D~YsliaL  606 (1018)
T KOG2002|consen  529 YIDAYLRLGCMARDKNNLYEASLLLKDALNID-SSNPNARSLLGNLHLKK-SEWKPAKKKFETILKKTSTKTDAYSLIAL  606 (1018)
T ss_pred             hHHHHHHhhHHHHhccCcHHHHHHHHHHHhcc-cCCcHHHHHHHHHHHhh-hhhcccccHHHHHHhhhccCCchhHHHHh
Confidence            45555555       56677888887766532 22333443333355666 77888888777766554555777766666


Q ss_pred             HHHHHH------------cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          342 MKVGIR------------LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYR  409 (493)
Q Consensus       342 i~~~~~------------~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~  409 (493)
                      -+.|..            .+..++|+++|.+..+.. +.|.+.=|-+--.++..|++.+|.++|.+.++... -+.-+|-
T Consensus       607 GN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~l  684 (1018)
T KOG2002|consen  607 GNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWL  684 (1018)
T ss_pred             hHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceee
Confidence            665542            345788999999877542 45788888899999999999999999999998754 2334688


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          410 VVIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       410 ~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      .+-+.|...|++..|.++|+.-. ...-.-+......|-.++-+.|.+.+|.+.+.........-...-||..+-
T Consensus       685 Nlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p~~~~v~FN~a~v  759 (1018)
T KOG2002|consen  685 NLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAPSNTSVKFNLALV  759 (1018)
T ss_pred             eHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCCccchHHhHHHHH
Confidence            89999999999999999999755 666666888899999999999999999998777666544444555665543

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

Probab=98.25  E-value=0.0058  Score=60.89  Aligned_cols=258  Identities=9%  Similarity=-0.060  Sum_probs=154.0

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcC----CCchhhh-HHHhhc-cC-cHHHHHHHHHHHHhc
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHH----ELKVPFK-LENFVS-LA-SKGVLEATAKGFVKG  276 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g----~~~~~~~-l~~~~~-~~-~~~~~~~li~~~~~~  276 (493)
                      .+...|++++|.++++...+.   .| |...+.. ...+...|    ..+.... +..... .+ .......+...+...
T Consensus        52 ~~~~~g~~~~A~~~~~~~l~~---~P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~  127 (355)
T cd05804          52 SAWIAGDLPKALALLEQLLDD---YPRDLLALKL-HLGAFGLGDFSGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEA  127 (355)
T ss_pred             HHHHcCCHHHHHHHHHHHHHH---CCCcHHHHHH-hHHHHHhcccccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHc
Confidence            556789999999999998754   23 3334432 22222222    2222221 111111 11 222345556678899


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH--HHHHHHHHHHHHcCCHHHH
Q 011102          277 GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ--QDCTAIMKVGIRLQKFGVV  354 (493)
Q Consensus       277 g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~--~~~~~li~~~~~~g~~~~A  354 (493)
                      |++++|.+.+++..+.. +.+...+..+-..+... |++++|...+++........++.  ..|-.+...+...|++++|
T Consensus       128 G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~-g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A  205 (355)
T cd05804         128 GQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQ-GRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAA  205 (355)
T ss_pred             CCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHc-CCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHH
Confidence            99999999999999865 23355667777888888 99999999999877642112333  3455678889999999999


Q ss_pred             HHHHHHHHHcCC-CCCHHHH-H--HHHHHHHcCCCHHHHHHH--HHHHHHCCC--CCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          355 ESLFHWFTHSGR-DPTVVMY-T--TLIHSRLSEKKCREALTV--VWNMEASNC--LFDLPAYRVVIKLFVALNDISRAIR  426 (493)
Q Consensus       355 ~~l~~~m~~~g~-~p~~~ty-~--~li~~~~~~g~~~~A~~l--~~~M~~~gi--~pd~~ty~~li~~~~~~g~~~~A~~  426 (493)
                      ..+|++...... .+..... +  .++.-+...|....+.+.  +........  ............++...|+.++|..
T Consensus       206 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~  285 (355)
T cd05804         206 LAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDK  285 (355)
T ss_pred             HHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHH
Confidence            999999854322 1222211 2  334444444533322222  211111111  1111222356677889999999999


Q ss_pred             HHHHHHHCCCC------C--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          427 YFSKLKEAGFC------P--TYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       427 ~~~~m~~~g~~------p--~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +++.+......      .  .+...-..--++...|+.++|.+++.+...
T Consensus       286 ~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~  335 (355)
T cd05804         286 LLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRD  335 (355)
T ss_pred             HHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99998742221      0  112222223335589999999999888764

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

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

Probab=98.20  E-value=0.00015  Score=69.83  Aligned_cols=150  Identities=19%  Similarity=0.108  Sum_probs=85.6

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHH----
Q 011102          271 KGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGI----  346 (493)
Q Consensus       271 ~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~----  346 (493)
                      ..+...|++++|++++..-      -+.......+..|.+. ++++.|.+.++.|.+.   ..|.. ...+..++.    
T Consensus       110 ~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~-~R~dlA~k~l~~~~~~---~eD~~-l~qLa~awv~l~~  178 (290)
T PF04733_consen  110 TILFHEGDYEEALKLLHKG------GSLELLALAVQILLKM-NRPDLAEKELKNMQQI---DEDSI-LTQLAEAWVNLAT  178 (290)
T ss_dssp             HHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHT-T-HHHHHHHHHHHHCC---SCCHH-HHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHc-CCHHHHHHHHHHHHhc---CCcHH-HHHHHHHHHHHHh
Confidence            3455567777777766532      3455555666677777 7777777777777643   23322 222333222    


Q ss_pred             HcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH-HHHH
Q 011102          347 RLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI-SRAI  425 (493)
Q Consensus       347 ~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~-~~A~  425 (493)
                      -..++.+|..+|+++.+ ...++..+.|.+..++...|++++|.+++.+..+..- -|..|...+|......|+. +.+.
T Consensus       179 g~e~~~~A~y~f~El~~-~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~-~~~d~LaNliv~~~~~gk~~~~~~  256 (290)
T PF04733_consen  179 GGEKYQDAFYIFEELSD-KFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDP-NDPDTLANLIVCSLHLGKPTEAAE  256 (290)
T ss_dssp             TTTCCCHHHHHHHHHHC-CS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHTT-TCHHHH
T ss_pred             CchhHHHHHHHHHHHHh-ccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCChhHHH
Confidence            22357777777777653 3456666777777777777777777777776544321 2344555566666666666 5566


Q ss_pred             HHHHHHHH
Q 011102          426 RYFSKLKE  433 (493)
Q Consensus       426 ~~~~~m~~  433 (493)
                      +++..++.
T Consensus       257 ~~l~qL~~  264 (290)
T PF04733_consen  257 RYLSQLKQ  264 (290)
T ss_dssp             HHHHHCHH
T ss_pred             HHHHHHHH
Confidence            66666663

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.

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

Probab=98.18  E-value=0.0038  Score=60.60  Aligned_cols=272  Identities=9%  Similarity=-0.018  Sum_probs=198.3

Q ss_pred             HHHHHHHHHh--CCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHH-Hhhcc---CcHHHHHHHHHH
Q 011102          199 LSFTVRELGH--MNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLE-NFVSL---ASKGVLEATAKG  272 (493)
Q Consensus       199 ~~~li~~~~~--~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~-~~~~~---~~~~~~~~li~~  272 (493)
                      -..+..++.+  .|++..|.++...-.+. +-.| ...|..-..+--..|+.+.+.... ...+.   .+.-++-+....
T Consensus        85 ~~~~~egl~~l~eG~~~qAEkl~~rnae~-~e~p-~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarl  162 (400)
T COG3071          85 RKALNEGLLKLFEGDFQQAEKLLRRNAEH-GEQP-VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARL  162 (400)
T ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHHhhhc-Ccch-HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHH
Confidence            3445555544  69999999999887765 5443 334555566666667755544432 22222   244467778888


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHH-------HHHHHHHHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQ-------DCTAIMKVG  345 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~-------~~~~li~~~  345 (493)
                      ....|+.+.|..-++++.+.+- -.+.........|.+. |.|..+..++..|.+. |.--|..       +|+.+++-.
T Consensus       163 ll~~~d~~aA~~~v~~ll~~~p-r~~~vlrLa~r~y~~~-g~~~~ll~~l~~L~ka-~~l~~~e~~~le~~a~~glL~q~  239 (400)
T COG3071         163 LLNRRDYPAARENVDQLLEMTP-RHPEVLRLALRAYIRL-GAWQALLAILPKLRKA-GLLSDEEAARLEQQAWEGLLQQA  239 (400)
T ss_pred             HHhCCCchhHHHHHHHHHHhCc-CChHHHHHHHHHHHHh-ccHHHHHHHHHHHHHc-cCCChHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999888653 3566778889999999 9999999999999998 6655533       678888877


Q ss_pred             HHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          346 IRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAI  425 (493)
Q Consensus       346 ~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~  425 (493)
                      ...+..+.-...|++...+ .+-+...-.+++.-+.+.|+.++|.++..+-.+++..|+..    ..-.+.+-++.+.=.
T Consensus       240 ~~~~~~~gL~~~W~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~~~~l~~~d~~~l~  314 (400)
T COG3071         240 RDDNGSEGLKTWWKNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RLIPRLRPGDPEPLI  314 (400)
T ss_pred             hccccchHHHHHHHhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HHHhhcCCCCchHHH
Confidence            7777777766677766432 13344445788889999999999999999999888877722    233455666666666


Q ss_pred             HHHHHHH-HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          426 RYFSKLK-EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       426 ~~~~~m~-~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      +..+.-. ..+-.|  ..+.+|=..|.+.+.|.+|.+.|+...  ...|+..+|+.+-+.
T Consensus       315 k~~e~~l~~h~~~p--~L~~tLG~L~~k~~~w~kA~~~leaAl--~~~~s~~~~~~la~~  370 (400)
T COG3071         315 KAAEKWLKQHPEDP--LLLSTLGRLALKNKLWGKASEALEAAL--KLRPSASDYAELADA  370 (400)
T ss_pred             HHHHHHHHhCCCCh--hHHHHHHHHHHHhhHHHHHHHHHHHHH--hcCCChhhHHHHHHH
Confidence            6655544 555555  677888899999999999999999655  478999999988764

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

Probab=98.17  E-value=0.0018  Score=65.41  Aligned_cols=272  Identities=15%  Similarity=0.037  Sum_probs=196.1

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhH--HHhhccC-cHHHHHHHHHHHHhcCCH
Q 011102          203 VRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKL--ENFVSLA-SKGVLEATAKGFVKGGNL  279 (493)
Q Consensus       203 i~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l--~~~~~~~-~~~~~~~li~~~~~~g~~  279 (493)
                      ..-+-..+++.+.+++++...+..++.++.  +..-|..+...|+...--.+  .....-| ...+|-++--.|--.|+.
T Consensus       251 ad~~y~~c~f~~c~kit~~lle~dpfh~~~--~~~~ia~l~el~~~n~Lf~lsh~LV~~yP~~a~sW~aVg~YYl~i~k~  328 (611)
T KOG1173|consen  251 ADRLYYGCRFKECLKITEELLEKDPFHLPC--LPLHIACLYELGKSNKLFLLSHKLVDLYPSKALSWFAVGCYYLMIGKY  328 (611)
T ss_pred             HHHHHHcChHHHHHHHhHHHHhhCCCCcch--HHHHHHHHHHhcccchHHHHHHHHHHhCCCCCcchhhHHHHHHHhcCc
Confidence            345667889999999999988765666554  45556677777763321111  1112223 445788888888888999


Q ss_pred             HHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc-CCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          280 KLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQR-DDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       280 ~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~-~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      .+|.+.|.+.....  |. ...|-..-+.|+-. +..++|...+...-+- .|.. -+..|.  ---|.+.++++.|.+.
T Consensus       329 seARry~SKat~lD--~~fgpaWl~fghsfa~e-~EhdQAmaaY~tAarl~~G~h-lP~LYl--gmey~~t~n~kLAe~F  402 (611)
T KOG1173|consen  329 SEARRYFSKATTLD--PTFGPAWLAFGHSFAGE-GEHDQAMAAYFTAARLMPGCH-LPSLYL--GMEYMRTNNLKLAEKF  402 (611)
T ss_pred             HHHHHHHHHHhhcC--ccccHHHHHHhHHhhhc-chHHHHHHHHHHHHHhccCCc-chHHHH--HHHHHHhccHHHHHHH
Confidence            99999998765532  22 12466667788888 8999999887765442 2221 122232  2357788999999999


Q ss_pred             HHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--CCC----CCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          358 FHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEAS--NCL----FDLPAYRVVIKLFVALNDISRAIRYFSK  430 (493)
Q Consensus       358 ~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~--gi~----pd~~ty~~li~~~~~~g~~~~A~~~~~~  430 (493)
                      |.+-.  ++.| |....+-+--.....+.+.+|...|+.....  .+.    .-..+++.|=++|.+.++.++|...|+.
T Consensus       403 f~~A~--ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~  480 (611)
T KOG1173|consen  403 FKQAL--AIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQK  480 (611)
T ss_pred             HHHHH--hcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHH
Confidence            98765  3344 6677777777777788999999999986621  111    2445688888999999999999999998


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHhhhh
Q 011102          431 LKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKE  487 (493)
Q Consensus       431 m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~~~~  487 (493)
                      -....- -|..||.++--.|...|+++.|.+.|.+..  .+.||..+-..+|+.+-+
T Consensus       481 aL~l~~-k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~aie  534 (611)
T KOG1173|consen  481 ALLLSP-KDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKLAIE  534 (611)
T ss_pred             HHHcCC-CchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHHHHH
Confidence            875443 388899999999999999999999999866  589999999999886544

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.17  E-value=0.0025  Score=61.95  Aligned_cols=223  Identities=12%  Similarity=0.033  Sum_probs=138.8

Q ss_pred             CCChHHHHHHHHHHHhCCCCCCCH--HHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHH
Q 011102          209 MNLPERALQTFCWAQKQPHLFPDD--RLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKGFVKGGNLKL  281 (493)
Q Consensus       209 ~g~~~~A~~l~~~m~~~~g~~pd~--~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~  281 (493)
                      .+..+.++.-+.++.......|+.  ..|...-..+.+.|+.+  +++..|..     ..+...|+.+-..|...|++++
T Consensus        39 ~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~--~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~  116 (296)
T PRK11189         39 TLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRA--LARNDFSQALALRPDMADAYNYLGIYLTQAGNFDA  116 (296)
T ss_pred             chHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHH--HHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHH
Confidence            345566666666666432333332  23444555566666633  33333332     1245678888899999999999


Q ss_pred             HHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          282 AWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHW  360 (493)
Q Consensus       282 A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~  360 (493)
                      |.+.|+...+..  |+ ..+|..+-..+... |++++|.+.|+...+.   .|+..........+...++.++|.+.|.+
T Consensus       117 A~~~~~~Al~l~--P~~~~a~~~lg~~l~~~-g~~~eA~~~~~~al~~---~P~~~~~~~~~~l~~~~~~~~~A~~~l~~  190 (296)
T PRK11189        117 AYEAFDSVLELD--PTYNYAYLNRGIALYYG-GRYELAQDDLLAFYQD---DPNDPYRALWLYLAESKLDPKQAKENLKQ  190 (296)
T ss_pred             HHHHHHHHHHhC--CCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHccCCHHHHHHHHHH
Confidence            999999998743  54 55677777778888 9999999999988764   34433222222234456789999999976


Q ss_pred             HHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC---CC--CC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          361 FTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS---NC--LF-DLPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       361 m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~---gi--~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      .... ..|+...| .+..  ...|+..++ +.+..+.+.   .+  .| ...+|..+-..+.+.|+.++|...|++..+.
T Consensus       191 ~~~~-~~~~~~~~-~~~~--~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~  265 (296)
T PRK11189        191 RYEK-LDKEQWGW-NIVE--FYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALAN  265 (296)
T ss_pred             HHhh-CCccccHH-HHHH--HHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            5432 23443332 2222  334555444 355555432   11  11 2357888888999999999999999998865


Q ss_pred             CCCCCHHHHHH
Q 011102          435 GFCPTYDIYRD  445 (493)
Q Consensus       435 g~~p~~~ty~~  445 (493)
                      +. ||.+-+..
T Consensus       266 ~~-~~~~e~~~  275 (296)
T PRK11189        266 NV-YNFVEHRY  275 (296)
T ss_pred             CC-chHHHHHH
Confidence            53 35555544

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

Probab=98.15  E-value=0.0011  Score=65.09  Aligned_cols=268  Identities=9%  Similarity=-0.023  Sum_probs=172.9

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC--c-----HHHHHHHHHhC-CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG--S-----LSFTVRELGHM-NLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHH  246 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~--~-----~~~li~~~~~~-g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g  246 (493)
                      ..+.+.|+++.|.+++.....++  +     -|.-.--|.+- .++..|.+.-+.........|  .....-=+.....|
T Consensus       427 ~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~--~a~~nkgn~~f~ng  504 (840)
T KOG2003|consen  427 GELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNA--AALTNKGNIAFANG  504 (840)
T ss_pred             HHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCH--HHhhcCCceeeecC
Confidence            56778899999988887665554  1     12222233333 356677776666553311211  11111011112345


Q ss_pred             CCchhhhHHHhhccC--cHH----HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHH
Q 011102          247 ELKVPFKLENFVSLA--SKG----VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMT  320 (493)
Q Consensus       247 ~~~~~~~l~~~~~~~--~~~----~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~  320 (493)
                      +  ..++...|.+-.  +..    .||+=+ .+-+.|++++|++.|-++..- +.-+..+.--+-+.|-.. .+..+|++
T Consensus       505 d--~dka~~~ykeal~ndasc~ealfnigl-t~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~l-ed~aqaie  579 (840)
T KOG2003|consen  505 D--LDKAAEFYKEALNNDASCTEALFNIGL-TAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELL-EDPAQAIE  579 (840)
T ss_pred             c--HHHHHHHHHHHHcCchHHHHHHHHhcc-cHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHh-hCHHHHHH
Confidence            5  455555565532  222    233322 245678899999988776431 112344444455556666 67788888


Q ss_pred             HHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          321 LLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       321 l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      ++-+....  +.-|....+-|-+.|-+.|+-..|.+.+-+--+ -++-|..+...|-.-|....-+++|...|++..  =
T Consensus       580 ~~~q~~sl--ip~dp~ilskl~dlydqegdksqafq~~ydsyr-yfp~nie~iewl~ayyidtqf~ekai~y~ekaa--l  654 (840)
T KOG2003|consen  580 LLMQANSL--IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR-YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAA--L  654 (840)
T ss_pred             HHHHhccc--CCCCHHHHHHHHHHhhcccchhhhhhhhhhccc-ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHH--h
Confidence            88766543  666788888889999999999988887755432 234577788888888888888999999998754  3


Q ss_pred             CCCCHHHHHHHHHHH-HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          401 CLFDLPAYRVVIKLF-VALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGR  455 (493)
Q Consensus       401 i~pd~~ty~~li~~~-~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~  455 (493)
                      +.|+.+-|..+|..| .+.|++..|+++++..- ..+.-|......|+..+...|-
T Consensus       655 iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~h-rkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  655 IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIH-RKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHH-HhCccchHHHHHHHHHhccccc
Confidence            679999999888665 56789999999998875 4466688888888888877774

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=98.13  E-value=2.6e-06  Score=52.02  Aligned_cols=29  Identities=28%  Similarity=0.303  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          372 MYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       372 ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      |||+||++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45555555555555555555555555444

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.

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

Probab=98.10  E-value=0.0039  Score=61.64  Aligned_cols=150  Identities=8%  Similarity=-0.047  Sum_probs=127.8

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTV  392 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  392 (493)
                      +++++|...|+...+-  -+-....|+.+-+-|....+...|.+-++.-.+-. +.|-..|-.|-++|.-.+...=|+-.
T Consensus       344 ~eHEKAv~YFkRALkL--Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyY  420 (559)
T KOG1155|consen  344 SEHEKAVMYFKRALKL--NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYY  420 (559)
T ss_pred             HhHHHHHHHHHHHHhc--CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHH
Confidence            7789999999988764  12345678889999999999999999999877432 56889999999999999999999999


Q ss_pred             HHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          393 VWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       393 ~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |++..+-  +| |...|.+|=++|.+.+++++|.+.|......|-. +...|..|-+.|-+.++.++|...|+.-.+
T Consensus       421 fqkA~~~--kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt-e~~~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  421 FQKALEL--KPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT-EGSALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHhc--CCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc-chHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            9987764  44 6789999999999999999999999998876643 668899999999999999999888776654

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

Probab=98.08  E-value=0.00031  Score=66.16  Aligned_cols=226  Identities=9%  Similarity=-0.018  Sum_probs=149.0

Q ss_pred             HHHHHHHHHcCCCchhhhHHH--hhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHH-HHHhcCC
Q 011102          236 ASTVEVLARHHELKVPFKLEN--FVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLI-LELGKNP  312 (493)
Q Consensus       236 ~~li~~~~~~g~~~~~~~l~~--~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li-~~~~~~~  312 (493)
                      +-+-++|.+.|....++.-..  ....+-..||--|-..|-+..+.+.|+.+|.+-.+.  .|-.+||-.=+ ..+-.. 
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi~eam-  303 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARIHEAM-  303 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHHHHHH-
Confidence            446666777776555443321  223445567777788888888888888888776653  36666664332 333344 


Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTV  392 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  392 (493)
                      +..++|.++++...+.  -..++....++-.+|.-.++.+.|++.|+.+.+.|+. +...|+.+--+|.-.+++|-++.-
T Consensus       304 ~~~~~a~~lYk~vlk~--~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~s  380 (478)
T KOG1129|consen  304 EQQEDALQLYKLVLKL--HPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPS  380 (478)
T ss_pred             HhHHHHHHHHHHHHhc--CCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHH
Confidence            6677888888777654  2345556666667777778888888888888877764 334455555566667778888877


Q ss_pred             HHHHHHCCCCCCHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          393 VWNMEASNCLFDLP--AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       393 ~~~M~~~gi~pd~~--ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |.+....--.|+..  .|-.|=......|++..|.+.|+--....-. +...||.|--.-.+.|++++|..+++....
T Consensus       381 f~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~-h~ealnNLavL~~r~G~i~~Arsll~~A~s  457 (478)
T KOG1129|consen  381 FQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQ-HGEALNNLAVLAARSGDILGARSLLNAAKS  457 (478)
T ss_pred             HHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcc-hHHHHHhHHHHHhhcCchHHHHHHHHHhhh
Confidence            77766543334432  2333434445677888888888777655432 667788887777899999999999888765

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

Probab=98.05  E-value=0.00031  Score=66.15  Aligned_cols=220  Identities=13%  Similarity=0.016  Sum_probs=89.4

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc----cCcHHHH-HHHHHHHHhcC
Q 011102          203 VRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS----LASKGVL-EATAKGFVKGG  277 (493)
Q Consensus       203 i~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~----~~~~~~~-~~li~~~~~~g  277 (493)
                      -+.|.+.|.+.+|...|+.-.++   .|-..||..|-++|.+..+  -..++..|.+    .|-.+|| .-+...+-..+
T Consensus       230 gkCylrLgm~r~AekqlqssL~q---~~~~dTfllLskvY~ridQ--P~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~  304 (478)
T KOG1129|consen  230 GKCYLRLGMPRRAEKQLQSSLTQ---FPHPDTFLLLSKVYQRIDQ--PERALLVIGEGLDSFPFDVTYLLGQARIHEAME  304 (478)
T ss_pred             HHHHHHhcChhhhHHHHHHHhhc---CCchhHHHHHHHHHHHhcc--HHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHH
Confidence            33444455555555555444433   2223344444444444444  2223322222    2222222 22223333344


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      +.++|.+++++..+.. ..++....++-.+|.-. ++.+-|+..+..+.+. |+ -+...|+.+--+|.-.+++|-++.-
T Consensus       305 ~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~-~~PE~AlryYRRiLqm-G~-~speLf~NigLCC~yaqQ~D~~L~s  380 (478)
T KOG1129|consen  305 QQEDALQLYKLVLKLH-PINVEAIACIAVGYFYD-NNPEMALRYYRRILQM-GA-QSPELFCNIGLCCLYAQQIDLVLPS  380 (478)
T ss_pred             hHHHHHHHHHHHHhcC-CccceeeeeeeeccccC-CChHHHHHHHHHHHHh-cC-CChHHHhhHHHHHHhhcchhhhHHH
Confidence            4455555554444321 11222333333344444 4445555555554444 33 2333344443344444445555444


Q ss_pred             HHHHHHcCCCCCH--HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          358 FHWFTHSGRDPTV--VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       358 ~~~m~~~g~~p~~--~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      |..-...--.|+.  ..|-.|-......|++.-|.+-|+-.....- -+...+|.|--.-.+.|++++|..+++..+
T Consensus       381 f~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~-~h~ealnNLavL~~r~G~i~~Arsll~~A~  456 (478)
T KOG1129|consen  381 FQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDA-QHGEALNNLAVLAARSGDILGARSLLNAAK  456 (478)
T ss_pred             HHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCc-chHHHHHhHHHHHhhcCchHHHHHHHHHhh
Confidence            4443332222222  2233344444444555555555544333221 123344444444444555555555544443

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.05  E-value=0.0006  Score=71.33  Aligned_cols=253  Identities=10%  Similarity=0.027  Sum_probs=151.9

Q ss_pred             hhccCCCCHHHHHHHHhhhcccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhH
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKL  254 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l  254 (493)
                      +.|...|+.++|.+...-+.....|..+-+.|.+..+.+-|.-.+-.|....|                       ++++
T Consensus       736 SfyvtiG~MD~AfksI~~IkS~~vW~nmA~McVkT~RLDVAkVClGhm~~aRg-----------------------aRAl  792 (1416)
T KOG3617|consen  736 SFYVTIGSMDAAFKSIQFIKSDSVWDNMASMCVKTRRLDVAKVCLGHMKNARG-----------------------ARAL  792 (1416)
T ss_pred             eEEEEeccHHHHHHHHHHHhhhHHHHHHHHHhhhhccccHHHHhhhhhhhhhh-----------------------HHHH
Confidence            45566677777777777776677777777777777777777766666653312                       1122


Q ss_pred             HHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC
Q 011102          255 ENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS  334 (493)
Q Consensus       255 ~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~  334 (493)
                      ..-.+.++ .+=.-+.-.-...|.+++|+.+|++-++.         . |++-+.+..|.|++|.++-+.=.+   +.. 
T Consensus       793 R~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~---------D-LlNKlyQs~g~w~eA~eiAE~~DR---iHL-  857 (1416)
T KOG3617|consen  793 RRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKRY---------D-LLNKLYQSQGMWSEAFEIAETKDR---IHL-  857 (1416)
T ss_pred             HHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHHH---------H-HHHHHHHhcccHHHHHHHHhhccc---eeh-
Confidence            11111111 00001111224567888888888877663         2 344444444888888877543322   222 


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHH-----------HHHc--------CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHW-----------FTHS--------GRDPTVVMYTTLIHSRLSEKKCREALTVVWN  395 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~-----------m~~~--------g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~  395 (493)
                      ..||-.--.-+-..++++.|++.|++           +.+.        .-..|...|..--.-+-..|+++.|+.++..
T Consensus       858 r~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~  937 (1416)
T KOG3617|consen  858 RNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSS  937 (1416)
T ss_pred             hhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHH
Confidence            22333333333344555555544442           2211        0112333344444445567888888888876


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCH
Q 011102          396 MEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDK  475 (493)
Q Consensus       396 M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~  475 (493)
                      .+.         |-++++..|-.|+.++|-++-++-.      |....-.|...|-..|++.+|...|-+..        
T Consensus       938 A~D---------~fs~VrI~C~qGk~~kAa~iA~esg------d~AAcYhlaR~YEn~g~v~~Av~FfTrAq--------  994 (1416)
T KOG3617|consen  938 AKD---------YFSMVRIKCIQGKTDKAARIAEESG------DKAACYHLARMYENDGDVVKAVKFFTRAQ--------  994 (1416)
T ss_pred             hhh---------hhhheeeEeeccCchHHHHHHHhcc------cHHHHHHHHHHhhhhHHHHHHHHHHHHHH--------
Confidence            654         6778888888999999998876642      55556678888999999999999888754        


Q ss_pred             HHHHHHHHhhhhcc
Q 011102          476 QTVVELLQIEKESR  489 (493)
Q Consensus       476 ~t~~~Ll~~~~~~r  489 (493)
                       +|+.-|++||++.
T Consensus       995 -afsnAIRlcKEnd 1007 (1416)
T KOG3617|consen  995 -AFSNAIRLCKEND 1007 (1416)
T ss_pred             -HHHHHHHHHHhcC
Confidence             6777888888764

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=98.03  E-value=4.8e-06  Score=50.79  Aligned_cols=30  Identities=20%  Similarity=0.403  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 011102          442 IYRDMIRIFMASGRLAKCRDVCKEAEMAGF  471 (493)
Q Consensus       442 ty~~li~~~~~~g~~~~A~~l~~~m~~~g~  471 (493)
                      ||++||++|++.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            556666666666666666666666655553

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.

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=98.02  E-value=0.00013  Score=58.21  Aligned_cols=70  Identities=9%  Similarity=0.195  Sum_probs=30.7

Q ss_pred             cCCCHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHcC--------CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          382 SEKKCREALTVVWNMEASNC-LFDLPAYRVVIKLFVALN--------DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFM  451 (493)
Q Consensus       382 ~~g~~~~A~~l~~~M~~~gi-~pd~~ty~~li~~~~~~g--------~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~  451 (493)
                      ..+++.....+|+.+++.|+ .|++.+|+.++.+.++..        ++-+.+.+++.|...+++|+..||+.++..+.
T Consensus        37 ~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYnivl~~Ll  115 (120)
T PF08579_consen   37 ENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYNIVLGSLL  115 (120)
T ss_pred             hhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHHH
Confidence            33444444444444444444 444444444444433322        22333444445554445555555555554443

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 [, , ].

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.01  E-value=0.0012  Score=61.84  Aligned_cols=185  Identities=11%  Similarity=0.017  Sum_probs=120.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH-H
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP----SIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ-Q  336 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~----~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~-~  336 (493)
                      ....+-.+...+.+.|++++|...|++.....  |+.    .++..+-..+.+. |++++|...++++.+...-.+.. .
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~a~~~la~~~~~~-~~~~~A~~~~~~~l~~~p~~~~~~~  108 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESRY--PFSPYAEQAQLDLAYAYYKS-GDYAEAIAAADRFIRLHPNHPDADY  108 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCchhHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHCcCCCchHH
Confidence            44567777788889999999999999887743  432    3556677788888 89999999999987652112221 1


Q ss_pred             HHHHHHHHHHHc--------CCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHH
Q 011102          337 DCTAIMKVGIRL--------QKFGVVESLFHWFTHSGRDPTV-VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPA  407 (493)
Q Consensus       337 ~~~~li~~~~~~--------g~~~~A~~l~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~t  407 (493)
                      .+..+-.++.+.        |+.++|.+.|+.+.+.  .|+. ..+..+.....    ....      ..        ..
T Consensus       109 a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~~----~~~~------~~--------~~  168 (235)
T TIGR03302       109 AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMDY----LRNR------LA--------GK  168 (235)
T ss_pred             HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHHH----HHHH------HH--------HH
Confidence            333344444443        6678888888887654  3432 22222111100    0000      00        01


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLKEAG--FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~~~g--~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      .-.+-..|.+.|+.++|...++...+..  -......+..+..++.+.|++++|..+++.+...
T Consensus       169 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       169 ELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            1244456889999999999999988542  1224578889999999999999999999888754

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).

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.98  E-value=0.00015  Score=57.73  Aligned_cols=80  Identities=15%  Similarity=0.270  Sum_probs=65.2

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHcCC--------CHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          339 TAIMKVGIRLQKFGVVESLFHWFTHSGR-DPTVVMYTTLIHSRLSEK--------KCREALTVVWNMEASNCLFDLPAYR  409 (493)
Q Consensus       339 ~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~~~ty~~li~~~~~~g--------~~~~A~~l~~~M~~~gi~pd~~ty~  409 (493)
                      ...|..+...+++.....+|+.+++.|+ .|++.+||.++.+.++..        ++-+++.+++.|...+++|+..||+
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            4556666677888888889999988888 889999998888887753        3456788899999999999999999


Q ss_pred             HHHHHHHHc
Q 011102          410 VVIKLFVAL  418 (493)
Q Consensus       410 ~li~~~~~~  418 (493)
                      .+|..+.+.
T Consensus       109 ivl~~Llkg  117 (120)
T PF08579_consen  109 IVLGSLLKG  117 (120)
T ss_pred             HHHHHHHHh
Confidence            999887653

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 [, , ].

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

Probab=97.96  E-value=0.014  Score=58.24  Aligned_cols=262  Identities=10%  Similarity=-0.103  Sum_probs=148.9

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHH-HHHHHHHcCCCchhhhHHHhhc----cC-cHHHHHH---HHH
Q 011102          201 FTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLAS-TVEVLARHHELKVPFKLENFVS----LA-SKGVLEA---TAK  271 (493)
Q Consensus       201 ~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~-li~~~~~~g~~~~~~~l~~~~~----~~-~~~~~~~---li~  271 (493)
                      .+-..+...|+.+.|...+..........++..-... -...+...|+++  +++..+..    .| +...++.   ...
T Consensus        11 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~--~A~~~~~~~l~~~P~~~~a~~~~~~~~~   88 (355)
T cd05804          11 AAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLP--KALALLEQLLDDYPRDLLALKLHLGAFG   88 (355)
T ss_pred             HHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHH--HHHHHHHHHHHHCCCcHHHHHHhHHHHH
Confidence            3344555567777766666655433122233322211 122234455543  33333322    23 3334442   111


Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCC
Q 011102          272 GFVKGGNLKLAWKLLMVAKDGGRMLDPS-IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQK  350 (493)
Q Consensus       272 ~~~~~g~~~~A~~l~~~m~~~g~~pd~~-t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~  350 (493)
                      .....+..+.+.+.++.  .....|+.. ....+-..+... |++++|.+.+++..+.  -..+...+..+-..|...|+
T Consensus        89 ~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~-G~~~~A~~~~~~al~~--~p~~~~~~~~la~i~~~~g~  163 (355)
T cd05804          89 LGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEA-GQYDRAEEAARRALEL--NPDDAWAVHAVAHVLEMQGR  163 (355)
T ss_pred             hcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhh--CCCCcHHHHHHHHHHHHcCC
Confidence            12234555666666654  222334433 333444566777 9999999999998875  23446677888899999999


Q ss_pred             HHHHHHHHHHHHHcCC-CCCH--HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC-CCCHHHH-H--HHHHHHHHcCCHHH
Q 011102          351 FGVVESLFHWFTHSGR-DPTV--VMYTTLIHSRLSEKKCREALTVVWNMEASNC-LFDLPAY-R--VVIKLFVALNDISR  423 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~-~p~~--~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi-~pd~~ty-~--~li~~~~~~g~~~~  423 (493)
                      +++|...+++.....- .|+.  ..|..+...+...|+.++|.+++++...... .+..... +  .++.-+...|..+.
T Consensus       164 ~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~  243 (355)
T cd05804         164 FKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDV  243 (355)
T ss_pred             HHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCCh
Confidence            9999999998775421 2333  3466788899999999999999999854322 2222221 2  33444444554444


Q ss_pred             HHHH--HHHHHHCCC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          424 AIRY--FSKLKEAGF--CPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       424 A~~~--~~~m~~~g~--~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      +.++  .........  ............++...|+.++|..+++.+...
T Consensus       244 ~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~  293 (355)
T cd05804         244 GDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGR  293 (355)
T ss_pred             HHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence            4333  211111111  111222235677778899999999999998763

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.

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

Probab=97.96  E-value=0.024  Score=56.38  Aligned_cols=282  Identities=10%  Similarity=0.009  Sum_probs=150.5

Q ss_pred             cCCCCHHHHHHHHhhhc----ccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhh
Q 011102          178 DSHKDVAEVLDKCGRFL----RKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFK  253 (493)
Q Consensus       178 ~~~~~~~~a~~~~~~m~----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~  253 (493)
                      -..|.+..|.++|++..    +...|.+.|+-=.+-..++.|..+++...   -+.|++.+|.....-=-+.|....+..
T Consensus       152 E~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV---~~HP~v~~wikyarFE~k~g~~~~aR~  228 (677)
T KOG1915|consen  152 EMLGNIAGARQIFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFV---LVHPKVSNWIKYARFEEKHGNVALARS  228 (677)
T ss_pred             HHhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHh---eecccHHHHHHHHHHHHhcCcHHHHHH
Confidence            33578888888888653    34599999998888899999999999887   456888887666555555554332221


Q ss_pred             HH-------------------------------------Hh--hccC---------------------------------
Q 011102          254 LE-------------------------------------NF--VSLA---------------------------------  261 (493)
Q Consensus       254 l~-------------------------------------~~--~~~~---------------------------------  261 (493)
                      +.                                     .|  +.+|                                 
T Consensus       229 VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk  308 (677)
T KOG1915|consen  229 VYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRK  308 (677)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhh
Confidence            10                                     00  0011                                 


Q ss_pred             ------------cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH--HHHHHH----H-H---HhcCCCCHHHHH
Q 011102          262 ------------SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS--IYAKLI----L-E---LGKNPDKYMLVM  319 (493)
Q Consensus       262 ------------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~--t~~~li----~-~---~~~~~~~~~~a~  319 (493)
                                  |-.+|--.+..--..|+.+...++|+..... ++|-..  -|.--|    + +   =... .+++.+.
T Consensus       309 ~qYE~~v~~np~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~-ed~ertr  386 (677)
T KOG1915|consen  309 FQYEKEVSKNPYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEA-EDVERTR  386 (677)
T ss_pred             hHHHHHHHhCCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHh-hhHHHHH
Confidence                        0012222333333334444444444444432 222100  011000    0 0   0112 3444444


Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHHHHHH----HcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 011102          320 TLLDELGQRDDLNLSQQDCTAIMKVGI----RLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWN  395 (493)
Q Consensus       320 ~l~~~m~~~~g~~p~~~~~~~li~~~~----~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~  395 (493)
                      ++++...+-  +.....||.-+--+|+    +..++..|.+++..-.  |..|-.-+|-.-|.-=.+.++++....+++.
T Consensus       387 ~vyq~~l~l--IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~efDRcRkLYEk  462 (677)
T KOG1915|consen  387 QVYQACLDL--IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLREFDRCRKLYEK  462 (677)
T ss_pred             HHHHHHHhh--cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            555444432  3334444443333332    3455555555555433  4456666666666666666666666666666


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          396 MEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG-FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       396 M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      ..+-+- -|..+|.-.-..=-..|+.+.|..+|+-..+.. +.-....|-+.|+-=...|.+++|..+++.+.+.
T Consensus       463 fle~~P-e~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  463 FLEFSP-ENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             HHhcCh-HhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh
Confidence            655432 244555555555556677777777776665432 2223344555555556677777777777777654

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.94  E-value=0.00014  Score=72.93  Aligned_cols=123  Identities=12%  Similarity=0.018  Sum_probs=88.1

Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHH
Q 011102          331 LNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS--GRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAY  408 (493)
Q Consensus       331 ~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty  408 (493)
                      ...+.....++++.+....+++++..++.+....  ...--..|..++|+.|...|..++|+.++..=...||-||..||
T Consensus        62 ~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~  141 (429)
T PF10037_consen   62 KPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSF  141 (429)
T ss_pred             CCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhH
Confidence            4456667777777777777777777777777654  22122233457888888888888888888777777888888888


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          409 RVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMAS  453 (493)
Q Consensus       409 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~  453 (493)
                      |.||+.+.+.|++..|.++..+|...+...+..|+..-+.+|.+.
T Consensus       142 n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  142 NLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            888888888888888888887777666666777777666666555

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 [].

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.91  E-value=0.00018  Score=72.16  Aligned_cols=125  Identities=11%  Similarity=0.060  Sum_probs=84.0

Q ss_pred             CCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHH
Q 011102          293 GRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDD-LNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVV  371 (493)
Q Consensus       293 g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g-~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~  371 (493)
                      +...+.+....+++.+... .+++++..++......+. ...-..|..++|..|.+.|..++++++++.=...|+-||..
T Consensus        61 ~~~vS~~dld~fvn~~~~~-~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~  139 (429)
T PF10037_consen   61 KKPVSSLDLDIFVNNVESK-DDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNF  139 (429)
T ss_pred             CCCCcHHHHHHHHhhcCCH-hHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChh
Confidence            3445666666677777766 667777777776654421 11223344577777777777777777777777777777777


Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          372 MYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL  418 (493)
Q Consensus       372 ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~  418 (493)
                      |||.||+.+.+.|++..|.++..+|...+...+..|+.--+.+|.+-
T Consensus       140 s~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  140 SFNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             hHHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            77777777777777777777777776666666666666666666554

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 [].

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=97.89  E-value=0.0044  Score=57.89  Aligned_cols=180  Identities=10%  Similarity=-0.066  Sum_probs=111.7

Q ss_pred             CHHHHHHHHHHHHHcCCCchhhhHHHhhc----cCc----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH--H
Q 011102          231 DDRLLASTVEVLARHHELKVPFKLENFVS----LAS----KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS--I  300 (493)
Q Consensus       231 d~~t~~~li~~~~~~g~~~~~~~l~~~~~----~~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~--t  300 (493)
                      ....+-.....+.+.|+++.+  +..+..    .++    ..++..+...|.+.|++++|...++++.+..-.....  +
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A--~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a  109 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEA--IKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYA  109 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHH--HHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHH
Confidence            445667777778888885544  333432    222    2367788899999999999999999998754211111  3


Q ss_pred             HHHHHHHHhcC-------CCCHHHHHHHHHHHhhcCCCCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHH
Q 011102          301 YAKLILELGKN-------PDKYMLVMTLLDELGQRDDLNLSQQ-DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVM  372 (493)
Q Consensus       301 ~~~li~~~~~~-------~~~~~~a~~l~~~m~~~~g~~p~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  372 (493)
                      +..+-..+.+.       .|+.++|.+.|+.+...   .|+.. .+..+... ..   ...      ...        ..
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~a~~~~-~~---~~~------~~~--------~~  168 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR---YPNSEYAPDAKKRM-DY---LRN------RLA--------GK  168 (235)
T ss_pred             HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH---CCCChhHHHHHHHH-HH---HHH------HHH--------HH
Confidence            33333334321       15688899999998765   24432 22222111 11   000      000        01


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEASN--CLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~~g--i~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      .-.+-..|.+.|+.++|...+.+..+..  -......+..+..++.+.|+.++|..+++.+..
T Consensus       169 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~  231 (235)
T TIGR03302       169 ELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGA  231 (235)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            1245566888899999999888877652  112346788888889999999999988888764

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).

>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=97.89  E-value=0.0012  Score=63.79  Aligned_cols=215  Identities=14%  Similarity=0.048  Sum_probs=134.2

Q ss_pred             ccCCCCHHHHHHHHhhhcccCc-HHHHHHHHHhC-CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhH
Q 011102          177 LDSHKDVAEVLDKCGRFLRKGS-LSFTVRELGHM-NLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKL  254 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~~~-~~~li~~~~~~-g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l  254 (493)
                      +-..|....++........... --.++..|... .+-+.++.-+.+.... ....+.. +..++.|..-...-+..+++
T Consensus        45 ~iAlg~~~~vl~ei~~~~~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~-~~~~~~~-~~~~~~A~i~~~~~~~~~AL  122 (290)
T PF04733_consen   45 YIALGQYDSVLSEIKKSSSPELQAVRLLAEYLSSPSDKESALEELKELLAD-QAGESNE-IVQLLAATILFHEGDYEEAL  122 (290)
T ss_dssp             HHHTT-HHHHHHHS-TTSSCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCT-S---CHH-HHHHHHHHHHCCCCHHHHHH
T ss_pred             HHHcCChhHHHHHhccCCChhHHHHHHHHHHHhCccchHHHHHHHHHHHHh-ccccccH-HHHHHHHHHHHHcCCHHHHH
Confidence            3334556666555543333321 11233444444 3445555555444333 2222222 23344444443333466777


Q ss_pred             HHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHh---cCCCCHHHHHHHHHHHhhcCCC
Q 011102          255 ENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELG---KNPDKYMLVMTLLDELGQRDDL  331 (493)
Q Consensus       255 ~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~---~~~~~~~~a~~l~~~m~~~~g~  331 (493)
                      .....-.+.......+..|.+.++++.|.+.++.|.+..  .|... ..+..++.   ..++.+.+|.-+|+++...  .
T Consensus       123 ~~l~~~~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~--eD~~l-~qLa~awv~l~~g~e~~~~A~y~f~El~~~--~  197 (290)
T PF04733_consen  123 KLLHKGGSLELLALAVQILLKMNRPDLAEKELKNMQQID--EDSIL-TQLAEAWVNLATGGEKYQDAFYIFEELSDK--F  197 (290)
T ss_dssp             CCCTTTTCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCS--CCHHH-HHHHHHHHHHHHTTTCCCHHHHHHHHHHCC--S
T ss_pred             HHHHccCcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcHHH-HHHHHHHHHHHhCchhHHHHHHHHHHHHhc--c
Confidence            666666667777889999999999999999999999864  45443 33444332   2225799999999999775  5


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH-HHHHHHHHHHHHC
Q 011102          332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC-REALTVVWNMEAS  399 (493)
Q Consensus       332 ~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~-~~A~~l~~~M~~~  399 (493)
                      .+++.+.|.+..++...|++++|.+++.+..+.. +-|..+...+|......|+. +.+.+.+.+++..
T Consensus       198 ~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~-~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  198 GSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD-PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             --SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            6889999999999999999999999999865432 33455666677777777777 7788899998864

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.

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

Probab=97.88  E-value=0.0033  Score=69.67  Aligned_cols=218  Identities=13%  Similarity=0.036  Sum_probs=167.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCC---CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDG-GRML---DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQD  337 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p---d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~  337 (493)
                      +...|-.-|......++.++|.+++++.... ++.-   -.-.|.++++.-... |.-+...++|++..+.  . -.-.+
T Consensus      1457 SSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~y-G~eesl~kVFeRAcqy--c-d~~~V 1532 (1710)
T KOG1070|consen 1457 SSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAY-GTEESLKKVFERACQY--C-DAYTV 1532 (1710)
T ss_pred             cchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhh-CcHHHHHHHHHHHHHh--c-chHHH
Confidence            3446888888899999999999999988753 1111   123577777766666 6678899999998775  2 22457


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC---HHHHHHHHHH
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD---LPAYRVVIKL  414 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd---~~ty~~li~~  414 (493)
                      |..|...|.+.++.++|-++|+.|.++=- -....|...+..+.+..+-+.|..++.+..+.  .|-   +....-.+..
T Consensus      1533 ~~~L~~iy~k~ek~~~A~ell~~m~KKF~-q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~--lPk~eHv~~IskfAqL 1609 (1710)
T KOG1070|consen 1533 HLKLLGIYEKSEKNDEADELLRLMLKKFG-QTRKVWIMYADFLLRQNEAEAARELLKRALKS--LPKQEHVEFISKFAQL 1609 (1710)
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHhc-chhhHHHHHHHHHhcccHHHHHHHHHHHHHhh--cchhhhHHHHHHHHHH
Confidence            88999999999999999999999975422 46678999999999999999999999987653  344   2334555566


Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHH--HHHHHHHhhhh
Q 011102          415 FVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQ--TVVELLQIEKE  487 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~--t~~~Ll~~~~~  487 (493)
                      -.+.|+.+.+..+|+.....--+ -...|+..|+.-.+.|+.+.+..+|++....++.|-..  -|..-|..++.
T Consensus      1610 EFk~GDaeRGRtlfEgll~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~ 1683 (1710)
T KOG1070|consen 1610 EFKYGDAERGRTLFEGLLSAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKS 1683 (1710)
T ss_pred             HhhcCCchhhHHHHHHHHhhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHh
Confidence            67899999999999998854322 45679999999999999999999999999999887543  45666665443

>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=97.85  E-value=0.00029  Score=63.10  Aligned_cols=105  Identities=10%  Similarity=0.134  Sum_probs=65.0

Q ss_pred             CCCHHHHHHHHHHHHHc-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHH
Q 011102          332 NLSQQDCTAIMKVGIRL-----QKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLP  406 (493)
Q Consensus       332 ~p~~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~  406 (493)
                      .-|..+|..+|+.|.+.     |.++-....+..|.+-|+..|..+|+.||+.+=+. .+-               |. .
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg-~fv---------------p~-n  106 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKG-KFV---------------PR-N  106 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCC-Ccc---------------cc-c
Confidence            45777777777777654     56777777777777777777777777777776652 211               11 0


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          407 AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGR  455 (493)
Q Consensus       407 ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~  455 (493)
                      .+.++..-|-  .+-+-|.++++.|...|+.||..|+..|++.+++.+.
T Consensus       107 ~fQ~~F~hyp--~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  107 FFQAEFMHYP--RQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHhccCc--HHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            1111111111  1335567777777777777777777777777766554

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

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

Probab=97.82  E-value=0.008  Score=54.35  Aligned_cols=208  Identities=12%  Similarity=-0.074  Sum_probs=159.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP-SIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~-~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      .+.--|--+|.+.|+...|..-+++..+..  |+. .+|..+-..|-+. |..+.|.+-|+.....  -.-+..+.|..-
T Consensus        36 ~arlqLal~YL~~gd~~~A~~nlekAL~~D--Ps~~~a~~~~A~~Yq~~-Ge~~~A~e~YrkAlsl--~p~~GdVLNNYG  110 (250)
T COG3063          36 KARLQLALGYLQQGDYAQAKKNLEKALEHD--PSYYLAHLVRAHYYQKL-GENDLADESYRKALSL--APNNGDVLNNYG  110 (250)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHHHHHHHHHc-CChhhHHHHHHHHHhc--CCCccchhhhhh
Confidence            357778889999999999999999999864  544 4677777778888 9999999999987654  122445677777


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      .-+|..|++++|...|++-...-.-+ -..||..+.-+..+.|+.+.|.+.|++-.+..-. ...+.-.+-....+.|++
T Consensus       111 ~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~~~~y  189 (250)
T COG3063         111 AFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYKAGDY  189 (250)
T ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHhcccc
Confidence            88899999999999998876532111 2467788888888999999999999997765321 234567777888999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHH
Q 011102          422 SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVE  480 (493)
Q Consensus       422 ~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~  480 (493)
                      -.|..+++.....+. ++..+.-..|..--+.|+.+.|.+.=..+.+  .-|...-|..
T Consensus       190 ~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r--~fP~s~e~q~  245 (250)
T COG3063         190 APARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQR--LFPYSEEYQT  245 (250)
T ss_pred             hHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHH--hCCCcHHHHh
Confidence            999999999886666 8888888888888899999888877555544  3455544443

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.80  E-value=0.052  Score=56.03  Aligned_cols=197  Identities=11%  Similarity=0.109  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC---HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC---------CCC
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD---PSIYAKLILELGKNPDKYMLVMTLLDELGQRD---------DLN  332 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd---~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~---------g~~  332 (493)
                      .|..+.+.|-..|+++.|..+|++..+...+--   ..+|-..-..=.+. .+++.|+++.+.....+         |-.
T Consensus       389 Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh-~~~~~Al~lm~~A~~vP~~~~~~~yd~~~  467 (835)
T KOG2047|consen  389 LWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRH-ENFEAALKLMRRATHVPTNPELEYYDNSE  467 (835)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhh-hhHHHHHHHHHhhhcCCCchhhhhhcCCC
Confidence            377788888889999999999998876543211   12232222333344 56777777766554321         111


Q ss_pred             C-------CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CCHHH-HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC
Q 011102          333 L-------SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRD-PTVVM-YTTLIHSRLSEKKCREALTVVWNMEASNCLF  403 (493)
Q Consensus       333 p-------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~t-y~~li~~~~~~g~~~~A~~l~~~M~~~gi~p  403 (493)
                      |       +...|+..++---..|-++....+|+.+.+..+. |-.+. |..++   -.+.-++++.+++++=...=--|
T Consensus       468 pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyAmfL---Eeh~yfeesFk~YErgI~LFk~p  544 (835)
T KOG2047|consen  468 PVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYAMFL---EEHKYFEESFKAYERGISLFKWP  544 (835)
T ss_pred             cHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHHHHH---HhhHHHHHHHHHHHcCCccCCCc
Confidence            1       2224555555555667788888888887754432 22211 11111   22333555555554311111113


Q ss_pred             CH-HHHHHHHHHHHH---cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH--HHcCCHHHHHHHHHHH
Q 011102          404 DL-PAYRVVIKLFVA---LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIF--MASGRLAKCRDVCKEA  466 (493)
Q Consensus       404 d~-~ty~~li~~~~~---~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~--~~~g~~~~A~~l~~~m  466 (493)
                      ++ ..|++-+.-+.+   .-+++.|..+|+...+ |+.|...-+--|+-+=  -+.|....|+.++++.
T Consensus       545 ~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyera  612 (835)
T KOG2047|consen  545 NVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERA  612 (835)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            33 234444433332   2256666666666665 5544332222222111  1335555666666554

>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=97.73  E-value=0.00047  Score=61.82  Aligned_cols=105  Identities=12%  Similarity=0.089  Sum_probs=72.3

Q ss_pred             cCcHHHHHHHHHHHHh-----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC
Q 011102          260 LASKGVLEATAKGFVK-----GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS  334 (493)
Q Consensus       260 ~~~~~~~~~li~~~~~-----~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~  334 (493)
                      ..+..+|..+|+.|.+     .|.++-....+..|.+-|+.-|..+|+.||+.+=+. .-.  -..+|+.+-..      
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg-~fv--p~n~fQ~~F~h------  114 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKG-KFV--PRNFFQAEFMH------  114 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCC-Ccc--cccHHHHHhcc------
Confidence            3456666677777654     488999999999999999999999999999998764 211  12222222111      


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK  385 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~  385 (493)
                                  .-.+.+-|++++++|...|+-||..++..|++.+++.+.
T Consensus       115 ------------yp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  115 ------------YPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             ------------CcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence                        112346677777777777777777777777777776664

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

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

Probab=97.72  E-value=0.083  Score=54.74  Aligned_cols=263  Identities=14%  Similarity=0.039  Sum_probs=157.3

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHH--HhhccC-cHHHHHHHHHHHHh
Q 011102          199 LSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLE--NFVSLA-SKGVLEATAKGFVK  275 (493)
Q Consensus       199 ~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~--~~~~~~-~~~~~~~li~~~~~  275 (493)
                      |......=-..|..++-..+|+....+  +.-....|-...+-.-..|++..+..+.  .|...+ +..+|-+-+..-..
T Consensus       553 Wlra~~~ek~hgt~Esl~Allqkav~~--~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~e  630 (913)
T KOG0495|consen  553 WLRAAMFEKSHGTRESLEALLQKAVEQ--CPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFE  630 (913)
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhc
Confidence            333333333344555555555555432  2223333444444444556544444432  233333 55688888888889


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC--------------------------
Q 011102          276 GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRD--------------------------  329 (493)
Q Consensus       276 ~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~--------------------------  329 (493)
                      +.+++.|..+|.+....  .|+...|..-+..---. +..++|.+++++..+..                          
T Consensus       631 n~e~eraR~llakar~~--sgTeRv~mKs~~~er~l-d~~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~a  707 (913)
T KOG0495|consen  631 NDELERARDLLAKARSI--SGTERVWMKSANLERYL-DNVEEALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMAREA  707 (913)
T ss_pred             cccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHh-hhHHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999887774  47777776555544444 67788888887766541                          


Q ss_pred             ---C---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----
Q 011102          330 ---D---LNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS----  399 (493)
Q Consensus       330 ---g---~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----  399 (493)
                         |   +.-..-.|-.|-+.=-+.|.+-.|..+|+.-.-++ +-|..-|-..|+.-.+.|..+.|..++.+..+.    
T Consensus       708 Y~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~s  786 (913)
T KOG0495|consen  708 YLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQECPSS  786 (913)
T ss_pred             HHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcc
Confidence               0   01111223333333345566666666666654332 446677888888888888888888777665431    


Q ss_pred             -------------------------CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC
Q 011102          400 -------------------------NCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASG  454 (493)
Q Consensus       400 -------------------------gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g  454 (493)
                                               .+.-|....-++-..|....+++.|.+.|.+-.+.+- -+..+|.-+..-+.+.|
T Consensus       787 g~LWaEaI~le~~~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~-d~GD~wa~fykfel~hG  865 (913)
T KOG0495|consen  787 GLLWAEAIWLEPRPQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDP-DNGDAWAWFYKFELRHG  865 (913)
T ss_pred             chhHHHHHHhccCcccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCC-ccchHHHHHHHHHHHhC
Confidence                                     1222333344444556666777888888887775542 25567777888888888


Q ss_pred             CHHHHHHHHHHHHH
Q 011102          455 RLAKCRDVCKEAEM  468 (493)
Q Consensus       455 ~~~~A~~l~~~m~~  468 (493)
                      .-++-.+++.....
T Consensus       866 ~eed~kev~~~c~~  879 (913)
T KOG0495|consen  866 TEEDQKEVLKKCET  879 (913)
T ss_pred             CHHHHHHHHHHHhc
Confidence            77777777766554

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

Probab=97.72  E-value=0.035  Score=50.34  Aligned_cols=164  Identities=13%  Similarity=0.026  Sum_probs=88.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      ..+|..+...|-+.|+.+.|.+-|++..+..  | +..+.|.-=.-+|.. |++++|.+.|++....+...--..+|..+
T Consensus        69 ~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~--p~~GdVLNNYG~FLC~q-g~~~eA~q~F~~Al~~P~Y~~~s~t~eN~  145 (250)
T COG3063          69 YLAHLVRAHYYQKLGENDLADESYRKALSLA--PNNGDVLNNYGAFLCAQ-GRPEEAMQQFERALADPAYGEPSDTLENL  145 (250)
T ss_pred             HHHHHHHHHHHHHcCChhhHHHHHHHHHhcC--CCccchhhhhhHHHHhC-CChHHHHHHHHHHHhCCCCCCcchhhhhh
Confidence            3456666666666666666666666555532  2 223344444445555 56666666666655554443344455555


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      .-+..+.|+.+.|...|+.-.+.  .|+ ..+.-.+-....+.|+...|...++.....+. ++..+.-..|..--..|+
T Consensus       146 G~Cal~~gq~~~A~~~l~raL~~--dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd  222 (250)
T COG3063         146 GLCALKAGQFDQAEEYLKRALEL--DPQFPPALLELARLHYKAGDYAPARLYLERYQQRGG-AQAESLLLGIRIAKRLGD  222 (250)
T ss_pred             HHHHhhcCCchhHHHHHHHHHHh--CcCCChHHHHHHHHHHhcccchHHHHHHHHHHhccc-ccHHHHHHHHHHHHHhcc
Confidence            55555666666666666555433  221 23344555555566666666666665555444 555555555555555666


Q ss_pred             HHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLK  432 (493)
Q Consensus       421 ~~~A~~~~~~m~  432 (493)
                      .+.|-++=..+.
T Consensus       223 ~~~a~~Y~~qL~  234 (250)
T COG3063         223 RAAAQRYQAQLQ  234 (250)
T ss_pred             HHHHHHHHHHHH
Confidence            555555444443

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.71  E-value=0.086  Score=54.53  Aligned_cols=309  Identities=15%  Similarity=0.172  Sum_probs=168.7

Q ss_pred             hhccCCCCHHHHHHHHhhhccc-------CcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCC
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRK-------GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHE  247 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~-------~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~  247 (493)
                      ..+-+.+++......|++.+..       ..|...|.-....|-++-++.+++...+-   .|..  -+-.|.-+++.++
T Consensus       110 q~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~---~P~~--~eeyie~L~~~d~  184 (835)
T KOG2047|consen  110 QFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV---APEA--REEYIEYLAKSDR  184 (835)
T ss_pred             HHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc---CHHH--HHHHHHHHHhccc
Confidence            3344566777766666644332       37777777777777777777777766533   3332  3555555666555


Q ss_pred             CchhhhH-HH----------------------h---hc--------------------cCcH--HHHHHHHHHHHhcCCH
Q 011102          248 LKVPFKL-EN----------------------F---VS--------------------LASK--GVLEATAKGFVKGGNL  279 (493)
Q Consensus       248 ~~~~~~l-~~----------------------~---~~--------------------~~~~--~~~~~li~~~~~~g~~  279 (493)
                      ++.+... ..                      +   ..                    ..|.  ..|++|.+.|.+.|.+
T Consensus       185 ~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~  264 (835)
T KOG2047|consen  185 LDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLF  264 (835)
T ss_pred             hHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhh
Confidence            4322211 00                      0   00                    0111  2599999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCC---------------C------CHHHHHHHHHHHhhcC---------
Q 011102          280 KLAWKLLMVAKDGGRMLDPSIYAKLILELGKNP---------------D------KYMLVMTLLDELGQRD---------  329 (493)
Q Consensus       280 ~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~---------------~------~~~~a~~l~~~m~~~~---------  329 (493)
                      +.|..+|++..+.-  .+..-|+.+.++|++..               +      +++-...-|+.+....         
T Consensus       265 ekarDvyeeai~~v--~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlL  342 (835)
T KOG2047|consen  265 EKARDVYEEAIQTV--MTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLLNSVLL  342 (835)
T ss_pred             HHHHHHHHHHHHhh--eehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHHHHHHH
Confidence            99999999877643  23333444444443210               0      1122222233222210         


Q ss_pred             ---------------------------------CCCCC------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-
Q 011102          330 ---------------------------------DLNLS------QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT-  369 (493)
Q Consensus       330 ---------------------------------g~~p~------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-  369 (493)
                                                       .+.|-      ...|..+-+-|-..|+++.|..+|++-.+-..+-- 
T Consensus       343 RQn~~nV~eW~kRV~l~e~~~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~  422 (835)
T KOG2047|consen  343 RQNPHNVEEWHKRVKLYEGNAAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVE  422 (835)
T ss_pred             hcCCccHHHHHhhhhhhcCChHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchH
Confidence                                             01111      11356777788889999999999998764332211 


Q ss_pred             --HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC----------CC-------CHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          370 --VVMYTTLIHSRLSEKKCREALTVVWNMEASNC----------LF-------DLPAYRVVIKLFVALNDISRAIRYFSK  430 (493)
Q Consensus       370 --~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi----------~p-------d~~ty~~li~~~~~~g~~~~A~~~~~~  430 (493)
                        ..+|..--..=.++.+++.|+++++.....--          .|       +...|+..++.--..|-++....+++.
T Consensus       423 dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdr  502 (835)
T KOG2047|consen  423 DLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDR  502 (835)
T ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence              23344434444556677778877766532110          11       112233333333334444444444444


Q ss_pred             HH------------------------------HCCCC----CCH-HHHHHHHHHHHH-c--CCHHHHHHHHHHHHHCCCc
Q 011102          431 LK------------------------------EAGFC----PTY-DIYRDMIRIFMA-S--GRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       431 m~------------------------------~~g~~----p~~-~ty~~li~~~~~-~--g~~~~A~~l~~~m~~~g~~  472 (493)
                      +.                              ++|+.    |++ ..|++.+.-+.+ -  -..+.|..+|++..+ |++
T Consensus       503 iidLriaTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~-~Cp  581 (835)
T KOG2047|consen  503 IIDLRIATPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD-GCP  581 (835)
T ss_pred             HHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh-cCC
Confidence            43                              24442    333 456666555543 2  368999999999998 888


Q ss_pred             cCHHHHHHHHHhhhhccCC
Q 011102          473 LDKQTVVELLQIEKESRIG  491 (493)
Q Consensus       473 pd~~t~~~Ll~~~~~~r~g  491 (493)
                      |...-+-.|+-+--+.+.|
T Consensus       582 p~~aKtiyLlYA~lEEe~G  600 (835)
T KOG2047|consen  582 PEHAKTIYLLYAKLEEEHG  600 (835)
T ss_pred             HHHHHHHHHHHHHHHHHhh
Confidence            8777666666543344444

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

Probab=97.70  E-value=0.061  Score=58.04  Aligned_cols=200  Identities=12%  Similarity=0.056  Sum_probs=144.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC--CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHH--
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRML--DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQD--  337 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p--d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~--  337 (493)
                      +.++.+.|-+.|.-.|+++.++.+...+...-..-  -...|--+-.+|-.. |++++|...|.+..+.   .+|..+  
T Consensus       269 nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~-Gd~ekA~~yY~~s~k~---~~d~~~l~  344 (1018)
T KOG2002|consen  269 NPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQ-GDFEKAFKYYMESLKA---DNDNFVLP  344 (1018)
T ss_pred             CcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhh-ccHHHHHHHHHHHHcc---CCCCcccc
Confidence            56678999999999999999999999888753111  122355677888888 9999999999887654   344433  


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCC----CHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYTTLIHSRLSEK----KCREALTVVWNMEASNCLFDLPAYRVVI  412 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~~~~~~g----~~~~A~~l~~~M~~~gi~pd~~ty~~li  412 (493)
                      +--+-.+|.+.|+++.|...|+...+.  .|| ..+.-+|-.-|+..+    ..++|..++.+-.+.- .-|...|-.+-
T Consensus       345 ~~GlgQm~i~~~dle~s~~~fEkv~k~--~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~-~~d~~a~l~la  421 (1018)
T KOG2002|consen  345 LVGLGQMYIKRGDLEESKFCFEKVLKQ--LPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQT-PVDSEAWLELA  421 (1018)
T ss_pred             ccchhHHHHHhchHHHHHHHHHHHHHh--CcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcc-cccHHHHHHHH
Confidence            446788999999999999999998755  444 455566666666654    4566666666654432 23556666666


Q ss_pred             HHHHHcCCHHHHHHHHH----HHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          413 KLFVALNDISRAIRYFS----KLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       413 ~~~~~~g~~~~A~~~~~----~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      ..+-... ...++.+|.    .|...+-.+-....|.+-......|.+++|.+.|+.....
T Consensus       422 ql~e~~d-~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~  481 (1018)
T KOG2002|consen  422 QLLEQTD-PWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGK  481 (1018)
T ss_pred             HHHHhcC-hHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhh
Confidence            6655544 434466655    3445666678888999999999999999999999998765

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

Probab=97.68  E-value=0.027  Score=62.80  Aligned_cols=199  Identities=8%  Similarity=-0.084  Sum_probs=93.7

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHH-----HHHHHHHHHHHcCCCchhhhHHHhhc----cCcHHHHHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDR-----LLASTVEVLARHHELKVPFKLENFVS----LASKGVLEA  268 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~-----t~~~li~~~~~~g~~~~~~~l~~~~~----~~~~~~~~~  268 (493)
                      .|-.-|....+.++.++|.+++++....  +.+...     .|.++++.-.-.|.  .+.....|.+    +....+|..
T Consensus      1460 ~WI~YMaf~LelsEiekAR~iaerAL~t--IN~REeeEKLNiWiA~lNlEn~yG~--eesl~kVFeRAcqycd~~~V~~~ 1535 (1710)
T KOG1070|consen 1460 LWIRYMAFHLELSEIEKARKIAERALKT--INFREEEEKLNIWIAYLNLENAYGT--EESLKKVFERACQYCDAYTVHLK 1535 (1710)
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHhhh--CCcchhHHHHHHHHHHHhHHHhhCc--HHHHHHHHHHHHHhcchHHHHHH
Confidence            4555566777777777777777777642  322111     23444433333332  1111122222    112234555


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHc
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRL  348 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~  348 (493)
                      |...|.+.+.+++|-++|+.|.+. +.-....|......+.+. ++-+.|.+++.+..+.---+--+....-....-.+.
T Consensus      1536 L~~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~-ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~ 1613 (1710)
T KOG1070|consen 1536 LLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQ-NEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKY 1613 (1710)
T ss_pred             HHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcc-cHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhc
Confidence            555555555555555555555543 113444555555555555 555555555555433200000122233333334455


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC
Q 011102          349 QKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF  403 (493)
Q Consensus       349 g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p  403 (493)
                      |+.+++..+|+.....- +.-...|+..|+.-.++|+.+.+.++|++....++.|
T Consensus      1614 GDaeRGRtlfEgll~ay-PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1614 GDAERGRTLFEGLLSAY-PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             CCchhhHHHHHHHHhhC-ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            55555555555544321 1123345555555555555555555555555554443

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.68  E-value=0.013  Score=63.07  Aligned_cols=159  Identities=10%  Similarity=0.082  Sum_probs=78.5

Q ss_pred             HHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCC
Q 011102          234 LLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPD  313 (493)
Q Consensus       234 t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~  313 (493)
                      .|+.+..|-.+.|.  ..+++..|..-.|...|--+|+...+.|.+++-.+.+...++..-.|...+  .||-+|++. +
T Consensus      1106 vWsqlakAQL~~~~--v~dAieSyikadDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~--eLi~AyAkt-~ 1180 (1666)
T KOG0985|consen 1106 VWSQLAKAQLQGGL--VKDAIESYIKADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDS--ELIFAYAKT-N 1180 (1666)
T ss_pred             HHHHHHHHHHhcCc--hHHHHHHHHhcCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchH--HHHHHHHHh-c
Confidence            44555555444444  344455555555555555555555555555555555555554444444332  455555555 5


Q ss_pred             CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHH
Q 011102          314 KYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVV  393 (493)
Q Consensus       314 ~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~  393 (493)
                      +..+..+++        ..||......+-+-|...|.++.|.-+|..         +.-|.-|-..+...|++..|.+--
T Consensus      1181 rl~elE~fi--------~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~---------vSN~a~La~TLV~LgeyQ~AVD~a 1243 (1666)
T KOG0985|consen 1181 RLTELEEFI--------AGPNVANIQQVGDRCFEEKMYEAAKLLYSN---------VSNFAKLASTLVYLGEYQGAVDAA 1243 (1666)
T ss_pred             hHHHHHHHh--------cCCCchhHHHHhHHHhhhhhhHHHHHHHHH---------hhhHHHHHHHHHHHHHHHHHHHHh
Confidence            544433332        224444444455555555555555544442         233555555555555555555443


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          394 WNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       394 ~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      ++.      -+..||--+-.+|...+.
T Consensus      1244 RKA------ns~ktWK~VcfaCvd~~E 1264 (1666)
T KOG0985|consen 1244 RKA------NSTKTWKEVCFACVDKEE 1264 (1666)
T ss_pred             hhc------cchhHHHHHHHHHhchhh
Confidence            322      234455555444444443

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.64  E-value=0.0028  Score=65.68  Aligned_cols=139  Identities=17%  Similarity=0.139  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      -|.-+.+.|+..|+++.|.++|-+.-         .++-.|..|.+. |+|++|.++-.+..   |-......|-+--.-
T Consensus       767 yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~-~kw~da~kla~e~~---~~e~t~~~yiakaed  833 (1636)
T KOG3616|consen  767 YYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKA-GKWEDAFKLAEECH---GPEATISLYIAKAED  833 (1636)
T ss_pred             cchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhcc-ccHHHHHHHHHHhc---CchhHHHHHHHhHHh
Confidence            37777788888888888888876432         356667788888 88888887766542   334455566666666


Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRA  424 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A  424 (493)
                      +-+.|++.+|+++|-.+.    .|+.     -|..|-+.|..++.+++..+-.-..+   ..|.-.+-.-|-..|++..|
T Consensus       834 ldehgkf~eaeqlyiti~----~p~~-----aiqmydk~~~~ddmirlv~k~h~d~l---~dt~~~f~~e~e~~g~lkaa  901 (1636)
T KOG3616|consen  834 LDEHGKFAEAEQLYITIG----EPDK-----AIQMYDKHGLDDDMIRLVEKHHGDHL---HDTHKHFAKELEAEGDLKAA  901 (1636)
T ss_pred             HHhhcchhhhhheeEEcc----CchH-----HHHHHHhhCcchHHHHHHHHhChhhh---hHHHHHHHHHHHhccChhHH
Confidence            667777777777776655    5654     35667777777777776654321111   12333333444445555555


Q ss_pred             HHHH
Q 011102          425 IRYF  428 (493)
Q Consensus       425 ~~~~  428 (493)
                      ..-|
T Consensus       902 e~~f  905 (1636)
T KOG3616|consen  902 EEHF  905 (1636)
T ss_pred             HHHH
Confidence            5444

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

Probab=97.61  E-value=0.0054  Score=61.08  Aligned_cols=191  Identities=11%  Similarity=0.071  Sum_probs=117.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC-CHHHHHHHHHHHHH
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNL-SQQDCTAIMKVGIR  347 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p-~~~~~~~li~~~~~  347 (493)
                      +-..|....+.++.++.|++..+..-. ++.+|-.--..+.-. +++++|..=|++...-   .| +...|-.+--+..|
T Consensus       366 ~a~~y~d~~~~~~~~~~F~~A~~ldp~-n~dvYyHRgQm~flL-~q~e~A~aDF~Kai~L---~pe~~~~~iQl~~a~Yr  440 (606)
T KOG0547|consen  366 RAAAYADENQSEKMWKDFNKAEDLDPE-NPDVYYHRGQMRFLL-QQYEEAIADFQKAISL---DPENAYAYIQLCCALYR  440 (606)
T ss_pred             HHHHHhhhhccHHHHHHHHHHHhcCCC-CCchhHhHHHHHHHH-HHHHHHHHHHHHHhhc---ChhhhHHHHHHHHHHHH
Confidence            344455555555555555555543311 122222211112222 4455666555555432   22 34455566666678


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----CCCCCH--HHHHHHHHHHHHcCC
Q 011102          348 LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS-----NCLFDL--PAYRVVIKLFVALND  420 (493)
Q Consensus       348 ~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-----gi~pd~--~ty~~li~~~~~~g~  420 (493)
                      .+++++++..|++-+++ ++--...||-.-..+...+++++|.+.|+...+.     ++-.+.  ...-+++-.-.+ ++
T Consensus       441 ~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~~qwk-~d  518 (606)
T KOG0547|consen  441 QHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLVLQWK-ED  518 (606)
T ss_pred             HHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhhhchh-hh
Confidence            88888999999887744 3445677888888888899999999888876542     222222  222233333344 78


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       421 ~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      +..|.++++.-.+..-+ ....|.+|-..-.+.|++++|.++|++-.
T Consensus       519 ~~~a~~Ll~KA~e~Dpk-ce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  519 INQAENLLRKAIELDPK-CEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             HHHHHHHHHHHHccCch-HHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            88888888887765433 45678899999999999999999998864

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=97.56  E-value=0.0029  Score=63.32  Aligned_cols=122  Identities=12%  Similarity=0.157  Sum_probs=76.3

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          339 TAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL  418 (493)
Q Consensus       339 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~  418 (493)
                      .+|+..+...++++.|.++|+++.+..  |++.  ..|...+...++-.+|.+++++..+. .+-|......-...|.+.
T Consensus       173 ~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev~--~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k  247 (395)
T PF09295_consen  173 DTLLKYLSLTQRYDEAIELLEKLRERD--PEVA--VLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSK  247 (395)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHhcC--CcHH--HHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhc
Confidence            445555555666777777777766542  4433  34666666666677777777766543 112444444445556777


Q ss_pred             CCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          419 NDISRAIRYFSKLKEAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       419 g~~~~A~~~~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      ++.+.|..+.++..+..  |+ ..+|..|..+|.+.|++++|+..++.+.
T Consensus       248 ~~~~lAL~iAk~av~ls--P~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  248 KKYELALEIAKKAVELS--PSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CCHHHHHHHHHHHHHhC--chhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            77777777777776532  43 4477777777777777777777777664

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.53  E-value=0.0068  Score=52.03  Aligned_cols=92  Identities=10%  Similarity=0.017  Sum_probs=49.1

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC
Q 011102          375 TLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASG  454 (493)
Q Consensus       375 ~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g  454 (493)
                      .+-..+...|++++|.+.|+....... .+...|..+-..+.+.|++++|...|+......- .+...+..+-.++.+.|
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 ASGYASWQEGDYSRAVIDFSWLVMAQP-WSWRAHIALAGTWMMLKEYTTAINFYGHALMLDA-SHPEPVYQTGVCLKMMG  106 (144)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCcHHHHHHHHHHHHcC
Confidence            344455555555556555555544321 2344555555555556666666666665554321 24455555555555666


Q ss_pred             CHHHHHHHHHHHHH
Q 011102          455 RLAKCRDVCKEAEM  468 (493)
Q Consensus       455 ~~~~A~~l~~~m~~  468 (493)
                      +.++|.+.|+...+
T Consensus       107 ~~~eAi~~~~~Al~  120 (144)
T PRK15359        107 EPGLAREAFQTAIK  120 (144)
T ss_pred             CHHHHHHHHHHHHH
Confidence            66666666655544

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

Probab=97.51  E-value=0.093  Score=53.48  Aligned_cols=264  Identities=12%  Similarity=0.031  Sum_probs=187.9

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+-...++.+.+.+++...+.+     .+..=|..+...|+..+-..+=..+.+.  ..-...+|-++-.-|--.|+..
T Consensus       252 d~~y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~--yP~~a~sW~aVg~YYl~i~k~s  329 (611)
T KOG1173|consen  252 DRLYYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL--YPSKALSWFAVGCYYLMIGKYS  329 (611)
T ss_pred             HHHHHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhcccchHHHHHHHHHHh--CCCCCcchhhHHHHHHHhcCcH
Confidence            44455688888888888777765     5566688888899888877777888754  3334567777766666667765


Q ss_pred             hhhhHHHhh-ccCcH--HHHHHHHHHHHhcCCHHHHHHHHHHHHhC--C-CCCCHHHHHHHHHHHhcCCCCHHHHHHHHH
Q 011102          250 VPFKLENFV-SLASK--GVLEATAKGFVKGGNLKLAWKLLMVAKDG--G-RMLDPSIYAKLILELGKNPDKYMLVMTLLD  323 (493)
Q Consensus       250 ~~~~l~~~~-~~~~~--~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g-~~pd~~t~~~li~~~~~~~~~~~~a~~l~~  323 (493)
                      .++....-. .+...  ..|-.+-+.|+-.|..|.|+..+...-+.  | -.|.  .|.  ---|.+. +..+.|.++|.
T Consensus       330 eARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~--LYl--gmey~~t-~n~kLAe~Ff~  404 (611)
T KOG1173|consen  330 EARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPS--LYL--GMEYMRT-NNLKLAEKFFK  404 (611)
T ss_pred             HHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchH--HHH--HHHHHHh-ccHHHHHHHHH
Confidence            555442211 12222  26888899999999999999988776652  2 1222  222  2246667 88999999998


Q ss_pred             HHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCC----CHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          324 ELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS--GRDP----TVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       324 ~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g~~p----~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      +....  ..-|+...+-+--.....+.+.+|...|+.-...  .+.+    -.-+++.|-++|.+.++.++|+..++...
T Consensus       405 ~A~ai--~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL  482 (611)
T KOG1173|consen  405 QALAI--APSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKAL  482 (611)
T ss_pred             HHHhc--CCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHH
Confidence            87653  3446677777766777788899999999876521  1111    23457888899999999999999999876


Q ss_pred             HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          398 ASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIF  450 (493)
Q Consensus       398 ~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~  450 (493)
                      .. ..-|..+|.++--.|...|+++.|.+.|.+-.  .+.||-.+-+.++..+
T Consensus       483 ~l-~~k~~~~~asig~iy~llgnld~Aid~fhKaL--~l~p~n~~~~~lL~~a  532 (611)
T KOG1173|consen  483 LL-SPKDASTHASIGYIYHLLGNLDKAIDHFHKAL--ALKPDNIFISELLKLA  532 (611)
T ss_pred             Hc-CCCchhHHHHHHHHHHHhcChHHHHHHHHHHH--hcCCccHHHHHHHHHH
Confidence            64 23577888888888999999999999998865  4568877777776644

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=97.50  E-value=0.0058  Score=63.65  Aligned_cols=190  Identities=12%  Similarity=0.111  Sum_probs=135.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      ..|.-+|..|+..|+..+|..+..+-.+  -+||+..|..+.+..... .-+++|.++++....+..     ..++-.  
T Consensus       425 emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d~-s~yEkawElsn~~sarA~-----r~~~~~--  494 (777)
T KOG1128|consen  425 EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHDP-SLYEKAWELSNYISARAQ-----RSLALL--  494 (777)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccCh-HHHHHHHHHhhhhhHHHH-----Hhhccc--
Confidence            4577788888888888888888877776  358888888888877777 778888888876533200     011111  


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL-PAYRVVIKLFVALNDIS  422 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~-~ty~~li~~~~~~g~~~  422 (493)
                       ..+.++++++.+.|+.-.+.. .--..+|-.+=.+..+.+++..|.+-|..-..  ..||- ..||.+-.+|.+.|+-.
T Consensus       495 -~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~aF~rcvt--L~Pd~~eaWnNls~ayi~~~~k~  570 (777)
T KOG1128|consen  495 -ILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVKAFHRCVT--LEPDNAEAWNNLSTAYIRLKKKK  570 (777)
T ss_pred             -cccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHHHHHHHhh--cCCCchhhhhhhhHHHHHHhhhH
Confidence             122677888888887644321 23456677777777778888888888877654  24554 57888888888888888


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          423 RAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +|...+.+-.+.. .-+-..|...+-...+.|.+++|.+.+.+|.+
T Consensus       571 ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  571 RAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             HHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence            8888888888766 33556677777777888888888888887754

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.48  E-value=0.0064  Score=51.23  Aligned_cols=103  Identities=12%  Similarity=0.035  Sum_probs=53.6

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA  452 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~  452 (493)
                      ...+...+...|+.++|.+.|+...+.+ ..+...+..+-..+.+.|++++|..+|+...+.+ ..+...|..+-..|..
T Consensus        20 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~   97 (135)
T TIGR02552        20 IYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECLLA   97 (135)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHH
Confidence            4444455555555555555555554432 1234445555555555566666666665554433 2234445555555666


Q ss_pred             cCCHHHHHHHHHHHHHCCCccCHHHHH
Q 011102          453 SGRLAKCRDVCKEAEMAGFKLDKQTVV  479 (493)
Q Consensus       453 ~g~~~~A~~l~~~m~~~g~~pd~~t~~  479 (493)
                      .|++++|.+.|+...+  +.|+...+.
T Consensus        98 ~g~~~~A~~~~~~al~--~~p~~~~~~  122 (135)
T TIGR02552        98 LGEPESALKALDLAIE--ICGENPEYS  122 (135)
T ss_pred             cCCHHHHHHHHHHHHH--hccccchHH
Confidence            6666666666665554  234444433

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=97.46  E-value=0.0048  Score=61.72  Aligned_cols=127  Identities=10%  Similarity=0.016  Sum_probs=102.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +...-.+|+..+...++++.|.++|+++.+..  |+..  ..+...+... ++-.+|.+++++..+.  ..-|......-
T Consensus       168 ~NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~--pev~--~~LA~v~l~~-~~E~~AI~ll~~aL~~--~p~d~~LL~~Q  240 (395)
T PF09295_consen  168 NNYLVDTLLKYLSLTQRYDEAIELLEKLRERD--PEVA--VLLARVYLLM-NEEVEAIRLLNEALKE--NPQDSELLNLQ  240 (395)
T ss_pred             chHHHHHHHHHHhhcccHHHHHHHHHHHHhcC--CcHH--HHHHHHHHhc-CcHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            33455677788888899999999999999875  6543  3467777777 7889999999998764  33466666666


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTV-VMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      ...|.+.++.+.|+++.++..+.  .|+. .+|..|..+|.+.|++++|+-.++.|-
T Consensus       241 a~fLl~k~~~~lAL~iAk~av~l--sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  241 AEFLLSKKKYELALEIAKKAVEL--SPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHh--CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            77889999999999999999865  6655 599999999999999999999999874

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.45  E-value=0.074  Score=51.97  Aligned_cols=110  Identities=12%  Similarity=0.141  Sum_probs=91.6

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLF  415 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~  415 (493)
                      .+.+..|.-+...|+...|.++-.+.+    .||..-|-..|.+|+..++|++-.++...    .-  ..+-|-.++.+|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s----kK--sPIGyepFv~~~  247 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS----KK--SPIGYEPFVEAC  247 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC----CC--CCCChHHHHHHH
Confidence            355666788888999999999998887    89999999999999999999998886543    22  347899999999


Q ss_pred             HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          416 VALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKE  465 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~  465 (493)
                      .+.|...+|..+...+          ++.--+..|.+.|++.+|.+.--+
T Consensus       248 ~~~~~~~eA~~yI~k~----------~~~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  248 LKYGNKKEASKYIPKI----------PDEERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             HHCCCHHHHHHHHHhC----------ChHHHHHHHHHCCCHHHHHHHHHH
Confidence            9999999999998772          347778889999999999775433

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

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.45  E-value=0.032  Score=60.26  Aligned_cols=186  Identities=17%  Similarity=0.122  Sum_probs=136.3

Q ss_pred             HHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHH
Q 011102          206 LGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKL  285 (493)
Q Consensus       206 ~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l  285 (493)
                      ...++..++|..+|+....      +....+.+|.-...     .+++.+.-.......+|+.+..+-.+.|.+.+|.+-
T Consensus      1058 ai~~~LyEEAF~ifkkf~~------n~~A~~VLie~i~~-----ldRA~efAe~~n~p~vWsqlakAQL~~~~v~dAieS 1126 (1666)
T KOG0985|consen 1058 AIENQLYEEAFAIFKKFDM------NVSAIQVLIENIGS-----LDRAYEFAERCNEPAVWSQLAKAQLQGGLVKDAIES 1126 (1666)
T ss_pred             HhhhhHHHHHHHHHHHhcc------cHHHHHHHHHHhhh-----HHHHHHHHHhhCChHHHHHHHHHHHhcCchHHHHHH
Confidence            3445566777777765432      34445555543332     222332233344567899999999999999999887


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Q 011102          286 LMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSG  365 (493)
Q Consensus       286 ~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  365 (493)
                      |-+.      -|+..|.-+|+...+. |.|++....+...+++ .-.|.+  =+.||-+|++.+++.+-+++..      
T Consensus      1127 yika------dDps~y~eVi~~a~~~-~~~edLv~yL~MaRkk-~~E~~i--d~eLi~AyAkt~rl~elE~fi~------ 1190 (1666)
T KOG0985|consen 1127 YIKA------DDPSNYLEVIDVASRT-GKYEDLVKYLLMARKK-VREPYI--DSELIFAYAKTNRLTELEEFIA------ 1190 (1666)
T ss_pred             HHhc------CCcHHHHHHHHHHHhc-CcHHHHHHHHHHHHHh-hcCccc--hHHHHHHHHHhchHHHHHHHhc------
Confidence            7643      4788999999999999 9999999998877766 555554  4689999999999988777654      


Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          366 RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYF  428 (493)
Q Consensus       366 ~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~  428 (493)
                       -||+.....+-+-|...|.++.|.-++.         ++..|..|-..+...|++..|.+--
T Consensus      1191 -gpN~A~i~~vGdrcf~~~~y~aAkl~y~---------~vSN~a~La~TLV~LgeyQ~AVD~a 1243 (1666)
T KOG0985|consen 1191 -GPNVANIQQVGDRCFEEKMYEAAKLLYS---------NVSNFAKLASTLVYLGEYQGAVDAA 1243 (1666)
T ss_pred             -CCCchhHHHHhHHHhhhhhhHHHHHHHH---------HhhhHHHHHHHHHHHHHHHHHHHHh
Confidence             7888888888999999999998888876         4556777777777777776665443

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=97.44  E-value=0.0074  Score=51.84  Aligned_cols=125  Identities=10%  Similarity=0.074  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH--HHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT---VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL--PAYRVV  411 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~---~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~--~ty~~l  411 (493)
                      .|..++..+ ..++...+...++.+.+.. ..+   ....-.+-..+...|++++|...|+........|+.  ...-.|
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            344444444 3566666666666666542 111   122223445666677777777777776665422221  122334


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          412 IKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKE  465 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~  465 (493)
                      -..+...|++++|...++......+  ....+...-+.|.+.|++++|...|+.
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            4556677777777777755433222  334455666667777777777777664

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.44  E-value=0.15  Score=57.79  Aligned_cols=264  Identities=10%  Similarity=-0.055  Sum_probs=162.8

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCCH----HHHHHHHHHHHHcCCCchhhhHH-----HhhccCc----HHHHHHHHH
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFPDD----RLLASTVEVLARHHELKVPFKLE-----NFVSLAS----KGVLEATAK  271 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~pd~----~t~~~li~~~~~~g~~~~~~~l~-----~~~~~~~----~~~~~~li~  271 (493)
                      .+...|++++|...++....... ..+.    ...+.+-..+...|+++.+....     ......+    ..++..+..
T Consensus       461 ~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~  539 (903)
T PRK04841        461 VAINDGDPEEAERLAELALAELP-LTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSE  539 (903)
T ss_pred             HHHhCCCHHHHHHHHHHHHhcCC-CccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHH
Confidence            44578999999999988765211 1122    23344455566678765443321     1111111    124566677


Q ss_pred             HHHhcCCHHHHHHHHHHHHh----CCCC--C-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC-CCCCC--HHHHHHH
Q 011102          272 GFVKGGNLKLAWKLLMVAKD----GGRM--L-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRD-DLNLS--QQDCTAI  341 (493)
Q Consensus       272 ~~~~~g~~~~A~~l~~~m~~----~g~~--p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~-g~~p~--~~~~~~l  341 (493)
                      .+...|++++|...+++..+    .|..  + ....+..+-..+... |++++|...+.+..... ...+.  ...+..+
T Consensus       540 ~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~-G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  618 (903)
T PRK04841        540 ILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEW-ARLDEAEQCARKGLEVLSNYQPQQQLQCLAML  618 (903)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHh-cCHHHHHHHHHHhHHhhhccCchHHHHHHHHH
Confidence            78889999999999887654    2221  1 122344444456667 99999999988764420 11122  3344445


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCC-CCHHHH-----HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH---HHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRD-PTVVMY-----TTLIHSRLSEKKCREALTVVWNMEASNCLFDL---PAYRVVI  412 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~ty-----~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~---~ty~~li  412 (493)
                      ...+...|+.++|.+.+++.....-. .....+     ...+..+...|+.+.|.+.+............   ..+..+-
T Consensus       619 a~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a  698 (903)
T PRK04841        619 AKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIA  698 (903)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHH
Confidence            66778899999999999887542111 111111     11234556689999999998775542211111   1234566


Q ss_pred             HHHHHcCCHHHHHHHHHHHHH----CCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          413 KLFVALNDISRAIRYFSKLKE----AGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEMAG  470 (493)
Q Consensus       413 ~~~~~~g~~~~A~~~~~~m~~----~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g  470 (493)
                      .++...|+.++|..++++...    .|..++ ..+...+-.++.+.|+.++|...+.+..+..
T Consensus       699 ~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        699 RAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            778899999999999998763    233322 2456667778889999999999999987643

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.44  E-value=0.049  Score=59.85  Aligned_cols=217  Identities=10%  Similarity=-0.006  Sum_probs=138.9

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcC
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGG  277 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g  277 (493)
                      .|..||..|-..+++++|.++.+...+...-.+...-|..+  .+...++.+.+-            .. .+++.+....
T Consensus        33 a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~--l~~q~~~~~~~~------------lv-~~l~~~~~~~   97 (906)
T PRK14720         33 ELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGI--LSLSRRPLNDSN------------LL-NLIDSFSQNL   97 (906)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHH--HHHhhcchhhhh------------hh-hhhhhccccc
Confidence            56778888888999999999998666542223333333333  333334322111            11 4566666666


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      ++..+.-+...|.+.+  -+...+-.+-.+|-+. |+.++|.++++++.+. . .-|....|-+-..|+.. ++++|+++
T Consensus        98 ~~~~ve~~~~~i~~~~--~~k~Al~~LA~~Ydk~-g~~~ka~~~yer~L~~-D-~~n~~aLNn~AY~~ae~-dL~KA~~m  171 (906)
T PRK14720         98 KWAIVEHICDKILLYG--ENKLALRTLAEAYAKL-NENKKLKGVWERLVKA-D-RDNPEIVKKLATSYEEE-DKEKAITY  171 (906)
T ss_pred             chhHHHHHHHHHHhhh--hhhHHHHHHHHHHHHc-CChHHHHHHHHHHHhc-C-cccHHHHHHHHHHHHHh-hHHHHHHH
Confidence            6655555666666643  3444666777777777 8888888888888775 3 45667777777777777 88888887


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH------------------C-CCCCCHHHHHHHHHHHHHc
Q 011102          358 FHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEA------------------S-NCLFDLPAYRVVIKLFVAL  418 (493)
Q Consensus       358 ~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~------------------~-gi~pd~~ty~~li~~~~~~  418 (493)
                      +.+-.+.               |...+++.++.++|.++..                  . |..--+.++-.+...|-+.
T Consensus       172 ~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~  236 (906)
T PRK14720        172 LKKAIYR---------------FIKKKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKAL  236 (906)
T ss_pred             HHHHHHH---------------HHhhhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhh
Confidence            7766533               3333444444444444433                  2 3333445566666788888


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          419 NDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFM  451 (493)
Q Consensus       419 g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~  451 (493)
                      .+++++..+++...+..-. |.....-++..|.
T Consensus       237 ~~~~~~i~iLK~iL~~~~~-n~~a~~~l~~~y~  268 (906)
T PRK14720        237 EDWDEVIYILKKILEHDNK-NNKAREELIRFYK  268 (906)
T ss_pred             hhhhHHHHHHHHHHhcCCc-chhhHHHHHHHHH
Confidence            9999999999999876544 6666777777776

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=97.42  E-value=0.012  Score=61.39  Aligned_cols=228  Identities=12%  Similarity=0.095  Sum_probs=154.3

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHH--hhccCcHHHHHHHHHHHHhcCC
Q 011102          201 FTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLEN--FVSLASKGVLEATAKGFVKGGN  278 (493)
Q Consensus       201 ~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~--~~~~~~~~~~~~li~~~~~~g~  278 (493)
                      .+-..+...|-...|+.+|+....          |.-+|.+|+..|+...++.+..  ....++...|..+.+......-
T Consensus       403 ~laell~slGitksAl~I~Erlem----------w~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~  472 (777)
T KOG1128|consen  403 LLAELLLSLGITKSALVIFERLEM----------WDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSL  472 (777)
T ss_pred             HHHHHHHHcchHHHHHHHHHhHHH----------HHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHH
Confidence            345577788888889888887653          4667778888887555554422  2335567778888888888888


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          279 LKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLF  358 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~  358 (493)
                      ++.|+++++.--..       .-..+-.-.... ++++++.+.|+.-.+..  ..-..+|-.+-.+..+.++++.|.+.|
T Consensus       473 yEkawElsn~~sar-------A~r~~~~~~~~~-~~fs~~~~hle~sl~~n--plq~~~wf~~G~~ALqlek~q~av~aF  542 (777)
T KOG1128|consen  473 YEKAWELSNYISAR-------AQRSLALLILSN-KDFSEADKHLERSLEIN--PLQLGTWFGLGCAALQLEKEQAAVKAF  542 (777)
T ss_pred             HHHHHHHhhhhhHH-------HHHhhccccccc-hhHHHHHHHHHHHhhcC--ccchhHHHhccHHHHHHhhhHHHHHHH
Confidence            88888888754322       111111111224 78888888888755441  234557777777778888999999988


Q ss_pred             HHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC-CC
Q 011102          359 HWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEA-GF  436 (493)
Q Consensus       359 ~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~-g~  436 (493)
                      ..-..-  .| +...||.+=.+|.+.|+-.+|...+.+..+-+ .-+...|-.-+....+.|.+++|.+.+..|.+- ..
T Consensus       543 ~rcvtL--~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rll~~~~~  619 (777)
T KOG1128|consen  543 HRCVTL--EPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDLRKK  619 (777)
T ss_pred             HHHhhc--CCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHHHHhhhh
Confidence            876632  45 45789999999999999999999999887766 334445666666778889999999988887621 11


Q ss_pred             CCCHHHHHHHHHHHH
Q 011102          437 CPTYDIYRDMIRIFM  451 (493)
Q Consensus       437 ~p~~~ty~~li~~~~  451 (493)
                      .-|..+-..++.+..
T Consensus       620 ~~d~~vl~~iv~~~~  634 (777)
T KOG1128|consen  620 YKDDEVLLIIVRTVL  634 (777)
T ss_pred             cccchhhHHHHHHHH
Confidence            124444444544443

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=97.40  E-value=0.011  Score=53.84  Aligned_cols=116  Identities=8%  Similarity=0.027  Sum_probs=54.9

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HcCCC--HHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSR-LSEKK--CREA  389 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~-~~~g~--~~~A  389 (493)
                      ++.+++...++...+.  -..|...|..+-..|...|++++|...|++..+.. .-+...+..+-.++ ...|+  .++|
T Consensus        53 ~~~~~~i~~l~~~L~~--~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         53 QTPEAQLQALQDKIRA--NPQNSEQWALLGEYYLWRNDYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             hhHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            4444444444444332  12344455555555555555555555555544332 12344444444432 34444  2555


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          390 LTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       390 ~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      .+++++..+..-. +...+..+-..+.+.|++++|...|+.+.
T Consensus       130 ~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~~~~~aL  171 (198)
T PRK10370        130 REMIDKALALDAN-EVTALMLLASDAFMQADYAQAIELWQKVL  171 (198)
T ss_pred             HHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            5555555443221 33444444455555555555555555554

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.39  E-value=0.015  Score=60.53  Aligned_cols=108  Identities=10%  Similarity=0.129  Sum_probs=67.6

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      .+-.....+.+|+.+++.++.+..  -.--|.-+.+-|+..|+++.|.++|-+.         -.++-.|.+|.++|+|+
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--ASGYYGEIADHYANKGDFEIAEELFTEA---------DLFKDAIDMYGKAGKWE  808 (1636)
T ss_pred             HHHhhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhc---------chhHHHHHHHhccccHH
Confidence            344455667777777777764422  1223666667777788888888877642         12566677788888888


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          423 RAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVC  463 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~  463 (493)
                      +|.++-.+.  .|-......|-+-..-+-+.|++.+|.+++
T Consensus       809 da~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeqly  847 (1636)
T KOG3616|consen  809 DAFKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQLY  847 (1636)
T ss_pred             HHHHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhhee
Confidence            877775543  343444555655555566666666666554

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.38  E-value=0.07  Score=57.72  Aligned_cols=129  Identities=9%  Similarity=-0.047  Sum_probs=74.7

Q ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 011102          297 DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ-QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTT  375 (493)
Q Consensus       297 d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~  375 (493)
                      +...+-.|-....+. |..++|..+++...+.   .||. .....+...+.+.+++++|+..++...... .-+....+.
T Consensus        85 ~~~~~~~La~i~~~~-g~~~ea~~~l~~~~~~---~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~  159 (694)
T PRK15179         85 TELFQVLVARALEAA-HRSDEGLAVWRGIHQR---FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILL  159 (694)
T ss_pred             cHHHHHHHHHHHHHc-CCcHHHHHHHHHHHhh---CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHH
Confidence            344555555555555 6666666666666543   3443 344455566666666666666666665431 223444555


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          376 LIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       376 li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      +-.++.+.|++++|.++|++....  .|| ..++..+=.++-+.|+.++|...|+...
T Consensus       160 ~a~~l~~~g~~~~A~~~y~~~~~~--~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~  215 (694)
T PRK15179        160 EAKSWDEIGQSEQADACFERLSRQ--HPEFENGYVGWAQSLTRRGALWRARDVLQAGL  215 (694)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            556666666666666666666652  222 4556666666666666666666666655

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=97.38  E-value=0.031  Score=51.58  Aligned_cols=154  Identities=10%  Similarity=-0.021  Sum_probs=95.1

Q ss_pred             HHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH
Q 011102          307 ELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC  386 (493)
Q Consensus       307 ~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~  386 (493)
                      .+... |+-+....+.......  ..-|...-+..+....+.|++.+|...|++... .-++|...||.+--+|-+.|+.
T Consensus        75 a~~~~-G~a~~~l~~~~~~~~~--~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~-l~p~d~~~~~~lgaaldq~Gr~  150 (257)
T COG5010          75 ALYLR-GDADSSLAVLQKSAIA--YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAAR-LAPTDWEAWNLLGAALDQLGRF  150 (257)
T ss_pred             HHHhc-ccccchHHHHhhhhcc--CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhc-cCCCChhhhhHHHHHHHHccCh
Confidence            33444 4555555555443322  233444555567777777777777777777653 2256777777777777777777


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          387 REALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       387 ~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      ++|..-|.+..+.-. -+...+|.|--.|.-.|+.+.|..++..-...+-. |...-..+.-.....|++++|.++...-
T Consensus       151 ~~Ar~ay~qAl~L~~-~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~a-d~~v~~NLAl~~~~~g~~~~A~~i~~~e  228 (257)
T COG5010         151 DEARRAYRQALELAP-NEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAA-DSRVRQNLALVVGLQGDFREAEDIAVQE  228 (257)
T ss_pred             hHHHHHHHHHHHhcc-CCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCC-chHHHHHHHHHHhhcCChHHHHhhcccc
Confidence            777777776655422 12345566666666777777777777776655443 4444555666667777777777665443

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.35  E-value=0.13  Score=49.45  Aligned_cols=54  Identities=11%  Similarity=0.172  Sum_probs=32.9

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHH
Q 011102          412 IKLFVALNDISRAIRYFSKLKEAGFCPTYDIYR-DMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~-~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      -.+++..|...+|+++|-.+....++ |..+|- .|..+|.+.++.+.|++++-.+
T Consensus       400 AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~  454 (557)
T KOG3785|consen  400 AQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKT  454 (557)
T ss_pred             HHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhc
Confidence            35556667777777777666544444 555554 3445666777777776665544

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=97.32  E-value=0.053  Score=49.21  Aligned_cols=130  Identities=6%  Similarity=-0.080  Sum_probs=88.5

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHHcCC--HHHH
Q 011102          348 LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKL-FVALND--ISRA  424 (493)
Q Consensus       348 ~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~-~~~~g~--~~~A  424 (493)
                      .++.+++...++...+.. +.|...|..|-..|...|+.++|...|++..+..- -|...+..+-.+ +...|+  .++|
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-PQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRG-ENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            455666666666654332 45777888888888888888888888887766432 245555665555 356666  4888


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHH
Q 011102          425 IRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVEL  481 (493)
Q Consensus       425 ~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~L  481 (493)
                      .+++++..+..-. +...+..+-..+.+.|++++|...|+++.+. ..|+..-+..+
T Consensus       130 ~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l-~~~~~~r~~~i  184 (198)
T PRK10370        130 REMIDKALALDAN-EVTALMLLASDAFMQADYAQAIELWQKVLDL-NSPRVNRTQLV  184 (198)
T ss_pred             HHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHHHHHHHHHHHHhh-CCCCccHHHHH
Confidence            8888888765543 6677777778888888888888888888664 34455444433

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

Probab=97.30  E-value=0.29  Score=50.91  Aligned_cols=278  Identities=13%  Similarity=0.024  Sum_probs=168.4

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHH---hhccCcHHHHHHHHHHHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLEN---FVSLASKGVLEATAKGFV  274 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~---~~~~~~~~~~~~li~~~~  274 (493)
                      +|+.--..|.+.+.++-|..+|......  +.-+...|...+..=-..|..+..+++..   +.-....+.|-....-+-
T Consensus       518 tw~~da~~~~k~~~~~carAVya~alqv--fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w  595 (913)
T KOG0495|consen  518 TWLDDAQSCEKRPAIECARAVYAHALQV--FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKW  595 (913)
T ss_pred             HHhhhHHHHHhcchHHHHHHHHHHHHhh--ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHH
Confidence            4555555666666666666666655532  23344445544444444444333333321   111223445555555566


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          275 KGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVV  354 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A  354 (493)
                      ..|++..|..++.+.-+..- -+...|-.-+.--..+ ..++.|..+|.....   ..|+..+|.--++.-.-.+++++|
T Consensus       596 ~agdv~~ar~il~~af~~~p-nseeiwlaavKle~en-~e~eraR~llakar~---~sgTeRv~mKs~~~er~ld~~eeA  670 (913)
T KOG0495|consen  596 KAGDVPAARVILDQAFEANP-NSEEIWLAAVKLEFEN-DELERARDLLAKARS---ISGTERVWMKSANLERYLDNVEEA  670 (913)
T ss_pred             hcCCcHHHHHHHHHHHHhCC-CcHHHHHHHHHHhhcc-ccHHHHHHHHHHHhc---cCCcchhhHHHhHHHHHhhhHHHH
Confidence            66777777777777766542 2455666666667777 777777777777654   345666666555555666777777


Q ss_pred             HHHHHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          355 ESLFHWFTHSGRDPTV-VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       355 ~~l~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      .+++++-.+.  -|+- -.|-.+-+.+-+.++++.|.+.+..=.+ .+.-.+..|-.|...=-+.|.+-.|..+++.-.-
T Consensus       671 ~rllEe~lk~--fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k-~cP~~ipLWllLakleEk~~~~~rAR~ildrarl  747 (913)
T KOG0495|consen  671 LRLLEEALKS--FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTK-KCPNSIPLWLLLAKLEEKDGQLVRARSILDRARL  747 (913)
T ss_pred             HHHHHHHHHh--CCchHHHHHHHhHHHHHHHHHHHHHHHHHhccc-cCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHh
Confidence            7777665533  3443 2344444555555566666555543111 2323344566666666788899999999998876


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHhhhh
Q 011102          434 AGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQIEKE  487 (493)
Q Consensus       434 ~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~~~~  487 (493)
                      ++-. |...|-..|..=.+.|..+.|..++.+..+. +.-+...|..-|.+.+.
T Consensus       748 kNPk-~~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~LWaEaI~le~~  799 (913)
T KOG0495|consen  748 KNPK-NALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGLLWAEAIWLEPR  799 (913)
T ss_pred             cCCC-cchhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccchhHHHHHHhccC
Confidence            5543 7788999999999999999999888777653 55556666666665443

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

Probab=97.30  E-value=0.032  Score=55.80  Aligned_cols=227  Identities=12%  Similarity=0.040  Sum_probs=156.0

Q ss_pred             CCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHH
Q 011102          209 MNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKGFVKGGNLKLAW  283 (493)
Q Consensus       209 ~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~  283 (493)
                      .|+...|.+-|+...+. .-.++. .|.-+-.+|....+-  .+-+..|..     ..+..+|..--..+.-.+++++|.
T Consensus       339 ~g~~~~a~~d~~~~I~l-~~~~~~-lyI~~a~~y~d~~~~--~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~  414 (606)
T KOG0547|consen  339 KGDSLGAQEDFDAAIKL-DPAFNS-LYIKRAAAYADENQS--EKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAI  414 (606)
T ss_pred             cCCchhhhhhHHHHHhc-Ccccch-HHHHHHHHHhhhhcc--HHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHH
Confidence            46777888888887754 222222 255555566665552  233333332     225567877777777888999999


Q ss_pred             HHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          284 KLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFT  362 (493)
Q Consensus       284 ~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~  362 (493)
                      .=|++.++..  |. ...|--+-.+..+. ++++++...|++.+++  +.-.+..||-.-..+...++++.|.+.|+.-.
T Consensus       415 aDF~Kai~L~--pe~~~~~iQl~~a~Yr~-~k~~~~m~~Fee~kkk--FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai  489 (606)
T KOG0547|consen  415 ADFQKAISLD--PENAYAYIQLCCALYRQ-HKIAESMKTFEEAKKK--FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAI  489 (606)
T ss_pred             HHHHHHhhcC--hhhhHHHHHHHHHHHHH-HHHHHHHHHHHHHHHh--CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHH
Confidence            9999988743  33 34555566666788 8999999999999886  66778899999999999999999999999876


Q ss_pred             HcCCC-----CCHH--HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          363 HSGRD-----PTVV--MYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       363 ~~g~~-----p~~~--ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      +..-.     .+..  .--+++-.- -.+++..|.+++....+..-+ ....|-+|-..-.+.|++++|.++|++-..  
T Consensus       490 ~LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~Ll~KA~e~Dpk-ce~A~~tlaq~~lQ~~~i~eAielFEksa~--  565 (606)
T KOG0547|consen  490 ELEPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENLLRKAIELDPK-CEQAYETLAQFELQRGKIDEAIELFEKSAQ--  565 (606)
T ss_pred             hhccccccccccchhhhhhhHhhhc-hhhhHHHHHHHHHHHHccCch-HHHHHHHHHHHHHHHhhHHHHHHHHHHHHH--
Confidence            43111     1111  111222222 338999999999988765322 346789999999999999999999997652  


Q ss_pred             CCCCHHHHHHHHHHHH
Q 011102          436 FCPTYDIYRDMIRIFM  451 (493)
Q Consensus       436 ~~p~~~ty~~li~~~~  451 (493)
                         -..|-.-++++|.
T Consensus       566 ---lArt~~E~~~a~s  578 (606)
T KOG0547|consen  566 ---LARTESEMVHAYS  578 (606)
T ss_pred             ---HHHhHHHHHHHHH
Confidence               1234455555554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=97.27  E-value=0.029  Score=56.18  Aligned_cols=159  Identities=13%  Similarity=0.047  Sum_probs=110.0

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHH
Q 011102          300 IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYTTLIH  378 (493)
Q Consensus       300 t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~  378 (493)
                      -|..-+..| .. |..++|+..++.+...  ..-|..-+....+.+.+.++..+|.+.++.+...  .|+ ...+-.+-+
T Consensus       309 ~YG~A~~~~-~~-~~~d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~  382 (484)
T COG4783         309 QYGRALQTY-LA-GQYDEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQ  382 (484)
T ss_pred             HHHHHHHHH-Hh-cccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHH
Confidence            344444333 34 6788888888887764  3334444455677888889999999999888765  566 555667778


Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          379 SRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAK  458 (493)
Q Consensus       379 ~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~  458 (493)
                      +|.+.|+..+|..++++-... .+-|...|..|-.+|...|+..+|..-..                  ++|...|++++
T Consensus       383 all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~A~A------------------E~~~~~G~~~~  443 (484)
T COG4783         383 ALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALLARA------------------EGYALAGRLEQ  443 (484)
T ss_pred             HHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHHHHH------------------HHHHhCCCHHH
Confidence            888889999998888886553 34567788889999999888887766543                  34566788888


Q ss_pred             HHHHHHHHHHCC--CccCHHHHHHHHH
Q 011102          459 CRDVCKEAEMAG--FKLDKQTVVELLQ  483 (493)
Q Consensus       459 A~~l~~~m~~~g--~~pd~~t~~~Ll~  483 (493)
                      |...+....+..  -.|+-.-+...|.
T Consensus       444 A~~~l~~A~~~~~~~~~~~aR~dari~  470 (484)
T COG4783         444 AIIFLMRASQQVKLGFPDWARADARID  470 (484)
T ss_pred             HHHHHHHHHHhccCCcHHHHHHHHHHH
Confidence            888777776542  2334333444443

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=97.25  E-value=0.013  Score=50.26  Aligned_cols=126  Identities=13%  Similarity=0.151  Sum_probs=70.2

Q ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCH--HHHHHHH
Q 011102          301 YAKLILELGKNPDKYMLVMTLLDELGQRDDLN-LSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTV--VMYTTLI  377 (493)
Q Consensus       301 ~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~-p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~--~ty~~li  377 (493)
                      |..++..+. . ++...+...++.+....+-. ......-.+-..+...|++++|...|++.......|+.  ...-.|.
T Consensus        15 y~~~~~~~~-~-~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA   92 (145)
T PF09976_consen   15 YEQALQALQ-A-GDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLA   92 (145)
T ss_pred             HHHHHHHHH-C-CCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHH
Confidence            334444443 3 56666766677766542111 01112223345666777777777777777765533322  2334456


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          378 HSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSK  430 (493)
Q Consensus       378 ~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~  430 (493)
                      ..+...|++++|+..++.......  ....+...=+.|.+.|+.++|...|+.
T Consensus        93 ~~~~~~~~~d~Al~~L~~~~~~~~--~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   93 RILLQQGQYDEALATLQQIPDEAF--KALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHcCCHHHHHHHHHhccCcch--HHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            667777777777777765332222  223344444567777777777777764

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=97.24  E-value=0.024  Score=48.58  Aligned_cols=89  Identities=8%  Similarity=-0.057  Sum_probs=37.6

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      -..+...|++++|...|+...... +.+...|..+-..+.+.|++++|...|+...+.. ..+...+..+-.++...|+.
T Consensus        31 g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~-p~~~~a~~~lg~~l~~~g~~  108 (144)
T PRK15359         31 GYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD-ASHPEPVYQTGVCLKMMGEP  108 (144)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCH
Confidence            333444444444444444443221 1233444444444444444444444444444321 12333444444444444444


Q ss_pred             HHHHHHHHHHH
Q 011102          422 SRAIRYFSKLK  432 (493)
Q Consensus       422 ~~A~~~~~~m~  432 (493)
                      ++|...|+...
T Consensus       109 ~eAi~~~~~Al  119 (144)
T PRK15359        109 GLAREAFQTAI  119 (144)
T ss_pred             HHHHHHHHHHH
Confidence            44444444443

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.24  E-value=0.021  Score=48.04  Aligned_cols=97  Identities=14%  Similarity=0.066  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLF  415 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~  415 (493)
                      .....+...+.+.|++++|.+.|+.....+ +.+...|..+-..|.+.|++++|...++...+.+ ..+...+..+-..|
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~   95 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAECL   95 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHHHH
Confidence            334455566677777777777777766543 3356667777777777777777777777765543 23445555566677


Q ss_pred             HHcCCHHHHHHHHHHHHHC
Q 011102          416 VALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~~  434 (493)
                      ...|+.++|...|+...+.
T Consensus        96 ~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        96 LALGEPESALKALDLAIEI  114 (135)
T ss_pred             HHcCCHHHHHHHHHHHHHh
Confidence            7777777777777776653

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.23  E-value=0.5  Score=53.58  Aligned_cols=264  Identities=11%  Similarity=-0.003  Sum_probs=151.7

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCC-----CCCHHHH--HHHHHHHHHcCCCchhhhHHH--hhccC--cH----HHHHH
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHL-----FPDDRLL--ASTVEVLARHHELKVPFKLEN--FVSLA--SK----GVLEA  268 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~-----~pd~~t~--~~li~~~~~~g~~~~~~~l~~--~~~~~--~~----~~~~~  268 (493)
                      ..+...|++++|..++........-     .++...-  ..+-..+...|+++.+.....  ....+  +.    ...+.
T Consensus       417 ~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~  496 (903)
T PRK04841        417 WLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSV  496 (903)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHH
Confidence            3445678888888888776542110     1111111  111222345566444333211  11111  11    23456


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCC---CC--HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc---CCCC--C-CHHH
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGGRM---LD--PSIYAKLILELGKNPDKYMLVMTLLDELGQR---DDLN--L-SQQD  337 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g~~---pd--~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~---~g~~--p-~~~~  337 (493)
                      +-..+...|++++|...+++.....-.   +.  ..++..+-..+... |++++|...+++....   .+..  + ....
T Consensus       497 lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~-G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  575 (903)
T PRK04841        497 LGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQ-GFLQAAYETQEKAFQLIEEQHLEQLPMHEFL  575 (903)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHhccccccHHHHH
Confidence            666777899999999998887642111   11  12334444556677 9999999988775432   1211  1 2233


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCCHHH--
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHS--GRDP--TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFDLPA--  407 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~--g~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd~~t--  407 (493)
                      +..+-..+...|++++|...+.+....  ...+  ....+..+...+...|+.++|.+.+.+....    +.......  
T Consensus       576 ~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~  655 (903)
T PRK04841        576 LRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANA  655 (903)
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHH
Confidence            445555677789999999998876532  1112  2344555667788899999999988887542    11111101  


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLKEAGFCPT---YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~---~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      -...+..+...|+.+.|..++...........   ...+..+..++...|++++|..++++...
T Consensus       656 ~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~  719 (903)
T PRK04841        656 DKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNE  719 (903)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            01123445668899999999877553221111   11234566778899999999999988764

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.21  E-value=0.042  Score=52.73  Aligned_cols=193  Identities=9%  Similarity=0.068  Sum_probs=126.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH-HHhcCC---CCHHHHHHHHHHHhhcCCCCCCHH-HHHHHHH
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLIL-ELGKNP---DKYMLVMTLLDELGQRDDLNLSQQ-DCTAIMK  343 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~-~~~~~~---~~~~~a~~l~~~m~~~~g~~p~~~-~~~~li~  343 (493)
                      |+-.|.+.+++.+|..+.+++.-  ..|-......++. ++++..   ..+.-|.+.|+-.... +..-|.. --.++-+
T Consensus       291 L~iYyL~q~dVqeA~~L~Kdl~P--ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~S-a~ecDTIpGRQsmAs  367 (557)
T KOG3785|consen  291 LIIYYLNQNDVQEAISLCKDLDP--TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGES-ALECDTIPGRQSMAS  367 (557)
T ss_pred             heeeecccccHHHHHHHHhhcCC--CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhccc-ccccccccchHHHHH
Confidence            44557889999999988776432  2232222222222 233321   3456777777766555 4443332 2234555


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHH-HHHHHHHcCCHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRV-VIKLFVALNDIS  422 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~-li~~~~~~g~~~  422 (493)
                      .+.-..++++.+-.++.++..=..-|.+-|| +.++++..|...+|+++|-......++ |..+|.+ |-++|.+.++.+
T Consensus       368 ~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~  445 (557)
T KOG3785|consen  368 YFFLSFQFDDVLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQ  445 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCch
Confidence            5566677889988888888776666777666 578899999999999999877655554 5566655 457789999999


Q ss_pred             HHHHHHHHHHHCCCCCCHHHH-HHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          423 RAIRYFSKLKEAGFCPTYDIY-RDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~~ty-~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      .|++++-.+...   .+..+. ..+.+-|-+.+.+--|-+.|++++..
T Consensus       446 lAW~~~lk~~t~---~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~l  490 (557)
T KOG3785|consen  446 LAWDMMLKTNTP---SERFSLLQLIANDCYKANEFYYAAKAFDELEIL  490 (557)
T ss_pred             HHHHHHHhcCCc---hhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHcc
Confidence            998888666532   233333 34455677888888888888888763

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.17  E-value=0.037  Score=60.78  Aligned_cols=196  Identities=10%  Similarity=-0.023  Sum_probs=123.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH-HHhcCCCCHHHHHHH------------------HHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLIL-ELGKNPDKYMLVMTL------------------LDE  324 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~-~~~~~~~~~~~a~~l------------------~~~  324 (493)
                      ..|..|+..|...+++++|.++.+.-.+..  |+...+-.+.. -+.+. ++..++..+                  ...
T Consensus        32 ~a~~~Li~~~~~~~~~deai~i~~~~l~~~--P~~i~~yy~~G~l~~q~-~~~~~~~lv~~l~~~~~~~~~~~ve~~~~~  108 (906)
T PRK14720         32 KELDDLIDAYKSENLTDEAKDICEEHLKEH--KKSISALYISGILSLSR-RPLNDSNLLNLIDSFSQNLKWAIVEHICDK  108 (906)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHhC--CcceehHHHHHHHHHhh-cchhhhhhhhhhhhcccccchhHHHHHHHH
Confidence            456677777777777777777777554432  44332211111 22222 334433333                  222


Q ss_pred             HhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC
Q 011102          325 LGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD  404 (493)
Q Consensus       325 m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd  404 (493)
                      |...   .-+...+-.+..+|-+.|+.++|..+|+++.+.. .-|....|-+-..|+.. ++++|++++.+....-+  |
T Consensus       109 i~~~---~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV~~~i--~  181 (906)
T PRK14720        109 ILLY---GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYLKKAIYRFI--K  181 (906)
T ss_pred             HHhh---hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHH--h
Confidence            2221   1223456677888889999999999999998776 56788899999999999 99999999988765411  1


Q ss_pred             HHHHHHHHH---HHHH--cCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          405 LPAYRVVIK---LFVA--LNDISRAIRYFSKLK-EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       405 ~~ty~~li~---~~~~--~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      ..-|+.+..   -+|.  ..+++.-.++.+.+. ..|..--+.++--+...|-...+|+++.++++...+.
T Consensus       182 ~kq~~~~~e~W~k~~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~  252 (906)
T PRK14720        182 KKQYVGIEEIWSKLVHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEH  252 (906)
T ss_pred             hhcchHHHHHHHHHHhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhc
Confidence            222333322   2222  223444444555554 2354555667777788888999999999999999864

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.13  E-value=0.02  Score=46.66  Aligned_cols=97  Identities=10%  Similarity=-0.010  Sum_probs=49.4

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC--CCCCHHHHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEASNC--LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG--FCPTYDIYRDMIR  448 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~~gi--~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g--~~p~~~ty~~li~  448 (493)
                      +-.+...+.+.|++++|.+.|..+.+..-  ......+..+...+.+.|++++|...|+.+....  -......+..+..
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~   84 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGM   84 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHH
Confidence            34444555555666666666655544311  0112234445555666666666666666655321  1111334555555


Q ss_pred             HHHHcCCHHHHHHHHHHHHHC
Q 011102          449 IFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       449 ~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      ++.+.|+.++|.+.++++.+.
T Consensus        85 ~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        85 SLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHhCChHHHHHHHHHHHHH
Confidence            566666666666666666554

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.

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.11  E-value=0.081  Score=53.65  Aligned_cols=150  Identities=17%  Similarity=0.178  Sum_probs=121.5

Q ss_pred             CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHH
Q 011102          314 KYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTV  392 (493)
Q Consensus       314 ~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l  392 (493)
                      +.+...+.++++.....++|+ .+|-..|+.-.|..-++.|..+|.+..+.+..+ ++..++++|.-||. ++..-|.++
T Consensus       346 ~~~~~~~~~~~ll~~~~~~~t-Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~cs-kD~~~AfrI  423 (656)
T KOG1914|consen  346 KEKKVHEIYNKLLKIEDIDLT-LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCS-KDKETAFRI  423 (656)
T ss_pred             hhhhhHHHHHHHHhhhccCCc-eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhc-CChhHHHHH
Confidence            356666777777665455565 467788888889889999999999999998888 89999999998886 677899999


Q ss_pred             HHH-HHHCCCCCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          393 VWN-MEASNCLFDLPA-YRVVIKLFVALNDISRAIRYFSKLKEAGFCPT--YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       393 ~~~-M~~~gi~pd~~t-y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |+- |+..|   |... -...++-+.+.++-..|..+|++....++.||  ...|..+|+-=...|+...+.++-+++..
T Consensus       424 FeLGLkkf~---d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  424 FELGLKKFG---DSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHHHHHhcC---CChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            986 55543   4333 35677888899999999999999998866655  47899999999999999999999887754

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.09  E-value=0.35  Score=47.69  Aligned_cols=85  Identities=18%  Similarity=0.131  Sum_probs=63.4

Q ss_pred             CCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHH
Q 011102          401 CLFDL-PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVV  479 (493)
Q Consensus       401 i~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~  479 (493)
                      +.|+- ...+.+-..|...|..+++..+++.-..  ..||...-+.|-+.+...+.+++|++.|......+ +-|..+..
T Consensus       433 ~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~d-P~~~~sl~  509 (564)
T KOG1174|consen  433 INPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQD-PKSKRTLR  509 (564)
T ss_pred             cCCccHHHHHHHHHHHHhhCccchHHHHHHHHHh--hccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcC-ccchHHHH
Confidence            34543 2345556778889999999999988764  34899999999999999999999999998877643 22566666


Q ss_pred             HHHHhhhhc
Q 011102          480 ELLQIEKES  488 (493)
Q Consensus       480 ~Ll~~~~~~  488 (493)
                      .|=+++|+.
T Consensus       510 Gl~~lEK~~  518 (564)
T KOG1174|consen  510 GLRLLEKSD  518 (564)
T ss_pred             HHHHHHhcc
Confidence            666666654

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=97.06  E-value=0.013  Score=44.57  Aligned_cols=92  Identities=14%  Similarity=0.083  Sum_probs=46.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMAS  453 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~  453 (493)
                      ..+...+...|++++|.+.+++..+..- .+...+..+...+...|++++|.+.|+....... .+..++..+...+...
T Consensus         4 ~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~~   81 (100)
T cd00189           4 LNLGNLYYKLGDYDEALEYYEKALELDP-DNADAYYNLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLGLAYYKL   81 (100)
T ss_pred             HHHHHHHHHHhcHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHHHHHHHH
Confidence            3344444555555555555555443311 1223444455555555666666666655544321 1234555555566666


Q ss_pred             CCHHHHHHHHHHHH
Q 011102          454 GRLAKCRDVCKEAE  467 (493)
Q Consensus       454 g~~~~A~~l~~~m~  467 (493)
                      |++++|.+.++...
T Consensus        82 ~~~~~a~~~~~~~~   95 (100)
T cd00189          82 GKYEEALEAYEKAL   95 (100)
T ss_pred             HhHHHHHHHHHHHH
Confidence            66666666655544

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.02  E-value=0.17  Score=47.66  Aligned_cols=251  Identities=10%  Similarity=0.091  Sum_probs=144.9

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH--cCCCchhhhHHHhhccCcHHHHHHHH---HHHHhcCC
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLAR--HHELKVPFKLENFVSLASKGVLEATA---KGFVKGGN  278 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~--~g~~~~~~~l~~~~~~~~~~~~~~li---~~~~~~g~  278 (493)
                      ..+-+.+.+.+|+++...|...    |+...-..-+.+-.+  .+++-..+.+  ....+...+-..+|   -...+.|+
T Consensus        86 QSLY~A~i~ADALrV~~~~~D~----~~L~~~~lqLqaAIkYse~Dl~g~rsL--veQlp~en~Ad~~in~gCllykegq  159 (459)
T KOG4340|consen   86 QSLYKACIYADALRVAFLLLDN----PALHSRVLQLQAAIKYSEGDLPGSRSL--VEQLPSENEADGQINLGCLLYKEGQ  159 (459)
T ss_pred             HHHHHhcccHHHHHHHHHhcCC----HHHHHHHHHHHHHHhcccccCcchHHH--HHhccCCCccchhccchheeecccc
Confidence            4556777888888888887643    222221222222222  2333223322  34444333222333   33458899


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCC-------------CCHH---------
Q 011102          279 LKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLN-------------LSQQ---------  336 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~-------------p~~~---------  336 (493)
                      .++|.+-|+...+-|=--....||.-+..|.+  ++...|++...++.++ |++             ||+.         
T Consensus       160 yEaAvqkFqaAlqvsGyqpllAYniALaHy~~--~qyasALk~iSEIieR-G~r~HPElgIGm~tegiDvrsvgNt~~lh  236 (459)
T KOG4340|consen  160 YEAAVQKFQAALQVSGYQPLLAYNLALAHYSS--RQYASALKHISEIIER-GIRQHPELGIGMTTEGIDVRSVGNTLVLH  236 (459)
T ss_pred             HHHHHHHHHHHHhhcCCCchhHHHHHHHHHhh--hhHHHHHHHHHHHHHh-hhhcCCccCccceeccCchhcccchHHHH
Confidence            99999999988875433456789988877765  5889999999998876 432             1211         


Q ss_pred             ------HHHHHHHHHHHcCCHHHHHHHHHHHH-HcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          337 ------DCTAIMKVGIRLQKFGVVESLFHWFT-HSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYR  409 (493)
Q Consensus       337 ------~~~~li~~~~~~g~~~~A~~l~~~m~-~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~  409 (493)
                            .+|.-...+.+.|+.+.|.+-+-+|. +.....|.+|...+.-.=. .+++.+..+-+.-+.+.+- .-..||.
T Consensus       237 ~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~nP-fP~ETFA  314 (459)
T KOG4340|consen  237 QSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQNP-FPPETFA  314 (459)
T ss_pred             HHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcCC-CChHHHH
Confidence                  23333344567899999999999885 2233445565544322111 2333333333333333332 2357999


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHc-CCHHHHHHHHHHH
Q 011102          410 VVIKLFVALNDISRAIRYFSKLKEAGFC-PTYDIYRDMIRIFMAS-GRLAKCRDVCKEA  466 (493)
Q Consensus       410 ~li~~~~~~g~~~~A~~~~~~m~~~g~~-p~~~ty~~li~~~~~~-g~~~~A~~l~~~m  466 (493)
                      .++-.|||..-++.|-+++-+=.....+ .+..-|+ |++++.-. -..++|++-++.+
T Consensus       315 NlLllyCKNeyf~lAADvLAEn~~lTyk~L~~Yly~-LLdaLIt~qT~pEea~KKL~~L  372 (459)
T KOG4340|consen  315 NLLLLYCKNEYFDLAADVLAENAHLTYKFLTPYLYD-LLDALITCQTAPEEAFKKLDGL  372 (459)
T ss_pred             HHHHHHhhhHHHhHHHHHHhhCcchhHHHhhHHHHH-HHHHHHhCCCCHHHHHHHHHHH
Confidence            9999999999999999888654322111 2334444 44554433 3456665544443

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.99  E-value=0.045  Score=51.35  Aligned_cols=194  Identities=12%  Similarity=0.084  Sum_probs=129.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH-H
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI-M  342 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l-i  342 (493)
                      -+++.+..+.+..++++|.+++.--.+..  | +....+.+-.+|... .++..|-..++.+...   .|...-|-.- -
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~--p~~rAgLSlLgyCYY~~-Q~f~~AA~CYeQL~ql---~P~~~qYrlY~A   85 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERS--PRSRAGLSLLGYCYYRL-QEFALAAECYEQLGQL---HPELEQYRLYQA   85 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcC--ccchHHHHHHHHHHHHH-HHHHHHHHHHHHHHhh---ChHHHHHHHHHH
Confidence            35667777788888888888887666543  4 555666677777777 7888888888888653   3555544432 3


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH--HcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSR--LSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~--~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      ..+.+.+.+.+|+++...|...   |+...=..-+.+-  ...+++..+..++++....|   +..+.+..-....+.|+
T Consensus        86 QSLY~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegq  159 (459)
T KOG4340|consen   86 QSLYKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQ  159 (459)
T ss_pred             HHHHHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeecccc
Confidence            4566778888888888888742   4444333333332  34567777777777654322   22222333333468899


Q ss_pred             HHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCc
Q 011102          421 ISRAIRYFSKLK-EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       421 ~~~A~~~~~~m~-~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~  472 (493)
                      .+.|.+-|+... -.|.. ....||.-+..| +.|+++.|+++..++.++|++
T Consensus       160 yEaAvqkFqaAlqvsGyq-pllAYniALaHy-~~~qyasALk~iSEIieRG~r  210 (459)
T KOG4340|consen  160 YEAAVQKFQAALQVSGYQ-PLLAYNLALAHY-SSRQYASALKHISEIIERGIR  210 (459)
T ss_pred             HHHHHHHHHHHHhhcCCC-chhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhh
Confidence            999999988877 45565 456688776655 557888999999998887764

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=96.97  E-value=0.5  Score=50.93  Aligned_cols=101  Identities=17%  Similarity=0.133  Sum_probs=46.9

Q ss_pred             hCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH--HcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHH
Q 011102          208 HMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLA--RHHELKVPFKLENFVS-----LASKGVLEATAKGFVKGGNLK  280 (493)
Q Consensus       208 ~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~--~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~  280 (493)
                      ..+++..|+.......++.   |+. .|..++.|+.  |.|+.+  ++......     ..|..|..++-..|...++.+
T Consensus        21 d~~qfkkal~~~~kllkk~---Pn~-~~a~vLkaLsl~r~gk~~--ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d   94 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKKH---PNA-LYAKVLKALSLFRLGKGD--EALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLD   94 (932)
T ss_pred             hhHHHHHHHHHHHHHHHHC---CCc-HHHHHHHHHHHHHhcCch--hHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhh
Confidence            4556667777666666542   221 2334444433  223221  12111111     013445555555555555566


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHH
Q 011102          281 LAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYML  317 (493)
Q Consensus       281 ~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~  317 (493)
                      +|..+|+...+.  .|+..-...+..+|.+. +.+.+
T Consensus        95 ~~~~~Ye~~~~~--~P~eell~~lFmayvR~-~~yk~  128 (932)
T KOG2053|consen   95 EAVHLYERANQK--YPSEELLYHLFMAYVRE-KSYKK  128 (932)
T ss_pred             HHHHHHHHHHhh--CCcHHHHHHHHHHHHHH-HHHHH
Confidence            666666555443  25544445555555555 44433

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=96.97  E-value=0.015  Score=55.98  Aligned_cols=144  Identities=10%  Similarity=0.019  Sum_probs=104.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGG-RMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      .+|-.++...-+.+..+.|..+|.+..+.+ +..+.....++|.-++.  ++.+.|..+|+...+.  +..+...|..-+
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E~~~~--~d~~~A~~Ife~glk~--f~~~~~~~~~Y~   77 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYYCN--KDPKRARKIFERGLKK--FPSDPDFWLEYL   77 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHHTC--S-HHHHHHHHHHHHHH--HTT-HHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhC--CCHHHHHHHHHHHHHH--CCCCHHHHHHHH
Confidence            368888888888888999999999998654 34555555666655543  4667799999998875  666788888889


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTV----VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLF  415 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~  415 (493)
                      +.+.+.|+.+.|..+|+.....  .|..    ..|...|+-=.+.|+++.+.++.+++.+.  .|+......+++-|
T Consensus        78 ~~l~~~~d~~~aR~lfer~i~~--l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry  150 (280)
T PF05843_consen   78 DFLIKLNDINNARALFERAISS--LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDRY  150 (280)
T ss_dssp             HHHHHTT-HHHHHHHHHHHCCT--SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT
T ss_pred             HHHHHhCcHHHHHHHHHHHHHh--cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHh
Confidence            9999999999999999988754  3333    48999999888999999999998888764  44544444444433

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.

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.97  E-value=0.18  Score=46.74  Aligned_cols=151  Identities=18%  Similarity=0.149  Sum_probs=102.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH--
Q 011102          270 AKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR--  347 (493)
Q Consensus       270 i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~--  347 (493)
                      ...|++.|++++|++......    ..+...  .=+..+.+. .+++-|.+.++.|.+-    -+..|.+.|-.+|.+  
T Consensus       115 a~i~~~~~~~deAl~~~~~~~----~lE~~A--l~VqI~lk~-~r~d~A~~~lk~mq~i----ded~tLtQLA~awv~la  183 (299)
T KOG3081|consen  115 AIIYMHDGDFDEALKALHLGE----NLEAAA--LNVQILLKM-HRFDLAEKELKKMQQI----DEDATLTQLAQAWVKLA  183 (299)
T ss_pred             hHHhhcCCChHHHHHHHhccc----hHHHHH--HHHHHHHHH-HHHHHHHHHHHHHHcc----chHHHHHHHHHHHHHHh
Confidence            345788889999988887621    123322  223345566 7788899888888764    355666655555544  


Q ss_pred             --cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH-HHH
Q 011102          348 --LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI-SRA  424 (493)
Q Consensus       348 --~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~-~~A  424 (493)
                        .+++.+|.-+|++|.+ ...|+.-+-|-+..++...|++++|..++++...+.-. |..|...+|-.--..|.- +-.
T Consensus       184 ~ggek~qdAfyifeE~s~-k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-dpetL~Nliv~a~~~Gkd~~~~  261 (299)
T KOG3081|consen  184 TGGEKIQDAFYIFEELSE-KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-DPETLANLIVLALHLGKDAEVT  261 (299)
T ss_pred             ccchhhhhHHHHHHHHhc-ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-CHHHHHHHHHHHHHhCCChHHH
Confidence              4668899999999874 24788888888888899999999999999988776432 344555555544445544 445


Q ss_pred             HHHHHHHHH
Q 011102          425 IRYFSKLKE  433 (493)
Q Consensus       425 ~~~~~~m~~  433 (493)
                      .+.+..++.
T Consensus       262 ~r~l~QLk~  270 (299)
T KOG3081|consen  262 ERNLSQLKL  270 (299)
T ss_pred             HHHHHHHHh
Confidence            567777764

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=96.96  E-value=0.1  Score=48.16  Aligned_cols=154  Identities=11%  Similarity=-0.009  Sum_probs=89.0

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          272 GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKF  351 (493)
Q Consensus       272 ~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~  351 (493)
                      .+.-.|+-+....+....... -.-|....+..+....+. |++.+|...|.+...-  -.+|...|+.+--+|-+.|++
T Consensus        75 a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~-g~~~~A~~~~rkA~~l--~p~d~~~~~~lgaaldq~Gr~  150 (257)
T COG5010          75 ALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRN-GNFGEAVSVLRKAARL--APTDWEAWNLLGAALDQLGRF  150 (257)
T ss_pred             HHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHh-cchHHHHHHHHHHhcc--CCCChhhhhHHHHHHHHccCh
Confidence            334444444444444432221 112333444466666666 6777777777666552  456666777777777777777


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          352 GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       352 ~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      ++|..-|.+..+.-. -+...+|.|--.|.-.|+.++|..++......+- -|...-..+.-.....|++++|.++...-
T Consensus       151 ~~Ar~ay~qAl~L~~-~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~-ad~~v~~NLAl~~~~~g~~~~A~~i~~~e  228 (257)
T COG5010         151 DEARRAYRQALELAP-NEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPA-ADSRVRQNLALVVGLQGDFREAEDIAVQE  228 (257)
T ss_pred             hHHHHHHHHHHHhcc-CCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCC-CchHHHHHHHHHHhhcCChHHHHhhcccc
Confidence            777777666554311 1223455666666666777777777777665543 24455566666667777777777665443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=96.95  E-value=0.076  Score=57.45  Aligned_cols=180  Identities=7%  Similarity=-0.052  Sum_probs=135.8

Q ss_pred             cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHH-HHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-HHH
Q 011102          260 LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSI-YAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-QQD  337 (493)
Q Consensus       260 ~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t-~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-~~~  337 (493)
                      |.+...+--|.....+.|..++|+.+|+...+.  .||... ...+...+.+. +++++|+...+.....   .|+ ...
T Consensus        83 ~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~-~~~eeA~~~~~~~l~~---~p~~~~~  156 (694)
T PRK15179         83 PHTELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQ-QGIEAGRAEIELYFSG---GSSSARE  156 (694)
T ss_pred             cccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHh-ccHHHHHHHHHHHhhc---CCCCHHH
Confidence            456778888999999999999999999999884  587664 45667788888 9999999999998765   354 445


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA  417 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~  417 (493)
                      ...+-.++.+.|++++|.++|++.... ..-+..++..+-..+-..|+.++|...|+...+. ..|....|+..+.    
T Consensus       157 ~~~~a~~l~~~g~~~~A~~~y~~~~~~-~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~-~~~~~~~~~~~~~----  230 (694)
T PRK15179        157 ILLEAKSWDEIGQSEQADACFERLSRQ-HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA-IGDGARKLTRRLV----  230 (694)
T ss_pred             HHHHHHHHHHhcchHHHHHHHHHHHhc-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-hCcchHHHHHHHH----
Confidence            667778889999999999999999873 2344788999999999999999999999998764 2355566776543    


Q ss_pred             cCCHHHHHHHHHHHHH----CCCCCCHHHHHHHHHHHHHc
Q 011102          418 LNDISRAIRYFSKLKE----AGFCPTYDIYRDMIRIFMAS  453 (493)
Q Consensus       418 ~g~~~~A~~~~~~m~~----~g~~p~~~ty~~li~~~~~~  453 (493)
                        ++..-..+++++.-    .|..........+|.-|.+.
T Consensus       231 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (694)
T PRK15179        231 --DLNADLAALRRLGVEGDGRDVPVSILVLEKMLQEIGRR  268 (694)
T ss_pred             --HHHHHHHHHHHcCcccccCCCceeeeeHHHHHHHHhhc
Confidence              44445566666652    23333445556666666544

>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=96.93  E-value=0.019  Score=43.59  Aligned_cols=94  Identities=14%  Similarity=0.050  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA  417 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~  417 (493)
                      +..+...+...|++++|..+|++..+.. ..+...+..+...+...|++++|.+.++....... .+..++..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHHHHHHH
Confidence            3445556666777777777777765432 22335566667777777777777777777655432 233466666677777


Q ss_pred             cCCHHHHHHHHHHHHH
Q 011102          418 LNDISRAIRYFSKLKE  433 (493)
Q Consensus       418 ~g~~~~A~~~~~~m~~  433 (493)
                      .|+.++|...+....+
T Consensus        81 ~~~~~~a~~~~~~~~~   96 (100)
T cd00189          81 LGKYEEALEAYEKALE   96 (100)
T ss_pred             HHhHHHHHHHHHHHHc
Confidence            7777777777766553

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=96.90  E-value=0.036  Score=53.30  Aligned_cols=129  Identities=19%  Similarity=0.181  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSG-RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKL  414 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~  414 (493)
                      .+|..+|...-+.+.++.|..+|.+..+.+ +..+++...++|.-+ ..++.+.|.++|+...+. +.-+..-|..-|+.
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 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALMEYY-CNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHHHH-TCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH-hCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            355666666666666666666666665332 234444444444322 234455566666665443 33344555666666


Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          415 FVALNDISRAIRYFSKLKEAGFCPTY----DIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +.+.|+.+.|..+|++.... + |..    ..|...|+-=.+.|+.+.+.++.+.+.+
T Consensus        80 l~~~~d~~~aR~lfer~i~~-l-~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISS-L-PKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCT-S-SCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHh-c-CchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            66666666666666666533 2 222    3666666666666666666666666654

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.

>PLN02789 farnesyltranstransferase

Probab=96.89  E-value=0.5  Score=46.32  Aligned_cols=47  Identities=6%  Similarity=-0.149  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Q 011102          316 MLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS  364 (493)
Q Consensus       316 ~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  364 (493)
                      ++++.+++.+.+.  -.-|..+|+-....+.+.|++++|++.++++.+.
T Consensus       125 ~~el~~~~kal~~--dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~  171 (320)
T PLN02789        125 NKELEFTRKILSL--DAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEE  171 (320)
T ss_pred             HHHHHHHHHHHHh--CcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            3444455444432  1223445555555555555555555555555443

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

Probab=96.83  E-value=0.75  Score=47.43  Aligned_cols=308  Identities=12%  Similarity=0.071  Sum_probs=177.3

Q ss_pred             HHHHHHHhhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHH
Q 011102          168 ISLARDIKGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVL  242 (493)
Q Consensus       168 ~~l~~~l~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~  242 (493)
                      ..+...++.+...+++++|+....+....+     .+..=+-++.+.+++++|+.+.+.-.   +..-+.+-+  +=.+|
T Consensus        13 ~~l~t~ln~~~~~~e~e~a~k~~~Kil~~~pdd~~a~~cKvValIq~~ky~~ALk~ikk~~---~~~~~~~~~--fEKAY   87 (652)
T KOG2376|consen   13 EALLTDLNRHGKNGEYEEAVKTANKILSIVPDDEDAIRCKVVALIQLDKYEDALKLIKKNG---ALLVINSFF--FEKAY   87 (652)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHHHHhcCCCcHhhHhhhHhhhhhhhHHHHHHHHHHhcc---hhhhcchhh--HHHHH
Confidence            466677888999999999999998877663     55555678889999999996654322   111111111  35666


Q ss_pred             HHcCCCchhhhHHHhhcc--CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-------------------------
Q 011102          243 ARHHELKVPFKLENFVSL--ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRM-------------------------  295 (493)
Q Consensus       243 ~~~g~~~~~~~l~~~~~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-------------------------  295 (493)
                      |--..-..++++..+...  .+..+...=...+-+.|++++|+.+|+.+.+++..                         
T Consensus        88 c~Yrlnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~l~~~~~q~v  167 (652)
T KOG2376|consen   88 CEYRLNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAALQVQLLQSV  167 (652)
T ss_pred             HHHHcccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhhhHHHHHhc
Confidence            654433356666555532  23445555556677889999999999988654421                         


Q ss_pred             --CCHHHHHHHHH---HHhcCCCCHHHHHHHHHHHhhc-------CCCC-----CCHHHH-HHHHHHHHHcCCHHHHHHH
Q 011102          296 --LDPSIYAKLIL---ELGKNPDKYMLVMTLLDELGQR-------DDLN-----LSQQDC-TAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       296 --pd~~t~~~li~---~~~~~~~~~~~a~~l~~~m~~~-------~g~~-----p~~~~~-~~li~~~~~~g~~~~A~~l  357 (493)
                        ....+|..+.+   .+... |++.+|++++....+-       +...     -...+. --|--.+-..|+.++|..+
T Consensus       168 ~~v~e~syel~yN~Ac~~i~~-gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~i  246 (652)
T KOG2376|consen  168 PEVPEDSYELLYNTACILIEN-GKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSI  246 (652)
T ss_pred             cCCCcchHHHHHHHHHHHHhc-ccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHH
Confidence              01224444433   23455 8899999998877211       0111     111111 1334466678999999999


Q ss_pred             HHHHHHcCCCCCH----HHHHHHHHHHHcCCCHH-HHHHHHHH----------------------------------H--
Q 011102          358 FHWFTHSGRDPTV----VMYTTLIHSRLSEKKCR-EALTVVWN----------------------------------M--  396 (493)
Q Consensus       358 ~~~m~~~g~~p~~----~ty~~li~~~~~~g~~~-~A~~l~~~----------------------------------M--  396 (493)
                      +....+... +|.    +.-|.|+..-....-++ .++..++.                                  |  
T Consensus       247 y~~~i~~~~-~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~tnk~~q  325 (652)
T KOG2376|consen  247 YVDIIKRNP-ADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALFTNKMDQ  325 (652)
T ss_pred             HHHHHHhcC-CCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence            988876543 332    22233322111111011 01110100                                  0  


Q ss_pred             -----HH-CCCCCCHHHHHHHHHHHHH--cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH----
Q 011102          397 -----EA-SNCLFDLPAYRVVIKLFVA--LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCK----  464 (493)
Q Consensus       397 -----~~-~gi~pd~~ty~~li~~~~~--~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~----  464 (493)
                           .. -+..|. ..+.+++..+.+  ......|.+++....+..-.-..+.--+++......|+++.|.+++.    
T Consensus       326 ~r~~~a~lp~~~p~-~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~  404 (652)
T KOG2376|consen  326 VRELSASLPGMSPE-SLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLE  404 (652)
T ss_pred             HHHHHHhCCccCch-HHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhh
Confidence                 00 122232 334445444322  22456667776666543322234556677888889999999999999    


Q ss_pred             ----HHHHCCCccCHHHHHHHHH
Q 011102          465 ----EAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       465 ----~m~~~g~~pd~~t~~~Ll~  483 (493)
                          ...+.+..|-.+.+-..+.
T Consensus       405 ~~~ss~~~~~~~P~~V~aiv~l~  427 (652)
T KOG2376|consen  405 SWKSSILEAKHLPGTVGAIVALY  427 (652)
T ss_pred             hhhhhhhhhccChhHHHHHHHHH
Confidence                7777888887777655544

>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=96.81  E-value=0.019  Score=47.84  Aligned_cols=54  Identities=9%  Similarity=0.042  Sum_probs=42.4

Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHHHHHHc
Q 011102          400 NCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIRIFMAS  453 (493)
Q Consensus       400 gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~~~~~~  453 (493)
                      ...|+..+..+++.+|+..|++..|.++.+... ..++..+..+|..|++-....
T Consensus        47 pl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~v~  101 (126)
T PF12921_consen   47 PLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAYVL  101 (126)
T ss_pred             CCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHh
Confidence            466888888888888888888888888888876 677777788888887765443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=96.81  E-value=0.064  Score=43.58  Aligned_cols=98  Identities=9%  Similarity=-0.055  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC--CCHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGR--DPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL--FDLPAYRVVI  412 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~--~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~--pd~~ty~~li  412 (493)
                      ++-.+...+.+.|++++|.+.|..+.+..-  ......+..+...+.+.|++++|.+.|+......-.  .....+..+-
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            344455566667777777777777654321  111344555667777777777777777776553211  1134455555


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHC
Q 011102          413 KLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       413 ~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      ..+.+.|+.++|.+.++++.+.
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHH
Confidence            6667777777777777777654

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.

>PLN02789 farnesyltranstransferase

Probab=96.79  E-value=0.6  Score=45.77  Aligned_cols=204  Identities=9%  Similarity=-0.090  Sum_probs=122.3

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCCHHH-HHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHhcC
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHLFPDDRL-LASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKGFVKGG  277 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t-~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~~g  277 (493)
                      ..+...++.++|+.+...+...   .|+..+ |+.--..+...|. ...+++..+..     ..+..+|+.---.+.+.|
T Consensus        45 a~l~~~e~serAL~lt~~aI~l---nP~~ytaW~~R~~iL~~L~~-~l~eeL~~~~~~i~~npknyqaW~~R~~~l~~l~  120 (320)
T PLN02789         45 AVYASDERSPRALDLTADVIRL---NPGNYTVWHFRRLCLEALDA-DLEEELDFAEDVAEDNPKNYQIWHHRRWLAEKLG  120 (320)
T ss_pred             HHHHcCCCCHHHHHHHHHHHHH---CchhHHHHHHHHHHHHHcch-hHHHHHHHHHHHHHHCCcchHHhHHHHHHHHHcC
Confidence            3556677889999999988853   555543 4433333444442 13344444332     234557876655566666


Q ss_pred             CH--HHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHc---CCH-
Q 011102          278 NL--KLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRL---QKF-  351 (493)
Q Consensus       278 ~~--~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~---g~~-  351 (493)
                      ..  ++++.+++++.+.. .-+..+|+..--.+... |+++++++.++.+.+. +. -|...|+-....+.+.   |.. 
T Consensus       121 ~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l-~~~~eeL~~~~~~I~~-d~-~N~sAW~~R~~vl~~~~~l~~~~  196 (320)
T PLN02789        121 PDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTL-GGWEDELEYCHQLLEE-DV-RNNSAWNQRYFVITRSPLLGGLE  196 (320)
T ss_pred             chhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHh-hhHHHHHHHHHHHHHH-CC-CchhHHHHHHHHHHhcccccccc
Confidence            63  77899998888754 24667888888888888 8999999999999876 33 3556676665555444   222 


Q ss_pred             ---HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC----CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          352 ---GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE----KKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA  417 (493)
Q Consensus       352 ---~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~----g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~  417 (493)
                         +++.+...+..... +-|...|+-+-..+...    ++..+|.+.+.+..+.++ .+......|++.|+.
T Consensus       197 ~~~e~el~y~~~aI~~~-P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~-~s~~al~~l~d~~~~  267 (320)
T PLN02789        197 AMRDSELKYTIDAILAN-PRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDS-NHVFALSDLLDLLCE  267 (320)
T ss_pred             ccHHHHHHHHHHHHHhC-CCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccC-CcHHHHHHHHHHHHh
Confidence               34555554444321 33556676666666653    233456666665444321 234445555555553

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=96.75  E-value=0.061  Score=53.89  Aligned_cols=128  Identities=9%  Similarity=-0.024  Sum_probs=102.8

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVVIKLF  415 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~  415 (493)
                      -|..-+. +...|++++|+..++.+... .+-|.+-+....+.+.+.++..+|.+.++.+...  .|+ ....-.+-.+|
T Consensus       309 ~YG~A~~-~~~~~~~d~A~~~l~~L~~~-~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~al  384 (484)
T COG4783         309 QYGRALQ-TYLAGQYDEALKLLQPLIAA-QPDNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQAL  384 (484)
T ss_pred             HHHHHHH-HHHhcccchHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHH
Confidence            3444444 34779999999999998755 2345666667778999999999999999998875  566 34455666889


Q ss_pred             HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          416 VALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      .+.|+..+|.++++...... +-|...|..|-++|...|+..+|..-..++...
T Consensus       385 l~~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~a~~A~AE~~~~  437 (484)
T COG4783         385 LKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAEALLARAEGYAL  437 (484)
T ss_pred             HhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHHHHHHHHHHHHh
Confidence            99999999999999987543 458899999999999999999999988887654

>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=96.74  E-value=0.019  Score=47.81  Aligned_cols=80  Identities=9%  Similarity=0.152  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHH---------------hCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhh
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAK---------------DGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQ  327 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~---------------~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~  327 (493)
                      ..++.++|.++++.|+++....+++..-               .....|+..+..+++.+|+.+ |++..|+++.+...+
T Consensus         2 e~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n-~~i~~al~~vd~fs~   80 (126)
T PF12921_consen    2 EELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYN-GDIFSALKLVDFFSR   80 (126)
T ss_pred             hHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhc-ccHHHHHHHHHHHHH
Confidence            3456666666666666666666665331               122345555555555555555 555555555555555


Q ss_pred             cCCCCCCHHHHHHHHH
Q 011102          328 RDDLNLSQQDCTAIMK  343 (493)
Q Consensus       328 ~~g~~p~~~~~~~li~  343 (493)
                      ..++..+..+|..|+.
T Consensus        81 ~Y~I~i~~~~W~~Ll~   96 (126)
T PF12921_consen   81 KYPIPIPKEFWRRLLE   96 (126)
T ss_pred             HcCCCCCHHHHHHHHH
Confidence            4455555555555544

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.68  E-value=0.014  Score=54.21  Aligned_cols=88  Identities=14%  Similarity=0.107  Sum_probs=62.4

Q ss_pred             CCHHHHHHHHHHHHHc-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC----------------HHHHHH
Q 011102          333 LSQQDCTAIMKVGIRL-----QKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK----------------CREALT  391 (493)
Q Consensus       333 p~~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~----------------~~~A~~  391 (493)
                      -|..+|-+.+..+...     +.++-....++.|.+.|+..|..+|+.||+.+-+..-                -+=+.+
T Consensus        65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~  144 (406)
T KOG3941|consen   65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIK  144 (406)
T ss_pred             ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHH
Confidence            4555555555555432     5566667777788888888888888888877655432                234678


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          392 VVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       392 l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      ++++|...|+.||..+-..||++|++.+-
T Consensus       145 vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  145 VLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            88888888888888888888888887764

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.66  E-value=0.32  Score=49.80  Aligned_cols=246  Identities=13%  Similarity=0.039  Sum_probs=161.4

Q ss_pred             HHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCC-CchhhhHHHhhcc--CcHHHHHHHHHHHHhcCCHHH
Q 011102          206 LGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHE-LKVPFKLENFVSL--ASKGVLEATAKGFVKGGNLKL  281 (493)
Q Consensus       206 ~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~-~~~~~~l~~~~~~--~~~~~~~~li~~~~~~g~~~~  281 (493)
                      +.+.|+.-+|.-+|+....+   .| +...|-.|=..-...++ .....|+....+.  .+....-+|.-.|...|.-..
T Consensus       295 lm~nG~L~~A~LafEAAVkq---dP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~  371 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQ---DPQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQ  371 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhh---ChHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHH
Confidence            46778888888888887765   23 22233322222222221 1122233333332  256677788889999999999


Q ss_pred             HHHHHHHHHhCCCC--------CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          282 AWKLLMVAKDGGRM--------LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGV  353 (493)
Q Consensus       282 A~~l~~~m~~~g~~--------pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~  353 (493)
                      |++.|+.-.....+        ++...-+.  ..+... ..+....++|-++....+.++|..+++.|---|--.|++++
T Consensus       372 Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~-~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdr  448 (579)
T KOG1125|consen  372 ALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDS-SHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDR  448 (579)
T ss_pred             HHHHHHHHHHhCccchhccccCccccccCC--cCCCCH-HHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHH
Confidence            99999887654311        01110000  222333 44566777777776655666777788888888888999999


Q ss_pred             HHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          354 VESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL--PAYRVVIKLFVALNDISRAIRYFSK  430 (493)
Q Consensus       354 A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~--~ty~~li~~~~~~g~~~~A~~~~~~  430 (493)
                      |.+.|+.....  +| |...||-|-..++...+..+|..-+.+..+.  +|+-  +=||. --.|...|.+++|.+.|-+
T Consensus       449 aiDcf~~AL~v--~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNl-gIS~mNlG~ykEA~~hlL~  523 (579)
T KOG1125|consen  449 AVDCFEAALQV--KPNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNL-GISCMNLGAYKEAVKHLLE  523 (579)
T ss_pred             HHHHHHHHHhc--CCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhh-hhhhhhhhhHHHHHHHHHH
Confidence            99999987754  45 6788999999999999999999999998874  5653  23554 4467889999999988875


Q ss_pred             HH---HCC------CCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          431 LK---EAG------FCPTYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       431 m~---~~g------~~p~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                      ..   .++      ..++...|.+|=.++.-.++.|-+.+.
T Consensus       524 AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a  564 (579)
T KOG1125|consen  524 ALSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEA  564 (579)
T ss_pred             HHHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHHh
Confidence            44   221      123456788887777777777655443

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=96.61  E-value=0.0054  Score=47.13  Aligned_cols=80  Identities=13%  Similarity=0.088  Sum_probs=34.6

Q ss_pred             CCHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          384 KKCREALTVVWNMEASNC-LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       384 g~~~~A~~l~~~M~~~gi-~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                      |++++|+.+++++.+..- .++...+-.+-.+|.+.|++++|..+++... .+. .+....-.+-.+|.+.|++++|.++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~~-~~~-~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKLK-LDP-SNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCHT-HHH-CHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHhC-CCC-CCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            455555555555544322 1122233334555555555555555555511 111 1112222334445555555555555


Q ss_pred             HHH
Q 011102          463 CKE  465 (493)
Q Consensus       463 ~~~  465 (493)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            543

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.55  E-value=0.069  Score=47.01  Aligned_cols=63  Identities=8%  Similarity=-0.090  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP--TVVMYTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      ..|..+...+...|++++|+..|++.......+  ...+|..+-..|...|+.++|++.++...+
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~  100 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALE  100 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344555555555666666666666554332121  123555555666666666666666655544

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.49  E-value=0.038  Score=51.51  Aligned_cols=104  Identities=13%  Similarity=0.077  Sum_probs=82.6

Q ss_pred             CCCCCHHHHHHHHHHHHcC-----CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC----------------HHH
Q 011102          365 GRDPTVVMYTTLIHSRLSE-----KKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND----------------ISR  423 (493)
Q Consensus       365 g~~p~~~ty~~li~~~~~~-----g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~----------------~~~  423 (493)
                      |-+.|..+|-+.+..+...     +.++-....++.|++-|+.-|..+|+.||+.+-|..-                -+-
T Consensus        62 ~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C  141 (406)
T KOG3941|consen   62 PEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNC  141 (406)
T ss_pred             cccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhH
Confidence            4467888888888877654     5677777888999999999999999999988765432                245


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH-HHHHHHHHHHHH
Q 011102          424 AIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRL-AKCRDVCKEAEM  468 (493)
Q Consensus       424 A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~-~~A~~l~~~m~~  468 (493)
                      +.+++++|...|+.||-.+-..||+++++.|.. .+..+++--|.+
T Consensus       142 ~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWmPk  187 (406)
T KOG3941|consen  142 AIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWMPK  187 (406)
T ss_pred             HHHHHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhhhh
Confidence            789999999999999999999999999988863 445555555543

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

Probab=96.48  E-value=1.3  Score=45.74  Aligned_cols=130  Identities=13%  Similarity=0.156  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHH--------HHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          351 FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVW--------NMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~--------~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      ...|.+++...-+..-.-..+.--+++.-....|+++.|.+++.        ...+.+-.|-.+  .+++..+.+.++-+
T Consensus       357 ~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V--~aiv~l~~~~~~~~  434 (652)
T KOG2376|consen  357 HKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTV--GAIVALYYKIKDND  434 (652)
T ss_pred             HhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHH--HHHHHHHHhccCCc
Confidence            44555555554433222224455566677777888888888887        444555555443  44555566666555


Q ss_pred             HHHHHHHHHHH----C--CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          423 RAIRYFSKLKE----A--GFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       423 ~A~~~~~~m~~----~--g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      .|..++.+-..    .  +-.--..++.-+..--.+.|+-++|..+++++.+.. .+|..+...++.
T Consensus       435 ~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n-~~d~~~l~~lV~  500 (652)
T KOG2376|consen  435 SASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFN-PNDTDLLVQLVT  500 (652)
T ss_pred             cHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhC-CchHHHHHHHHH
Confidence            55555544331    0  001112233333333456788888888888887642 456666555554

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=96.48  E-value=0.0071  Score=46.44  Aligned_cols=79  Identities=11%  Similarity=0.135  Sum_probs=38.4

Q ss_pred             CCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHHHHHH
Q 011102          349 QKFGVVESLFHWFTHSGR-DPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL-PAYRVVIKLFVALNDISRAIR  426 (493)
Q Consensus       349 g~~~~A~~l~~~m~~~g~-~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~-~ty~~li~~~~~~g~~~~A~~  426 (493)
                      |+++.|+.+|+++.+..- .++...+-.+-.+|.+.|++++|.++++. .  ...|+. ...-.+-.+|.+.|++++|.+
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~--~~~~~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-L--KLDPSNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-H--THHHCHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-h--CCCCCCHHHHHHHHHHHHHhCCHHHHHH
Confidence            556666666666654422 11233344456666666666666666655 1  111222 222223444566666666666


Q ss_pred             HHHH
Q 011102          427 YFSK  430 (493)
Q Consensus       427 ~~~~  430 (493)
                      +|++
T Consensus        80 ~l~~   83 (84)
T PF12895_consen   80 ALEK   83 (84)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            6553

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=96.46  E-value=0.071  Score=53.22  Aligned_cols=101  Identities=13%  Similarity=0.068  Sum_probs=70.1

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      ..+...|++++|+++|++..+.. .-+...|..+-.+|.+.|++++|+..+++..+..- .+...|..+-.+|...|+++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P-~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDP-SLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHhCCHH
Confidence            45567788888888888877542 23566777777888888888888888888766421 24556777777788888888


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          423 RAIRYFSKLKEAGFCPTYDIYRDMI  447 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~~ty~~li  447 (493)
                      +|...|++..+..  |+......++
T Consensus        88 eA~~~~~~al~l~--P~~~~~~~~l  110 (356)
T PLN03088         88 TAKAALEKGASLA--PGDSRFTKLI  110 (356)
T ss_pred             HHHHHHHHHHHhC--CCCHHHHHHH
Confidence            8888888877533  4444444343

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

Probab=96.45  E-value=1.4  Score=45.91  Aligned_cols=264  Identities=17%  Similarity=0.128  Sum_probs=168.9

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH------HcCCCchhhhHHHhhc----cCcHHH-H
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLA------RHHELKVPFKLENFVS----LASKGV-L  266 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~------~~g~~~~~~~l~~~~~----~~~~~~-~  266 (493)
                      .|..+..++--.|+...|..+.+.......-.|+...|.-....+-      +.|.  ...++.....    ..|... -
T Consensus       145 ~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~--~q~ale~L~~~e~~i~Dkla~~  222 (700)
T KOG1156|consen  145 SWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGS--LQKALEHLLDNEKQIVDKLAFE  222 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHccc--HHHHHHHHHhhhhHHHHHHHHh
Confidence            7888888888899999999999999875234577777766554443      3343  2333332221    123222 3


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH-HHhcCCCCHHHHHHHHHHHhhcC----------------
Q 011102          267 EATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLIL-ELGKNPDKYMLVMTLLDELGQRD----------------  329 (493)
Q Consensus       267 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~-~~~~~~~~~~~a~~l~~~m~~~~----------------  329 (493)
                      .+-.+.+.+.+++++|..++..+....  ||-.-|.-.+. ++++..+..+....+|....+..                
T Consensus       223 e~ka~l~~kl~~lEeA~~~y~~Ll~rn--Pdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~  300 (700)
T KOG1156|consen  223 ETKADLLMKLGQLEEAVKVYRRLLERN--PDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNG  300 (700)
T ss_pred             hhHHHHHHHHhhHHhHHHHHHHHHhhC--chhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCc
Confidence            556677889999999999999999876  88887775544 44334133333335555554421                


Q ss_pred             -----------------CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH----cC----------CCCCHHH--HHHH
Q 011102          330 -----------------DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTH----SG----------RDPTVVM--YTTL  376 (493)
Q Consensus       330 -----------------g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~----~g----------~~p~~~t--y~~l  376 (493)
                                       |+   +.++..+.+-|-.-.+.+-.+++.-.+..    .|          -.|....  +-.+
T Consensus       301 eel~~~vdkyL~~~l~Kg~---p~vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~l  377 (700)
T KOG1156|consen  301 EELKEIVDKYLRPLLSKGV---PSVFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFL  377 (700)
T ss_pred             chhHHHHHHHHHHHhhcCC---CchhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHH
Confidence                             11   11333444433322222222222222221    11          1455544  4568


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          377 IHSRLSEKKCREALTVVWNMEASNCLFDLP-AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGR  455 (493)
Q Consensus       377 i~~~~~~g~~~~A~~l~~~M~~~gi~pd~~-ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~  455 (493)
                      +..|-+.|+++.|+..++....+  .|+.+ -|-+=-+.+..+|++++|..++++-.+-.. ||...-.--..-..++.+
T Consensus       378 aqh~D~~g~~~~A~~yId~AIdH--TPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~-aDR~INsKcAKYmLrAn~  454 (700)
T KOG1156|consen  378 AQHYDKLGDYEVALEYIDLAIDH--TPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDT-ADRAINSKCAKYMLRANE  454 (700)
T ss_pred             HHHHHHcccHHHHHHHHHHHhcc--CchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccc-hhHHHHHHHHHHHHHccc
Confidence            88999999999999999987764  45543 344445789999999999999999886554 466555455566678899


Q ss_pred             HHHHHHHHHHHHHCCC
Q 011102          456 LAKCRDVCKEAEMAGF  471 (493)
Q Consensus       456 ~~~A~~l~~~m~~~g~  471 (493)
                      .++|.++.....+.|.
T Consensus       455 i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  455 IEEAEEVLSKFTREGF  470 (700)
T ss_pred             cHHHHHHHHHhhhccc
Confidence            9999999998888775

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.42  E-value=0.81  Score=42.63  Aligned_cols=173  Identities=8%  Similarity=0.035  Sum_probs=114.9

Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          283 WKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFT  362 (493)
Q Consensus       283 ~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~  362 (493)
                      .++.+.+......-+...-..-...|+.. +++++|++..+...       +......=+..+.|..+++-|.+.+++|.
T Consensus        93 ~~l~E~~a~~~~~sn~i~~l~aa~i~~~~-~~~deAl~~~~~~~-------~lE~~Al~VqI~lk~~r~d~A~~~lk~mq  164 (299)
T KOG3081|consen   93 ASLYELVADSTDGSNLIDLLLAAIIYMHD-GDFDEALKALHLGE-------NLEAAALNVQILLKMHRFDLAEKELKKMQ  164 (299)
T ss_pred             HHHHHHHHhhccchhHHHHHHhhHHhhcC-CChHHHHHHHhccc-------hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34445555544333333322333457777 99999999887622       12222333455667888999999999998


Q ss_pred             HcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC
Q 011102          363 HSGRDPTVVMYTTLIHSRLS----EKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCP  438 (493)
Q Consensus       363 ~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p  438 (493)
                      +-   -+-.|.+-|-+++.+    .+++.+|.-+|++|-+ ...|+..+-+....++...|++++|..++++..++.-. 
T Consensus       165 ~i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~-k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-  239 (299)
T KOG3081|consen  165 QI---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSE-KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-  239 (299)
T ss_pred             cc---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhc-ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-
Confidence            32   234556656665554    4679999999999965 46788899999999999999999999999999876654 


Q ss_pred             CHHHHHHHHHHHHHcCCHH-HHHHHHHHHHH
Q 011102          439 TYDIYRDMIRIFMASGRLA-KCRDVCKEAEM  468 (493)
Q Consensus       439 ~~~ty~~li~~~~~~g~~~-~A~~l~~~m~~  468 (493)
                      +..|...+|-.-...|.-. -..+.+.++..
T Consensus       240 dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~  270 (299)
T KOG3081|consen  240 DPETLANLIVLALHLGKDAEVTERNLSQLKL  270 (299)
T ss_pred             CHHHHHHHHHHHHHhCCChHHHHHHHHHHHh
Confidence            4555555555444555543 34455666554

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.35  E-value=0.3  Score=43.11  Aligned_cols=84  Identities=7%  Similarity=-0.094  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT--VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIK  413 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~  413 (493)
                      .+..+...|...|++++|...|++..+....+.  ...|..+...+.+.|++++|...+.+..+.  .| +...+..+-.
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~  114 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHH
Confidence            445555566666677777776666654322221  345666666666677777777766665543  23 2334444444


Q ss_pred             HHHHcCCHH
Q 011102          414 LFVALNDIS  422 (493)
Q Consensus       414 ~~~~~g~~~  422 (493)
                      .|...|+..
T Consensus       115 ~~~~~g~~~  123 (172)
T PRK02603        115 IYHKRGEKA  123 (172)
T ss_pred             HHHHcCChH
Confidence            555555543

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=96.19  E-value=0.24  Score=43.78  Aligned_cols=129  Identities=7%  Similarity=-0.166  Sum_probs=82.3

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD--PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd--~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      ..|..+...+.+.|++++|...|++..+....+.  ...+..+-..+.+. |++++|...+.+....  ..-+...+..+
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~-g~~~~A~~~~~~al~~--~p~~~~~~~~l  112 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASN-GEHDKALEYYHQALEL--NPKQPSALNNI  112 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CcccHHHHHHH
Confidence            3567777788888999999999998876543332  35667777778888 8999999988887764  12245556666


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      ...|...|+...+..-++...                     ..+++|.+++++....  .|+.  |..++..+...|+
T Consensus       113 g~~~~~~g~~~~a~~~~~~A~---------------------~~~~~A~~~~~~a~~~--~p~~--~~~~~~~~~~~~~  166 (172)
T PRK02603        113 AVIYHKRGEKAEEAGDQDEAE---------------------ALFDKAAEYWKQAIRL--APNN--YIEAQNWLKTTGR  166 (172)
T ss_pred             HHHHHHcCChHhHhhCHHHHH---------------------HHHHHHHHHHHHHHhh--Cchh--HHHHHHHHHhcCc
Confidence            677777777555444333322                     1256667777665542  2332  5555555555443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.18  E-value=0.75  Score=48.69  Aligned_cols=126  Identities=12%  Similarity=0.145  Sum_probs=100.3

Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          318 VMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       318 a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      -+.+.+.+....|......+.+--+.-+...|+..+|.++-.+.+    -||..-|-.=+.+++..++|++-+++-+.++
T Consensus       667 Ll~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskk  742 (829)
T KOG2280|consen  667 LLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKK  742 (829)
T ss_pred             HHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC
Confidence            344455555444444555566777778888999999999999998    8999999999999999999999888877664


Q ss_pred             HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          398 ASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       398 ~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                      .      .+-|--.+.+|.+.|+.++|.+++.+..      +   +.-.+.+|.+.|++.+|.++
T Consensus       743 s------PIGy~PFVe~c~~~~n~~EA~KYiprv~------~---l~ekv~ay~~~~~~~eAad~  792 (829)
T KOG2280|consen  743 S------PIGYLPFVEACLKQGNKDEAKKYIPRVG------G---LQEKVKAYLRVGDVKEAADL  792 (829)
T ss_pred             C------CCCchhHHHHHHhcccHHHHhhhhhccC------C---hHHHHHHHHHhccHHHHHHH
Confidence            3      4568889999999999999999997653      1   11578899999999998775

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.14  E-value=1.2  Score=43.60  Aligned_cols=86  Identities=9%  Similarity=0.063  Sum_probs=70.8

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRI  449 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~  449 (493)
                      ..+.+..|.-+...|+...|.++-.+.   +| ||..-|-..|.+++..++|++-.++...    .  -..+-|..++++
T Consensus       177 ~~Sl~~Ti~~li~~~~~k~A~kl~k~F---kv-~dkrfw~lki~aLa~~~~w~eL~~fa~s----k--KsPIGyepFv~~  246 (319)
T PF04840_consen  177 GLSLNDTIRKLIEMGQEKQAEKLKKEF---KV-PDKRFWWLKIKALAENKDWDELEKFAKS----K--KSPIGYEPFVEA  246 (319)
T ss_pred             cCCHHHHHHHHHHCCCHHHHHHHHHHc---CC-cHHHHHHHHHHHHHhcCCHHHHHHHHhC----C--CCCCChHHHHHH
Confidence            345667788888899999999887765   33 8999999999999999999988876543    1  234779999999


Q ss_pred             HHHcCCHHHHHHHHHH
Q 011102          450 FMASGRLAKCRDVCKE  465 (493)
Q Consensus       450 ~~~~g~~~~A~~l~~~  465 (493)
                      |.+.|+..+|..++..
T Consensus       247 ~~~~~~~~eA~~yI~k  262 (319)
T PF04840_consen  247 CLKYGNKKEASKYIPK  262 (319)
T ss_pred             HHHCCCHHHHHHHHHh
Confidence            9999999999998887

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

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.10  E-value=1.2  Score=41.33  Aligned_cols=185  Identities=11%  Similarity=0.105  Sum_probs=114.3

Q ss_pred             cCCHHHHHHHHHHHHh---CC-CCCCHHH-HHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH-HHHHcC
Q 011102          276 GGNLKLAWKLLMVAKD---GG-RMLDPSI-YAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK-VGIRLQ  349 (493)
Q Consensus       276 ~g~~~~A~~l~~~m~~---~g-~~pd~~t-~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~-~~~~~g  349 (493)
                      ..+.++..+++.+|..   +| ..++..+ |.-++-+.... |+.+.|..+++.+..+  + |...-.-.|=. -+-..|
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~-~~~~lAq~C~~~L~~~--f-p~S~RV~~lkam~lEa~~  100 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDT-GRDDLAQKCINQLRDR--F-PGSKRVGKLKAMLLEATG  100 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHh-cchHHHHHHHHHHHHh--C-CCChhHHHHHHHHHHHhh
Confidence            3556777777766653   33 4455543 44455555566 7778888888887765  3 33222111111 123457


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Q 011102          350 KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFS  429 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~  429 (493)
                      ++++|.++++.+.+.. +-|.++|--=+...-..|+--+|++-+.+-.+ .+.-|...|.-+-..|...|++++|.-.++
T Consensus       101 ~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~-~F~~D~EAW~eLaeiY~~~~~f~kA~fClE  178 (289)
T KOG3060|consen  101 NYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLD-KFMNDQEAWHELAEIYLSEGDFEKAAFCLE  178 (289)
T ss_pred             chhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHH-HhcCcHHHHHHHHHHHHhHhHHHHHHHHHH
Confidence            7888888888887664 44666666555556666666677777666554 355678888888888888888888888888


Q ss_pred             HHHHCCCCCC-HHHHHHHHHHHHHcC---CHHHHHHHHHHHHH
Q 011102          430 KLKEAGFCPT-YDIYRDMIRIFMASG---RLAKCRDVCKEAEM  468 (493)
Q Consensus       430 ~m~~~g~~p~-~~ty~~li~~~~~~g---~~~~A~~l~~~m~~  468 (493)
                      +|.-..  |. ...+..+-+.+--.|   +.+-|.++|....+
T Consensus       179 E~ll~~--P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alk  219 (289)
T KOG3060|consen  179 ELLLIQ--PFNPLYFQRLAEVLYTQGGAENLELARKYYERALK  219 (289)
T ss_pred             HHHHcC--CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            887432  33 333344444433332   45667777777665

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.10  E-value=0.026  Score=41.09  Aligned_cols=62  Identities=11%  Similarity=0.116  Sum_probs=32.9

Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVEL  481 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~L  481 (493)
                      +.|++++|.++|+.+....-. |...+-.+..+|.+.|++++|.++++++..  ..||...|..+
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~-~~~~~~~la~~~~~~g~~~~A~~~l~~~~~--~~~~~~~~~~l   64 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPD-NPEARLLLAQCYLKQGQYDEAEELLERLLK--QDPDNPEYQQL   64 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTT-SHHHHHHHHHHHHHTT-HHHHHHHHHCCHG--GGTTHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--HCcCHHHHHHH
Confidence            456666666666665543221 445555566666666666666666666554  24444444433

...

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=96.08  E-value=0.79  Score=49.05  Aligned_cols=212  Identities=12%  Similarity=0.122  Sum_probs=124.0

Q ss_pred             HhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHH-hhccCcHHHHHHHHHHHHhcCCHHHHHHH
Q 011102          207 GHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLEN-FVSLASKGVLEATAKGFVKGGNLKLAWKL  285 (493)
Q Consensus       207 ~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~-~~~~~~~~~~~~li~~~~~~g~~~~A~~l  285 (493)
                      .+.|..++|+.+|.+-++.          ..|=+.|-..|.|+.+-.+.. -++..-..||-.-...+-..++.+.|++.
T Consensus       811 ieLgMlEeA~~lYr~ckR~----------DLlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~Aley  880 (1416)
T KOG3617|consen  811 IELGMLEEALILYRQCKRY----------DLLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEY  880 (1416)
T ss_pred             HHHhhHHHHHHHHHHHHHH----------HHHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHH
Confidence            4567788888888877754          222233444555444333321 12222334665556666666777777777


Q ss_pred             HHHHHhCC-------------------CCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHH
Q 011102          286 LMVAKDGG-------------------RMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGI  346 (493)
Q Consensus       286 ~~~m~~~g-------------------~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~  346 (493)
                      |++-..+.                   .+.|...|... ..|....|+.+.|+.++...+.          |-+++...|
T Consensus       881 yEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WW-gqYlES~GemdaAl~~Y~~A~D----------~fs~VrI~C  949 (1416)
T KOG3617|consen  881 YEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWW-GQYLESVGEMDAALSFYSSAKD----------YFSMVRIKC  949 (1416)
T ss_pred             HHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHH-HHHHhcccchHHHHHHHHHhhh----------hhhheeeEe
Confidence            76432110                   11222222222 2333333777777777766543          456777788


Q ss_pred             HcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC-------
Q 011102          347 RLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN-------  419 (493)
Q Consensus       347 ~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g-------  419 (493)
                      -.|++++|-++-++      .-|...+--|-+.|-..|++.+|..+|.+.+         +|...|+.|-.++       
T Consensus       950 ~qGk~~kAa~iA~e------sgd~AAcYhlaR~YEn~g~v~~Av~FfTrAq---------afsnAIRlcKEnd~~d~L~n 1014 (1416)
T KOG3617|consen  950 IQGKTDKAARIAEE------SGDKAACYHLARMYENDGDVVKAVKFFTRAQ---------AFSNAIRLCKENDMKDRLAN 1014 (1416)
T ss_pred             eccCchHHHHHHHh------cccHHHHHHHHHHhhhhHHHHHHHHHHHHHH---------HHHHHHHHHHhcCHHHHHHH
Confidence            88999999888775      4477778888899999999999999998754         3444444433222       


Q ss_pred             --------CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          420 --------DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       420 --------~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                              +.-.|-++|++.   |..     +.--+..|-++|.+.+|+++
T Consensus      1015 lal~s~~~d~v~aArYyEe~---g~~-----~~~AVmLYHkAGm~~kALel 1057 (1416)
T KOG3617|consen 1015 LALMSGGSDLVSAARYYEEL---GGY-----AHKAVMLYHKAGMIGKALEL 1057 (1416)
T ss_pred             HHhhcCchhHHHHHHHHHHc---chh-----hhHHHHHHHhhcchHHHHHH
Confidence                    333444555443   211     23344557788888887765

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

Probab=96.00  E-value=2  Score=43.26  Aligned_cols=81  Identities=14%  Similarity=-0.014  Sum_probs=57.2

Q ss_pred             HHHHhhccCCCCHHHHHHHHhhhccc----C-cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc
Q 011102          171 ARDIKGLDSHKDVAEVLDKCGRFLRK----G-SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARH  245 (493)
Q Consensus       171 ~~~l~~~~~~~~~~~a~~~~~~m~~~----~-~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~  245 (493)
                      .+....--++..+..|..+|++....    + .|---+..=-..|++..|.++|+.-.   ...||...|.+.|+.=.+-
T Consensus       111 lkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqiferW~---~w~P~eqaW~sfI~fElRy  187 (677)
T KOG1915|consen  111 LKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIFERWM---EWEPDEQAWLSFIKFELRY  187 (677)
T ss_pred             HHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHHHHHH---cCCCcHHHHHHHHHHHHHh
Confidence            33445556677888888888854332    2 33333444445688999999997665   4589999999999998888


Q ss_pred             CCCchhhhH
Q 011102          246 HELKVPFKL  254 (493)
Q Consensus       246 g~~~~~~~l  254 (493)
                      +.++.+..+
T Consensus       188 keieraR~I  196 (677)
T KOG1915|consen  188 KEIERARSI  196 (677)
T ss_pred             hHHHHHHHH
Confidence            887766665

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=95.98  E-value=0.19  Score=44.17  Aligned_cols=113  Identities=13%  Similarity=0.058  Sum_probs=80.1

Q ss_pred             HHHHHHHHH-HHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHcCCHHHHHHHHH
Q 011102          353 VVESLFHWF-THSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF--DLPAYRVVIKLFVALNDISRAIRYFS  429 (493)
Q Consensus       353 ~A~~l~~~m-~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p--d~~ty~~li~~~~~~g~~~~A~~~~~  429 (493)
                      .+...+..+ ...+..--...|..+...+...|++++|+..|++.......+  ...+|..+-..+.+.|+.++|...++
T Consensus        17 ~~~~~l~~~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~   96 (168)
T CHL00033         17 IVADILLRILPTTSGEKEAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYF   96 (168)
T ss_pred             cchhhhhHhccCCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            334444444 233333345677888888889999999999999987653222  23578888889999999999999999


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHH-------HcCCHHHHHHHHHHH
Q 011102          430 KLKEAGFCPTYDIYRDMIRIFM-------ASGRLAKCRDVCKEA  466 (493)
Q Consensus       430 ~m~~~g~~p~~~ty~~li~~~~-------~~g~~~~A~~l~~~m  466 (493)
                      ...... +....++..+...+.       ..|++++|...+++-
T Consensus        97 ~Al~~~-~~~~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033         97 QALERN-PFLPQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHHhC-cCcHHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            887542 223456666666776       788888776666654

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=95.97  E-value=1.1  Score=43.04  Aligned_cols=26  Identities=19%  Similarity=0.093  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAK  290 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~  290 (493)
                      .|.-.-+.|-..|++++|.+.|.+..
T Consensus        37 ~y~~Aa~~fk~~~~~~~A~~ay~kAa   62 (282)
T PF14938_consen   37 LYEKAANCFKLAKDWEKAAEAYEKAA   62 (282)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccchhHHHHHHHH
Confidence            35556666666677777776666553

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=95.95  E-value=3.2  Score=45.09  Aligned_cols=216  Identities=11%  Similarity=0.034  Sum_probs=130.0

Q ss_pred             CCCHHHHHHHHhhhcccC---cHHHHHHHH--HhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhH
Q 011102          180 HKDVAEVLDKCGRFLRKG---SLSFTVREL--GHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKL  254 (493)
Q Consensus       180 ~~~~~~a~~~~~~m~~~~---~~~~li~~~--~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l  254 (493)
                      .+++..|+...++...+.   .|..++.++  .+.|+.++|..+++..... +.. |..|...+...|-+.++.+  +++
T Consensus        22 ~~qfkkal~~~~kllkk~Pn~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~-~~~-D~~tLq~l~~~y~d~~~~d--~~~   97 (932)
T KOG2053|consen   22 SSQFKKALAKLGKLLKKHPNALYAKVLKALSLFRLGKGDEALKLLEALYGL-KGT-DDLTLQFLQNVYRDLGKLD--EAV   97 (932)
T ss_pred             hHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHhcCchhHHHHHhhhccC-CCC-chHHHHHHHHHHHHHhhhh--HHH
Confidence            466777777777666553   677777765  5789999999998887654 333 8889999999999999854  444


Q ss_pred             HHhhc----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCC---------HHHHHHH
Q 011102          255 ENFVS----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDK---------YMLVMTL  321 (493)
Q Consensus       255 ~~~~~----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~---------~~~a~~l  321 (493)
                      +.|..    -|+......+..+|.+.+++.+-.++=-+|.+ ...-....|=++|+-+.+.-..         ..-|...
T Consensus        98 ~~Ye~~~~~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK-~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m  176 (932)
T KOG2053|consen   98 HLYERANQKYPSEELLYHLFMAYVREKSYKKQQKAALQLYK-NFPKRAYYFWSVISLILQSIFSENELLDPILLALAEKM  176 (932)
T ss_pred             HHHHHHHhhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCcccchHHHHHHHHHHhccCCcccccchhHHHHHHH
Confidence            44443    45666667788888888887664444434433 1223444444555544433111         1244555


Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH-HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          322 LDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLF-HWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       322 ~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~-~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      ++.+.+.+|-.-+..-.-.-...+-..|++++|++++ ....+.-..-+...-|--+.-+...++|.+..++-.++...|
T Consensus       177 ~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~  256 (932)
T KOG2053|consen  177 VQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKG  256 (932)
T ss_pred             HHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhC
Confidence            5555555332222222222234445566677777777 334433333444445566666666777777766666666554

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=95.94  E-value=0.83  Score=46.96  Aligned_cols=240  Identities=12%  Similarity=0.032  Sum_probs=154.2

Q ss_pred             ccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHHcCCCch
Q 011102          177 LDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDD-RLLASTVEVLARHHELKV  250 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~-~t~~~li~~~~~~g~~~~  250 (493)
                      +-+.|++.+|.-.|+....++     .|--|=..-+.+++-..|+..+++..+   +.|+. ...-.|.-.|...|.  .
T Consensus       295 lm~nG~L~~A~LafEAAVkqdP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~---LdP~NleaLmaLAVSytNeg~--q  369 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQDPQHAEAWQKLGITQAENENEQNAISALRRCLE---LDPTNLEALMALAVSYTNEGL--Q  369 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhChHHHHHHHHhhhHhhhccchHHHHHHHHHHHh---cCCccHHHHHHHHHHHhhhhh--H
Confidence            345688999988888665554     676666667777777788888888764   45543 345555555555554  3


Q ss_pred             hhhHHHhh---ccCcHHHHHHHH---------HHHHhcCCHHHHHHHHHHH-HhCCCCCCHHHHHHHHHHHhcCCCCHHH
Q 011102          251 PFKLENFV---SLASKGVLEATA---------KGFVKGGNLKLAWKLLMVA-KDGGRMLDPSIYAKLILELGKNPDKYML  317 (493)
Q Consensus       251 ~~~l~~~~---~~~~~~~~~~li---------~~~~~~g~~~~A~~l~~~m-~~~g~~pd~~t~~~li~~~~~~~~~~~~  317 (493)
                      ..++..+.   ...-...|...-         ..+.....+....++|-++ .+.+.++|+.....|=--|.-. |.+++
T Consensus       370 ~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls-~efdr  448 (579)
T KOG1125|consen  370 NQALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLS-GEFDR  448 (579)
T ss_pred             HHHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcc-hHHHH
Confidence            33433222   111111110000         1223333455566666555 4566667888887776677777 99999


Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          318 VMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       318 a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      |...|+.....  -.-|...||-|-..++...+.++|..-|++-.+.  +|+ +.+..-|--+|...|.+++|.+.|=+.
T Consensus       449 aiDcf~~AL~v--~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqL--qP~yVR~RyNlgIS~mNlG~ykEA~~hlL~A  524 (579)
T KOG1125|consen  449 AVDCFEAALQV--KPNDYLLWNRLGATLANGNRSEEAISAYNRALQL--QPGYVRVRYNLGISCMNLGAYKEAVKHLLEA  524 (579)
T ss_pred             HHHHHHHHHhc--CCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhc--CCCeeeeehhhhhhhhhhhhHHHHHHHHHHH
Confidence            99999998764  2335678999999999999999999999998765  565 334444555688999999999887664


Q ss_pred             ---HHC------CCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          397 ---EAS------NCLFDLPAYRVVIKLFVALNDISRAIR  426 (493)
Q Consensus       397 ---~~~------gi~pd~~ty~~li~~~~~~g~~~~A~~  426 (493)
                         .++      +..++...|.+|=.++.-.++.|.+.+
T Consensus       525 L~mq~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~  563 (579)
T KOG1125|consen  525 LSMQRKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQE  563 (579)
T ss_pred             HHhhhcccccccCCcchHHHHHHHHHHHHHcCCchHHHH
Confidence               333      122344567766666666666554433

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=95.88  E-value=0.53  Score=49.37  Aligned_cols=63  Identities=11%  Similarity=0.048  Sum_probs=41.9

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          404 DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +...|.++--.....|++++|...+++..+..  |+...|..+-..+...|+.++|.+.+++...
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~  481 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFN  481 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            33555555444445677777777777776544  5667777777777777777777777766654

>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=95.80  E-value=0.05  Score=39.56  Aligned_cols=49  Identities=10%  Similarity=0.007  Sum_probs=19.5

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          348 LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       348 ~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      .|++++|.++|++..+.. +-+...+-.+...|.+.|++++|.++++.+.
T Consensus         4 ~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~   52 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLL   52 (68)
T ss_dssp             TTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCH
T ss_pred             ccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            344444444444443221 1133333344444444444444444444433

...

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=95.78  E-value=0.25  Score=49.27  Aligned_cols=101  Identities=10%  Similarity=-0.024  Sum_probs=75.4

Q ss_pred             HHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Q 011102          306 LELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK  385 (493)
Q Consensus       306 ~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~  385 (493)
                      ..+... |++++|+++|.+..+.  -.-+...|..+-.+|.+.|++++|+..++...+.. ..+...|..+-.+|...|+
T Consensus        10 ~~a~~~-~~~~~Ai~~~~~Al~~--~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088         10 KEAFVD-DDFALAVDLYTQAIDL--DPNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCC
Confidence            344556 8899999999988765  22356677778888889999999999998887642 2356778888888899999


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          386 CREALTVVWNMEASNCLFDLPAYRVVI  412 (493)
Q Consensus       386 ~~~A~~l~~~M~~~gi~pd~~ty~~li  412 (493)
                      +++|...|++..+.  .|+.......+
T Consensus        86 ~~eA~~~~~~al~l--~P~~~~~~~~l  110 (356)
T PLN03088         86 YQTAKAALEKGASL--APGDSRFTKLI  110 (356)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            99999999887764  45555544443

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

Probab=95.77  E-value=3.1  Score=43.56  Aligned_cols=193  Identities=10%  Similarity=0.006  Sum_probs=117.4

Q ss_pred             CCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHHcCCCchh-
Q 011102          179 SHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPD-DRLLASTVEVLARHHELKVP-  251 (493)
Q Consensus       179 ~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd-~~t~~~li~~~~~~g~~~~~-  251 (493)
                      ..|+-++|.+....-.+.+     .|.++=-.+-...++++|+..|......   .|| ...|.-+--.-...++++.. 
T Consensus        53 ~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~---~~dN~qilrDlslLQ~QmRd~~~~~  129 (700)
T KOG1156|consen   53 CLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKI---EKDNLQILRDLSLLQIQMRDYEGYL  129 (700)
T ss_pred             cccchHHHHHHHHHHhccCcccchhHHHHHHHHhhhhhHHHHHHHHHHHHhc---CCCcHHHHHHHHHHHHHHHhhhhHH
Confidence            3477777777766544433     4554444445567899999999888743   344 33443332222333333211 


Q ss_pred             hhH-HHhhc-cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHH------HhcCCCCHHHHHHHH
Q 011102          252 FKL-ENFVS-LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGG-RMLDPSIYAKLILE------LGKNPDKYMLVMTLL  322 (493)
Q Consensus       252 ~~l-~~~~~-~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~pd~~t~~~li~~------~~~~~~~~~~a~~l~  322 (493)
                      ... ..+.. ......|..+.-++.-.|+...|..++++..+.- -.|+...|.....-      ..+. |..++|++-+
T Consensus       130 ~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~-g~~q~ale~L  208 (700)
T KOG1156|consen  130 ETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEA-GSLQKALEHL  208 (700)
T ss_pred             HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHc-ccHHHHHHHH
Confidence            111 11222 2245578899999999999999999999998765 35777776644332      3455 6677777766


Q ss_pred             HHHhhcCCCCCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011102          323 DELGQRDDLNLSQQD-CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSR  380 (493)
Q Consensus       323 ~~m~~~~g~~p~~~~-~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~  380 (493)
                      ..-+..  + .|... --+--+-+.+.+++++|..+|..+...  .||.+-|+-.+..+
T Consensus       209 ~~~e~~--i-~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Yy~~l~~~  262 (700)
T KOG1156|consen  209 LDNEKQ--I-VDKLAFEETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDYYEGLEKA  262 (700)
T ss_pred             HhhhhH--H-HHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHHHHHHHHH
Confidence            655432  2 23222 234456677888888888888888765  67776666554433

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=95.69  E-value=2.5  Score=41.92  Aligned_cols=134  Identities=13%  Similarity=0.079  Sum_probs=77.2

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHH-HHHH-HHcCC
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVV-IKLF-VALND  420 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~l-i~~~-~~~g~  420 (493)
                      ..+...|++++|.-.|+.-+... +-+..+|.-|+.+|...|++.+|.-+-+..... +.-+..+.+.+ -..| -...-
T Consensus       342 ~lL~~~~R~~~A~IaFR~Aq~La-p~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~  419 (564)
T KOG1174|consen  342 RLLIALERHTQAVIAFRTAQMLA-PYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRM  419 (564)
T ss_pred             HHHHhccchHHHHHHHHHHHhcc-hhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchh
Confidence            45556677777777777654321 235677788888888888777777665553221 11122332222 0111 11122


Q ss_pred             HHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHH
Q 011102          421 ISRAIRYFSKLKEAGFCPTY-DIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELL  482 (493)
Q Consensus       421 ~~~A~~~~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll  482 (493)
                      -++|.++++.-..  +.|+- ..-+.+...+...|+.+++..+++.-..  ..||...-+.|=
T Consensus       420 rEKAKkf~ek~L~--~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~--~~~D~~LH~~Lg  478 (564)
T KOG1174|consen  420 REKAKKFAEKSLK--INPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLI--IFPDVNLHNHLG  478 (564)
T ss_pred             HHHHHHHHHhhhc--cCCccHHHHHHHHHHHHhhCccchHHHHHHHHHh--hccccHHHHHHH
Confidence            3566666665442  33443 3345666778889999999999988765  466666555443

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=95.66  E-value=0.091  Score=44.96  Aligned_cols=72  Identities=19%  Similarity=0.245  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HCCCccCHHHHH
Q 011102          407 AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE-----MAGFKLDKQTVV  479 (493)
Q Consensus       407 ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~-----~~g~~pd~~t~~  479 (493)
                      +...++..+...|++++|.++.+.+....- -|...|..+|.+|...|+..+|.++|+.+.     +.|+.|+..|-.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP-~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDP-YDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHST-T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            345566666777777777777777775432 366677777888888888877777777764     347777776643

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.63  E-value=1.8  Score=41.91  Aligned_cols=127  Identities=11%  Similarity=0.154  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH--cC----CHHHHHHHHHHHHHcCC---CCCHHHHHHHHHHHHcCCC
Q 011102          315 YMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR--LQ----KFGVVESLFHWFTHSGR---DPTVVMYTTLIHSRLSEKK  385 (493)
Q Consensus       315 ~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~--~g----~~~~A~~l~~~m~~~g~---~p~~~ty~~li~~~~~~g~  385 (493)
                      +.+...+++.|.+. |++-+..+|-+..-....  ..    ...+|..+|+.|++...   .++-+.+.+|+..  ...+
T Consensus        78 ~~~~~~~y~~L~~~-gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~  154 (297)
T PF13170_consen   78 FKEVLDIYEKLKEA-GFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSED  154 (297)
T ss_pred             HHHHHHHHHHHHHh-ccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--cccc
Confidence            34455555566655 565555555442222222  11    14456666666665421   2344445555443  2222


Q ss_pred             ----HHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHHcC-C--HHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          386 ----CREALTVVWNMEASNCLFDLP-AYRVVIKLFVALN-D--ISRAIRYFSKLKEAGFCPTYDIYR  444 (493)
Q Consensus       386 ----~~~A~~l~~~M~~~gi~pd~~-ty~~li~~~~~~g-~--~~~A~~~~~~m~~~g~~p~~~ty~  444 (493)
                          .++++..++.+.+.|+..+-. -+.+-|-+++... .  +..+.++++.+.+.|+++....|.
T Consensus       155 ~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp  221 (297)
T PF13170_consen  155 VEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYP  221 (297)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCcccccccc
Confidence                244555566665555543321 2222222222211 1  335556666666666666655554

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=95.62  E-value=0.9  Score=46.42  Aligned_cols=129  Identities=12%  Similarity=0.025  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      +|...|+.-.+..-++.|..+|.+..+.+..+ ++..++++|.-+|..  +.+-|.++|+-=.+.  +.-+..--...++
T Consensus       368 v~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~csk--D~~~AfrIFeLGLkk--f~d~p~yv~~Yld  443 (656)
T KOG1914|consen  368 VYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYCSK--DKETAFRIFELGLKK--FGDSPEYVLKYLD  443 (656)
T ss_pred             ehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHhcC--ChhHHHHHHHHHHHh--cCCChHHHHHHHH
Confidence            34555555555555555666666665555555 555555555555543  445555555543332  1122222344455


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPT--VVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      -+...++-..|..+|+.....+..||  ...|..+|.-=..-|++..+.++-+++.
T Consensus       444 fL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~  499 (656)
T KOG1914|consen  444 FLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRF  499 (656)
T ss_pred             HHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            55555555555566655555544433  2455556555555566555555555543

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.60  E-value=0.67  Score=38.19  Aligned_cols=86  Identities=13%  Similarity=0.023  Sum_probs=42.3

Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC---HHH-HHHHHHHHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPT--VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD---LPA-YRVVIKLFVA  417 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd---~~t-y~~li~~~~~  417 (493)
                      ++-..|+.++|..+|++-.+.|....  ...+-.+-++|...|+.++|+.+|++.....  |+   ... ...+-.++..
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~--p~~~~~~~l~~f~Al~L~~   87 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF--PDDELNAALRVFLALALYN   87 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHH
Confidence            34445666666666666555554443  2334445555556666666666666554321  22   111 1111224455


Q ss_pred             cCCHHHHHHHHHHH
Q 011102          418 LNDISRAIRYFSKL  431 (493)
Q Consensus       418 ~g~~~~A~~~~~~m  431 (493)
                      .|+.++|...+-..
T Consensus        88 ~gr~~eAl~~~l~~  101 (120)
T PF12688_consen   88 LGRPKEALEWLLEA  101 (120)
T ss_pred             CCCHHHHHHHHHHH
Confidence            56666666555443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=95.40  E-value=0.79  Score=37.76  Aligned_cols=55  Identities=20%  Similarity=0.089  Sum_probs=28.8

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCCCCHH--HHHHHHHHHhcCCCCHHHHHHHHHHHhh
Q 011102          272 GFVKGGNLKLAWKLLMVAKDGGRMLDPS--IYAKLILELGKNPDKYMLVMTLLDELGQ  327 (493)
Q Consensus       272 ~~~~~g~~~~A~~l~~~m~~~g~~pd~~--t~~~li~~~~~~~~~~~~a~~l~~~m~~  327 (493)
                      ++-..|+.++|..+|++....|...+..  .+-.+-..+-.. |++++|..+|++...
T Consensus        10 a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~L-G~~deA~~~L~~~~~   66 (120)
T PF12688_consen   10 AHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNL-GRYDEALALLEEALE   66 (120)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHH
Confidence            3445566666666666666665443321  222333344444 666666666665544

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=95.14  E-value=0.15  Score=43.59  Aligned_cols=68  Identities=24%  Similarity=0.385  Sum_probs=30.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HCCCCCCHHH
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-----EAGFCPTYDI  442 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-----~~g~~p~~~t  442 (493)
                      ..++..+...|++++|.++...+..... -|...|..+|.+|...|+..+|.++|+.+.     +.|+.|+..|
T Consensus        66 ~~l~~~~~~~~~~~~a~~~~~~~l~~dP-~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   66 ERLAEALLEAGDYEEALRLLQRALALDP-YDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHHHHHST-T-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHhccCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            4444444555555555555555444321 244455555555555555555555555443     3455555443

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.11  E-value=2.8  Score=38.92  Aligned_cols=156  Identities=11%  Similarity=0.103  Sum_probs=116.7

Q ss_pred             CCHHHHHHHHHHHhhcC--C-CCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHcCC
Q 011102          313 DKYMLVMTLLDELGQRD--D-LNLSQQ-DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTV----VMYTTLIHSRLSEK  384 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~--g-~~p~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~ty~~li~~~~~~g  384 (493)
                      .+.++.++++.++....  | ..++.. .|-.++-+...+|+.+.|..+++.+...-  |..    ..+..++   -..|
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~l---Ea~~  100 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLL---EATG  100 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHH---HHhh
Confidence            46788888888876531  3 445543 45666777788999999999999987653  332    2233333   3468


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCK  464 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~  464 (493)
                      ++++|+++++...+.. +-|.++|--=|...-..|+--+|.+-+.+..+. +.-|...|.-+-+.|...|++++|.-.++
T Consensus       101 ~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClE  178 (289)
T KOG3060|consen  101 NYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLE  178 (289)
T ss_pred             chhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHH
Confidence            8999999999998876 456778877777777778888888888887753 55699999999999999999999999999


Q ss_pred             HHHHCCCccCHHH
Q 011102          465 EAEMAGFKLDKQT  477 (493)
Q Consensus       465 ~m~~~g~~pd~~t  477 (493)
                      +|.-  +.|-...
T Consensus       179 E~ll--~~P~n~l  189 (289)
T KOG3060|consen  179 ELLL--IQPFNPL  189 (289)
T ss_pred             HHHH--cCCCcHH
Confidence            9975  4454333

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=95.09  E-value=2.6  Score=44.03  Aligned_cols=51  Identities=16%  Similarity=0.139  Sum_probs=26.7

Q ss_pred             cHHHHHHHHHhCCChH--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhh
Q 011102          198 SLSFTVRELGHMNLPE--RALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPF  252 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~--~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~  252 (493)
                      .+++.=.+|.+-.+..  +-+.=+++|+.+ |-.||.....   ..|+-.|++..+.
T Consensus       600 ~f~~ARkAY~rVRdl~~L~li~EL~~~k~r-ge~P~~iLlA---~~~Ay~gKF~EAA  652 (1081)
T KOG1538|consen  600 DFETARKAYIRVRDLRYLELISELEERKKR-GETPNDLLLA---DVFAYQGKFHEAA  652 (1081)
T ss_pred             hhHHHHHHHHHHhccHHHHHHHHHHHHHhc-CCCchHHHHH---HHHHhhhhHHHHH
Confidence            4555556666655433  333334566665 7778765433   3344455544433

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.04  E-value=3  Score=38.92  Aligned_cols=145  Identities=9%  Similarity=0.052  Sum_probs=97.0

Q ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH---
Q 011102          302 AKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIH---  378 (493)
Q Consensus       302 ~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~---  378 (493)
                      +.++..+.-. +.+.-...++++..+. .-..+++....|...-.+.|+.+.|...|++..+..-+.|..+.+.++.   
T Consensus       181 y~~~~~llG~-kEy~iS~d~~~~vi~~-~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  181 YSMANCLLGM-KEYVLSVDAYHSVIKY-YPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHhcc-hhhhhhHHHHHHHHHh-CCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            3455555555 6777777888888776 5566778888888888889999999999998876655666666666654   


Q ss_pred             --HHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          379 --SRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFM  451 (493)
Q Consensus       379 --~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~  451 (493)
                        .|.-.+++.+|...+.+.....- -|.+.-|.=--+..-.|+..+|.+.++.|+..  .|...+-++++--++
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~-~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~es~~~nL~  330 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDP-RNAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHESVLFNLT  330 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCC-CchhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhhhHHHHHH
Confidence              34445678888888877665421 23333343333333457889999999888754  366666565554443

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.04  E-value=1.4  Score=37.20  Aligned_cols=84  Identities=11%  Similarity=-0.019  Sum_probs=35.8

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC
Q 011102          340 AIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN  419 (493)
Q Consensus       340 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g  419 (493)
                      .+|..+.+.+........++.+...+. .+...+|.+|..|++.+ ..+.++.+..      ..+......++..|.+.+
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~~   83 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKAK   83 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHcC
Confidence            344444444444445555544444331 34444455555554432 2222233221      112222333555555555


Q ss_pred             CHHHHHHHHHHH
Q 011102          420 DISRAIRYFSKL  431 (493)
Q Consensus       420 ~~~~A~~~~~~m  431 (493)
                      .++++..++..+
T Consensus        84 l~~~~~~l~~k~   95 (140)
T smart00299       84 LYEEAVELYKKD   95 (140)
T ss_pred             cHHHHHHHHHhh
Confidence            555555555444

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=95.03  E-value=3.1  Score=39.03  Aligned_cols=175  Identities=14%  Similarity=0.044  Sum_probs=108.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HH---HHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Q 011102          270 AKGFVKGGNLKLAWKLLMVAKDGGRMLDPS-IY---AKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVG  345 (493)
Q Consensus       270 i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~-t~---~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~  345 (493)
                      ...+.+.|++++|.+.|+++...-  |+.. .-   -.+..++.+. +++++|...+++..+...-.|+ ..|...+.+.
T Consensus        39 A~~~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~-~~y~~A~~~~e~fi~~~P~~~~-~~~a~Y~~g~  114 (243)
T PRK10866         39 AQQKLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKN-ADLPLAQAAIDRFIRLNPTHPN-IDYVLYMRGL  114 (243)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHhCcCCCc-hHHHHHHHHH
Confidence            334456789999999999988754  3332 22   1345667788 8999999999888766323333 2444444443


Q ss_pred             HH--cC---------------CH---HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH
Q 011102          346 IR--LQ---------------KF---GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL  405 (493)
Q Consensus       346 ~~--~g---------------~~---~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~  405 (493)
                      +.  .+               +.   .+|.+.               +..+|+-|=...-..+|...+..++..   --.
T Consensus       115 ~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~---------------~~~li~~yP~S~ya~~A~~rl~~l~~~---la~  176 (243)
T PRK10866        115 TNMALDDSALQGFFGVDRSDRDPQHARAAFRD---------------FSKLVRGYPNSQYTTDATKRLVFLKDR---LAK  176 (243)
T ss_pred             hhhhcchhhhhhccCCCccccCHHHHHHHHHH---------------HHHHHHHCcCChhHHHHHHHHHHHHHH---HHH
Confidence            31  10               11   122233               334444444445566666655555432   111


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH--CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLKE--AGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~~--~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      .- -.+..-|.+.|.+..|..-|+.+.+  .+........-.++.+|...|..++|.+....+.
T Consensus       177 ~e-~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        177 YE-LSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HH-HHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            11 1455668899999999999999884  2333445666788899999999999988776654

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.86  E-value=1.3  Score=36.80  Aligned_cols=139  Identities=12%  Similarity=0.094  Sum_probs=78.8

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          275 KGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVV  354 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A  354 (493)
                      -.|.+++..++..+...+   -+..-||.+|.-.... -+-+...+.++.+.+-.++    .          .+|++...
T Consensus        14 ldG~V~qGveii~k~v~S---sni~E~NWvICNiiDa-a~C~yvv~~LdsIGkiFDi----s----------~C~NlKrV   75 (161)
T PF09205_consen   14 LDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDA-ADCDYVVETLDSIGKIFDI----S----------KCGNLKRV   75 (161)
T ss_dssp             HTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH---HHHHHHHHHHHGGGS-G----G----------G-S-THHH
T ss_pred             HhchHHHHHHHHHHHcCc---CCccccceeeeecchh-hchhHHHHHHHHHhhhcCc----h----------hhcchHHH
Confidence            357788888888887765   3666777777766666 5666677777777554222    1          22333333


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          355 ESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       355 ~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      ...+-.+-     .+..-...-++.+...|+-+.-.++..++.+ +-.++....-.+-.||.+.|+..++.+++.+.-+.
T Consensus        76 i~C~~~~n-----~~se~vD~ALd~lv~~~kkDqLdki~~~l~k-n~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACek  149 (161)
T PF09205_consen   76 IECYAKRN-----KLSEYVDLALDILVKQGKKDQLDKIYNELKK-NEEINPEFLVKIANAYKKLGNTREANELLKEACEK  149 (161)
T ss_dssp             HHHHHHTT--------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHT
T ss_pred             HHHHHHhc-----chHHHHHHHHHHHHHhccHHHHHHHHHHHhh-ccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHh
Confidence            33322221     1223345566677777777777777777654 33466666677777888888888888888777777


Q ss_pred             CCC
Q 011102          435 GFC  437 (493)
Q Consensus       435 g~~  437 (493)
                      |++
T Consensus       150 G~k  152 (161)
T PF09205_consen  150 GLK  152 (161)
T ss_dssp             T-H
T ss_pred             chH
Confidence            764

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=94.85  E-value=2.7  Score=44.15  Aligned_cols=146  Identities=12%  Similarity=0.026  Sum_probs=95.2

Q ss_pred             CCCCCCHHHHHHHHHHHhcC----CCCHHHHHHHHHHHhhcCCCCCCH-HHHHHHHHHHHHc--------CCHHHHHHHH
Q 011102          292 GGRMLDPSIYAKLILELGKN----PDKYMLVMTLLDELGQRDDLNLSQ-QDCTAIMKVGIRL--------QKFGVVESLF  358 (493)
Q Consensus       292 ~g~~pd~~t~~~li~~~~~~----~~~~~~a~~l~~~m~~~~g~~p~~-~~~~~li~~~~~~--------g~~~~A~~l~  358 (493)
                      .+...|...|...+.+....    .+....|..+|++..+.   .|+- ..|..+..+|...        .++..+.+..
T Consensus       331 ~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l---dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~  407 (517)
T PRK10153        331 QGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS---EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTEL  407 (517)
T ss_pred             ccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHH
Confidence            44567888888888875442    13467888898888764   3553 3333332323221        1223334444


Q ss_pred             HHHHHc-CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC
Q 011102          359 HWFTHS-GRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFC  437 (493)
Q Consensus       359 ~~m~~~-g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~  437 (493)
                      ...... ....+...|.++--.+...|++++|...+++..+.+  |+...|..+-..+...|+.++|.+.+++-...  .
T Consensus       408 ~~a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L--~  483 (517)
T PRK10153        408 DNIVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFNL--R  483 (517)
T ss_pred             HHhhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--C
Confidence            432222 233455777777666667799999999999988765  68888999999999999999999999887643  3


Q ss_pred             CCHHHHH
Q 011102          438 PTYDIYR  444 (493)
Q Consensus       438 p~~~ty~  444 (493)
                      |...||.
T Consensus       484 P~~pt~~  490 (517)
T PRK10153        484 PGENTLY  490 (517)
T ss_pred             CCCchHH
Confidence            5544543

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=94.83  E-value=0.16  Score=36.48  Aligned_cols=55  Identities=16%  Similarity=0.158  Sum_probs=34.4

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          413 KLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       413 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ..+.+.|++++|...|+...+..- -+...+..+-..+...|++++|..+|++..+
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQDP-DNPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCST-THHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345666777777777777665441 2555566666666677777777777776654

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=94.71  E-value=0.15  Score=36.61  Aligned_cols=53  Identities=9%  Similarity=-0.046  Sum_probs=24.4

Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      .+.+.|++++|.+.|++..+.. +-+...+..+-..+...|++++|...|++..
T Consensus         6 ~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~   58 (65)
T PF13432_consen    6 ALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERAL   58 (65)
T ss_dssp             HHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3444455555555555554332 1133444444445555555555555555443

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=94.63  E-value=5  Score=42.47  Aligned_cols=260  Identities=10%  Similarity=-0.000  Sum_probs=118.2

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhCCCCCC----CHHHHHHHHHHHHHcCCCchhhh-H-HHhhccC----cHHHHHHHHHH
Q 011102          203 VRELGHMNLPERALQTFCWAQKQPHLFP----DDRLLASTVEVLARHHELKVPFK-L-ENFVSLA----SKGVLEATAKG  272 (493)
Q Consensus       203 i~~~~~~g~~~~A~~l~~~m~~~~g~~p----d~~t~~~li~~~~~~g~~~~~~~-l-~~~~~~~----~~~~~~~li~~  272 (493)
                      |++|  -|++++|.++|-+|.++ .+..    ..--|-.+++.+-. |.-+.... + ..+..+.    +...|..-...
T Consensus       743 i~~~--~g~feeaek~yld~drr-DLAielr~klgDwfrV~qL~r~-g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~y  818 (1189)
T KOG2041|consen  743 ISAF--YGEFEEAEKLYLDADRR-DLAIELRKKLGDWFRVYQLIRN-GGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKY  818 (1189)
T ss_pred             Hhhh--hcchhHhhhhhhccchh-hhhHHHHHhhhhHHHHHHHHHc-cCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444  37888999998888765 2211    11123333333222 21111111 1 0111111    22345555566


Q ss_pred             HHhcCCHHHHHHHHHHHHhCC--------CCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGG--------RMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g--------~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      |.++|+.+.-.+.+-....-|        ++-|....-.+-.++.+. |.-++|.+.|-+-..     |     -+.++.
T Consensus       819 Y~~~~~~e~~~ecly~le~f~~LE~la~~Lpe~s~llp~~a~mf~sv-GMC~qAV~a~Lr~s~-----p-----kaAv~t  887 (1189)
T KOG2041|consen  819 YSYCGDTENQIECLYRLELFGELEVLARTLPEDSELLPVMADMFTSV-GMCDQAVEAYLRRSL-----P-----KAAVHT  887 (1189)
T ss_pred             HHhccchHhHHHHHHHHHhhhhHHHHHHhcCcccchHHHHHHHHHhh-chHHHHHHHHHhccC-----c-----HHHHHH
Confidence            666665554443333322211        222222333444555555 555555555433211     1     234455


Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHH--------------HHHHHHHcCCCHHHHHHHHHHHHH----CCCCCCHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYT--------------TLIHSRLSEKKCREALTVVWNMEA----SNCLFDLP  406 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~--------------~li~~~~~~g~~~~A~~l~~~M~~----~gi~pd~~  406 (493)
                      |...+++.+|.++-+...    -|.+.|.-              --|.-+.++|+.-+|-+++.+|.+    ++.+|-..
T Consensus       888 Cv~LnQW~~avelaq~~~----l~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae~e~~K~~p~lr~  963 (1189)
T KOG2041|consen  888 CVELNQWGEAVELAQRFQ----LPQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAEREQEKYVPYLRL  963 (1189)
T ss_pred             HHHHHHHHHHHHHHHhcc----chhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhHHHhhccCCHHHH
Confidence            555566666666555443    34333321              123445566777777777777754    23433221


Q ss_pred             H----HHHHH-HHH----------HHcCCHHHHHHHHHHHHH---CCCC------CCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          407 A----YRVVI-KLF----------VALNDISRAIRYFSKLKE---AGFC------PTYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       407 t----y~~li-~~~----------~~~g~~~~A~~~~~~m~~---~g~~------p~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                      -    ..+|+ .-+          -+.|..++|..++++-..   ..+.      ....+|-+|.+--...|.++.|++.
T Consensus       964 KklYVL~AlLvE~h~~~ik~~~~~~~~g~~~dat~lles~~l~~~~ri~~n~WrgAEAyHFmilAQrql~eg~v~~Al~T 1043 (1189)
T KOG2041|consen  964 KKLYVLGALLVENHRQTIKELRKIDKHGFLEDATDLLESGLLAEQSRILENTWRGAEAYHFMILAQRQLFEGRVKDALQT 1043 (1189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhhcCcchhhhhhhhhhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHhchHHHHHHH
Confidence            1    11211 111          134566666665544321   0011      1233344444555667888888775


Q ss_pred             HHHHHH-CCCccCHHHHHHH
Q 011102          463 CKEAEM-AGFKLDKQTVVEL  481 (493)
Q Consensus       463 ~~~m~~-~g~~pd~~t~~~L  481 (493)
                      --.+.+ ..+-|....|+.|
T Consensus      1044 al~L~DYEd~lpP~eiySll 1063 (1189)
T KOG2041|consen 1044 ALILSDYEDFLPPAEIYSLL 1063 (1189)
T ss_pred             HhhhccHhhcCCHHHHHHHH
Confidence            433332 2356666666554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=94.62  E-value=0.66  Score=44.06  Aligned_cols=96  Identities=13%  Similarity=-0.006  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC--CCCHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTV----VMYTTLIHSRLSEKKCREALTVVWNMEASNC--LFDLPAYR  409 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi--~pd~~ty~  409 (493)
                      ..|...+.-+.+.|++++|...|+.+.+.  -|+.    ..+-.+-..|...|++++|...|+.+.+.--  ......+-
T Consensus       144 ~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~  221 (263)
T PRK10803        144 TDYNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMF  221 (263)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHH
Confidence            34555555555566777777777776644  2322    3455666666666777777777666654310  00112223


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          410 VVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       410 ~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      .+...+...|+.++|..+|+.+.+
T Consensus       222 klg~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        222 KVGVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            333445566666666666666553

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=94.35  E-value=3.3  Score=41.58  Aligned_cols=146  Identities=12%  Similarity=0.055  Sum_probs=111.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHH-HHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGG-RMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDC-TAI  341 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~-~~l  341 (493)
                      .+|...|+.-.+..-++.|..+|-+..+.| +.+++..++++|.-++..  +...|..+|+-=...  + ||...| +-.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~~--d~~ta~~ifelGl~~--f-~d~~~y~~ky  472 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYATG--DRATAYNIFELGLLK--F-PDSTLYKEKY  472 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhcC--CcchHHHHHHHHHHh--C-CCchHHHHHH
Confidence            468889999888888999999999999999 778999999999988874  678889999874443  2 444444 566


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPT--VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA  417 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~  417 (493)
                      +.-+.+.++-+.|..+|+.-.++ +..+  ...|..+|+--..-|++..|..+=+.|.+.  .|-..+-....+.|+-
T Consensus       473 l~fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry~i  547 (660)
T COG5107         473 LLFLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRYAI  547 (660)
T ss_pred             HHHHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHHhh
Confidence            77888899999999999954321 1122  467899999888999999998888888763  4555555555555543

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.32  E-value=2.8  Score=35.32  Aligned_cols=124  Identities=10%  Similarity=0.106  Sum_probs=59.5

Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 011102          303 KLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS  382 (493)
Q Consensus       303 ~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~  382 (493)
                      .+|..+.+. +....+..+++.+... +. .+...+|.+|..|++... ++..+.+..      ..+......+++.|.+
T Consensus        12 ~vv~~~~~~-~~~~~l~~yLe~~~~~-~~-~~~~~~~~li~ly~~~~~-~~ll~~l~~------~~~~yd~~~~~~~c~~   81 (140)
T smart00299       12 EVVELFEKR-NLLEELIPYLESALKL-NS-ENPALQTKLIELYAKYDP-QKEIERLDN------KSNHYDIEKVGKLCEK   81 (140)
T ss_pred             HHHHHHHhC-CcHHHHHHHHHHHHcc-Cc-cchhHHHHHHHHHHHHCH-HHHHHHHHh------ccccCCHHHHHHHHHH
Confidence            445555555 5566666666665554 32 455566666666665432 233333331      1222223335555555


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          383 EKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL-NDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFM  451 (493)
Q Consensus       383 ~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~-g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~  451 (493)
                      .+.++++.-++..+..         |...+..+.+. ++.+.|.+++.+-      -+...|..++..+.
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            5556666655554422         22222222223 5566666655541      24445655555543

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=94.23  E-value=4.5  Score=39.15  Aligned_cols=138  Identities=10%  Similarity=0.067  Sum_probs=83.7

Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011102          212 PERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKD  291 (493)
Q Consensus       212 ~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  291 (493)
                      +++.+++++.|.+. |++-+.++|-+..-.......-+...                         ....|..+|+.|++
T Consensus        78 ~~~~~~~y~~L~~~-gFk~~~y~~laA~~i~~~~~~~~~~~-------------------------~~~ra~~iy~~mKk  131 (297)
T PF13170_consen   78 FKEVLDIYEKLKEA-GFKRSEYLYLAALIILEEEEKEDYDE-------------------------IIQRAKEIYKEMKK  131 (297)
T ss_pred             HHHHHHHHHHHHHh-ccCccChHHHHHHHHHHhcccccHHH-------------------------HHHHHHHHHHHHHH
Confidence            34567788888887 89888887776444443322111111                         24789999999998


Q ss_pred             CC---CCCCHHHHHHHHHHHhcCCC-CHHHHHHHHHHHhhcCCCCCCHH-HHHHHHHHHHHcCC---HHHHHHHHHHHHH
Q 011102          292 GG---RMLDPSIYAKLILELGKNPD-KYMLVMTLLDELGQRDDLNLSQQ-DCTAIMKVGIRLQK---FGVVESLFHWFTH  363 (493)
Q Consensus       292 ~g---~~pd~~t~~~li~~~~~~~~-~~~~a~~l~~~m~~~~g~~p~~~-~~~~li~~~~~~g~---~~~A~~l~~~m~~  363 (493)
                      ..   ..++...+..++..-..... -.+.+..+++.+.+. |+..+.. -+.+-|-+++....   +..+.++++.+++
T Consensus       132 ~H~fLTs~~D~~~a~lLA~~~~~~e~l~~~~E~~Y~~L~~~-~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~  210 (297)
T PF13170_consen  132 KHPFLTSPEDYPFAALLAMTSEDVEELAERMEQCYQKLADA-GFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKK  210 (297)
T ss_pred             hCccccCccchhHHHHHhcccccHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHH
Confidence            76   34667778888766222211 135667777777775 5544322 23333333332211   4577788888888


Q ss_pred             cCCCCCHHHHHHH
Q 011102          364 SGRDPTVVMYTTL  376 (493)
Q Consensus       364 ~g~~p~~~ty~~l  376 (493)
                      .|+++....|.++
T Consensus       211 ~~~kik~~~yp~l  223 (297)
T PF13170_consen  211 NGVKIKYMHYPTL  223 (297)
T ss_pred             cCCccccccccHH
Confidence            8888777776654

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.21  E-value=2.2  Score=35.46  Aligned_cols=67  Identities=13%  Similarity=0.186  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCc
Q 011102          405 LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       405 ~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~  472 (493)
                      ..-....++.+.++|+-|.-.++..++.+ .-+++....-.+-.||.+.|+..++.+++.+..++|++
T Consensus        86 se~vD~ALd~lv~~~kkDqLdki~~~l~k-n~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   86 SEYVDLALDILVKQGKKDQLDKIYNELKK-NEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             -HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHhh-ccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            34456778888999999999999999875 33477888888999999999999999999999999975

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=94.10  E-value=1.5  Score=43.79  Aligned_cols=127  Identities=16%  Similarity=0.169  Sum_probs=101.5

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHcCCCHHHHHHHHHH-HHHCCCCCCHHHH-HHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSG-RDPTVVMYTTLIHSRLSEKKCREALTVVWN-MEASNCLFDLPAY-RVV  411 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~ty~~li~~~~~~g~~~~A~~l~~~-M~~~gi~pd~~ty-~~l  411 (493)
                      ..+|...|++-.|..-++.|..+|-+..+.| +.+++..|+++|.-+|. |+..-|.++|+- |+.   -||...| +-.
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~---f~d~~~y~~ky  472 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK---FPDSTLYKEKY  472 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh---CCCchHHHHHH
Confidence            3467788898889999999999999999988 77999999999998876 677889999986 444   3666554 456


Q ss_pred             HHHHHHcCCHHHHHHHHHHHH----HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          412 IKLFVALNDISRAIRYFSKLK----EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~----~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +.-+..-++-+.|..+|+.-.    +...   ...|..+|+-=..-|+...|..+=+.|.+
T Consensus       473 l~fLi~inde~naraLFetsv~r~~~~q~---k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         473 LLFLIRINDEENARALFETSVERLEKTQL---KRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHHHHHhCcHHHHHHHHHHhHHHHHHhhh---hHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            677788899999999999443    3222   45899999999999999888887777754

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=94.02  E-value=1.6  Score=37.67  Aligned_cols=88  Identities=15%  Similarity=0.125  Sum_probs=55.7

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      -.-+...|++++|..+|+-+...  .| +..-|-.|--.+-..|++.+|++.+........ -|...+-.+=.++.+.|+
T Consensus        42 A~~ly~~G~l~~A~~~f~~L~~~--Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~lG~  118 (157)
T PRK15363         42 AMQLMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLACDN  118 (157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHcCC
Confidence            33445667777777777766533  33 344455555666666777777777777665543 345566666667777777


Q ss_pred             HHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLK  432 (493)
Q Consensus       421 ~~~A~~~~~~m~  432 (493)
                      .+.|.+-|+.-.
T Consensus       119 ~~~A~~aF~~Ai  130 (157)
T PRK15363        119 VCYAIKALKAVV  130 (157)
T ss_pred             HHHHHHHHHHHH
Confidence            777777776554

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=93.90  E-value=1.1  Score=38.60  Aligned_cols=85  Identities=8%  Similarity=-0.066  Sum_probs=36.7

Q ss_pred             HHcCCCHHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          380 RLSEKKCREALTVVWNMEASNCLFDLP-AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAK  458 (493)
Q Consensus       380 ~~~~g~~~~A~~l~~~M~~~gi~pd~~-ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~  458 (493)
                      +...|++++|.++|+-...-  .|... -|-.|=-.|-..|++++|...|........ -|...+-.+-.++...|+.+.
T Consensus        45 ly~~G~l~~A~~~f~~L~~~--Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~-ddp~~~~~ag~c~L~lG~~~~  121 (157)
T PRK15363         45 LMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKI-DAPQAPWAAAECYLACDNVCY  121 (157)
T ss_pred             HHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHHHHcCCHHH
Confidence            34445555555555443332  12222 222222333334455555555554443332 234444444444555555555


Q ss_pred             HHHHHHHHH
Q 011102          459 CRDVCKEAE  467 (493)
Q Consensus       459 A~~l~~~m~  467 (493)
                      |.+-|+...
T Consensus       122 A~~aF~~Ai  130 (157)
T PRK15363        122 AIKALKAVV  130 (157)
T ss_pred             HHHHHHHHH
Confidence            555554443

>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=93.84  E-value=0.27  Score=36.74  Aligned_cols=60  Identities=17%  Similarity=0.350  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH----CCC-CCC-HHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          407 AYRVVIKLFVALNDISRAIRYFSKLKE----AGF-CPT-YDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       407 ty~~li~~~~~~g~~~~A~~~~~~m~~----~g~-~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      +|+.+-..|...|++++|...|++..+    .|- .|+ ..+|..+-..|...|++++|++.+++.
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            344455555555555555555554431    110 111 344555555666666666666665554

...

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=93.74  E-value=1.3  Score=42.12  Aligned_cols=98  Identities=16%  Similarity=0.070  Sum_probs=73.8

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-C-CCCHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL----PAYRVVIKLFVALNDISRAIRYFSKLKEAG-F-CPTYDIY  443 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~----~ty~~li~~~~~~g~~~~A~~~~~~m~~~g-~-~p~~~ty  443 (493)
                      ...|..-+.-+.+.|++++|...|+...+.  .|+.    ..+-.+-..|...|++++|...|+.+.+.- - ......+
T Consensus       143 ~~~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        143 NTDYNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAM  220 (263)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHH
Confidence            345666666667789999999999998875  2443    356677788999999999999999998432 1 1123444


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          444 RDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       444 ~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      -.+...+...|+.++|.++|++..+.
T Consensus       221 ~klg~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        221 FKVGVIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            45566778999999999999999864

>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=93.73  E-value=0.44  Score=34.55  Aligned_cols=61  Identities=20%  Similarity=0.268  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHH
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASG-RLAKCRDVCKEAE  467 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g-~~~~A~~l~~~m~  467 (493)
                      .+|..+=..+.+.|++++|...|++..+..- -+...|..+-.+|.+.| ++++|.+.+++..
T Consensus         4 ~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p-~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al   65 (69)
T PF13414_consen    4 EAWYNLGQIYFQQGDYEEAIEYFEKAIELDP-NNAEAYYNLGLAYMKLGKDYEEAIEDFEKAL   65 (69)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHHHST-THHHHHHHHHHHHHHTTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhCccHHHHHHHHHHHH
Confidence            3445555555666666666666666554331 14445555555566666 4666666655544

...

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.68  E-value=1.5  Score=40.91  Aligned_cols=143  Identities=10%  Similarity=-0.005  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH-
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK-  343 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~-  343 (493)
                      +-+.++..+.-.|.+.-.+.++.+.++..-+-++...+.|.+.-.+. |+.+.|...|+..++. .-+.|..+++.++. 
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~-GD~k~a~~yf~~vek~-~~kL~~~q~~~~V~~  256 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQI-GDIKTAEKYFQDVEKV-TQKLDGLQGKIMVLM  256 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhc-ccHHHHHHHHHHHHHH-HhhhhccchhHHHHh
Confidence            44667777777788888888999988877777888888999999999 9999999999988765 34455555555543 


Q ss_pred             ----HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          344 ----VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVI  412 (493)
Q Consensus       344 ----~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li  412 (493)
                          .|.-.+++.+|...|+++.... ..|.+.-|.=.-...-.|+..+|.+.++.|.+.  .|...+-++++
T Consensus       257 n~a~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l~es~~  326 (366)
T KOG2796|consen  257 NSAFLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYLHESVL  326 (366)
T ss_pred             hhhhheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccchhhhHH
Confidence                3445677889999998887542 234454554333444468999999999999875  46655555444

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=93.38  E-value=7  Score=36.66  Aligned_cols=177  Identities=8%  Similarity=-0.063  Sum_probs=103.8

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCCHH-HHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHH
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFPDDR-LLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAW  283 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~pd~~-t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~  283 (493)
                      .+.+.|++++|.+.|+.+...   -|+.. .-.+                            .--+..+|-+.+++++|.
T Consensus        41 ~~~~~g~y~~Ai~~f~~l~~~---yP~s~~a~~a----------------------------~l~la~ayy~~~~y~~A~   89 (243)
T PRK10866         41 QKLQDGNWKQAITQLEALDNR---YPFGPYSQQV----------------------------QLDLIYAYYKNADLPLAQ   89 (243)
T ss_pred             HHHHCCCHHHHHHHHHHHHHh---CCCChHHHHH----------------------------HHHHHHHHHhcCCHHHHH
Confidence            445688999999999998864   23221 1111                            012566777888899999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHhcCC----------------CC---HHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          284 KLLMVAKDGGRMLDPSIYAKLILELGKNP----------------DK---YMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       284 ~l~~~m~~~g~~pd~~t~~~li~~~~~~~----------------~~---~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      ..|++..+.--.-...-|.-.+.|.+...                .+   ..+|.+.|+.+                |.-
T Consensus        90 ~~~e~fi~~~P~~~~~~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~l----------------i~~  153 (243)
T PRK10866         90 AAIDRFIRLNPTHPNIDYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKL----------------VRG  153 (243)
T ss_pred             HHHHHHHHhCcCCCchHHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHH----------------HHH
Confidence            99988887542222334444444443210                01   12333444444                444


Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHHcCCHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS--NCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~--gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      |-...-..+|...+..+...    =...--.+..-|.+.|.+..|..-|+.+.+.  +-.......-.++.+|.+.|..+
T Consensus       154 yP~S~ya~~A~~rl~~l~~~----la~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~  229 (243)
T PRK10866        154 YPNSQYTTDATKRLVFLKDR----LAKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNA  229 (243)
T ss_pred             CcCChhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChH
Confidence            44444455565555444321    0111114455677888888888888888765  34444556677888888888888


Q ss_pred             HHHHHHHHHH
Q 011102          423 RAIRYFSKLK  432 (493)
Q Consensus       423 ~A~~~~~~m~  432 (493)
                      +|..+...+.
T Consensus       230 ~a~~~~~~l~  239 (243)
T PRK10866        230 QADKVAKIIA  239 (243)
T ss_pred             HHHHHHHHHh
Confidence            8888776654

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=93.33  E-value=2.7  Score=43.18  Aligned_cols=156  Identities=12%  Similarity=0.144  Sum_probs=97.8

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          274 VKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGV  353 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~  353 (493)
                      .-.|+++++.++.+.=.-..- ....-.+.++.-+-+. |..+.|+++-..-..+             .+...++|+++.
T Consensus       272 v~~~d~~~v~~~i~~~~ll~~-i~~~~~~~i~~fL~~~-G~~e~AL~~~~D~~~r-------------FeLAl~lg~L~~  336 (443)
T PF04053_consen  272 VLRGDFEEVLRMIAASNLLPN-IPKDQGQSIARFLEKK-GYPELALQFVTDPDHR-------------FELALQLGNLDI  336 (443)
T ss_dssp             HHTT-HHH-----HHHHTGGG---HHHHHHHHHHHHHT-T-HHHHHHHSS-HHHH-------------HHHHHHCT-HHH
T ss_pred             HHcCChhhhhhhhhhhhhccc-CChhHHHHHHHHHHHC-CCHHHHHhhcCChHHH-------------hHHHHhcCCHHH
Confidence            345778887666641111000 1244467777777777 8888888776544332             334557788888


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          354 VESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       354 A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      |.++-++.      .+...|..|-+...+.|+++-|++.|.+...         |..|+--|.-.|+.+.-.++.+.-..
T Consensus       337 A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~  401 (443)
T PF04053_consen  337 ALEIAKEL------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEE  401 (443)
T ss_dssp             HHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHH
Confidence            88776543      3667888888888899999999888887643         67777778888888777777766666


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          434 AGFCPTYDIYRDMIRIFMASGRLAKCRDVCKE  465 (493)
Q Consensus       434 ~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~  465 (493)
                      .|-      +|....++.-.|++++..+++.+
T Consensus       402 ~~~------~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  402 RGD------INIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             TT-------HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             ccC------HHHHHHHHHHcCCHHHHHHHHHH
Confidence            553      56677777777888887776654

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.

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=93.33  E-value=7.9  Score=37.16  Aligned_cols=33  Identities=18%  Similarity=0.041  Sum_probs=20.7

Q ss_pred             CHHHHHHHHhhhcccCcHHHHHHHHHhCCChHHHHHHHHHHH
Q 011102          182 DVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQ  223 (493)
Q Consensus       182 ~~~~a~~~~~~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~  223 (493)
                      +.++|.+.|         .-.-..|-..|++++|.+.|...-
T Consensus        30 ~~e~Aa~~y---------~~Aa~~fk~~~~~~~A~~ay~kAa   62 (282)
T PF14938_consen   30 DYEEAADLY---------EKAANCFKLAKDWEKAAEAYEKAA   62 (282)
T ss_dssp             HHHHHHHHH---------HHHHHHHHHTT-CHHHHHHHHHHH
T ss_pred             CHHHHHHHH---------HHHHHHHHHHhccchhHHHHHHHH
Confidence            555665553         334667777778888877776654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=93.27  E-value=0.72  Score=33.79  Aligned_cols=55  Identities=13%  Similarity=0.198  Sum_probs=33.4

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          413 KLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       413 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ..|.+.+++++|.++++.+....-. +...|...-..+.+.|++++|.+.|+...+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPD-DPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3456666666666666666654322 444555556666666666666666666664

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.20  E-value=5.6  Score=41.31  Aligned_cols=162  Identities=14%  Similarity=0.108  Sum_probs=87.3

Q ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHH-----HHHHHHHHHHH----cCCHHHHHHHHHHHHHcCCCCCHHH
Q 011102          302 AKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQ-----DCTAIMKVGIR----LQKFGVVESLFHWFTHSGRDPTVVM  372 (493)
Q Consensus       302 ~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~-----~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t  372 (493)
                      ..++...+-. |+-+.+++++.+-.+..++.-...     .|..++..++-    ....+.|.++++.+.+.  -|+..-
T Consensus       192 ~kll~~vGF~-gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~--yP~s~l  268 (468)
T PF10300_consen  192 LKLLSFVGFS-GDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR--YPNSAL  268 (468)
T ss_pred             HHHHhhcCcC-CcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh--CCCcHH
Confidence            3455555555 666666666666554433332221     34444443332    34566777777777644  466555


Q ss_pred             HHHHH-HHHHcCCCHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          373 YTTLI-HSRLSEKKCREALTVVWNMEASNC---LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR  448 (493)
Q Consensus       373 y~~li-~~~~~~g~~~~A~~l~~~M~~~gi---~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~  448 (493)
                      |...- +.+...|++++|.+.|++......   +.....|--+.-.+.-.++|++|.+.|..+.+.. .....+|.-+..
T Consensus       269 fl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a  347 (468)
T PF10300_consen  269 FLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAA  347 (468)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHH
Confidence            54443 333445777777777775442110   1112223333344666778888888888887432 123444444433


Q ss_pred             HH-HHcCCH-------HHHHHHHHHHH
Q 011102          449 IF-MASGRL-------AKCRDVCKEAE  467 (493)
Q Consensus       449 ~~-~~~g~~-------~~A~~l~~~m~  467 (493)
                      +| ...|+.       ++|.++|.+..
T Consensus       348 ~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  348 ACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            33 345666       77777777764

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.

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

Probab=93.20  E-value=14  Score=39.67  Aligned_cols=286  Identities=11%  Similarity=-0.010  Sum_probs=155.8

Q ss_pred             ccCCCCHHHHHHHHhhhccc-----CcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH-Hc-CCCc
Q 011102          177 LDSHKDVAEVLDKCGRFLRK-----GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLA-RH-HELK  249 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~-----~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~-~~-g~~~  249 (493)
                      +..+|+++.+.+.|++...-     ..|+.+-..|...|.-..|+.+.+.-... .-.|+..+--.++...| +. +..+
T Consensus       333 l~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~-~~~ps~~s~~Lmasklc~e~l~~~e  411 (799)
T KOG4162|consen  333 LSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKK-SEQPSDISVLLMASKLCIERLKLVE  411 (799)
T ss_pred             HHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhccc-ccCCCcchHHHHHHHHHHhchhhhh
Confidence            45568888888888854432     37888888888888888888888766543 22244333333332222 21 1110


Q ss_pred             h----hh-hHH-------------------------------------------Hhhc-----cCcHHHHHHHHHHHHhc
Q 011102          250 V----PF-KLE-------------------------------------------NFVS-----LASKGVLEATAKGFVKG  276 (493)
Q Consensus       250 ~----~~-~l~-------------------------------------------~~~~-----~~~~~~~~~li~~~~~~  276 (493)
                      .    +. ++.                                           .+.+     +.|..+---+---|+..
T Consensus       412 egldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp~~if~lalq~A~~  491 (799)
T KOG4162|consen  412 EGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDPLVIFYLALQYAEQ  491 (799)
T ss_pred             hHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHH
Confidence            0    00 000                                           0000     00111111233346777


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC------------------CHHH-
Q 011102          277 GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNL------------------SQQD-  337 (493)
Q Consensus       277 g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p------------------~~~~-  337 (493)
                      ++++.|++..++..+.+-.-+...|.-+.-.+... +++.+|+.+.+......|...                  ...| 
T Consensus       492 R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~-kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~~~~~~e~~l~t~  570 (799)
T KOG4162|consen  492 RQLTSALDYAREALALNRGDSAKAWHLLALVLSAQ-KRLKEALDVVDAALEEFGDNHVLMDGKIHIELTFNDREEALDTC  570 (799)
T ss_pred             HhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhh-hhhHHHHHHHHHHHHHhhhhhhhchhhhhhhhhcccHHHHHHHH
Confidence            88999999999988887677888887777777766 777777777665433212100                  0111 


Q ss_pred             --------------------------------------------------------------------------------
Q 011102          338 --------------------------------------------------------------------------------  337 (493)
Q Consensus       338 --------------------------------------------------------------------------------  337 (493)
                                                                                                      
T Consensus       571 ~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~~~~~~~~~~~~~  650 (799)
T KOG4162|consen  571 IHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSSTVLPGPDSLWYLLQ  650 (799)
T ss_pred             HHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCcccccCCCCchHHHHH
Confidence                                                                                            


Q ss_pred             --HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHH
Q 011102          338 --CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL-PAYRVVIKL  414 (493)
Q Consensus       338 --~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~-~ty~~li~~  414 (493)
                        |...-+.+.+.+..++|...+.+.... ..-....|.-.-..+-..|++++|.+.|.....  +.||. .+.+++-..
T Consensus       651 ~lwllaa~~~~~~~~~~~a~~CL~Ea~~~-~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~--ldP~hv~s~~Ala~~  727 (799)
T KOG4162|consen  651 KLWLLAADLFLLSGNDDEARSCLLEASKI-DPLSASVYYLRGLLLEVKGQLEEAKEAFLVALA--LDPDHVPSMTALAEL  727 (799)
T ss_pred             HHHHHHHHHHHhcCCchHHHHHHHHHHhc-chhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHh--cCCCCcHHHHHHHHH
Confidence              122223333333344443333332211 011222233333344445556666666655443  33443 455666666


Q ss_pred             HHHcCCHHHHHH--HHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          415 FVALNDISRAIR--YFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       415 ~~~~g~~~~A~~--~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +.+.|+-..|..  ++.++.+.+- -+...|-.+-..+-+.|+.++|.+.|+...+
T Consensus       728 lle~G~~~la~~~~~L~dalr~dp-~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~q  782 (799)
T KOG4162|consen  728 LLELGSPRLAEKRSLLSDALRLDP-LNHEAWYYLGEVFKKLGDSKQAAECFQAALQ  782 (799)
T ss_pred             HHHhCCcchHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHccchHHHHHHHHHHHh
Confidence            777776666666  7777766553 2666777777777777777777777766543

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=93.18  E-value=4  Score=44.95  Aligned_cols=160  Identities=9%  Similarity=-0.050  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHH--HHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCT--AIM  342 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~--~li  342 (493)
                      .|..|-..|+..-+...|.+.|+..-+.. .-|...+..+.+.|++. ..|+.|..+.-...+.  -..-...+|  -.-
T Consensus       494 af~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~-~~we~a~~I~l~~~qk--a~a~~~k~nW~~rG  569 (1238)
T KOG1127|consen  494 AFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEE-STWEEAFEICLRAAQK--APAFACKENWVQRG  569 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhcc-ccHHHHHHHHHHHhhh--chHHHHHhhhhhcc
Confidence            46666666666666777777777665532 12334556666777777 6777777662222111  000111111  122


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH--HHHHcCC
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIK--LFVALND  420 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~--~~~~~g~  420 (493)
                      -.|-+.++...|..-|+.-.+.. +.|...|..|..+|.+.|+...|+++|.+....  .|+. +|.-.-.  .-|..|+
T Consensus       570 ~yyLea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~L--rP~s-~y~~fk~A~~ecd~Gk  645 (1238)
T KOG1127|consen  570 PYYLEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGRYSHALKVFTKASLL--RPLS-KYGRFKEAVMECDNGK  645 (1238)
T ss_pred             ccccCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCceehHHHhhhhhHhc--CcHh-HHHHHHHHHHHHHhhh
Confidence            23445556666666665544221 235666777777777777777777777655432  3432 3332222  2355566


Q ss_pred             HHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLK  432 (493)
Q Consensus       421 ~~~A~~~~~~m~  432 (493)
                      ..+|...+....
T Consensus       646 Ykeald~l~~ii  657 (1238)
T KOG1127|consen  646 YKEALDALGLII  657 (1238)
T ss_pred             HHHHHHHHHHHH
Confidence            666666665543

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.16  E-value=6.5  Score=40.83  Aligned_cols=163  Identities=13%  Similarity=0.081  Sum_probs=112.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH------HHHHHHHHHHhcC---CCCHHHHHHHHHHHhhcCCCCCCHH
Q 011102          266 LEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP------SIYAKLILELGKN---PDKYMLVMTLLDELGQRDDLNLSQQ  336 (493)
Q Consensus       266 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~------~t~~~li~~~~~~---~~~~~~a~~l~~~m~~~~g~~p~~~  336 (493)
                      +..++....=.|+-+.+++.+.+-.+.+-.-.+      .+|..++..++..   +...+.|.++++.+.++   -|+..
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~---yP~s~  267 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR---YPNSA  267 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh---CCCcH
Confidence            456677777789999999999887664322222      3466666665554   47889999999999876   38877


Q ss_pred             HHHHHH-HHHHHcCCHHHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          337 DCTAIM-KVGIRLQKFGVVESLFHWFTHSG---RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVI  412 (493)
Q Consensus       337 ~~~~li-~~~~~~g~~~~A~~l~~~m~~~g---~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li  412 (493)
                      .|...- ..+...|++++|.+.|++.....   -+.....|--+.-.+.-.++|++|.+.|..+.+..- ....+|.-+.
T Consensus       268 lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~-WSka~Y~Y~~  346 (468)
T PF10300_consen  268 LFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESK-WSKAFYAYLA  346 (468)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhccc-cHHHHHHHHH
Confidence            776553 46677899999999999654211   122344455566678888999999999999987532 2344454444


Q ss_pred             HH-HHHcCCH-------HHHHHHHHHHH
Q 011102          413 KL-FVALNDI-------SRAIRYFSKLK  432 (493)
Q Consensus       413 ~~-~~~~g~~-------~~A~~~~~~m~  432 (493)
                      .+ +...|+.       ++|.++|.+..
T Consensus       347 a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  347 AACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            33 3445666       88888888764

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.

>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=93.09  E-value=0.57  Score=33.94  Aligned_cols=58  Identities=9%  Similarity=-0.011  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC-CHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK-KCREALTVVWN  395 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g-~~~~A~~l~~~  395 (493)
                      +|..+-..+.+.|++++|+..|++..+.. +-+...|..+-.+|.+.| ++++|++.++.
T Consensus         5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~   63 (69)
T PF13414_consen    5 AWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEK   63 (69)
T ss_dssp             HHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHH
Confidence            34444444444455555555554443321 113334444444444444 34444444444

...

>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=92.86  E-value=0.33  Score=36.26  Aligned_cols=61  Identities=18%  Similarity=0.136  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CC-CCC-HHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEAS----NC-LFD-LPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi-~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      .+|+.+-..|...|++++|++.|++..+.    |- .|+ ..+++.+-..|...|++++|.+++++-
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            34555555666666666666666554322    11 122 345555556666666666666666654

...

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

Probab=92.32  E-value=19  Score=38.83  Aligned_cols=201  Identities=11%  Similarity=0.032  Sum_probs=127.3

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +..+|..|.-+....|+++.+.+.|++....- .-....|+.+-..|... |.-..|..++++-... .-.|+..+--.+
T Consensus       322 d~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~-~~~~e~w~~~als~saa-g~~s~Av~ll~~~~~~-~~~ps~~s~~Lm  398 (799)
T KOG4162|consen  322 DAAIFDHLTFALSRCGQFEVLAEQFEQALPFS-FGEHERWYQLALSYSAA-GSDSKAVNLLRESLKK-SEQPSDISVLLM  398 (799)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh-hhhHHHHHHHHHHHHHh-ccchHHHHHHHhhccc-ccCCCcchHHHH
Confidence            55678888888888999999999998776432 22344566666667666 7778888888776543 222433332222


Q ss_pred             HH-HH-HHcCCHHHHHHHHHHHHH--cCC--CCCHHHHHHHHHHHHcCC-----------CHHHHHHHHHHHHHC-CCCC
Q 011102          342 MK-VG-IRLQKFGVVESLFHWFTH--SGR--DPTVVMYTTLIHSRLSEK-----------KCREALTVVWNMEAS-NCLF  403 (493)
Q Consensus       342 i~-~~-~~~g~~~~A~~l~~~m~~--~g~--~p~~~ty~~li~~~~~~g-----------~~~~A~~l~~~M~~~-gi~p  403 (493)
                      +. .| .+.|.++++++.-.+...  .|.  ......|-.+--+|...-           ...++++.+++..+. +-.|
T Consensus       399 asklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp  478 (799)
T KOG4162|consen  399 ASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDP  478 (799)
T ss_pred             HHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence            22 22 233556666655555443  111  122333444443443221           235677778877654 4556


Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          404 DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      ++.-|-++=  |+-.++++.|.+...+..+-+-.-+...|..|.-.+.-.+++.+|+.+.+...
T Consensus       479 ~~if~lalq--~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al  540 (799)
T KOG4162|consen  479 LVIFYLALQ--YAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAAL  540 (799)
T ss_pred             hHHHHHHHH--HHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence            666665554  45567889999998888877656688888888888888899999988877654

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=92.19  E-value=2.7  Score=42.53  Aligned_cols=64  Identities=8%  Similarity=0.015  Sum_probs=45.9

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 011102          334 SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTV----VMYTTLIHSRLSEKKCREALTVVWNMEAS  399 (493)
Q Consensus       334 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~ty~~li~~~~~~g~~~~A~~l~~~M~~~  399 (493)
                      +...++.+-.+|.+.|++++|...|++-.+.  .|+.    .+|..+-.+|...|+.++|++.+++..+.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4556777777888888888888888775544  4542    35777778888888888888887776663

>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=92.11  E-value=4.1  Score=41.84  Aligned_cols=149  Identities=21%  Similarity=0.174  Sum_probs=96.6

Q ss_pred             CCCCHHHHHHHHh------hhcccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhh
Q 011102          179 SHKDVAEVLDKCG------RFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPF  252 (493)
Q Consensus       179 ~~~~~~~a~~~~~------~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~  252 (493)
                      -.++++++.+...      ..+ ++-.+.+++-+-+.|..+.|+++-.+-..+             .+...+.|+++  .
T Consensus       273 ~~~d~~~v~~~i~~~~ll~~i~-~~~~~~i~~fL~~~G~~e~AL~~~~D~~~r-------------FeLAl~lg~L~--~  336 (443)
T PF04053_consen  273 LRGDFEEVLRMIAASNLLPNIP-KDQGQSIARFLEKKGYPELALQFVTDPDHR-------------FELALQLGNLD--I  336 (443)
T ss_dssp             HTT-HHH-----HHHHTGGG---HHHHHHHHHHHHHTT-HHHHHHHSS-HHHH-------------HHHHHHCT-HH--H
T ss_pred             HcCChhhhhhhhhhhhhcccCC-hhHHHHHHHHHHHCCCHHHHHhhcCChHHH-------------hHHHHhcCCHH--H
Confidence            3577777544433      222 345788899999999999999987654332             23445677744  4


Q ss_pred             hHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCC
Q 011102          253 KLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLN  332 (493)
Q Consensus       253 ~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~  332 (493)
                      |+..-.+..+...|..|-+...+.|+++-|.+.|.+..+         |..|+--|.-. |+.+...++.+....+ |  
T Consensus       337 A~~~a~~~~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~-g~~~~L~kl~~~a~~~-~--  403 (443)
T PF04053_consen  337 ALEIAKELDDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSST-GDREKLSKLAKIAEER-G--  403 (443)
T ss_dssp             HHHHCCCCSTHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHC-T-HHHHHHHHHHHHHT-T--
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHh-CCHHHHHHHHHHHHHc-c--
Confidence            444466677888999999999999999999999987655         56666667777 7777777777766655 2  


Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          333 LSQQDCTAIMKVGIRLQKFGVVESLFHW  360 (493)
Q Consensus       333 p~~~~~~~li~~~~~~g~~~~A~~l~~~  360 (493)
                          -+|....++.-.|++++..+++.+
T Consensus       404 ----~~n~af~~~~~lgd~~~cv~lL~~  427 (443)
T PF04053_consen  404 ----DINIAFQAALLLGDVEECVDLLIE  427 (443)
T ss_dssp             -----HHHHHHHHHHHT-HHHHHHHHHH
T ss_pred             ----CHHHHHHHHHHcCCHHHHHHHHHH
Confidence                256666677777887777776654

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.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=91.91  E-value=7.9  Score=43.55  Aligned_cols=134  Identities=13%  Similarity=0.078  Sum_probs=77.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHh----cCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          267 EATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELG----KNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       267 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~----~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      +-.++.--+.|.+++|+.++.        ||...+..+..+|+    .. ..+++|--+|+...+.          .-.+
T Consensus       912 ~e~~n~I~kh~Ly~~aL~ly~--------~~~e~~k~i~~~ya~hL~~~-~~~~~Aal~Ye~~Gkl----------ekAl  972 (1265)
T KOG1920|consen  912 PECKNYIKKHGLYDEALALYK--------PDSEKQKVIYEAYADHLREE-LMSDEAALMYERCGKL----------EKAL  972 (1265)
T ss_pred             HHHHHHHHhcccchhhhheec--------cCHHHHHHHHHHHHHHHHHh-ccccHHHHHHHHhccH----------HHHH
Confidence            333344444455555554443        67666665554443    34 5666666666554332          3456


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHH--HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVM--YTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t--y~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      .+|-.+|+|++|+.+-.+|..   ..|...  --.|+.-+...++.-+|-++..+-.+.        +.-.+.-||++..
T Consensus       973 ~a~~~~~dWr~~l~~a~ql~~---~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd--------~~~av~ll~ka~~ 1041 (1265)
T KOG1920|consen  973 KAYKECGDWREALSLAAQLSE---GKDELVILAEELVSRLVEQRKHYEAAKILLEYLSD--------PEEAVALLCKAKE 1041 (1265)
T ss_pred             HHHHHhccHHHHHHHHHhhcC---CHHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcC--------HHHHHHHHhhHhH
Confidence            777777888888877777651   112221  256777777778877777777765442        2334455666666


Q ss_pred             HHHHHHHHHH
Q 011102          421 ISRAIRYFSK  430 (493)
Q Consensus       421 ~~~A~~~~~~  430 (493)
                      |++|.++-..
T Consensus      1042 ~~eAlrva~~ 1051 (1265)
T KOG1920|consen 1042 WEEALRVASK 1051 (1265)
T ss_pred             HHHHHHHHHh
Confidence            7777665443

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=91.78  E-value=6  Score=43.66  Aligned_cols=156  Identities=11%  Similarity=0.066  Sum_probs=95.6

Q ss_pred             HHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC
Q 011102          305 ILELGKNPDKYMLVMTLLDELGQRDDLNLS-QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE  383 (493)
Q Consensus       305 i~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~  383 (493)
                      +.+|.+.  +...|+..|-...+.   .++ ...|+.|-..|+..-+...|.+.|++-.+.. .-|...+-.+.+.|++.
T Consensus       466 a~~~~rK--~~~~al~ali~alrl---d~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~  539 (1238)
T KOG1127|consen  466 ALGCMRK--NSALALHALIRALRL---DVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEE  539 (1238)
T ss_pred             HHHHhhh--hHHHHHHHHHHHHhc---ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhcc
Confidence            3444443  345555555444332   122 3467888888888878888888888766331 23566777888888888


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH--HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          384 KKCREALTVVWNMEASNCLFDLPAYRVVIKL--FVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRD  461 (493)
Q Consensus       384 g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~--~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~  461 (493)
                      .++++|..+.-.--+. -..-...+|.+-.+  |-+.++...|..-|+.-.....+ |...|..+..+|.++|++..|.+
T Consensus       540 ~~we~a~~I~l~~~qk-a~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPk-D~n~W~gLGeAY~~sGry~~AlK  617 (1238)
T KOG1127|consen  540 STWEEAFEICLRAAQK-APAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPK-DYNLWLGLGEAYPESGRYSHALK  617 (1238)
T ss_pred             ccHHHHHHHHHHHhhh-chHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCch-hHHHHHHHHHHHHhcCceehHHH
Confidence            8888888873222111 11111223333333  55667777777777766644432 66777777778888888888877


Q ss_pred             HHHHHHH
Q 011102          462 VCKEAEM  468 (493)
Q Consensus       462 l~~~m~~  468 (493)
                      +|.+...
T Consensus       618 vF~kAs~  624 (1238)
T KOG1127|consen  618 VFTKASL  624 (1238)
T ss_pred             hhhhhHh
Confidence            7776653

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=91.68  E-value=9.2  Score=33.95  Aligned_cols=127  Identities=12%  Similarity=0.053  Sum_probs=68.3

Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC---CCCCCHHH
Q 011102          331 LNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS---NCLFDLPA  407 (493)
Q Consensus       331 ~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~---gi~pd~~t  407 (493)
                      ..|++..--.|-.++.+.|+..+|...|++-..--+.-|....-.+-++....++...|...++.+.+.   +-.||.  
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~--  162 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDG--  162 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCc--
Confidence            345555555666666666666666666666654334445555556666666666666666666665543   223332  


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRD  461 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~  461 (493)
                      .-.+-..|...|+..+|+.-|+...+.---|-...|  .-..+.+.|+.++|..
T Consensus       163 ~Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~ar~~--Y~e~La~qgr~~ea~a  214 (251)
T COG4700         163 HLLFARTLAAQGKYADAESAFEVAISYYPGPQARIY--YAEMLAKQGRLREANA  214 (251)
T ss_pred             hHHHHHHHHhcCCchhHHHHHHHHHHhCCCHHHHHH--HHHHHHHhcchhHHHH
Confidence            223345566666666666666666543222222222  2223445555554433

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=91.61  E-value=2.9  Score=42.31  Aligned_cols=65  Identities=6%  Similarity=-0.145  Sum_probs=55.7

Q ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH----HHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Q 011102          296 LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ----QDCTAIMKVGIRLQKFGVVESLFHWFTHS  364 (493)
Q Consensus       296 pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~----~~~~~li~~~~~~g~~~~A~~l~~~m~~~  364 (493)
                      .+...|+.+-.+|.+. |++++|+..|++..+.   .|+.    .+|..+-.+|.+.|++++|++.+++..+.
T Consensus        73 ~~a~a~~NLG~AL~~l-GryeEAIa~f~rALeL---~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         73 KTAEDAVNLGLSLFSK-GRVKDALAQFETALEL---NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhh---CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4566888999999999 9999999999997654   4664    46899999999999999999999998864

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.58  E-value=2.6  Score=40.06  Aligned_cols=96  Identities=14%  Similarity=0.103  Sum_probs=50.9

Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~~~~g~~~~  423 (493)
                      +.+.+++++|+..|.+-.+.. +-|.+-|.-=-.+|++.|.++.|++=.+....  +.|. ..+|..|=.+|...|++++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~-P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELD-PTNAVYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcC-CCcchHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcHHH
Confidence            445566666666666655331 22445555555666666666666555444332  1222 2355555556666666666


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHH
Q 011102          424 AIRYFSKLKEAGFCPTYDIYRD  445 (493)
Q Consensus       424 A~~~~~~m~~~g~~p~~~ty~~  445 (493)
                      |.+.|+.-.+  +.|+-.+|-.
T Consensus       168 A~~aykKaLe--ldP~Ne~~K~  187 (304)
T KOG0553|consen  168 AIEAYKKALE--LDPDNESYKS  187 (304)
T ss_pred             HHHHHHhhhc--cCCCcHHHHH
Confidence            6666555443  3455555543

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=91.51  E-value=3.4  Score=43.26  Aligned_cols=74  Identities=15%  Similarity=0.194  Sum_probs=40.0

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHH-----------HHHHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVM-----------YTTLIHSRL  381 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t-----------y~~li~~~~  381 (493)
                      ..+..|-++|..|...          .++++.....+++.+|..+-+...+.  .||+..           |---=++|-
T Consensus       761 ~~~gLAaeIF~k~gD~----------ksiVqlHve~~~W~eAFalAe~hPe~--~~dVy~pyaqwLAE~DrFeEAqkAfh  828 (1081)
T KOG1538|consen  761 DSPGLAAEIFLKMGDL----------KSLVQLHVETQRWDEAFALAEKHPEF--KDDVYMPYAQWLAENDRFEEAQKAFH  828 (1081)
T ss_pred             cccchHHHHHHHhccH----------HHHhhheeecccchHhHhhhhhCccc--cccccchHHHHhhhhhhHHHHHHHHH
Confidence            5556666666666433          34556666667777776666654432  334321           222334555


Q ss_pred             cCCCHHHHHHHHHHHHH
Q 011102          382 SEKKCREALTVVWNMEA  398 (493)
Q Consensus       382 ~~g~~~~A~~l~~~M~~  398 (493)
                      ++|+-.+|.++++++-.
T Consensus       829 kAGr~~EA~~vLeQLtn  845 (1081)
T KOG1538|consen  829 KAGRQREAVQVLEQLTN  845 (1081)
T ss_pred             HhcchHHHHHHHHHhhh
Confidence            55555666665555543

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.34  E-value=16  Score=39.17  Aligned_cols=92  Identities=7%  Similarity=0.074  Sum_probs=67.7

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          365 GRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYR  444 (493)
Q Consensus       365 g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~  444 (493)
                      |..-.--|.+--+.-+...|+..+|.++-.+.+    .||..-|--=+.+++..++|++-+++-+.++.      ..-|.
T Consensus       679 ~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskks------PIGy~  748 (829)
T KOG2280|consen  679 GGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKKS------PIGYL  748 (829)
T ss_pred             ccccccCcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccCC------CCCch
Confidence            333444455556666777788888888777654    38888888888999999999888777766652      34467


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHH
Q 011102          445 DMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       445 ~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      -.+.+|.+.|+.+||.+++...
T Consensus       749 PFVe~c~~~~n~~EA~KYiprv  770 (829)
T KOG2280|consen  749 PFVEACLKQGNKDEAKKYIPRV  770 (829)
T ss_pred             hHHHHHHhcccHHHHhhhhhcc
Confidence            7888899999999998887654

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=91.33  E-value=1.7  Score=31.79  Aligned_cols=53  Identities=15%  Similarity=0.089  Sum_probs=23.5

Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          379 SRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       379 ~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      .|.+.+++++|.++++.+...+- -+...+...-..+.+.|++++|.+.|+...
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l   56 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELDP-DDPELWLQRARCLFQLGRYEEALEDLERAL   56 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhCc-ccchhhHHHHHHHHHhccHHHHHHHHHHHH
Confidence            34444555555555554444311 122333333344445555555555555444

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=91.16  E-value=3.6  Score=39.18  Aligned_cols=99  Identities=7%  Similarity=-0.069  Sum_probs=43.3

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEAS-NCLFDLPA-YRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDM  446 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-gi~pd~~t-y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~l  446 (493)
                      |...|-.|-..|.+.|+.+.|..-|....+. |-.|+... |...+..-.....-.++..+|+++....- -|+.+-..|
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~-~~iral~lL  233 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDP-ANIRALSLL  233 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCC-ccHHHHHHH
Confidence            4455555555555555555555555544332 22222211 11111111112233445555555553321 133444444


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Q 011102          447 IRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       447 i~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      -..+...|++.+|...|+.|.+
T Consensus       234 A~~afe~g~~~~A~~~Wq~lL~  255 (287)
T COG4235         234 AFAAFEQGDYAEAAAAWQMLLD  255 (287)
T ss_pred             HHHHHHcccHHHHHHHHHHHHh
Confidence            4455555555555555555554

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=91.00  E-value=10  Score=34.34  Aligned_cols=172  Identities=13%  Similarity=0.081  Sum_probs=83.3

Q ss_pred             HHHhcCCHHHHHHHHHHHHhCCCC--CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcC
Q 011102          272 GFVKGGNLKLAWKLLMVAKDGGRM--LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQ  349 (493)
Q Consensus       272 ~~~~~g~~~~A~~l~~~m~~~g~~--pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g  349 (493)
                      .+.+.|++++|.+.|+.+...--.  --....-.+..++.+. |++++|...+++..+...-.| ...+...+.+.+...
T Consensus        14 ~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~-~~y~~A~~~~~~fi~~yP~~~-~~~~A~Y~~g~~~~~   91 (203)
T PF13525_consen   14 EALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQ-GDYEEAIAAYERFIKLYPNSP-KADYALYMLGLSYYK   91 (203)
T ss_dssp             HHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHT-T-HHHHHHHHHHHHHH-TT-T-THHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHCCCCc-chhhHHHHHHHHHHH
Confidence            345566777777777776653211  1122333455666666 677777777776655421112 122333333332221


Q ss_pred             CHHHHHHHHHHHHHcCCCCC-------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          350 KFGVVESLFHWFTHSGRDPT-------VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g~~p~-------~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      ......         ....|       ...+..+|.-|=......+|...+.++.+.   --..- -.+-.-|.+.|.+.
T Consensus        92 ~~~~~~---------~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~---la~~e-~~ia~~Y~~~~~y~  158 (203)
T PF13525_consen   92 QIPGIL---------RSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNR---LAEHE-LYIARFYYKRGKYK  158 (203)
T ss_dssp             HHHHHH----------TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHH---HHHHH-HHHHHHHHCTT-HH
T ss_pred             hCccch---------hcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHH---HHHHH-HHHHHHHHHcccHH
Confidence            111111         00111       234555666666666666665555554431   00111 12345578888888


Q ss_pred             HHHHHHHHHHHCCCCCCH----HHHHHHHHHHHHcCCHHHHH
Q 011102          423 RAIRYFSKLKEAGFCPTY----DIYRDMIRIFMASGRLAKCR  460 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~----~ty~~li~~~~~~g~~~~A~  460 (493)
                      .|..-++.+.+.=  |+.    ...-.|+.+|-+.|..+.|.
T Consensus       159 aA~~r~~~v~~~y--p~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  159 AAIIRFQYVIENY--PDTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             HHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHHHHC--CCCchHHHHHHHHHHHHHHhCChHHHH
Confidence            8888888877431  332    34466777788888776443

>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]

Probab=91.00  E-value=8.8  Score=36.64  Aligned_cols=147  Identities=7%  Similarity=0.072  Sum_probs=79.6

Q ss_pred             HHHHHHhhhcccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhcc----
Q 011102          185 EVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSL----  260 (493)
Q Consensus       185 ~a~~~~~~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~----  260 (493)
                      -+.++|.........|.+|+.+.+.+.-+.-.++         +.|+..+-...-.-+...|--+.    ..|.+.    
T Consensus       185 F~~~lFk~~~~Ek~i~~lis~Lrkg~md~rLmef---------fPpnkrs~E~Fak~Ft~agL~el----vey~~~q~~~  251 (412)
T KOG2297|consen  185 FAVKLFKEWLVEKDINDLISSLRKGKMDDRLMEF---------FPPNKRSVEHFAKYFTDAGLKEL----VEYHRNQQSE  251 (412)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHhcChHhHHHHh---------cCCcchhHHHHHHHHhHhhHHHH----HHHHHHHHHH
Confidence            3566777777777778888777665543333222         34555555555555555553111    111111    


Q ss_pred             -CcHHHHHHHHHHHHhcCCHHHHHHHH-HHHHhCCCCCCHH----HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC
Q 011102          261 -ASKGVLEATAKGFVKGGNLKLAWKLL-MVAKDGGRMLDPS----IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS  334 (493)
Q Consensus       261 -~~~~~~~~li~~~~~~g~~~~A~~l~-~~m~~~g~~pd~~----t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~  334 (493)
                       .-...-..|..-..+...+++..... ++|++.++ |++.    .|+.+|++---+.+.---|.+.++.          
T Consensus       252 ~a~kElq~~L~~q~s~e~p~~evi~~VKee~k~~nl-Pe~eVi~ivWs~iMsaveWnKkeelva~qalrh----------  320 (412)
T KOG2297|consen  252 GARKELQKELQEQVSEEDPVKEVILYVKEEMKRNNL-PETEVIGIVWSGIMSAVEWNKKEELVAEQALRH----------  320 (412)
T ss_pred             HHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcCC-CCceEEeeeHhhhhHHHhhchHHHHHHHHHHHH----------
Confidence             01123345555566666677766655 55666554 5543    5777776654441111222333332          


Q ss_pred             HHHHHHHHHHHHHcCCHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~  355 (493)
                      ..+|..|+.++|..|+.+.++
T Consensus       321 lK~yaPLL~af~s~g~sEL~L  341 (412)
T KOG2297|consen  321 LKQYAPLLAAFCSQGQSELEL  341 (412)
T ss_pred             HHhhhHHHHHHhcCChHHHHH
Confidence            346788888888888877554

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=90.71  E-value=3.1  Score=39.58  Aligned_cols=79  Identities=20%  Similarity=0.288  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HCCCCCCHHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-----EAGFCPTYDIYR  444 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-----~~g~~p~~~ty~  444 (493)
                      ..++..++..+...|+.+.+...++++..... -|...|..++.+|.+.|+...|.+.|+.+.     +.|+.|-..+..
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp-~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~  231 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDP-YDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRA  231 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHH
Confidence            45555666666666666666666666555432 355566666666666666666666665554     345555555555


Q ss_pred             HHHHH
Q 011102          445 DMIRI  449 (493)
Q Consensus       445 ~li~~  449 (493)
                      ...+.
T Consensus       232 ~y~~~  236 (280)
T COG3629         232 LYEEI  236 (280)
T ss_pred             HHHHH
Confidence            44444

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=90.09  E-value=25  Score=36.24  Aligned_cols=372  Identities=14%  Similarity=0.067  Sum_probs=195.3

Q ss_pred             cCCCccccchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhhhhhhhhhhhccCCchhHHHHH
Q 011102           92 ADNDFIWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLASSRASICKQVYKNPSFLISLA  171 (493)
Q Consensus        92 ~~~~~~~~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~l~~l~  171 (493)
                      +.++..+++|+++.|..+|-+-..-.++|.+-|+--.          .+|+..+....|+..+.-  +..-.|..-.++.
T Consensus         7 ~kgnaa~s~~d~~~ai~~~t~ai~l~p~nhvlySnrs----------aa~a~~~~~~~al~da~k--~~~l~p~w~kgy~   74 (539)
T KOG0548|consen    7 EKGNAAFSSGDFETAIRLFTEAIMLSPTNHVLYSNRS----------AAYASLGSYEKALKDATK--TRRLNPDWAKGYS   74 (539)
T ss_pred             HHHHhhcccccHHHHHHHHHHHHccCCCccchhcchH----------HHHHHHhhHHHHHHHHHH--HHhcCCchhhHHH
Confidence            4566788899999999999887333455887777777          778888887776322111  1111122222333


Q ss_pred             HHHhhccCCCCHHHHHHHHhhhcccC-cHHHHHHHHHhCCChHHH-HHHHH----HHHhCCCC-----CCCHHHHHHHHH
Q 011102          172 RDIKGLDSHKDVAEVLDKCGRFLRKG-SLSFTVRELGHMNLPERA-LQTFC----WAQKQPHL-----FPDDRLLASTVE  240 (493)
Q Consensus       172 ~~l~~~~~~~~~~~a~~~~~~m~~~~-~~~~li~~~~~~g~~~~A-~~l~~----~m~~~~g~-----~pd~~t~~~li~  240 (493)
                      +.-.++.-.|++++|+..|.+-+..+ +--.|..++...-..+.+ -+.|.    ++... +.     ......|..++.
T Consensus        75 r~Gaa~~~lg~~~eA~~ay~~GL~~d~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~-~~p~t~~~~~~~~~~~~l~  153 (539)
T KOG0548|consen   75 RKGAALFGLGDYEEAILAYSEGLEKDPSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLA-NLPLTNYSLSDPAYVKILE  153 (539)
T ss_pred             HhHHHHHhcccHHHHHHHHHHHhhcCCchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhh-cChhhhhhhccHHHHHHHH
Confidence            33333444599999999999877765 333334444433322211 11110    11000 00     000111233332


Q ss_pred             HHHHcC-----CCc---hhhhHH--------Hhh---------------cc----C---cH----------HHHHHHHHH
Q 011102          241 VLARHH-----ELK---VPFKLE--------NFV---------------SL----A---SK----------GVLEATAKG  272 (493)
Q Consensus       241 ~~~~~g-----~~~---~~~~l~--------~~~---------------~~----~---~~----------~~~~~li~~  272 (493)
                      .+-+..     .+.   ...++-        .+.               .+    +   +.          .-+..+.++
T Consensus       154 ~~~~~p~~l~~~l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgna  233 (539)
T KOG0548|consen  154 IIQKNPTSLKLYLNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNA  233 (539)
T ss_pred             HhhcCcHhhhcccccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHH
Confidence            221110     000   000000        000               00    0   00          025567777


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHH-HHHHHHHhcCCCCHHHHHHHHHHHhhcCC-----CCCCHHHHHHHHHHHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLDPSIY-AKLILELGKNPDKYMLVMTLLDELGQRDD-----LNLSQQDCTAIMKVGI  346 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd~~t~-~~li~~~~~~~~~~~~a~~l~~~m~~~~g-----~~p~~~~~~~li~~~~  346 (493)
                      .-+..+++.|.+-+....+..   ...+| +..-.+|... |.+.+....-+.-.+.++     .+.=...+..+-++|.
T Consensus       234 aykkk~f~~a~q~y~~a~el~---~~it~~~n~aA~~~e~-~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~a~~  309 (539)
T KOG0548|consen  234 AYKKKDFETAIQHYAKALELA---TDITYLNNIAAVYLER-GKYAECIELCEKAVEVGRELRADYKLIAKALARLGNAYT  309 (539)
T ss_pred             HHHhhhHHHHHHHHHHHHhHh---hhhHHHHHHHHHHHhc-cHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhhhhh
Confidence            777888888888888777754   33344 3444456666 666555544443333211     0000112223445777


Q ss_pred             HcCCHHHHHHHHHHHHHcCCCCCHHHHHH-------------------------HHHHHHcCCCHHHHHHHHHHHHHCCC
Q 011102          347 RLQKFGVVESLFHWFTHSGRDPTVVMYTT-------------------------LIHSRLSEKKCREALTVVWNMEASNC  401 (493)
Q Consensus       347 ~~g~~~~A~~l~~~m~~~g~~p~~~ty~~-------------------------li~~~~~~g~~~~A~~l~~~M~~~gi  401 (493)
                      +.++++.|...|.+....-..||..+=..                         =-+.+.+.|++..|.+-+.++.... 
T Consensus       310 k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~-  388 (539)
T KOG0548|consen  310 KREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRD-  388 (539)
T ss_pred             hHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-
Confidence            77888888888887665444454443111                         1235567788888998888887765 


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHH
Q 011102          402 LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTY-DIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVE  480 (493)
Q Consensus       402 ~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~  480 (493)
                      +-|...|+.---+|.+.|.+..|++=-+.-.+.  .|+. .-|.-=-.++.-..++++|.+.|++-.+.  .|+..-+..
T Consensus       389 P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL--~p~~~kgy~RKg~al~~mk~ydkAleay~eale~--dp~~~e~~~  464 (539)
T KOG0548|consen  389 PEDARLYSNRAACYLKLGEYPEALKDAKKCIEL--DPNFIKAYLRKGAALRAMKEYDKALEAYQEALEL--DPSNAEAID  464 (539)
T ss_pred             CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhc--CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc--CchhHHHHH
Confidence            345678888888888888888887765554443  2322 11211122222334677777777776653  355555544


Q ss_pred             HHHhh
Q 011102          481 LLQIE  485 (493)
Q Consensus       481 Ll~~~  485 (493)
                      -++-|
T Consensus       465 ~~~rc  469 (539)
T KOG0548|consen  465 GYRRC  469 (539)
T ss_pred             HHHHH
Confidence            44444

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=90.01  E-value=30  Score=36.99  Aligned_cols=267  Identities=12%  Similarity=0.021  Sum_probs=144.9

Q ss_pred             CCCHHHHHHHHhhhcccCcHHHHHHHHHhCCChHHHHHHHHH----------------HHhCCCCCCCHHHHHHHHHHHH
Q 011102          180 HKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCW----------------AQKQPHLFPDDRLLASTVEVLA  243 (493)
Q Consensus       180 ~~~~~~a~~~~~~m~~~~~~~~li~~~~~~g~~~~A~~l~~~----------------m~~~~g~~pd~~t~~~li~~~~  243 (493)
                      -|.+++|.+.+-.+.+++   ..|..+.+.|+|-...++++.                |-+.   -.+...|......|.
T Consensus       747 ~g~feeaek~yld~drrD---LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~---fa~~~~We~A~~yY~  820 (1189)
T KOG2041|consen  747 YGEFEEAEKLYLDADRRD---LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGET---FAEMMEWEEAAKYYS  820 (1189)
T ss_pred             hcchhHhhhhhhccchhh---hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence            488899999888776664   223344444444444444332                1110   112233445555555


Q ss_pred             HcCCCch-hhhH---HHhhc-------cC-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcC
Q 011102          244 RHHELKV-PFKL---ENFVS-------LA-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKN  311 (493)
Q Consensus       244 ~~g~~~~-~~~l---~~~~~-------~~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~  311 (493)
                      ..|+.+. .+.+   +.|.+       ++ +....-.+.+++...|.-++|.+.|-+--.    |     .+.++.|...
T Consensus       821 ~~~~~e~~~ecly~le~f~~LE~la~~Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~----p-----kaAv~tCv~L  891 (1189)
T KOG2041|consen  821 YCGDTENQIECLYRLELFGELEVLARTLPEDSELLPVMADMFTSVGMCDQAVEAYLRRSL----P-----KAAVHTCVEL  891 (1189)
T ss_pred             hccchHhHHHHHHHHHhhhhHHHHHHhcCcccchHHHHHHHHHhhchHHHHHHHHHhccC----c-----HHHHHHHHHH
Confidence            5555321 1111   12222       12 333566778888888888888887754322    2     2345666666


Q ss_pred             CCCHHHHHHHHHHHhhcCCCCCCHHHH--------------HHHHHHHHHcCCHHHHHHHHHHHHH----cCCCCCH---
Q 011102          312 PDKYMLVMTLLDELGQRDDLNLSQQDC--------------TAIMKVGIRLQKFGVVESLFHWFTH----SGRDPTV---  370 (493)
Q Consensus       312 ~~~~~~a~~l~~~m~~~~g~~p~~~~~--------------~~li~~~~~~g~~~~A~~l~~~m~~----~g~~p~~---  370 (493)
                       ++|.+|.++-+...-     |.+.+.              ---|..+.+.|+.-+|-+++.+|.+    ++.++-.   
T Consensus       892 -nQW~~avelaq~~~l-----~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae~e~~K~~p~lr~Kk  965 (1189)
T KOG2041|consen  892 -NQWGEAVELAQRFQL-----PQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAEREQEKYVPYLRLKK  965 (1189)
T ss_pred             -HHHHHHHHHHHhccc-----hhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhHHHhhccCCHHHHHH
Confidence             788888877654321     111111              1246677788888788888888853    3443322   


Q ss_pred             -HHHHHHH-HHH----------HcCCCHHHHHHHHHHHHHC---CCC----CCHHHHHHHHHH--HHHcCCHHHHHHHHH
Q 011102          371 -VMYTTLI-HSR----------LSEKKCREALTVVWNMEAS---NCL----FDLPAYRVVIKL--FVALNDISRAIRYFS  429 (493)
Q Consensus       371 -~ty~~li-~~~----------~~~g~~~~A~~l~~~M~~~---gi~----pd~~ty~~li~~--~~~~g~~~~A~~~~~  429 (493)
                       +...+|+ .-+          -..|..++|.++++.-...   .+.    -....|.-+|-+  -...|.++.|.+.--
T Consensus       966 lYVL~AlLvE~h~~~ik~~~~~~~~g~~~dat~lles~~l~~~~ri~~n~WrgAEAyHFmilAQrql~eg~v~~Al~Tal 1045 (1189)
T KOG2041|consen  966 LYVLGALLVENHRQTIKELRKIDKHGFLEDATDLLESGLLAEQSRILENTWRGAEAYHFMILAQRQLFEGRVKDALQTAL 1045 (1189)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhcCcchhhhhhhhhhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHhchHHHHHHHHh
Confidence             1122221 111          1246677777766543211   111    123344444444  566789999988766


Q ss_pred             HHH-HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          430 KLK-EAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       430 ~m~-~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      .+. -..+-|....|+.|.-+-|....+-.+-+.|-+++
T Consensus      1046 ~L~DYEd~lpP~eiySllALaaca~raFGtCSKAfmkLe 1084 (1189)
T KOG2041|consen 1046 ILSDYEDFLPPAEIYSLLALAACAVRAFGTCSKAFMKLE 1084 (1189)
T ss_pred             hhccHhhcCCHHHHHHHHHHHHhhhhhhhhhHHHHHHHH
Confidence            666 34566888889888777666655555555444444

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.99  E-value=6.5  Score=42.52  Aligned_cols=175  Identities=13%  Similarity=0.055  Sum_probs=90.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH----hcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          267 EATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILEL----GKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       267 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~----~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      ..-|+.+++...++.|..+-+.   .+  .|..+...++..|    .+. |++++|..-+.+-...  +.|     ..+|
T Consensus       338 e~kL~iL~kK~ly~~Ai~LAk~---~~--~d~d~~~~i~~kYgd~Ly~K-gdf~~A~~qYI~tI~~--le~-----s~Vi  404 (933)
T KOG2114|consen  338 ETKLDILFKKNLYKVAINLAKS---QH--LDEDTLAEIHRKYGDYLYGK-GDFDEATDQYIETIGF--LEP-----SEVI  404 (933)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHh---cC--CCHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHccc--CCh-----HHHH
Confidence            3455566666666666555432   22  2333333444333    233 6777776666555432  333     2345


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      .-|-...++.+--..++.+.+.|. -+...-+.||.+|.+.++.++-.++.+.-. .|..-  .-.-..+..|-+.+-++
T Consensus       405 ~kfLdaq~IknLt~YLe~L~~~gl-a~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~~--fd~e~al~Ilr~snyl~  480 (933)
T KOG2114|consen  405 KKFLDAQRIKNLTSYLEALHKKGL-ANSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEWF--FDVETALEILRKSNYLD  480 (933)
T ss_pred             HHhcCHHHHHHHHHHHHHHHHccc-ccchhHHHHHHHHHHhcchHHHHHHHhcCC-Cccee--eeHHHHHHHHHHhChHH
Confidence            555555555555666666666664 333444667777777777776666665443 33221  11344555566666666


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          423 RAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      +|..+-.....     +......++   -..|++++|++.+..|
T Consensus       481 ~a~~LA~k~~~-----he~vl~ill---e~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  481 EAELLATKFKK-----HEWVLDILL---EDLHNYEEALRYISSL  516 (933)
T ss_pred             HHHHHHHHhcc-----CHHHHHHHH---HHhcCHHHHHHHHhcC
Confidence            66655444322     222223333   2346666666665554

>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=89.80  E-value=13  Score=32.52  Aligned_cols=33  Identities=15%  Similarity=0.182  Sum_probs=17.3

Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHH
Q 011102          285 LLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLV  318 (493)
Q Consensus       285 l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a  318 (493)
                      .++-+.+.|+.|+...|..+|+.+.+. |++...
T Consensus        16 YirSl~~~~i~~~~~L~~lli~lLi~~-~~~~~L   48 (167)
T PF07035_consen   16 YIRSLNQHNIPVQHELYELLIDLLIRN-GQFSQL   48 (167)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHc-CCHHHH
Confidence            334444555555555555555555555 544333

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=89.69  E-value=23  Score=35.29  Aligned_cols=31  Identities=13%  Similarity=0.093  Sum_probs=23.2

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          439 TYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       439 ~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      |---+.+++.++.-.|+.++|.+..+.|.+.
T Consensus       304 dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  304 DYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            4445577788888888888888888888754

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=89.61  E-value=9.7  Score=38.45  Aligned_cols=139  Identities=12%  Similarity=0.132  Sum_probs=91.5

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCC------HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH
Q 011102          274 VKGGNLKLAWKLLMVAKDGGRMLD------PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR  347 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~~~g~~pd------~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~  347 (493)
                      -+.+++.+|.++|.+..+..- -+      .+.-+.+|++|...  +.+.....+.+..+..|-.+-...|-.+  .+.+
T Consensus        17 qkq~~~~esEkifskI~~e~~-~~~f~lkeEvl~grilnAffl~--nld~Me~~l~~l~~~~~~s~~l~LF~~L--~~Y~   91 (549)
T PF07079_consen   17 QKQKKFQESEKIFSKIYDEKE-SSPFLLKEEVLGGRILNAFFLN--NLDLMEKQLMELRQQFGKSAYLPLFKAL--VAYK   91 (549)
T ss_pred             HHHhhhhHHHHHHHHHHHHhh-cchHHHHHHHHhhHHHHHHHHh--hHHHHHHHHHHHHHhcCCchHHHHHHHH--HHHH
Confidence            467899999999998877532 22      22345778888875  6777777777777653332222222222  2246


Q ss_pred             cCCHHHHHHHHHHHHHc--CCCC------------CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCCHHHHH
Q 011102          348 LQKFGVVESLFHWFTHS--GRDP------------TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFDLPAYR  409 (493)
Q Consensus       348 ~g~~~~A~~l~~~m~~~--g~~p------------~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd~~ty~  409 (493)
                      .+.+++|.+.+..-.+.  +..|            |.+-=+..++++...|++.++..++++|...    .+..|..+|+
T Consensus        92 ~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd  171 (549)
T PF07079_consen   92 QKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYD  171 (549)
T ss_pred             hhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHH
Confidence            78888888888766544  3332            2222356777888888888888888887654    3447888888


Q ss_pred             HHHHHHHH
Q 011102          410 VVIKLFVA  417 (493)
Q Consensus       410 ~li~~~~~  417 (493)
                      .++-.+++
T Consensus       172 ~~vlmlsr  179 (549)
T PF07079_consen  172 RAVLMLSR  179 (549)
T ss_pred             HHHHHHhH
Confidence            87777765

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=89.60  E-value=4.8  Score=38.28  Aligned_cols=99  Identities=16%  Similarity=0.015  Sum_probs=61.4

Q ss_pred             hcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHH
Q 011102          309 GKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCR  387 (493)
Q Consensus       309 ~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~  387 (493)
                      .+. +++.+|+..|.+..+-  ..-|.+-|.---.+|++.|.++.|++=.+.-...  .| -..+|..|=.+|...|+++
T Consensus        92 m~~-~~Y~eAv~kY~~AI~l--~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~~  166 (304)
T KOG0553|consen   92 MKN-KDYQEAVDKYTEAIEL--DPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKYE  166 (304)
T ss_pred             HHh-hhHHHHHHHHHHHHhc--CCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcHH
Confidence            345 6777777777776653  2234555555667777777777776665554422  23 2456777777777777777


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          388 EALTVVWNMEASNCLFDLPAYRVVIKL  414 (493)
Q Consensus       388 ~A~~l~~~M~~~gi~pd~~ty~~li~~  414 (493)
                      +|.+.|+...+  +.|+-.+|-.=|..
T Consensus       167 ~A~~aykKaLe--ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  167 EAIEAYKKALE--LDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHHhhhc--cCCCcHHHHHHHHH
Confidence            77777765543  46666666554443

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=89.60  E-value=22  Score=34.76  Aligned_cols=282  Identities=14%  Similarity=0.061  Sum_probs=172.4

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC--cHHHHHH---HHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHH--HHHHHcCC
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG--SLSFTVR---ELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTV--EVLARHHE  247 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~--~~~~li~---~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li--~~~~~~g~  247 (493)
                      +.+...|++.+|+..|....+-+  .|-++.+   .|...|+...|+.=|....   .++||-.. ..+-  ..+.+.|.
T Consensus        46 k~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVl---elKpDF~~-ARiQRg~vllK~Ge  121 (504)
T KOG0624|consen   46 KELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVL---ELKPDFMA-ARIQRGVVLLKQGE  121 (504)
T ss_pred             HHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHH---hcCccHHH-HHHHhchhhhhccc
Confidence            34445577888888777655443  6655543   6677777778887777776   34677432 1111  22456676


Q ss_pred             CchhhhHHHh--hccCcHH----------------HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHH
Q 011102          248 LKVPFKLENF--VSLASKG----------------VLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILEL  308 (493)
Q Consensus       248 ~~~~~~l~~~--~~~~~~~----------------~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~  308 (493)
                      ++.+++-+..  ...++..                ..-..+..+.-.|+...|+.....+.+-  .| |...|..--.+|
T Consensus       122 le~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi--~~Wda~l~~~Rakc~  199 (504)
T KOG0624|consen  122 LEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEI--QPWDASLRQARAKCY  199 (504)
T ss_pred             HHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhc--CcchhHHHHHHHHHH
Confidence            5554443221  1112111                1234455667788888998888888773  34 344455556677


Q ss_pred             hcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHH------------
Q 011102          309 GKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTL------------  376 (493)
Q Consensus       309 ~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~l------------  376 (493)
                      ... |....|+.=++...+-  -.-++.++--+-.-+...|+.+.++...++..+.  .||--.+-..            
T Consensus       200 i~~-~e~k~AI~Dlk~askL--s~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKl--dpdHK~Cf~~YKklkKv~K~le  274 (504)
T KOG0624|consen  200 IAE-GEPKKAIHDLKQASKL--SQDNTEGHYKISQLLYTVGDAENSLKEIRECLKL--DPDHKLCFPFYKKLKKVVKSLE  274 (504)
T ss_pred             Hhc-CcHHHHHHHHHHHHhc--cccchHHHHHHHHHHHhhhhHHHHHHHHHHHHcc--CcchhhHHHHHHHHHHHHHHHH
Confidence            777 8888887666555432  1234444445556677888888888888777643  5654332211            


Q ss_pred             -HHHHHcCCCHHHHHHHHHHHHHCCCCCCHHH---HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHH
Q 011102          377 -IHSRLSEKKCREALTVVWNMEASNCLFDLPA---YRVVIKLFVALNDISRAIRYFSKLKEAGFCPT-YDIYRDMIRIFM  451 (493)
Q Consensus       377 -i~~~~~~g~~~~A~~l~~~M~~~gi~pd~~t---y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~li~~~~  451 (493)
                       +......++|.++++-.+...+..-.-..++   +..+-.++...|++.+|++.-.+..+.  .|| +.++.-=..+|.
T Consensus       275 s~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~--d~~dv~~l~dRAeA~l  352 (504)
T KOG0624|consen  275 SAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDI--DPDDVQVLCDRAEAYL  352 (504)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhc--CchHHHHHHHHHHHHh
Confidence             1233445666666666666444322211223   344556677888999999988888753  354 778877778888


Q ss_pred             HcCCHHHHHHHHHHHHHC
Q 011102          452 ASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       452 ~~g~~~~A~~l~~~m~~~  469 (493)
                      -...+++|..=|+...+.
T Consensus       353 ~dE~YD~AI~dye~A~e~  370 (504)
T KOG0624|consen  353 GDEMYDDAIHDYEKALEL  370 (504)
T ss_pred             hhHHHHHHHHHHHHHHhc
Confidence            888888888888777653

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=89.30  E-value=21  Score=34.19  Aligned_cols=231  Identities=11%  Similarity=-0.038  Sum_probs=124.6

Q ss_pred             HhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHH
Q 011102          207 GHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLL  286 (493)
Q Consensus       207 ~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~  286 (493)
                      .+.|+.+.|..++........ ..+......+..                       ..||.-...+.+..+++.|...+
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~-~~~~~~~~~La~-----------------------~~yn~G~~l~~~~~~~~~a~~wL   59 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLN-SLDPDMAEELAR-----------------------VCYNIGKSLLSKKDKYEEAVKWL   59 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHh-cCCcHHHHHHHH-----------------------HHHHHHHHHHHcCCChHHHHHHH
Confidence            457888888888887765421 112222222222                       23444444444443555555555


Q ss_pred             HHHHhC--------CCCCCH-----HHHHHHHHHHhcCCCC---HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCC
Q 011102          287 MVAKDG--------GRMLDP-----SIYAKLILELGKNPDK---YMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQK  350 (493)
Q Consensus       287 ~~m~~~--------g~~pd~-----~t~~~li~~~~~~~~~---~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~  350 (493)
                      ++..+.        ...|+.     .++..++.+|... +.   .++|..+++.+....+-+  ..++-.-|..+.+.++
T Consensus        60 ~~a~~~l~~~~~~~~~~~~~~elr~~iL~~La~~~l~~-~~~~~~~ka~~~l~~l~~e~~~~--~~~~~L~l~il~~~~~  136 (278)
T PF08631_consen   60 QRAYDILEKPGKMDKLSPDGSELRLSILRLLANAYLEW-DTYESVEKALNALRLLESEYGNK--PEVFLLKLEILLKSFD  136 (278)
T ss_pred             HHHHHHHHhhhhccccCCcHHHHHHHHHHHHHHHHHcC-CChHHHHHHHHHHHHHHHhCCCC--cHHHHHHHHHHhccCC
Confidence            443322        233443     3456677777776 44   456677777776653333  3445455666666899


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHH---HcCCCHHHHHHHHHHHHHCCCCCCHH--HHHHHHHH---HHHc----
Q 011102          351 FGVVESLFHWFTHSGRDPTVVMYTTLIHSR---LSEKKCREALTVVWNMEASNCLFDLP--AYRVVIKL---FVAL----  418 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~~p~~~ty~~li~~~---~~~g~~~~A~~l~~~M~~~gi~pd~~--ty~~li~~---~~~~----  418 (493)
                      .+++.+++..|...-. -....+..++..+   ... ....|...+..+....+.|...  .=..++..   ..+.    
T Consensus       137 ~~~~~~~L~~mi~~~~-~~e~~~~~~l~~i~~l~~~-~~~~a~~~ld~~l~~r~~~~~~~~~e~~vl~~~~~~~~~~~~~  214 (278)
T PF08631_consen  137 EEEYEEILMRMIRSVD-HSESNFDSILHHIKQLAEK-SPELAAFCLDYLLLNRFKSSEDQWLEKLVLTRVLLTTQSKDLS  214 (278)
T ss_pred             hhHHHHHHHHHHHhcc-cccchHHHHHHHHHHHHhh-CcHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHcCCcccc
Confidence            9999999999986521 1334455555555   333 3456777777776665555553  11112221   1111    


Q ss_pred             --CCHHHHHHHHHHHH-HCCCCCCHHHHHHHHH-------HHHHcCCHHHHHHHHHHH
Q 011102          419 --NDISRAIRYFSKLK-EAGFCPTYDIYRDMIR-------IFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       419 --g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~-------~~~~~g~~~~A~~l~~~m  466 (493)
                        ++++...++++... ..+-+.+..+-.++..       .+.+.+++++|.+.|+--
T Consensus       215 ~~~~i~~l~~~~~~v~~~~~~~ls~~~~~a~~~LLW~~~~~~~~~k~y~~A~~w~~~a  272 (278)
T PF08631_consen  215 SSEKIESLEELLSIVEHSLGKQLSAEAASAIHTLLWNKGKKHYKAKNYDEAIEWYELA  272 (278)
T ss_pred             chhHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Confidence              12555556666433 2333334444333322       245678999999988743

It is also involved in sporulation [].

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.20  E-value=3.6  Score=39.38  Aligned_cols=47  Identities=17%  Similarity=0.106  Sum_probs=23.8

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          350 KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      +.++++.++..=.+.|+-||.++++.+|+.+.+.++..+|..+.-.|
T Consensus       115 ~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~  161 (418)
T KOG4570|consen  115 DPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEV  161 (418)
T ss_pred             ChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHH
Confidence            34445555444444555555555555555555555555555544443

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=89.11  E-value=10  Score=32.23  Aligned_cols=80  Identities=13%  Similarity=0.181  Sum_probs=37.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCC---C--CCCHHHHHHHHHHHHHcCC-HHHHHHHHHHHHHCCCCCCHHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEASN---C--LFDLPAYRVVIKLFVALND-ISRAIRYFSKLKEAGFCPTYDIYRDM  446 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~~g---i--~pd~~ty~~li~~~~~~g~-~~~A~~~~~~m~~~g~~p~~~ty~~l  446 (493)
                      .|+++.-....+++...+.+++.+..-.   +  .-|..+|.+++.+.++..- ---+..+|+-|++.+.+++..-|..|
T Consensus        42 iN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~~~~~~t~~dy~~l  121 (145)
T PF13762_consen   42 INCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKKNDIEFTPSDYSCL  121 (145)
T ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            4555555555555555555554442110   0  1223345555555544443 22334445555555555555555555


Q ss_pred             HHHHHH
Q 011102          447 IRIFMA  452 (493)
Q Consensus       447 i~~~~~  452 (493)
                      |.++.+
T Consensus       122 i~~~l~  127 (145)
T PF13762_consen  122 IKAALR  127 (145)
T ss_pred             HHHHHc
Confidence            555444

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=89.08  E-value=5.8  Score=35.17  Aligned_cols=60  Identities=5%  Similarity=-0.021  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT--VVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      .+..+.+-|++.|+.+.|.+.|.++.+....+.  ...+-.+|....-.+++..+...+.+.
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            344555555555555555555555554433332  223344444444555555555544443

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.

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=88.65  E-value=27  Score=34.70  Aligned_cols=242  Identities=14%  Similarity=-0.007  Sum_probs=142.8

Q ss_pred             hCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHH----HHHcCCCchhhhHHHhhc-----cC-cHHHHHHHHHHHHhcC
Q 011102          208 HMNLPERALQTFCWAQKQPHLFPDDRLLASTVEV----LARHHELKVPFKLENFVS-----LA-SKGVLEATAKGFVKGG  277 (493)
Q Consensus       208 ~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~----~~~~g~~~~~~~l~~~~~-----~~-~~~~~~~li~~~~~~g  277 (493)
                      -.|+.+.|.+-|+.|...      ..|--.=+.+    --+.|.-+   +-..|.+     -+ -.-.+.+.+...|..|
T Consensus       132 ~eG~~~~Ar~kfeAMl~d------PEtRllGLRgLyleAqr~Gare---aAr~yAe~Aa~~Ap~l~WA~~AtLe~r~~~g  202 (531)
T COG3898         132 LEGDYEDARKKFEAMLDD------PETRLLGLRGLYLEAQRLGARE---AARHYAERAAEKAPQLPWAARATLEARCAAG  202 (531)
T ss_pred             hcCchHHHHHHHHHHhcC------hHHHHHhHHHHHHHHHhcccHH---HHHHHHHHHHhhccCCchHHHHHHHHHHhcC
Confidence            368888888888888753      2222221222    22333322   2222222     11 2235788999999999


Q ss_pred             CHHHHHHHHHHHHhCC-CCCCHHH--HHHHHHHHhc--CCCCHHHHHHHHHHHhhcCCCCCCHHHHH-HHHHHHHHcCCH
Q 011102          278 NLKLAWKLLMVAKDGG-RMLDPSI--YAKLILELGK--NPDKYMLVMTLLDELGQRDDLNLSQQDCT-AIMKVGIRLQKF  351 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g-~~pd~~t--~~~li~~~~~--~~~~~~~a~~l~~~m~~~~g~~p~~~~~~-~li~~~~~~g~~  351 (493)
                      +|+.|+++++.-++.. +.++..-  -..|+.+-..  ...+...|...-.+..   .+.||.+--. ..-.+|.+.|++
T Consensus       203 dWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~---KL~pdlvPaav~AAralf~d~~~  279 (531)
T COG3898         203 DWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEAN---KLAPDLVPAAVVAARALFRDGNL  279 (531)
T ss_pred             ChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHh---hcCCccchHHHHHHHHHHhccch
Confidence            9999999998776643 4455432  2234433221  1123444444333322   3455544322 234678899999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCCC-HHHHHHHHHHHHHcCCHHHHHHHHH
Q 011102          352 GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS-NCLFD-LPAYRVVIKLFVALNDISRAIRYFS  429 (493)
Q Consensus       352 ~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~  429 (493)
                      .++-.+++.+.+..-.|++.    ++..+.+.|+  .+++-+++.+.. .++|| ..+--++..+-...|++..|..--+
T Consensus       280 rKg~~ilE~aWK~ePHP~ia----~lY~~ar~gd--ta~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Ae  353 (531)
T COG3898         280 RKGSKILETAWKAEPHPDIA----LLYVRARSGD--TALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAE  353 (531)
T ss_pred             hhhhhHHHHHHhcCCChHHH----HHHHHhcCCC--cHHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHH
Confidence            99999999999876666642    3344455554  333333333221 23444 4566667777888888887776555


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHC
Q 011102          430 KLKEAGFCPTYDIYRDMIRIFMAS-GRLAKCRDVCKEAEMA  469 (493)
Q Consensus       430 ~m~~~g~~p~~~ty~~li~~~~~~-g~~~~A~~l~~~m~~~  469 (493)
                      ....  ..|....|-.|.+.-.-. |+-.++...+-+-.+.
T Consensus       354 aa~r--~~pres~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         354 AAAR--EAPRESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             HHhh--hCchhhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence            5432  358888888887776544 8888888887777654

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=88.40  E-value=6.3  Score=33.52  Aligned_cols=95  Identities=6%  Similarity=0.049  Sum_probs=73.3

Q ss_pred             HHHHHCCCCCCHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHCC---C--CCCHHHHHHHHHHHHHcCC-HHHHHHHHHH
Q 011102          394 WNMEASNCLFDLP--AYRVVIKLFVALNDISRAIRYFSKLKEAG---F--CPTYDIYRDMIRIFMASGR-LAKCRDVCKE  465 (493)
Q Consensus       394 ~~M~~~gi~pd~~--ty~~li~~~~~~g~~~~A~~~~~~m~~~g---~--~p~~~ty~~li~~~~~~g~-~~~A~~l~~~  465 (493)
                      ..|++.+..++..  ..|+++.-....+.+.....+++.+..-.   +  .-+-.+|.+++.+.++..- ---+..+|+-
T Consensus        26 ~y~~~~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~  105 (145)
T PF13762_consen   26 PYMQEENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNF  105 (145)
T ss_pred             HHhhhcccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHH
Confidence            3455566666654  46888888888899998888888874110   0  2356679999999977766 4557889999


Q ss_pred             HHHCCCccCHHHHHHHHHhhhhc
Q 011102          466 AEMAGFKLDKQTVVELLQIEKES  488 (493)
Q Consensus       466 m~~~g~~pd~~t~~~Ll~~~~~~  488 (493)
                      |++.+.+++..-|..||+.|..+
T Consensus       106 Lk~~~~~~t~~dy~~li~~~l~g  128 (145)
T PF13762_consen  106 LKKNDIEFTPSDYSCLIKAALRG  128 (145)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHcC
Confidence            99999999999999999988765

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=88.23  E-value=11  Score=38.12  Aligned_cols=115  Identities=15%  Similarity=0.034  Sum_probs=76.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH--hcCCCCHHHHHHHHHHHhhc-CCCCC-------
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILEL--GKNPDKYMLVMTLLDELGQR-DDLNL-------  333 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~--~~~~~~~~~a~~l~~~m~~~-~g~~p-------  333 (493)
                      +.-+-+|++|...+ .+.....+.+..+.-  | ...|-.+..++  .+. +.+.+|.+.+..-... .+.++       
T Consensus        47 vl~grilnAffl~n-ld~Me~~l~~l~~~~--~-~s~~l~LF~~L~~Y~~-k~~~kal~~ls~w~~~~~~~~~~~Ld~ni  121 (549)
T PF07079_consen   47 VLGGRILNAFFLNN-LDLMEKQLMELRQQF--G-KSAYLPLFKALVAYKQ-KEYRKALQALSVWKEQIKGTESPWLDTNI  121 (549)
T ss_pred             HHhhHHHHHHHHhh-HHHHHHHHHHHHHhc--C-CchHHHHHHHHHHHHh-hhHHHHHHHHHHHHhhhcccccchhhhhH
Confidence            34678889988654 666666666665532  3 23344444432  344 7888888887765443 11222       


Q ss_pred             -----CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHHHcC
Q 011102          334 -----SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSG----RDPTVVMYTTLIHSRLSE  383 (493)
Q Consensus       334 -----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g----~~p~~~ty~~li~~~~~~  383 (493)
                           |-..=+..++.+.+.|++.++..+++.|...=    +..++.+||-++-.+.+.
T Consensus       122 ~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vlmlsrS  180 (549)
T PF07079_consen  122 QQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVLMLSRS  180 (549)
T ss_pred             HHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHHHHhHH
Confidence                 12223577889999999999999999887644    448999999988777764

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=87.89  E-value=26  Score=33.51  Aligned_cols=157  Identities=10%  Similarity=-0.011  Sum_probs=94.1

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHH
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAW  283 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~  283 (493)
                      ..|...|-++.+   +..+....--.|+..+...++..+-.          +.-....|...|--|-..|.+.|+.+.|.
T Consensus       110 g~y~~vg~~~q~---~~r~~~~~a~~~~~~~~~~l~a~Le~----------~L~~nP~d~egW~~Lg~~ym~~~~~~~A~  176 (287)
T COG4235         110 GLYQAVGAPEQP---ADRLADPLAQPPAEQEMEALIARLET----------HLQQNPGDAEGWDLLGRAYMALGRASDAL  176 (287)
T ss_pred             hhhhhcCCcccc---chhhhcccccCCCcccHHHHHHHHHH----------HHHhCCCCchhHHHHHHHHHHhcchhHHH
Confidence            345555666655   33333331223454445555433221          11233446778999999999999999999


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHhc--CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          284 KLLMVAKDGGRMLDPSIYAKLILELGK--NPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWF  361 (493)
Q Consensus       284 ~l~~~m~~~g~~pd~~t~~~li~~~~~--~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m  361 (493)
                      .-|....+.- .+++..+..+-.++..  .+....++.++|+++...  -.-|+.+-.-|-..+...|++.+|...|+.|
T Consensus       177 ~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~--D~~~iral~lLA~~afe~g~~~~A~~~Wq~l  253 (287)
T COG4235         177 LAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALAL--DPANIRALSLLAFAAFEQGDYAEAAAAWQML  253 (287)
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            9999887731 1344444444333322  224557888899988764  1234444555556788888999999999888


Q ss_pred             HHcCCCCCHHHHHHHHH
Q 011102          362 THSGRDPTVVMYTTLIH  378 (493)
Q Consensus       362 ~~~g~~p~~~ty~~li~  378 (493)
                      .+.  .|.-..+..+|.
T Consensus       254 L~~--lp~~~~rr~~ie  268 (287)
T COG4235         254 LDL--LPADDPRRSLIE  268 (287)
T ss_pred             Hhc--CCCCCchHHHHH
Confidence            865  343344455444

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=87.59  E-value=13  Score=35.36  Aligned_cols=118  Identities=9%  Similarity=0.039  Sum_probs=60.0

Q ss_pred             CHHHHHHHHHHHHh-CCCCCCHHHHHHHHHHHhc-CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          278 NLKLAWKLLMVAKD-GGRMLDPSIYAKLILELGK-NPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       278 ~~~~A~~l~~~m~~-~g~~pd~~t~~~li~~~~~-~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~  355 (493)
                      .+.+|+++|+...- ..+--|..+...+++.... .......-.++.+-+....+-.++..+...+|..+++.+++..-.
T Consensus       143 ~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~  222 (292)
T PF13929_consen  143 IVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLF  222 (292)
T ss_pred             HHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHH
Confidence            34556666552211 2234455555555555544 211222222333333333244556666666666666666666666


Q ss_pred             HHHHHHHHc-CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 011102          356 SLFHWFTHS-GRDPTVVMYTTLIHSRLSEKKCREALTVVWN  395 (493)
Q Consensus       356 ~l~~~m~~~-g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~  395 (493)
                      ++++.-... +..-|..-|...|+.-...|+..-..+++++
T Consensus       223 ~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~  263 (292)
T PF13929_consen  223 QFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDD  263 (292)
T ss_pred             HHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhC
Confidence            666655433 4444566666666666666665555555543

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.59  E-value=8.6  Score=36.92  Aligned_cols=48  Identities=10%  Similarity=0.113  Sum_probs=25.5

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      +.++++-++..=.+-|+-||..+++.+|+.+.+.+++.+|.++.-.|.
T Consensus       115 ~pq~~i~~l~npIqYGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  115 DPQKAIYTLVNPIQYGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             ChHHHHHHHhCcchhccccchhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            344555555554555555555555555555555555555555544444

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=87.19  E-value=60  Score=37.00  Aligned_cols=115  Identities=9%  Similarity=0.044  Sum_probs=73.6

Q ss_pred             CCCHHHHHHHHHHH----HHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHH-
Q 011102          332 NLSQQDCTAIMKVG----IRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLP-  406 (493)
Q Consensus       332 ~p~~~~~~~li~~~----~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~-  406 (493)
                      .|+...+..+..+|    ...+.+++|--.|+..-+         ----+.+|-.+|+|.+|+.+..+|...   -|.. 
T Consensus       932 ~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gk---------lekAl~a~~~~~dWr~~l~~a~ql~~~---~de~~  999 (1265)
T KOG1920|consen  932 KPDSEKQKVIYEAYADHLREELMSDEAALMYERCGK---------LEKALKAYKECGDWREALSLAAQLSEG---KDELV  999 (1265)
T ss_pred             ccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhcc---------HHHHHHHHHHhccHHHHHHHHHhhcCC---HHHHH
Confidence            45555555444443    455667777666654321         123467788888888888888777532   1222 


Q ss_pred             -HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          407 -AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       407 -ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                       +--.|+.-+...++.-+|-++..+....        +.-.+..||+...|++|..+-..-
T Consensus      1000 ~~a~~L~s~L~e~~kh~eAa~il~e~~sd--------~~~av~ll~ka~~~~eAlrva~~~ 1052 (1265)
T KOG1920|consen 1000 ILAEELVSRLVEQRKHYEAAKILLEYLSD--------PEEAVALLCKAKEWEEALRVASKA 1052 (1265)
T ss_pred             HHHHHHHHHHHHcccchhHHHHHHHHhcC--------HHHHHHHHhhHhHHHHHHHHHHhc
Confidence             2356777788889888888888776532        344566677888888888765543

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=87.17  E-value=7.3  Score=37.14  Aligned_cols=79  Identities=9%  Similarity=-0.003  Sum_probs=66.5

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCCCCHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEA-----SNCLFDLPAYR  409 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~-----~gi~pd~~ty~  409 (493)
                      ..++..++..+..+|+.+.+.+.++++.... +-|...|-.||.+|.+.|+...|+..++.+.+     .|+.|-..+..
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~  231 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRA  231 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHH
Confidence            5678889999999999999999999987542 44788899999999999999999999998865     48999888777


Q ss_pred             HHHHH
Q 011102          410 VVIKL  414 (493)
Q Consensus       410 ~li~~  414 (493)
                      .....
T Consensus       232 ~y~~~  236 (280)
T COG3629         232 LYEEI  236 (280)
T ss_pred             HHHHH
Confidence            66555

>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=87.00  E-value=20  Score=31.34  Aligned_cols=133  Identities=14%  Similarity=0.158  Sum_probs=84.9

Q ss_pred             HHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC--CHHHHHHHHHHHH
Q 011102          320 TLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK--KCREALTVVWNME  397 (493)
Q Consensus       320 ~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g--~~~~A~~l~~~M~  397 (493)
                      +.+..+.+. ++.|+...|..+|+.+.+.|++..    +..+...++-+|.......+-.+....  -..-|++++.++.
T Consensus        15 EYirSl~~~-~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~   89 (167)
T PF07035_consen   15 EYIRSLNQH-NIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLG   89 (167)
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhh
Confidence            444445555 788898999999999999988554    455556677777776666665444432  1334445554443


Q ss_pred             HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          398 ASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       398 ~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      .        .+..+++.+...|++-+|.++.+.....    +......++++-.+.++...-..+++-..++
T Consensus        90 ~--------~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~  149 (167)
T PF07035_consen   90 T--------AYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEER  149 (167)
T ss_pred             h--------hHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            2        3677888888899999999888775321    2223355677777777766555555555443

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=86.64  E-value=21  Score=31.23  Aligned_cols=199  Identities=18%  Similarity=0.067  Sum_probs=84.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhC-CCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH-
Q 011102          266 LEATAKGFVKGGNLKLAWKLLMVAKDG-GRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK-  343 (493)
Q Consensus       266 ~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~-  343 (493)
                      +......+...+.+..+...+...... ........+......+... +.+..+...+...... ...+ ......... 
T Consensus        62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~  138 (291)
T COG0457          62 LLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEAL-GKYEEALELLEKALAL-DPDP-DLAEALLALG  138 (291)
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHH-hhHHHHHHHHHHHHcC-CCCc-chHHHHHHHH
Confidence            333444444444444444444444331 1112223333333333333 4445555555544432 1111 111111111 


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGR--DPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~--~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      .+...|+++.|...|.+......  ......+......+...++.++|...+.+............+..+-..+...++.
T Consensus       139 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (291)
T COG0457         139 ALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKY  218 (291)
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhhCcccchHHHHHhhHHHHHcccH
Confidence            45555555555555555532110  0122333333333445555556665555554432111244455555555555556


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          422 SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       422 ~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +.|...+.......-. ....+..+...+...|..+++...+.+..+
T Consensus       219 ~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (291)
T COG0457         219 EEALEYYEKALELDPD-NAEALYNLALLLLELGRYEEALEALEKALE  264 (291)
T ss_pred             HHHHHHHHHHHhhCcc-cHHHHhhHHHHHHHcCCHHHHHHHHHHHHH
Confidence            6666665555532211 123333333333344555555555555443

>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=86.20  E-value=11  Score=33.52  Aligned_cols=97  Identities=13%  Similarity=0.022  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHH---HCCCCCCHHHHHH
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL--PAYRVVIKLFVALNDISRAIRYFSKLK---EAGFCPTYDIYRD  445 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~--~ty~~li~~~~~~g~~~~A~~~~~~m~---~~g~~p~~~ty~~  445 (493)
                      ..+..+..-|++.|+.++|++.+.++.+....+..  ..+-.+|......|++..+.....+..   +.|-.++...--.
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk  116 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLK  116 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence            55777788888888888888888888876554443  356777788888888888877776655   3332222222112


Q ss_pred             HHHH--HHHcCCHHHHHHHHHHHH
Q 011102          446 MIRI--FMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       446 li~~--~~~~g~~~~A~~l~~~m~  467 (493)
                      ...|  +...|++.+|-++|-+..
T Consensus       117 ~~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  117 VYEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHHhchHHHHHHHHHccC
Confidence            2222  234678888887776654

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.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.16  E-value=12  Score=35.13  Aligned_cols=97  Identities=12%  Similarity=0.011  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCCC-HHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGR--DPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS-NCLFD-LPAYRVV  411 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~--~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-gi~pd-~~ty~~l  411 (493)
                      ..|+.-++.| +.|++..|...|....+..-  .-....+-.|-.++...|+.++|..+|..+.+. +-.|- ..++--|
T Consensus       143 ~~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKl  221 (262)
T COG1729         143 KLYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKL  221 (262)
T ss_pred             HHHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHH
Confidence            3577666654 56668888888877765421  112234566777888888888888888777654 11121 1345555


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Q 011102          412 IKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      -....+.|+.++|..+|++..+
T Consensus       222 g~~~~~l~~~d~A~atl~qv~k  243 (262)
T COG1729         222 GVSLGRLGNTDEACATLQQVIK  243 (262)
T ss_pred             HHHHHHhcCHHHHHHHHHHHHH
Confidence            5666777778888887777763

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=85.85  E-value=31  Score=32.95  Aligned_cols=144  Identities=10%  Similarity=0.102  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHc-CC-CHHHHHHHHHHHHH-CCCCCCHHHHHHHHH
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTH-SGRDPTVVMYTTLIHSRLS-EK-KCREALTVVWNMEA-SNCLFDLPAYRVVIK  413 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~-~g~~p~~~ty~~li~~~~~-~g-~~~~A~~l~~~M~~-~gi~pd~~ty~~li~  413 (493)
                      |..|+.   +...+.+|+++|+.... ..+--|...-..|++.... .+ ....-.++.+-+.. .|-.++..+...+|.
T Consensus       134 Y~~LVk---~N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~  210 (292)
T PF13929_consen  134 YWDLVK---RNKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILE  210 (292)
T ss_pred             HHHHHH---hhHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHH
Confidence            555443   23346778888874332 2345567777777777776 22 33334445554443 356788889999999


Q ss_pred             HHHHcCCHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH-----HHHCCCccCHHHHHHHHHh
Q 011102          414 LFVALNDISRAIRYFSKLKEA-GFCPTYDIYRDMIRIFMASGRLAKCRDVCKE-----AEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       414 ~~~~~g~~~~A~~~~~~m~~~-g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~-----m~~~g~~pd~~t~~~Ll~~  484 (493)
                      .+++.+++..-.++++.-... +..-|...|..+|+.....|+..-..++.++     +++.|+..+...-..|-++
T Consensus       211 ~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~~~L~~~L~~L  287 (292)
T PF13929_consen  211 ILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVTDELRSQLSEL  287 (292)
T ss_pred             HHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCCHHHHHHHHHH
Confidence            999999999999999887744 5666889999999999999999877776655     2455666677666666554

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=85.76  E-value=7.2  Score=30.83  Aligned_cols=59  Identities=17%  Similarity=0.224  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHH
Q 011102          388 EALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIR  448 (493)
Q Consensus       388 ~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~  448 (493)
                      +..+-++.+....+.|+.....+.+.+|.+.+++..|.++|+..+ +.|-+  ...|..+++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~--~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNK--KEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT---TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCh--HHHHHHHHH
Confidence            455555555556667777777777777777777777777777766 33322  225665554

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 ....

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=85.23  E-value=27  Score=31.13  Aligned_cols=99  Identities=9%  Similarity=0.009  Sum_probs=45.7

Q ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc---CCCCCHHH
Q 011102          296 LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS---GRDPTVVM  372 (493)
Q Consensus       296 pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~---g~~p~~~t  372 (493)
                      |+..---.|-.++.+. |+..+|...|++...- -+.-|....-.+-++....+++..|...++++-+.   +-.||.  
T Consensus        87 pTvqnr~rLa~al~el-Gr~~EA~~hy~qalsG-~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~--  162 (251)
T COG4700          87 PTVQNRYRLANALAEL-GRYHEAVPHYQQALSG-IFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDG--  162 (251)
T ss_pred             hhHHHHHHHHHHHHHh-hhhhhhHHHHHHHhcc-ccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCc--
Confidence            3333333444444444 5555555555554432 23344444444445555555555555555554432   122332  


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      --.+-..|...|+..+|+.-|+....
T Consensus       163 ~Ll~aR~laa~g~~a~Aesafe~a~~  188 (251)
T COG4700         163 HLLFARTLAAQGKYADAESAFEVAIS  188 (251)
T ss_pred             hHHHHHHHHhcCCchhHHHHHHHHHH
Confidence            12333445555555555555555444

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=84.87  E-value=41  Score=32.96  Aligned_cols=67  Identities=10%  Similarity=0.082  Sum_probs=48.7

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          403 FDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCP---TYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       403 pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p---~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      ....+|..+...+.+.|.++.|...+..+...+...   +....-.-.+.+...|+.++|...+++..+.
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            345678888889999999999999998887644211   2233344556677888999999988888763

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.79  E-value=14  Score=34.82  Aligned_cols=98  Identities=12%  Similarity=0.054  Sum_probs=74.7

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCH-HHHHHH
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEASNC--LFDLPAYRVVIKLFVALNDISRAIRYFSKLK-EAGFCPTY-DIYRDM  446 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi--~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~-~ty~~l  446 (493)
                      ..|+.-++.| +.|++.+|.+.|..-.+..-  .-....+=.|-..+...|+.++|..+|..+. +.+-.|-. ..+--|
T Consensus       143 ~~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKl  221 (262)
T COG1729         143 KLYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKL  221 (262)
T ss_pred             HHHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHH
Confidence            3688777755 55679999999999887521  1122345568899999999999999999988 44443433 566677


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHC
Q 011102          447 IRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       447 i~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      -....+.|+.++|..+|++..+.
T Consensus       222 g~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         222 GVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHH
Confidence            77888999999999999999864

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=84.69  E-value=27  Score=30.71  Aligned_cols=131  Identities=9%  Similarity=-0.029  Sum_probs=66.6

Q ss_pred             HHcCCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHH-HH--HHHcCCH
Q 011102          346 IRLQKFGVVESLFHWFTHSGRDPTVV-MYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVI-KL--FVALNDI  421 (493)
Q Consensus       346 ~~~g~~~~A~~l~~~m~~~g~~p~~~-ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li-~~--~~~~g~~  421 (493)
                      ++.++.++|+.-|.++.+.|..--.+ .---+-......|+-..|...|++.-...-.|-..-=.+=+ .+  +...|.+
T Consensus        69 A~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gsy  148 (221)
T COG4649          69 AQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGSY  148 (221)
T ss_pred             HHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhccccH
Confidence            45566666666666666554432111 11111223445666777777777665554444333111111 11  3456666


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHH
Q 011102          422 SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       422 ~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~  476 (493)
                      ++...-.+-+...|-.--...-.+|--+-.+.|++.+|.+.|+.+....-.|-.+
T Consensus       149 ~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da~aprni  203 (221)
T COG4649         149 DDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAPRNI  203 (221)
T ss_pred             HHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccccCcHHH
Confidence            6666665555433322222333445455556777777777777766554455433

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.62  E-value=20  Score=39.02  Aligned_cols=79  Identities=11%  Similarity=0.138  Sum_probs=38.7

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFG  352 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~  352 (493)
                      +.+.|++++|...|-+-... +.|     ..+|.-|-.. .++..-..+++.+.+. |+ .+...-+.||++|.|.++.+
T Consensus       378 Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfLda-q~IknLt~YLe~L~~~-gl-a~~dhttlLLncYiKlkd~~  448 (933)
T KOG2114|consen  378 LYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFLDA-QRIKNLTSYLEALHKK-GL-ANSDHTTLLLNCYIKLKDVE  448 (933)
T ss_pred             HHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhcCH-HHHHHHHHHHHHHHHc-cc-ccchhHHHHHHHHHHhcchH
Confidence            34556666665555443321 111     2234444444 4555555555555554 44 23344455666666666655


Q ss_pred             HHHHHHHH
Q 011102          353 VVESLFHW  360 (493)
Q Consensus       353 ~A~~l~~~  360 (493)
                      .-.++.+.
T Consensus       449 kL~efI~~  456 (933)
T KOG2114|consen  449 KLTEFISK  456 (933)
T ss_pred             HHHHHHhc
Confidence            55544443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=84.56  E-value=31  Score=31.21  Aligned_cols=152  Identities=10%  Similarity=0.053  Sum_probs=83.1

Q ss_pred             HhcCCCCHHHHHHHHHHHhhcC-CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH
Q 011102          308 LGKNPDKYMLVMTLLDELGQRD-DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC  386 (493)
Q Consensus       308 ~~~~~~~~~~a~~l~~~m~~~~-g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~  386 (493)
                      +... |++.+|.+.|+.+.... +-.--....-.+..++.+.|+++.|...|+++.+.--.-...-+...+.|.+.....
T Consensus        15 ~~~~-g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~~~~   93 (203)
T PF13525_consen   15 ALQQ-GDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYYKQI   93 (203)
T ss_dssp             HHHC-T-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHHHHH
T ss_pred             HHHC-CCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHhC
Confidence            3344 78899999998887652 112223345566778888899999999998876542221223344444444432222


Q ss_pred             HHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          387 REALTVVWNMEASNC---LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVC  463 (493)
Q Consensus       387 ~~A~~l~~~M~~~gi---~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~  463 (493)
                      ....     +.....   .--..+|..+|.-|-......+|...+..+.+.=    ...--.+.+-|.+.|.+..|..-+
T Consensus        94 ~~~~-----~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~l----a~~e~~ia~~Y~~~~~y~aA~~r~  164 (203)
T PF13525_consen   94 PGIL-----RSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNRL----AEHELYIARFYYKRGKYKAAIIRF  164 (203)
T ss_dssp             HHHH------TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHH----HHHHHHHHHHHHCTT-HHHHHHHH
T ss_pred             ccch-----hcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHcccHHHHHHHH
Confidence            2221     000000   0012356667777777777777777666665210    011122556678888888888888


Q ss_pred             HHHHHC
Q 011102          464 KEAEMA  469 (493)
Q Consensus       464 ~~m~~~  469 (493)
                      +.+.+.
T Consensus       165 ~~v~~~  170 (203)
T PF13525_consen  165 QYVIEN  170 (203)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            887764

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=84.49  E-value=42  Score=32.74  Aligned_cols=202  Identities=9%  Similarity=-0.066  Sum_probs=127.0

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH----HHHHHHcCC
Q 011102          275 KGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI----MKVGIRLQK  350 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l----i~~~~~~g~  350 (493)
                      -.|+..+|...++++.+. .+.|...++-.=++|.-. |+...-...++++...  ..+|...|+-+    --++..+|-
T Consensus       115 ~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~-G~~~~~k~ai~kIip~--wn~dlp~~sYv~GmyaFgL~E~g~  190 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYN-GNQIGKKNAIEKIIPK--WNADLPCYSYVHGMYAFGLEECGI  190 (491)
T ss_pred             ccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhc-cchhhhhhHHHHhccc--cCCCCcHHHHHHHHHHhhHHHhcc
Confidence            357778888888888764 456777888788888888 8888888888888754  45665444433    234457899


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          351 FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS---NCLFDLPAYRVVIKLFVALNDISRAIRY  427 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~---gi~pd~~ty~~li~~~~~~g~~~~A~~~  427 (493)
                      +++|++.-++-.+-+ .-|..+-.++-+.+-.+|++.++.++..+-...   +-..-...|=..--.+...+.++.|+++
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 YDDAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEI  269 (491)
T ss_pred             chhHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHH
Confidence            999999888765432 456777888889999999999999988765432   1111122233333345666899999999


Q ss_pred             HHHHH-HCCCCCCHHHH---HHHHHHHHHcCCHHHHHHHHHHHHH-----CCCccCHHHHHHH
Q 011102          428 FSKLK-EAGFCPTYDIY---RDMIRIFMASGRLAKCRDVCKEAEM-----AGFKLDKQTVVEL  481 (493)
Q Consensus       428 ~~~m~-~~g~~p~~~ty---~~li~~~~~~g~~~~A~~l~~~m~~-----~g~~pd~~t~~~L  481 (493)
                      |+.=. ..--+-|.+.-   .-+.....+.-.+.+-.++-+.+-.     ..+.-|+.||-.+
T Consensus       270 yD~ei~k~l~k~Da~a~~~~ld~dgv~~~~d~~~kld~la~~l~d~a~~~~d~~~~itt~~~~  332 (491)
T KOG2610|consen  270 YDREIWKRLEKDDAVARDVYLDLDGVDLRSDLWRKLDKLADSLTDKAMWYQDWLFDITTIWAL  332 (491)
T ss_pred             HHHHHHHHhhccchhhhhhhhhhhhHHhHHHHHHHHHhhhhhhcchhhhhhhhhhhhhHHhhh
Confidence            98654 32223344332   2223333344444444444444432     2445556665544

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=84.47  E-value=8.9  Score=30.01  Aligned_cols=62  Identities=16%  Similarity=0.223  Sum_probs=40.0

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIR  448 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~  448 (493)
                      +.-++.+-++.+....+.|+.....+.++||.+.+++..|.++|+..+ +.|.  +...|..+++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~--~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGA--HKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccC--chhhHHHHHH
Confidence            444555666666666677777777777777777777777777777666 3332  3445665554

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.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=84.24  E-value=40  Score=32.28  Aligned_cols=142  Identities=12%  Similarity=0.078  Sum_probs=80.1

Q ss_pred             HhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHH
Q 011102          308 LGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCR  387 (493)
Q Consensus       308 ~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~  387 (493)
                      .... |++.+|..+|+.....  ..-+...--.+..+|...|+++.|..+++.+...--.........=|.-+.+.....
T Consensus       144 ~~~~-e~~~~a~~~~~~al~~--~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~  220 (304)
T COG3118         144 LIEA-EDFGEAAPLLKQALQA--APENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATP  220 (304)
T ss_pred             hhhc-cchhhHHHHHHHHHHh--CcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCC
Confidence            3444 7777777777776554  112234445666777788888888888887654322222222223334444444444


Q ss_pred             HHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHH--HCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          388 EALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLK--EAGFCPTYDIYRDMIRIFMASGRL  456 (493)
Q Consensus       388 ~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~--~~g~~p~~~ty~~li~~~~~~g~~  456 (493)
                      +..++-.+...   .| |...--.+-..+...|+.++|.+.+-.+.  +.|.. |...=..|++.+.--|.-
T Consensus       221 ~~~~l~~~~aa---dPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~-d~~~Rk~lle~f~~~g~~  288 (304)
T COG3118         221 EIQDLQRRLAA---DPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFE-DGEARKTLLELFEAFGPA  288 (304)
T ss_pred             CHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccc-CcHHHHHHHHHHHhcCCC
Confidence            44444444433   25 44444556666777888888877665555  34444 445556666666666633

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=84.04  E-value=2.7  Score=26.11  Aligned_cols=26  Identities=19%  Similarity=0.300  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          442 IYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       442 ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      +|+.|-..|.+.|++++|.+++++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46778888888888888888888744

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=83.95  E-value=16  Score=31.01  Aligned_cols=81  Identities=5%  Similarity=-0.101  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSG--RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIK  413 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~  413 (493)
                      ..|+.-...+ +.|++++|.+.|+.+...-  -.-....--.|+.+|.+.+++++|...+++..+..-.--.+-|.-.+.
T Consensus        12 ~ly~~a~~~l-~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~   90 (142)
T PF13512_consen   12 ELYQEAQEAL-QKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMR   90 (142)
T ss_pred             HHHHHHHHHH-HhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHH
Confidence            3344433333 5567777777777766431  111234445566677777777777777766555432111234555555


Q ss_pred             HHHH
Q 011102          414 LFVA  417 (493)
Q Consensus       414 ~~~~  417 (493)
                      |++.
T Consensus        91 gL~~   94 (142)
T PF13512_consen   91 GLSY   94 (142)
T ss_pred             HHHH
Confidence            5544

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=83.66  E-value=16  Score=37.54  Aligned_cols=100  Identities=14%  Similarity=0.104  Sum_probs=54.6

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHH
Q 011102          375 TLIHSRLSEKKCREALTVVWNMEASN-CLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGF-CPTYDIYRDMIRIFMA  452 (493)
Q Consensus       375 ~li~~~~~~g~~~~A~~l~~~M~~~g-i~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~-~p~~~ty~~li~~~~~  452 (493)
                      -|-..+-+.|+.++|.+.|.+|.+.. ..-+....-.||.++...+...++..++.+..+... +--..+|+..+-.+-.
T Consensus       264 RLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaRa  343 (539)
T PF04184_consen  264 RLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKARA  343 (539)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHHh
Confidence            34555556788888888888776532 222334566777888888888888887777643222 1123445543332222


Q ss_pred             cCCHHHHHHHHHHHHHCCCccCHHHH
Q 011102          453 SGRLAKCRDVCKEAEMAGFKLDKQTV  478 (493)
Q Consensus       453 ~g~~~~A~~l~~~m~~~g~~pd~~t~  478 (493)
                      .|+--    --+...++|+.|....-
T Consensus       344 v~d~f----s~e~a~rRGls~ae~~a  365 (539)
T PF04184_consen  344 VGDKF----SPEAASRRGLSPAEMNA  365 (539)
T ss_pred             hcccc----CchhhhhcCCChhHHHH
Confidence            22211    01223456776666553

The molecular function of this protein is uncertain.

>PRK15331 chaperone protein SicA; Provisional

Probab=83.14  E-value=13  Score=32.39  Aligned_cols=87  Identities=10%  Similarity=-0.025  Sum_probs=55.6

Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRA  424 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A  424 (493)
                      +...|++++|..+|.-+...+. -|..-|..|-.++-..+++++|...|...-..+. -|...+--.=.+|...|+.+.|
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~d~-~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A  124 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIYDF-YNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCc-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHH
Confidence            3467888888888887765321 2333355565666667788888888877554332 2222233444567777888888


Q ss_pred             HHHHHHHHH
Q 011102          425 IRYFSKLKE  433 (493)
Q Consensus       425 ~~~~~~m~~  433 (493)
                      ...|+...+
T Consensus       125 ~~~f~~a~~  133 (165)
T PRK15331        125 RQCFELVNE  133 (165)
T ss_pred             HHHHHHHHh
Confidence            888877765

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=82.27  E-value=3.2  Score=25.72  Aligned_cols=26  Identities=15%  Similarity=0.158  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAK  290 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~  290 (493)
                      +|+.|-..|.+.|++++|.++|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46677788888888888888887743

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=82.21  E-value=66  Score=33.31  Aligned_cols=112  Identities=11%  Similarity=-0.002  Sum_probs=52.5

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHH-HHHHHHHHHHcC
Q 011102          271 KGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQD-CTAIMKVGIRLQ  349 (493)
Q Consensus       271 ~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~-~~~li~~~~~~g  349 (493)
                      ++|.+.++.+.|...|.+.......||..+=         . ...++++...+...   -+.|.... .-.--+.+.+.|
T Consensus       306 ~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~---------l-k~~Ek~~k~~e~~a---~~~pe~A~e~r~kGne~Fk~g  372 (539)
T KOG0548|consen  306 NAYTKREDYEGAIKYYQKALTEHRTPDLLSK---------L-KEAEKALKEAERKA---YINPEKAEEEREKGNEAFKKG  372 (539)
T ss_pred             hhhhhHHhHHHHHHHHHHHhhhhcCHHHHHH---------H-HHHHHHHHHHHHHH---hhChhHHHHHHHHHHHHHhcc
Confidence            3555567777777777776554444443321         1 12222222222221   11222110 001133444556


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          350 KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      ++..|...|.++.... +-|...|...--+|.+.|.+..|++=-+.-
T Consensus       373 dy~~Av~~YteAIkr~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~  418 (539)
T KOG0548|consen  373 DYPEAVKHYTEAIKRD-PEDARLYSNRAACYLKLGEYPEALKDAKKC  418 (539)
T ss_pred             CHHHHHHHHHHHHhcC-CchhHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            6666666666655443 335555666666666666665555544433

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=82.19  E-value=30  Score=29.34  Aligned_cols=85  Identities=12%  Similarity=0.135  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011102          299 SIYAKLILELGKNPDKYMLVMTLLDELGQRDDL-NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLI  377 (493)
Q Consensus       299 ~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~-~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li  377 (493)
                      ..|+.-...+- . |++++|.+.|+.+..+.-. .-....--.++.+|.+.|++++|...++.+.+..-.---+-|-..+
T Consensus        12 ~ly~~a~~~l~-~-~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~   89 (142)
T PF13512_consen   12 ELYQEAQEALQ-K-GNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYM   89 (142)
T ss_pred             HHHHHHHHHHH-h-CCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            34444444433 3 7888888888888775211 1234455677888889999999998888887654333335566666


Q ss_pred             HHHHcCCC
Q 011102          378 HSRLSEKK  385 (493)
Q Consensus       378 ~~~~~~g~  385 (493)
                      .|++.-..
T Consensus        90 ~gL~~~~~   97 (142)
T PF13512_consen   90 RGLSYYEQ   97 (142)
T ss_pred             HHHHHHHH
Confidence            66665443

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=81.86  E-value=19  Score=28.50  Aligned_cols=76  Identities=14%  Similarity=0.103  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHHcCCH--HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          407 AYRVVIKLFVALNDI--SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       407 ty~~li~~~~~~g~~--~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      .|++=...|....+.  -+..+-++.+....+.|+.....+.+.+|-|.+++..|.++|+-.+.+ +.+....|..+++
T Consensus        10 eF~ary~~~F~~~~iD~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K-~~~~~~~Y~~~lq   87 (108)
T PF02284_consen   10 EFDARYEKYFNRPDIDGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK-CGNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHHH-TT--HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TTT-TTHHHHHHH
T ss_pred             HHHHHHHHHhCCccccHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-ccChHHHHHHHHH
Confidence            344444445544433  366777888888999999999999999999999999999999998754 2333338888887

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 ....

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=81.43  E-value=30  Score=28.89  Aligned_cols=91  Identities=13%  Similarity=0.000  Sum_probs=63.8

Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCCCHHHHHHHH---HHHHHcC
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS-NCLFDLPAYRVVI---KLFVALN  419 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-gi~pd~~ty~~li---~~~~~~g  419 (493)
                      +++..|+++.|++.|.+-... .+-....||.--+++.-.|+.++|++=+++..+. |-+ ......+.+   ..|...|
T Consensus        52 alaE~g~Ld~AlE~F~qal~l-~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-trtacqa~vQRg~lyRl~g  129 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL-APERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TRTACQAFVQRGLLYRLLG  129 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh-cccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHhC
Confidence            567889999999999876532 1346678999999999999999999888887654 333 222222222   3366778


Q ss_pred             CHHHHHHHHHHHHHCCC
Q 011102          420 DISRAIRYFSKLKEAGF  436 (493)
Q Consensus       420 ~~~~A~~~~~~m~~~g~  436 (493)
                      +.+.|..=|+.-.+-|-
T Consensus       130 ~dd~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  130 NDDAARADFEAAAQLGS  146 (175)
T ss_pred             chHHHHHhHHHHHHhCC
Confidence            88888888877665553

>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]

Probab=80.53  E-value=57  Score=31.43  Aligned_cols=141  Identities=7%  Similarity=0.020  Sum_probs=68.9

Q ss_pred             hHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCC----------CCHHHHHHHH
Q 011102          253 KLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNP----------DKYMLVMTLL  322 (493)
Q Consensus       253 ~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~----------~~~~~a~~l~  322 (493)
                      ++..|.........|.+|..+.+.+.-+.-+++|        +|+..+-...-..+...+          .....|.+-+
T Consensus       186 ~~~lFk~~~~Ek~i~~lis~Lrkg~md~rLmeff--------Ppnkrs~E~Fak~Ft~agL~elvey~~~q~~~~a~kEl  257 (412)
T KOG2297|consen  186 AVKLFKEWLVEKDINDLISSLRKGKMDDRLMEFF--------PPNKRSVEHFAKYFTDAGLKELVEYHRNQQSEGARKEL  257 (412)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHhcChHhHHHHhc--------CCcchhHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHH
Confidence            3344554444555677777777777666555554        355444333333333320          1222222111


Q ss_pred             HHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH-HHHHHcCCCCCH----HHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          323 DELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLF-HWFTHSGRDPTV----VMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       323 ~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~-~~m~~~g~~p~~----~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      +               ..|.+-..+...+++..... ++|++..+ |+.    +.|.++|++---+    +-.++..+-.
T Consensus       258 q---------------~~L~~q~s~e~p~~evi~~VKee~k~~nl-Pe~eVi~ivWs~iMsaveWn----Kkeelva~qa  317 (412)
T KOG2297|consen  258 Q---------------KELQEQVSEEDPVKEVILYVKEEMKRNNL-PETEVIGIVWSGIMSAVEWN----KKEELVAEQA  317 (412)
T ss_pred             H---------------HHHHHHhccCCCHHHHHHHHHHHHHhcCC-CCceEEeeeHhhhhHHHhhc----hHHHHHHHHH
Confidence            1               12222233334455555444 45665554 444    3466666654433    3333322211


Q ss_pred             HCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          398 ASNCLFDLPAYRVVIKLFVALNDISRAI  425 (493)
Q Consensus       398 ~~gi~pd~~ty~~li~~~~~~g~~~~A~  425 (493)
                      -    --..+|.-|+.++|..|+.+.++
T Consensus       318 l----rhlK~yaPLL~af~s~g~sEL~L  341 (412)
T KOG2297|consen  318 L----RHLKQYAPLLAAFCSQGQSELEL  341 (412)
T ss_pred             H----HHHHhhhHHHHHHhcCChHHHHH
Confidence            1    12457899999999999876553

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=80.46  E-value=50  Score=30.80  Aligned_cols=166  Identities=11%  Similarity=0.059  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc-CCCCCCH--HHHHHHHHHHHHcCCHHHHH
Q 011102          279 LKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQR-DDLNLSQ--QDCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~-~g~~p~~--~~~~~li~~~~~~g~~~~A~  355 (493)
                      .+.|.-+.++|.+..  --..-|+.-...|..+ |..+.|-..++..-+. .++.|+.  ..|..-+...-..++...|.
T Consensus        74 yEqaamLake~~kls--Evvdl~eKAs~lY~E~-GspdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~  150 (308)
T KOG1585|consen   74 YEQAAMLAKELSKLS--EVVDLYEKASELYVEC-GSPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAF  150 (308)
T ss_pred             HHHHHHHHHHHHHhH--HHHHHHHHHHHHHHHh-CCcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHH
Confidence            344555555554421  1122355566666666 6666655555543211 1244442  23333333333333333333


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          356 SLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFDL-PAYRVVIKLFVALNDISRAIRYFSK  430 (493)
Q Consensus       356 ~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd~-~ty~~li~~~~~~g~~~~A~~~~~~  430 (493)
                      +++               ...-..|.+..++++|-..|.+-...    .--++. ..|.+.|-.+....++..|.+.++.
T Consensus       151 el~---------------gk~sr~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~  215 (308)
T KOG1585|consen  151 ELY---------------GKCSRVLVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRD  215 (308)
T ss_pred             HHH---------------HHhhhHhhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcc
Confidence            333               33445566777777766555432211    111222 2355666667777899999999987


Q ss_pred             HH---HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          431 LK---EAGFCPTYDIYRDMIRIFMASGRLAKCRDVC  463 (493)
Q Consensus       431 m~---~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~  463 (493)
                      -.   ...-.-+..+...||.+| ..|+.+++.+++
T Consensus       216 ~~qip~f~~sed~r~lenLL~ay-d~gD~E~~~kvl  250 (308)
T KOG1585|consen  216 CSQIPAFLKSEDSRSLENLLTAY-DEGDIEEIKKVL  250 (308)
T ss_pred             hhcCccccChHHHHHHHHHHHHh-ccCCHHHHHHHH
Confidence            43   222234677888899888 558888877653

---

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	493
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-07
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-05

>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 = 52.5 bits (125), Expect = 3e-07
 Identities = 85/544 (15%), Positives = 160/544 (29%), Gaps = 172/544 (31%)

Query: 49  KLPKNLQNPRRTKLPPDFGVNLFLKKPSDEYDPIKADSVEEQEADN-DFIWESEELEAIS 107
                +    R      F     L K  +         VEE    N  F+    + E   
Sbjct: 56  MSKDAVSGTLRL-----FW--TLLSKQEEMVQ----KFVEEVLRINYKFLMSPIKTEQRQ 104

Query: 108 -SLFQGRIPQKPGRLYRERPL--PLPLPHRLRP--------LELPTPKKRV--------- 147
            S+      ++  RLY +  +     +  RL+P        LEL  P K V         
Sbjct: 105 PSMMTRMYIEQRDRLYNDNQVFAKYNVS-RLQPYLKLRQALLEL-RPAKNVLIDGVLGSG 162

Query: 148 --CLASS--RASICKQVYKNPSFLISLARDIKGLDSHKDVAEVLDKCGRFLRKGSLSFTV 203
              +A     +   +       F ++L       +S + V E+L K    L +   ++T 
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNC----NSPETVLEMLQK---LLYQIDPNWTS 215

Query: 204 RELGHMNLPER------ALQTFCWAQKQPH--LFPDD--------------RLLAST--- 238
           R     N+  R       L+    ++   +  L   +              ++L +T   
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK 275

Query: 239 -----VEVLARHH----ELKVPFKLENFVSLASKGVLEATAKGF---VKGGN-LKLA--- 282
                +      H       +    +   SL  K  L+   +     V   N  +L+   
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK-YLDCRPQDLPREVLTTNPRRLSIIA 334

Query: 283 ------------------WKLLMVAKDGGRMLDPSIYAKLILELGKNPD----------- 313
                              KL  + +    +L+P+ Y K+   L   P            
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394

Query: 314 -----KYMLVMTLLDELGQRDDLNLSQQDCT-AIMKVGIRLQKFGVVESLFH-------- 359
                    VM ++++L +   +    ++ T +I  + + L+     E   H        
Sbjct: 395 IWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYN 454

Query: 360 ------------------WFTHSG-------RDPTVVMYTTLIHS-RLSEKKCREALTVV 393
                             +++H G           + ++  +    R  E+K R   +  
Sbjct: 455 IPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHD-STA 513

Query: 394 WNMEAS--NCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTY--DIYR----D 445
           WN   S  N L  L  Y+     ++  ND     R  + + +  F P    ++      D
Sbjct: 514 WNASGSILNTLQQLKFYKP----YICDNDPKYE-RLVNAILD--FLPKIEENLICSKYTD 566

Query: 446 MIRI 449
           ++RI
Sbjct: 567 LLRI 570

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 46.7 bits (109), Expect = 2e-05
 Identities = 22/164 (13%), Positives = 53/164 (32%), Gaps = 4/164 (2%)

Query: 324 ELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL---FHWFTHSGRDPTVVMYTTLIHSR 380
               +  L+  QQ   A  K  +   +  +   L    H      +  T+ MY  ++   
Sbjct: 116 GQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGW 175

Query: 381 LSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAI-RYFSKLKEAGFCPT 439
             +   +E + V++ ++ +    DL +Y   ++     +  +  I R   ++ + G    
Sbjct: 176 ARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQ 235

Query: 440 YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ 483
                 ++     +  L     V     +           +LL+
Sbjct: 236 ALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLR 279

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	493
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.95
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.94
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.87
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.86
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.8
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.77
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.77
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.72
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.61
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.61
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.58
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.57
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.55
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.55
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.55
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.54
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.53
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.53
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.52
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.48
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.45
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.44
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.43
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.43
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.41
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.4
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.4
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.4
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.36
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.31
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.3
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.3
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.23
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.22
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.22
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.21
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.2
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.18
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.16
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.16
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.16
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.14
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.12
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.1
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.08
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.07
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.07
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.05
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.05
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.04
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.03
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.01
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.01
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.0
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.0
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.0
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	98.99
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	98.95
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.95
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	98.93
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	98.89
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.88
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	98.87
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.85
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	98.85
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.85
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	98.83
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.81
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.79
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	98.77
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.77
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.74
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	98.7
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.68
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.68
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.67
4g1t_A	472	Interferon-induced protein with tetratricopeptide	98.66
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.63
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	98.62
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.62
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	98.61
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	98.56
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.53
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.46
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.44
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	98.42
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.38
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.34
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.33
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.33
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.33
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.31
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.3
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.29
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.27
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.25
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.23
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.23
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.22
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.21
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.17
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.15
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.15
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.14
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.14
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.13
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.13
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.13
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.12
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.11
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.11
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.1
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.1
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.02
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.01
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.01
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	97.99
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.97
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.95
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	97.94
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	97.92
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	97.86
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.84
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.82
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.81
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.81
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.79
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	97.79
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.75
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.72
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.72
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.71
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.69
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	97.69
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.69
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	97.68
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	97.68
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.67
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	97.65
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.64
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	97.64
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.62
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	97.61
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.61
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.6
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.6
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.57
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.56
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.56
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	97.55
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.49
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.48
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.48
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.47
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.47
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	97.47
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	97.46
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	97.45
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.44
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.43
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.41
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	97.39
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	97.36
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	97.34
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	97.34
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.27
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.14
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.13
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.12
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.11
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.08
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.07
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.06
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.04
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	97.01
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.98
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	96.94
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	96.91
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	96.86
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	96.85
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.82
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	96.8
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.78
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.6
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	96.48
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	96.44
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.43
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	96.32
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	96.25
2l6j_A	111	TPR repeat-containing protein associated with HSP;	96.17
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.16
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	96.06
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.01
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.98
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	95.95
2l6j_A	111	TPR repeat-containing protein associated with HSP;	95.89
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	95.86
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.84
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	95.81
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	95.74
2kat_A	115	Uncharacterized protein; NESG, structure, structur	95.7
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.53
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	95.52
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.44
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	95.36
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	95.3
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	95.27
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	95.2
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	95.09
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	94.86
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	94.8
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	94.59
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	94.11
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	93.93
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	93.64
1pc2_A	152	Mitochondria fission protein; unknown function; NM	93.33
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	93.31
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	93.0
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	92.19
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	91.42
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	90.42
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	89.99
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	89.58
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	88.99
1pc2_A	152	Mitochondria fission protein; unknown function; NM	88.01
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	87.89
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	86.34
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	86.26
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	84.78
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	84.49
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	84.31
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	83.94
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	83.2
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	81.7

>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=1.8e-35  Score=306.39  Aligned_cols=187  Identities=12%  Similarity=0.134  Sum_probs=113.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCC---------HHHHHHHHHHHhhcCCCCCC
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDK---------YMLVMTLLDELGQRDDLNLS  334 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~---------~~~a~~l~~~m~~~~g~~p~  334 (493)
                      .+++.+|++|++.|++++|+++|++|.+.|+.||.+|||+||.+|++. +.         +++|.++|++|... |+.||
T Consensus        27 ~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~-~~~~~~~~~~~l~~A~~lf~~M~~~-G~~Pd  104 (501)
T 4g26_A           27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLA-EAATESSPNPGLSRGFDIFKQMIVD-KVVPN  104 (501)
T ss_dssp             HHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTC-CCCSSSSCCHHHHHHHHHHHHHHHT-TCCCC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhC-CchhhhhhcchHHHHHHHHHHHHHh-CCCCC
Confidence            345566666666666666666666666666666666666666666654 32         45555666666555 56666


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKL  414 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~  414 (493)
                      ..|||+||++|++.|++++|.++|++|.+.|+.||.+|||+||.+|++.|++++|.++|++|.+.|+.||..||++||.+
T Consensus       105 ~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~  184 (501)
T 4g26_A          105 EATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKV  184 (501)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            66666666666666666666666666666666666666666666666666666666666666666666666666666666


Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          415 FVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA  452 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~  452 (493)
                      |++.|++++|.++|++|.+.|+.|+..||++++..|+.
T Consensus       185 ~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          185 SMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             HhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            66666666666666666666666666666666555554

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=100.00  E-value=5.8e-35  Score=302.54  Aligned_cols=203  Identities=15%  Similarity=0.107  Sum_probs=180.3

Q ss_pred             HHHHHHHHHHHhCCCCCCHH-HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCC--------
Q 011102          280 KLAWKLLMVAKDGGRMLDPS-IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQK--------  350 (493)
Q Consensus       280 ~~A~~l~~~m~~~g~~pd~~-t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~--------  350 (493)
                      ..+..+.+++++.++...+. .++.+|++|++. |++++|+++|++|.+. |+.||..|||+||++|++.+.        
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~-G~~~~A~~lf~~M~~~-Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~   84 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEALLKQKLDMCSKK-GDVLEALRLYDEARRN-GVQLSQYHYNVLLYVCSLAEAATESSPNP   84 (501)
T ss_dssp             -----------------CHHHHHHHHHHHTTTS-CCHHHHHHHHHHHHHH-TCCCCHHHHHHHHHHHTTCCCCSSSSCCH
T ss_pred             chHHHHHHHHHHhcccCCCHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHc-CCCCCHhHHHHHHHHHHhCCchhhhhhcc
Confidence            45667778888888776654 689999999999 9999999999999998 999999999999999998765        


Q ss_pred             -HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Q 011102          351 -FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFS  429 (493)
Q Consensus       351 -~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~  429 (493)
                       +++|.++|++|.+.|+.||.+|||+||++|++.|++++|.++|++|.+.|+.||..|||+||.+|++.|++++|.++|+
T Consensus        85 ~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~  164 (501)
T 4g26_A           85 GLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDA  164 (501)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHH
Confidence             7899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          430 KLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       430 ~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      +|.+.|+.||..||++||++|++.|++++|.++|++|.+.|+.|+..||++|+..
T Consensus       165 ~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~  219 (501)
T 4g26_A          165 HMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEW  219 (501)
T ss_dssp             HHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHH
T ss_pred             HHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999984

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.95  E-value=2.1e-26  Score=243.96  Aligned_cols=361  Identities=8%  Similarity=-0.065  Sum_probs=203.8

Q ss_pred             cccchhHHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHHhhhh---hhhhhhhhccCCchhHHHHHHH
Q 011102           97 IWESEELEAISSLFQGRIPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRVCLAS---SRASICKQVYKNPSFLISLARD  173 (493)
Q Consensus        97 ~~~~~~~~~a~~lf~~m~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~~~a~---~~~~~~~~~~~~~~~l~~l~~~  173 (493)
                      ....|+++.|..+|+.|. +..|+..++..+.          ..|...|..++|.   ......+   ....   .....
T Consensus        94 ~~~~g~~~~A~~~~~~~~-~~~p~~~~~~~l~----------~~~~~~g~~~~A~~~~~~~~~~~---~~~~---~~~~l  156 (597)
T 2xpi_A           94 ALMQQQYKCAAFVGEKVL-DITGNPNDAFWLA----------QVYCCTGDYARAKCLLTKEDLYN---RSSA---CRYLA  156 (597)
T ss_dssp             HHHTTCHHHHHHHHHHHH-HHHCCHHHHHHHH----------HHHHHTTCHHHHHHHHHHTCGGG---TCHH---HHHHH
T ss_pred             HHHccCchHHHHHHHHHH-hhCCCchHHHHHH----------HHHHHcCcHHHHHHHHHHHhccc---cchh---HHHHH
Confidence            445788999999999882 2345556666666          6666666666661   1111011   1111   22334


Q ss_pred             HhhccCCCCHHHHHHHHhhh-ccc--------------------CcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCH
Q 011102          174 IKGLDSHKDVAEVLDKCGRF-LRK--------------------GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDD  232 (493)
Q Consensus       174 l~~~~~~~~~~~a~~~~~~m-~~~--------------------~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~  232 (493)
                      ...+.+.|++++|+++|++. +..                    .+|+.++.+|.+.|++++|+++|+.|.+. +.. +.
T Consensus       157 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~p~-~~  234 (597)
T 2xpi_A          157 AFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMV-DAK-CY  234 (597)
T ss_dssp             HHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTT-CH
T ss_pred             HHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-Cch-hh
Confidence            46677889999999999843 332                    27888999999999999999999988754 211 11


Q ss_pred             HHHHHH--------------------------------------HHHHHHcCCCchhhhHHHhhcc----CcHHHHHHHH
Q 011102          233 RLLAST--------------------------------------VEVLARHHELKVPFKLENFVSL----ASKGVLEATA  270 (493)
Q Consensus       233 ~t~~~l--------------------------------------i~~~~~~g~~~~~~~l~~~~~~----~~~~~~~~li  270 (493)
                      ..+..+                                      +.+|.+.|+  ..+++..|..+    .+..+|+.++
T Consensus       235 ~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~--~~~A~~~~~~~~~~~~~~~~~~~l~  312 (597)
T 2xpi_A          235 EAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDE--LRRAEDYLSSINGLEKSSDLLLCKA  312 (597)
T ss_dssp             HHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHH--HHHHHHHHHTSTTGGGCHHHHHHHH
T ss_pred             HHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcch--HHHHHHHHHHhhcCCchHHHHHHHH
Confidence            122211                                      222222232  12222223322    2444555555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCC---------------------------------CCCCHHHHHHHHHHHhcCCCCHHH
Q 011102          271 KGFVKGGNLKLAWKLLMVAKDGG---------------------------------RMLDPSIYAKLILELGKNPDKYML  317 (493)
Q Consensus       271 ~~~~~~g~~~~A~~l~~~m~~~g---------------------------------~~pd~~t~~~li~~~~~~~~~~~~  317 (493)
                      .+|.+.|++++|.++|++|.+.+                                 ...+..+|+.+...|.+. |++++
T Consensus       313 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~  391 (597)
T 2xpi_A          313 DTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCV-NKISE  391 (597)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHT-TCHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHh-ccHHH
Confidence            55555555555555555554432                                 122455555566666666 66666


Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          318 VMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       318 a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      |.++|+++.+.  ...+..+|+.++.+|.+.|++++|.++|+++.+.+ +.+..+|+.++.+|.+.|++++|.++|++|.
T Consensus       392 A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  468 (597)
T 2xpi_A          392 ARRYFSKSSTM--DPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSY  468 (597)
T ss_dssp             HHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            66666665543  12245566666666666666666666666655432 2355566666666666666666666666665


Q ss_pred             HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 011102          398 ASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEA----GFCPT--YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGF  471 (493)
Q Consensus       398 ~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~----g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~  471 (493)
                      +... .+..+|+.+...|.+.|++++|.++|+++.+.    +..|+  ..+|..+..+|.+.|++++|.++|+++.+.+ 
T Consensus       469 ~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-  546 (597)
T 2xpi_A          469 ALFQ-YDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-  546 (597)
T ss_dssp             HHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HhCC-CChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-
Confidence            4321 24556666666666666666666666666543    44555  5566666666666666666666666665543 


Q ss_pred             ccCHHHHHHHHHh
Q 011102          472 KLDKQTVVELLQI  484 (493)
Q Consensus       472 ~pd~~t~~~Ll~~  484 (493)
                      ..+..+|..+..+
T Consensus       547 p~~~~~~~~l~~~  559 (597)
T 2xpi_A          547 TNDANVHTAIALV  559 (597)
T ss_dssp             SCCHHHHHHHHHH
T ss_pred             CCChHHHHHHHHH
Confidence            2245555555543

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.94  E-value=7.6e-26  Score=239.70  Aligned_cols=299  Identities=6%  Similarity=-0.085  Sum_probs=257.0

Q ss_pred             HhhccCCCCHHHHHHHHhhhcc--cC--cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          174 IKGLDSHKDVAEVLDKCGRFLR--KG--SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       174 l~~~~~~~~~~~a~~~~~~m~~--~~--~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      +..+.+.|++++|.+.|+++..  .+  +|+.++.+|.+.|++++|+++|+.+.+. + ..+..+|+.++.++.+.|+++
T Consensus       279 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~-~~~~~~~~~l~~~~~~~g~~~  356 (597)
T 2xpi_A          279 LNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDVLAITTKILEI-D-PYNLDVYPLHLASLHESGEKN  356 (597)
T ss_dssp             SCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C-TTCCTTHHHHHHHHHHHTCHH
T ss_pred             HHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHc-C-cccHHHHHHHHHHHHHhCCHH
Confidence            3566788999999999998876  23  8999999999999999999999999865 3 236678999999999999955


Q ss_pred             hhhhHHHhhcc-----CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHH
Q 011102          250 VPFKLENFVSL-----ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDE  324 (493)
Q Consensus       250 ~~~~l~~~~~~-----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~  324 (493)
                      .  ++..+..+     .+..+|+.++.+|.+.|++++|.++|+++.+.. ..+..+|+.++.+|.+. |++++|.++|++
T Consensus       357 ~--A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~  432 (597)
T 2xpi_A          357 K--LYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIE-GEHDQAISAYTT  432 (597)
T ss_dssp             H--HHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH-TCHHHHHHHHHH
T ss_pred             H--HHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc-CCHHHHHHHHHH
Confidence            4  44444433     367789999999999999999999999998743 23578999999999999 999999999999


Q ss_pred             HhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----C
Q 011102          325 LGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS----N  400 (493)
Q Consensus       325 m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----g  400 (493)
                      +.+.  ...+..+|+.++.+|.+.|++++|.++|+++.+.. +.+..+|+.++..|.+.|++++|.++|++|.+.    +
T Consensus       433 ~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  509 (597)
T 2xpi_A          433 AARL--FQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQ  509 (597)
T ss_dssp             HHHT--TTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHh--CccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccc
Confidence            9875  34578999999999999999999999999998653 457899999999999999999999999999876    7


Q ss_pred             CCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccC-HHH
Q 011102          401 CLFD--LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLD-KQT  477 (493)
Q Consensus       401 i~pd--~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t  477 (493)
                      ..|+  ..+|..+..+|.+.|++++|.++|+++.+.+ ..+..+|..+..+|.+.|++++|.++|+++.+.  .|+ ...
T Consensus       510 ~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~  586 (597)
T 2xpi_A          510 SNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLS-TNDANVHTAIALVYLHKKIPGLAITHLHESLAI--SPNEIMA  586 (597)
T ss_dssp             CCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHH
T ss_pred             cchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCChHH
Confidence            7888  7899999999999999999999999998765 348899999999999999999999999999874  454 445


Q ss_pred             HHHHHHh
Q 011102          478 VVELLQI  484 (493)
Q Consensus       478 ~~~Ll~~  484 (493)
                      |..|-.+
T Consensus       587 ~~~l~~~  593 (597)
T 2xpi_A          587 SDLLKRA  593 (597)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHH
Confidence            5444443

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.87  E-value=1.2e-22  Score=216.79  Aligned_cols=136  Identities=13%  Similarity=0.138  Sum_probs=98.1

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHH---HcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q 011102          334 SQQDCTAIMKVGIRLQKFGVVESLFHWFT---HSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRV  410 (493)
Q Consensus       334 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~---~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~  410 (493)
                      -..|||+||++||++|++++|.++|++|.   ..|+.||++|||+||+|||+.|++++|.++|++|.+.|+.||.+|||+
T Consensus       126 ~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYnt  205 (1134)
T 3spa_A          126 QQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA  205 (1134)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHH
Confidence            34577777777777777777777777765   347777888888888888888888888888888877777788888888


Q ss_pred             HHHHHHHcCC-HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccC
Q 011102          411 VIKLFVALND-ISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLD  474 (493)
Q Consensus       411 li~~~~~~g~-~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd  474 (493)
                      ||+++|+.|+ .++|.++|++|.+.|+.||.+||++++.++.+.+    +++.++++ ..++.|+
T Consensus       206 LI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~----vL~~Vrkv-~P~f~p~  265 (1134)
T 3spa_A          206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRAT----VLKAVHKV-KPTFSLP  265 (1134)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHH----HHHHHGGG-CCCCCCC
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHH----HHHHHHHh-CcccCCC
Confidence            8887777776 4677777788877777788888877777666543    33333333 3455554

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.86  E-value=8.1e-22  Score=210.53  Aligned_cols=118  Identities=14%  Similarity=0.141  Sum_probs=110.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH---CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHH
Q 011102          367 DPTVVMYTTLIHSRLSEKKCREALTVVWNMEA---SNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIY  443 (493)
Q Consensus       367 ~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~---~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty  443 (493)
                      .--..|||+||++||+.|++++|.++|++|.+   .|+.||++|||+||+|||+.|++++|.++|++|.+.|+.||++||
T Consensus       124 ~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTY  203 (1134)
T 3spa_A          124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSY  203 (1134)
T ss_dssp             CHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHH
Confidence            34467999999999999999999999988764   589999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCC-HHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          444 RDMIRIFMASGR-LAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       444 ~~li~~~~~~g~-~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      |+||++||+.|+ .++|.++|++|.+.|+.||.+||++++..
T Consensus       204 ntLI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~  245 (1134)
T 3spa_A          204 AAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSE  245 (1134)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCH
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccCh
Confidence            999999999998 57899999999999999999999977653

>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=99.80  E-value=5.9e-18  Score=169.33  Aligned_cols=293  Identities=12%  Similarity=-0.015  Sum_probs=227.3

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCH-HHHHHHHHHHHHcCCC
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDD-RLLASTVEVLARHHEL  248 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~-~t~~~li~~~~~~g~~  248 (493)
                      ..+.+.|++++|+..|.++....     .|..+...+.+.|++++|++.|+.+.+.   .|+. ..+..+-..+...|++
T Consensus        75 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~  151 (388)
T 1w3b_A           75 NVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQY---NPDLYCVRSDLGNLLKALGRL  151 (388)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH---CTTCTHHHHHHHHHHHTTSCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHccCH
Confidence            44566788899988888765432     6788888889999999999999888754   3443 3556666677777875


Q ss_pred             chhhhHHHhhcc-----CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHH
Q 011102          249 KVPFKLENFVSL-----ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLD  323 (493)
Q Consensus       249 ~~~~~l~~~~~~-----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~  323 (493)
                      +.+  +..|...     .+..+|+.+...|.+.|++++|.+.|+++.+.. +-+...|..+-..+... |++++|...++
T Consensus       152 ~~A--~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~-~~~~~A~~~~~  227 (388)
T 1w3b_A          152 EEA--KACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEA-RIFDRAVAAYL  227 (388)
T ss_dssp             HHH--HHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTT-TCTTHHHHHHH
T ss_pred             HHH--HHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHc-CCHHHHHHHHH
Confidence            443  3334332     245688889999999999999999999988754 22456777777888888 89999999998


Q ss_pred             HHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC
Q 011102          324 ELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF  403 (493)
Q Consensus       324 ~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p  403 (493)
                      +....  -.-+..++..+...|.+.|++++|.+.|+++.+.. +.+..+|+.+...|.+.|++++|.+.|+++.+.. ..
T Consensus       228 ~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~  303 (388)
T 1w3b_A          228 RALSL--SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PT  303 (388)
T ss_dssp             HHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TT
T ss_pred             HHHhh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cc
Confidence            87664  12357888899999999999999999999988653 2356789999999999999999999999988753 45


Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccC-HHHHHHH
Q 011102          404 DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLD-KQTVVEL  481 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~L  481 (493)
                      +..+|+.+...+.+.|++++|...|+++.+.. +.+..+|..+...|.+.|++++|.+.|+++.+  +.|+ ...|..+
T Consensus       304 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~--~~p~~~~a~~~l  379 (388)
T 1w3b_A          304 HADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASVLQQQGKLQEALMHYKEAIR--ISPTFADAYSNM  379 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHT--TCTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCCHHHHHhH
Confidence            77889999999999999999999999988643 34578899999999999999999999999986  4554 3344433

>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=99.77  E-value=3.4e-15  Score=149.19  Aligned_cols=295  Identities=9%  Similarity=-0.036  Sum_probs=243.5

Q ss_pred             ccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCch
Q 011102          177 LDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELKV  250 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~~  250 (493)
                      +...++.++|...+.......     .|..+...|.+.|++++|++.|+.+.+.   .| +..+|..+..++.+.|+++.
T Consensus        43 ~~~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~  119 (388)
T 1w3b_A           43 HFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRL---KPDFIDGYINLAAALVAAGDMEG  119 (388)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHSCSSH
T ss_pred             HHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHc---CcchHHHHHHHHHHHHHcCCHHH
Confidence            455688999998887655433     7899999999999999999999999854   34 45579999999999999776


Q ss_pred             hhhHHHhhc----cC-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Q 011102          251 PFKLENFVS----LA-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDEL  325 (493)
Q Consensus       251 ~~~l~~~~~----~~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m  325 (493)
                      +...  |..    .| +..++..+-..|.+.|++++|.++|+++.+.. +-+..+|+.+...+.+. |++++|...|+++
T Consensus       120 A~~~--~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~a  195 (388)
T 1w3b_A          120 AVQA--YVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQ-GEIWLAIHHFEKA  195 (388)
T ss_dssp             HHHH--HHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTT-TCHHHHHHHHHHH
T ss_pred             HHHH--HHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc-CCHHHHHHHHHHH
Confidence            5543  332    22 44578888899999999999999999998853 23467899999999999 9999999999999


Q ss_pred             hhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH
Q 011102          326 GQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL  405 (493)
Q Consensus       326 ~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~  405 (493)
                      ...  -.-+...|..+-..+...|++++|...|++..+.. +-+..+|+.+...|.+.|++++|.+.|+++.+... -+.
T Consensus       196 l~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~  271 (388)
T 1w3b_A          196 VTL--DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQP-HFP  271 (388)
T ss_dssp             HHH--CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCS-SCH
T ss_pred             Hhc--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCH
Confidence            875  23356788999999999999999999999887652 23588999999999999999999999999988532 246


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      .+|..+...+.+.|++++|...|+++.+.. +.+..+|..+...+.+.|++++|.+.++++.+.. +.+..++..+..+
T Consensus       272 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  348 (388)
T 1w3b_A          272 DAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHADSLNNLANIKREQGNIEEAVRLYRKALEVF-PEFAAAHSNLASV  348 (388)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHH
Confidence            789999999999999999999999998653 4588999999999999999999999999998642 3346666666553

>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=99.77  E-value=1.6e-15  Score=154.27  Aligned_cols=298  Identities=10%  Similarity=0.014  Sum_probs=239.7

Q ss_pred             HHHHHhhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Q 011102          170 LARDIKGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLAR  244 (493)
Q Consensus       170 l~~~l~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~  244 (493)
                      +......+.+.|++++|+..|.++....     .|..+...|.+.|++++|++.|+.+.+. + ..+..++..+..++.+
T Consensus        29 ~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-~-p~~~~~~~~l~~~~~~  106 (450)
T 2y4t_A           29 HLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQL-K-MDFTAARLQRGHLLLK  106 (450)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc-C-CCcHHHHHHHHHHHHH
Confidence            3333456677899999999999876543     7888889999999999999999999865 2 2357789999999999


Q ss_pred             cCCCchhhhHHHhhcc----C-cH---HHHHHHHH------------HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 011102          245 HHELKVPFKLENFVSL----A-SK---GVLEATAK------------GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKL  304 (493)
Q Consensus       245 ~g~~~~~~~l~~~~~~----~-~~---~~~~~li~------------~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~l  304 (493)
                      .|+++.  ++..|...    + +.   .+|..++.            .+.+.|++++|.++|+++.+.. +.+..++..+
T Consensus       107 ~g~~~~--A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l  183 (450)
T 2y4t_A          107 QGKLDE--AEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRELR  183 (450)
T ss_dssp             TTCHHH--HHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             cCCHHH--HHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHH
Confidence            998554  44444432    2 23   55665544            4899999999999999998753 3467889999


Q ss_pred             HHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHH--------
Q 011102          305 ILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTL--------  376 (493)
Q Consensus       305 i~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~l--------  376 (493)
                      ...|.+. |++++|.++|+++.+.  ...+..+|..+...|.+.|++++|.+.|+++.+.. +.+...+..+        
T Consensus       184 ~~~~~~~-g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~~~~~~~~~~  259 (450)
T 2y4t_A          184 AECFIKE-GEPRKAISDLKAASKL--KNDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNK  259 (450)
T ss_dssp             HHHHHHT-TCGGGGHHHHHHHHHH--HCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHC-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHH
Confidence            9999999 9999999999998775  23568899999999999999999999999998642 2344555555        


Q ss_pred             ----HHHHHcCCCHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          377 ----IHSRLSEKKCREALTVVWNMEASNCLFD-----LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMI  447 (493)
Q Consensus       377 ----i~~~~~~g~~~~A~~l~~~M~~~gi~pd-----~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li  447 (493)
                          ...|.+.|++++|.+.|+++.+.  .|+     ...|..+...+.+.|++++|...++++.+.. +.+...|..+.
T Consensus       260 ~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~~~l~  336 (450)
T 2y4t_A          260 LIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNALKDRA  336 (450)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHH
Confidence                88999999999999999999874  355     4578889999999999999999999988653 23689999999


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHCCCccCHH-HHHHH
Q 011102          448 RIFMASGRLAKCRDVCKEAEMAGFKLDKQ-TVVEL  481 (493)
Q Consensus       448 ~~~~~~g~~~~A~~l~~~m~~~g~~pd~~-t~~~L  481 (493)
                      .+|...|++++|.+.++++.+  +.|+.. .+..+
T Consensus       337 ~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~l  369 (450)
T 2y4t_A          337 EAYLIEEMYDEAIQDYETAQE--HNENDQQIREGL  369 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHT--TSSSCHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHH--hCcchHHHHHHH
Confidence            999999999999999999987  556543 44333

>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=99.72  E-value=1.3e-14  Score=147.40  Aligned_cols=273  Identities=10%  Similarity=-0.008  Sum_probs=222.8

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhcc-----CcHHHHHHHHHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSL-----ASKGVLEATAKG  272 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~-----~~~~~~~~li~~  272 (493)
                      .|..+...|.+.|++++|+.+|+.+.+.  ...+..+|..+..++...|+++.  ++..+...     .+..+|..+...
T Consensus        28 ~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~l~~~~~~~g~~~~--A~~~~~~al~~~p~~~~~~~~l~~~  103 (450)
T 2y4t_A           28 KHLELGKKLLAAGQLADALSQFHAAVDG--DPDNYIAYYRRATVFLAMGKSKA--ALPDLTKVIQLKMDFTAARLQRGHL  103 (450)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHH--HHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHCCCHHH--HHHHHHHHHhcCCCcHHHHHHHHHH
Confidence            6778888999999999999999999864  23478889999999999998544  44444432     256789999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCH----HHHHHHHHH------------HhcCCCCHHHHHHHHHHHhhcCCCCCCHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLDP----SIYAKLILE------------LGKNPDKYMLVMTLLDELGQRDDLNLSQQ  336 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd~----~t~~~li~~------------~~~~~~~~~~a~~l~~~m~~~~g~~p~~~  336 (493)
                      |.+.|++++|.+.|+++.+..  |+.    ..+..+...            +.+. |++++|...|+++...  ...+..
T Consensus       104 ~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~  178 (450)
T 2y4t_A          104 LLKQGKLDEAEDDFKKVLKSN--PSENEEKEAQSQLIKSDEMQRLRSQALNAFGS-GDYTAAIAFLDKILEV--CVWDAE  178 (450)
T ss_dssp             HHHTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHH--CTTCHH
T ss_pred             HHHcCCHHHHHHHHHHHHhcC--CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCChH
Confidence            999999999999999999854  554    455555443            7888 9999999999999875  345788


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHH----
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVV----  411 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~l----  411 (493)
                      .+..+..+|.+.|++++|.++|+++.+.. +.+..+|+.+...|...|++++|.+.|+++.+.  .|+ ...+..+    
T Consensus       179 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~~~~~~  255 (450)
T 2y4t_A          179 LRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVK  255 (450)
T ss_dssp             HHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHHHHHHHHHHH
Confidence            99999999999999999999999987642 457899999999999999999999999999864  344 3344444    


Q ss_pred             --------HHHHHHcCCHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHH
Q 011102          412 --------IKLFVALNDISRAIRYFSKLKEAGFCPT-----YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTV  478 (493)
Q Consensus       412 --------i~~~~~~g~~~~A~~~~~~m~~~g~~p~-----~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~  478 (493)
                              ...|.+.|++++|..+|+++.+..  |+     ..+|..+...+.+.|++++|.+.++++.+.. +.+..+|
T Consensus       256 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~-p~~~~~~  332 (450)
T 2y4t_A          256 KLNKLIESAEELIRDGRYTDATSKYESVMKTE--PSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME-PDNVNAL  332 (450)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHH
Confidence                    788999999999999999998643  44     4588999999999999999999999987642 2356777


Q ss_pred             HHHHHhh
Q 011102          479 VELLQIE  485 (493)
Q Consensus       479 ~~Ll~~~  485 (493)
                      ..+..++
T Consensus       333 ~~l~~~~  339 (450)
T 2y4t_A          333 KDRAEAY  339 (450)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7766654

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.61  E-value=8.5e-12  Score=121.83  Aligned_cols=295  Identities=11%  Similarity=0.018  Sum_probs=229.6

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+...|++++|+..|.+.....     .|..+-..+.+.|++++|+..|+.+.+. . .-+...|..+...+...|+++
T Consensus        11 ~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~-~~~~~~~~~l~~~~~~~~~~~   88 (359)
T 3ieg_A           11 KKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIAL-K-MDFTAARLQRGHLLLKQGKLD   88 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-C-CCcchHHHHHHHHHHHcCChH
Confidence            34556799999999999775543     6777888999999999999999998864 1 225678899999999999855


Q ss_pred             hhhhHHHhhc----cC----cHHHHHHH------------HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHh
Q 011102          250 VPFKLENFVS----LA----SKGVLEAT------------AKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELG  309 (493)
Q Consensus       250 ~~~~l~~~~~----~~----~~~~~~~l------------i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~  309 (493)
                      .+.  ..+..    .+    +...+..+            ...+...|++++|.++|+++.+.. +.+...+..+...+.
T Consensus        89 ~A~--~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~  165 (359)
T 3ieg_A           89 EAE--DDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELRELRAECFI  165 (359)
T ss_dssp             HHH--HHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHH--HHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHH
Confidence            444  33332    22    23344444            578899999999999999998754 246778888889999


Q ss_pred             cCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHH------------HHH
Q 011102          310 KNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYT------------TLI  377 (493)
Q Consensus       310 ~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~------------~li  377 (493)
                      .. |++++|...+++....  ...+...+..+...|.+.|++++|.+.|++..+.. +.+...+.            .+.
T Consensus       166 ~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~a  241 (359)
T 3ieg_A          166 KE-GEPRKAISDLKAASKL--KSDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD-QDHKRCFAHYKQVKKLNKLIESA  241 (359)
T ss_dssp             HT-TCHHHHHHHHHHHHTT--CSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HC-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-ccchHHHHHHHHHHHHHHHHHHH
Confidence            99 9999999999999875  34577899999999999999999999999987653 22333333            236


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCCCH-----HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          378 HSRLSEKKCREALTVVWNMEASNCLFDL-----PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA  452 (493)
Q Consensus       378 ~~~~~~g~~~~A~~l~~~M~~~gi~pd~-----~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~  452 (493)
                      ..+.+.|++++|.+.++++.+..  |+.     ..|..+-..+.+.|++++|...|+...+.. ..+..+|..+...|.+
T Consensus       242 ~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~  318 (359)
T 3ieg_A          242 EELIRDGRYTDATSKYESVMKTE--PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQME-PDNVNALKDRAEAYLI  318 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC--CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHH
Confidence            67899999999999999988753  332     234556788999999999999999998653 2378899999999999


Q ss_pred             cCCHHHHHHHHHHHHHCCCccC-HHHHHHHHH
Q 011102          453 SGRLAKCRDVCKEAEMAGFKLD-KQTVVELLQ  483 (493)
Q Consensus       453 ~g~~~~A~~l~~~m~~~g~~pd-~~t~~~Ll~  483 (493)
                      .|++++|.+.|++..+.  .|+ ...+..|.+
T Consensus       319 ~g~~~~A~~~~~~a~~~--~p~~~~~~~~l~~  348 (359)
T 3ieg_A          319 EEMYDEAIQDYEAAQEH--NENDQQIREGLEK  348 (359)
T ss_dssp             TTCHHHHHHHHHHHHTT--CTTCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhc--CCCChHHHHHHHH
Confidence            99999999999999874  455 444444444

>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=99.61  E-value=6.8e-13  Score=128.39  Aligned_cols=273  Identities=9%  Similarity=-0.093  Sum_probs=202.7

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKG  272 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~  272 (493)
                      .+..+...+...|++++|+++|+.+.+...  .+...+..++..+...|+++.  ++..+..     ..+..+|..+...
T Consensus        24 ~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p--~~~~~~~~~~~~~~~~~~~~~--A~~~~~~~~~~~~~~~~~~~~l~~~   99 (330)
T 3hym_B           24 VVVSLAERHYYNCDFKMCYKLTSVVMEKDP--FHASCLPVHIGTLVELNKANE--LFYLSHKLVDLYPSNPVSWFAVGCY   99 (330)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCTTTHHHHHHHHHHHTCHHH--HHHHHHHHHHHCTTSTHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCC--CChhhHHHHHHHHHHhhhHHH--HHHHHHHHHHhCcCCHHHHHHHHHH
Confidence            556666677777888888888877765422  223345556666677776433  3332322     1245678888888


Q ss_pred             HHhcC-CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          273 FVKGG-NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKF  351 (493)
Q Consensus       273 ~~~~g-~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~  351 (493)
                      +...| ++++|.+.|++..+.. +.+...|..+...+... |++++|.+.+++..+.  ...+...+..+...|...|++
T Consensus       100 ~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~a~~~--~~~~~~~~~~l~~~~~~~~~~  175 (330)
T 3hym_B          100 YLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVE-SEHDQAMAAYFTAAQL--MKGCHLPMLYIGLEYGLTNNS  175 (330)
T ss_dssp             HHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHH-TCHHHHHHHHHHHHHH--TTTCSHHHHHHHHHHHHTTCH
T ss_pred             HHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHc-cCHHHHHHHHHHHHHh--ccccHHHHHHHHHHHHHHhhH
Confidence            88899 8999999999988754 23466788888888888 9999999999998765  223456677788899999999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--------CCCCHHHHHHHHHHHHHcCCHHH
Q 011102          352 GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN--------CLFDLPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       352 ~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g--------i~pd~~ty~~li~~~~~~g~~~~  423 (493)
                      ++|.+.|++..+.. +.+...|..+...|...|++++|.+.+++..+..        ...+..+|..+...|.+.|++++
T Consensus       176 ~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  254 (330)
T 3hym_B          176 KLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAE  254 (330)
T ss_dssp             HHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHH
Confidence            99999999987553 4467889999999999999999999999876531        13345788889999999999999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccC-HHHHHHHH
Q 011102          424 AIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLD-KQTVVELL  482 (493)
Q Consensus       424 A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~Ll  482 (493)
                      |...|++..+..- .+...|..+...|.+.|++++|.+.+++..+  +.|+ ...+..+-
T Consensus       255 A~~~~~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~l~  311 (330)
T 3hym_B          255 ALDYHRQALVLIP-QNASTYSAIGYIHSLMGNFENAVDYFHTALG--LRRDDTFSVTMLG  311 (330)
T ss_dssp             HHHHHHHHHHHST-TCSHHHHHHHHHHHHHTCHHHHHHHHHTTTT--TCSCCHHHHHHHH
T ss_pred             HHHHHHHHHhhCc-cchHHHHHHHHHHHHhccHHHHHHHHHHHHc--cCCCchHHHHHHH
Confidence            9999999886542 3677888899999999999999999998765  4454 44444433

>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=99.58  E-value=7.6e-13  Score=130.48  Aligned_cols=276  Identities=9%  Similarity=-0.055  Sum_probs=210.0

Q ss_pred             CCHHHHHH-HHhhhcc---------cCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCch
Q 011102          181 KDVAEVLD-KCGRFLR---------KGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKV  250 (493)
Q Consensus       181 ~~~~~a~~-~~~~m~~---------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~  250 (493)
                      +++++|++ .+.+...         ...+..+-..+.+.|++++|+..|+.+.+.  ...+..+|..+...+.+.|+++.
T Consensus        39 ~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~  116 (368)
T 1fch_A           39 SDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQ--DPKHMEAWQYLGTTQAENEQELL  116 (368)
T ss_dssp             -------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCcCHHH
Confidence            55566665 5552221         225777888999999999999999999865  23467788899999999998554


Q ss_pred             hhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHH---------------HHHHHh
Q 011102          251 PFKLENFVS-----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPS-IYAK---------------LILELG  309 (493)
Q Consensus       251 ~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~-t~~~---------------li~~~~  309 (493)
                        ++..+..     ..+..+|..+...|.+.|++++|.+.|+++.+..  |+.. .+..               .+..+.
T Consensus       117 --A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  192 (368)
T 1fch_A          117 --AISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLL  192 (368)
T ss_dssp             --HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--TTTGGGCC---------------CTTHHHH
T ss_pred             --HHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--cCcHHHHHHHHHHhhhhcccHHHHHHHHHh
Confidence              4433433     2356789999999999999999999999998864  3221 1111               244444


Q ss_pred             cCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHH
Q 011102          310 KNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREA  389 (493)
Q Consensus       310 ~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A  389 (493)
                      .. |++++|...|+++.....-.++..++..+...|.+.|++++|...|++..+.. +.+..+|+.+...|.+.|++++|
T Consensus       193 ~~-~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A  270 (368)
T 1fch_A          193 SD-SLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEA  270 (368)
T ss_dssp             HH-HHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hc-ccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHH
Confidence            66 89999999999988762222258899999999999999999999999987652 34678999999999999999999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC----------CCHHHHHHHHHHHHHcCCHHHH
Q 011102          390 LTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFC----------PTYDIYRDMIRIFMASGRLAKC  459 (493)
Q Consensus       390 ~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~----------p~~~ty~~li~~~~~~g~~~~A  459 (493)
                      .+.|+++.+.. ..+...+..+...|.+.|++++|...|++..+..-.          ....+|..+..+|.+.|++++|
T Consensus       271 ~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  349 (368)
T 1fch_A          271 VAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAY  349 (368)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGH
T ss_pred             HHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhH
Confidence            99999987753 245788999999999999999999999988743211          1268899999999999999999


Q ss_pred             HHHHHH
Q 011102          460 RDVCKE  465 (493)
Q Consensus       460 ~~l~~~  465 (493)
                      ..++++
T Consensus       350 ~~~~~~  355 (368)
T 1fch_A          350 GAADAR  355 (368)
T ss_dssp             HHHHTT
T ss_pred             HHhHHH
Confidence            988763

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.57  E-value=1.2e-12  Score=125.80  Aligned_cols=255  Identities=7%  Similarity=-0.012  Sum_probs=193.6

Q ss_pred             HHHHHhCCChHHHHHHHHHHHhCCCCCCCH--HHHHHHHHHHHHcCCCchhhhHHHhhc--cCcHHHHHHHHHHHHhcCC
Q 011102          203 VRELGHMNLPERALQTFCWAQKQPHLFPDD--RLLASTVEVLARHHELKVPFKLENFVS--LASKGVLEATAKGFVKGGN  278 (493)
Q Consensus       203 i~~~~~~g~~~~A~~l~~~m~~~~g~~pd~--~t~~~li~~~~~~g~~~~~~~l~~~~~--~~~~~~~~~li~~~~~~g~  278 (493)
                      |+-....|++..|+..++...   ...|+.  .....+..++...|+.  ..++..+..  .++..++..+...+.+.|+
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~---~~~p~~~~e~~~~l~r~yi~~g~~--~~al~~~~~~~~~~~~a~~~la~~~~~~~~   80 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVK---PSSPERDVERDVFLYRAYLAQRKY--GVVLDEIKPSSAPELQAVRMFAEYLASHSR   80 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSC---CCSHHHHHHHHHHHHHHHHHTTCH--HHHHHHSCTTSCHHHHHHHHHHHHHHCSTT
T ss_pred             HHHHHHHHHHHHHHHHHHhcc---cCCchhhHHHHHHHHHHHHHCCCH--HHHHHHhcccCChhHHHHHHHHHHHcCCCc
Confidence            445566788888888887653   334443  2445567788888874  444444433  2345578888999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHH-HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          279 LKLAWKLLMVAKDGGRMLDPS-IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~pd~~-t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      .++|++.++++...+..|+.. .+..+-..+.+. |++++|++.++.       ..+...+..+...|.+.|++++|.+.
T Consensus        81 ~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~-g~~~~Al~~l~~-------~~~~~~~~~l~~~~~~~g~~~~A~~~  152 (291)
T 3mkr_A           81 RDAIVAELDREMSRSVDVTNTTFLLMAASIYFYD-QNPDAALRTLHQ-------GDSLECMAMTVQILLKLDRLDLARKE  152 (291)
T ss_dssp             HHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHT-TCHHHHHHHHTT-------CCSHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHC-CCHHHHHHHHhC-------CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            999999999999887666544 445555778888 999999999976       35778899999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHH---HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          358 FHWFTHSGRDPTVVMY---TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       358 ~~~m~~~g~~p~~~ty---~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      |+++.+..  |+...+   .+.+..+...|++++|..+|+++.+. ...+...|+.+-.++.+.|++++|...|++..+.
T Consensus       153 l~~~~~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~  229 (291)
T 3mkr_A          153 LKKMQDQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDK  229 (291)
T ss_dssp             HHHHHHHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            99998763  553211   23344555669999999999999876 3457888999999999999999999999998865


Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHH-HHHHHHHHHHCCCccCHH
Q 011102          435 GFCPTYDIYRDMIRIFMASGRLAK-CRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       435 g~~p~~~ty~~li~~~~~~g~~~~-A~~l~~~m~~~g~~pd~~  476 (493)
                      .- -+..++..++..+...|+.++ +.++++++.+  +.|+..
T Consensus       230 ~p-~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~--~~P~~~  269 (291)
T 3mkr_A          230 DS-GHPETLINLVVLSQHLGKPPEVTNRYLSQLKD--AHRSHP  269 (291)
T ss_dssp             CT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH--HCTTCH
T ss_pred             CC-CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH--hCCCCh
Confidence            42 377889999999999999876 5788888876  345443

>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=99.55  E-value=1.2e-14  Score=144.75  Aligned_cols=248  Identities=8%  Similarity=0.027  Sum_probs=108.2

Q ss_pred             CCCCHHHHHHHHhhhcccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhh
Q 011102          179 SHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFV  258 (493)
Q Consensus       179 ~~~~~~~a~~~~~~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~  258 (493)
                      +.|++++|.+.+++...+..|+.+..++.+.|++++|++.|...       +|..+|..++.++...|+++.+.......
T Consensus        15 ~~~~ld~A~~fae~~~~~~vWs~La~A~l~~g~~~eAIdsfika-------~D~~~y~~V~~~ae~~g~~EeAi~yl~~a   87 (449)
T 1b89_A           15 HIGNLDRAYEFAERCNEPAVWSQLAKAQLQKGMVKEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMA   87 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCCChHHHHHHHHHHHHcCCHHHHHHHHHcC-------CCHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence            45789999999999988889999999999999999999999643       36678899999999989876655532221


Q ss_pred             --ccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHH
Q 011102          259 --SLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQ  336 (493)
Q Consensus       259 --~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~  336 (493)
                        ..++..+.+.++.+|.+.|+++++.++++       .|+..+|+.+.+.|... |.+++|..+|..+          .
T Consensus        88 rk~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~-g~yeeA~~~Y~~a----------~  149 (449)
T 1b89_A           88 RKKARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDE-KMYDAAKLLYNNV----------S  149 (449)
T ss_dssp             ---------------------CHHHHTTTTT-------CC-----------------CTTTHHHHHHHT----------T
T ss_pred             HHhCccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHc-CCHHHHHHHHHHh----------h
Confidence              13345678899999999999999988885       27888999999999999 9999999999877          2


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .|..+.+++.+.|++++|.+.+.++      .+..+|..++.+|+..|+++.|......+.   +.|+.  ...++..|.
T Consensus       150 n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~---~~ad~--l~~lv~~Ye  218 (449)
T 1b89_A          150 NFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV---VHADE--LEELINYYQ  218 (449)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT---TCHHH--HHHHHHHHH
T ss_pred             hHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH---hCHhh--HHHHHHHHH
Confidence            5889999999999999999999987      378999999999999999999965544322   33433  556888999


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc--CCHHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMAS--GRLAKCRDVC  463 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~--g~~~~A~~l~  463 (493)
                      +.|++++|..+++.-.... .-....|+-|--+|++-  ++..+.+++|
T Consensus       219 k~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~  266 (449)
T 1b89_A          219 DRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELF  266 (449)
T ss_dssp             HTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            9999999999998877444 45677888887777765  3444444444

>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=99.55  E-value=2.9e-14  Score=141.97  Aligned_cols=219  Identities=10%  Similarity=0.093  Sum_probs=51.0

Q ss_pred             CCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 011102          209 MNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMV  288 (493)
Q Consensus       209 ~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~  288 (493)
                      .|+.++|.++++.+..       ..+|..+..++.+.|++  .+++..|...+|..+|..++..+...|++++|.+.++.
T Consensus        16 ~~~ld~A~~fae~~~~-------~~vWs~La~A~l~~g~~--~eAIdsfika~D~~~y~~V~~~ae~~g~~EeAi~yl~~   86 (449)
T 1b89_A           16 IGNLDRAYEFAERCNE-------PAVWSQLAKAQLQKGMV--KEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQM   86 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCHHHHHHHHHhCCC-------hHHHHHHHHHHHHcCCH--HHHHHHHHcCCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            3445555555554421       12445555555555542  23333344444444555555555555555555554443


Q ss_pred             HHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC
Q 011102          289 AKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP  368 (493)
Q Consensus       289 m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  368 (493)
                      ..+.  .+++.+.+.++.+|.+. |+++++.++++        .|+..+|+.+.+.|...|++++|...|..+       
T Consensus        87 ark~--~~~~~i~~~Li~~Y~Kl-g~l~e~e~f~~--------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a-------  148 (449)
T 1b89_A           87 ARKK--ARESYVETELIFALAKT-NRLAELEEFIN--------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-------  148 (449)
T ss_dssp             -------------------------CHHHHTTTTT--------CC----------------CTTTHHHHHHHT-------
T ss_pred             HHHh--CccchhHHHHHHHHHHh-CCHHHHHHHHc--------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh-------
Confidence            3332  23344445555555555 55555444442        133345555555555555555555555543       


Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR  448 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~  448 (493)
                        ..|..|..++.+.|++++|.+.+.++      -+..+|..++.+|+..|+++.|......     +..+..-...++.
T Consensus       149 --~n~~~LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~-----L~~~ad~l~~lv~  215 (449)
T 1b89_A          149 --SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELIN  215 (449)
T ss_dssp             --TCHHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTT-----TTTCHHHHHHHHH
T ss_pred             --hhHHHHHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHH-----HHhCHhhHHHHHH
Confidence              13555555555555555555555544      1445555555555555555555333222     1122222334555


Q ss_pred             HHHHcCCHHHHHHHHHHHH
Q 011102          449 IFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       449 ~~~~~g~~~~A~~l~~~m~  467 (493)
                      .|.+.|++++|..+++...
T Consensus       216 ~Yek~G~~eEai~lLe~aL  234 (449)
T 1b89_A          216 YYQDRGYFEELITMLEAAL  234 (449)
T ss_dssp             HHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHCCCHHHHHHHHHHHh
Confidence            5555555555555554443

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.55  E-value=1.1e-12  Score=129.48  Aligned_cols=259  Identities=9%  Similarity=-0.101  Sum_probs=193.8

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKG  272 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~  272 (493)
                      .|..+-..+.+.|++++|+++|+.+...  ...+..+|..+...+.+.|+++.  ++..|..     ..+..+|..+...
T Consensus        67 ~~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~--A~~~~~~al~~~p~~~~~~~~l~~~  142 (365)
T 4eqf_A           67 GAFEEGLKRLKEGDLPVTILFMEAAILQ--DPGDAEAWQFLGITQAENENEQA--AIVALQRCLELQPNNLKALMALAVS  142 (365)
T ss_dssp             THHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHH--HHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHCCCHHH--HHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            4666666777788888888888877753  12356677777788888777443  3333332     2246688899999


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCC-----------HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLD-----------PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd-----------~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      |.+.|++++|.+.|+++.+..  |+           ...+..+...+.+. |++++|.++|+++.....-..+..++..+
T Consensus       143 ~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~al~~~p~~~~~~~~~~l  219 (365)
T 4eqf_A          143 YTNTSHQQDACEALKNWIKQN--PKYKYLVKNKKGSPGLTRRMSKSPVDS-SVLEGVKELYLEAAHQNGDMIDPDLQTGL  219 (365)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC--HHHHCC-------------------CC-HHHHHHHHHHHHHHHHSCSSCCHHHHHHH
T ss_pred             HHccccHHHHHHHHHHHHHhC--ccchHHHhhhccchHHHHHHHHHHhhh-hhHHHHHHHHHHHHHhCcCccCHHHHHHH
Confidence            999999999999999998743  32           22334456778888 99999999999998762222368899999


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      ...|.+.|++++|.+.|++..+.. +.+..+|+.+...|.+.|++++|.+.|+++.+.. .-+..+|..+-..|.+.|++
T Consensus       220 ~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~  297 (365)
T 4eqf_A          220 GVLFHLSGEFNRAIDAFNAALTVR-PEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAY  297 (365)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCH
Confidence            999999999999999999987653 4468899999999999999999999999987753 23478899999999999999


Q ss_pred             HHHHHHHHHHHHCC--C-C--------CCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          422 SRAIRYFSKLKEAG--F-C--------PTYDIYRDMIRIFMASGRLAKCRDVCKE  465 (493)
Q Consensus       422 ~~A~~~~~~m~~~g--~-~--------p~~~ty~~li~~~~~~g~~~~A~~l~~~  465 (493)
                      ++|...|++..+..  . .        .+...|..+-.++...|+.+.|.++.+.
T Consensus       298 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          298 REAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            99999999887422  1 1        1367899999999999999988877654

>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=99.54  E-value=2.7e-12  Score=123.93  Aligned_cols=258  Identities=9%  Similarity=-0.077  Sum_probs=191.3

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKG  272 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~  272 (493)
                      .|-..-..+.+.|++++|+.+|+.+.+. . .-+..++..+...+.+.|+++.  ++..+..     ..+..+|..+...
T Consensus        23 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~-~~~~~~~~~l~~~~~~~~~~~~--A~~~~~~a~~~~~~~~~~~~~la~~   98 (327)
T 3cv0_A           23 NPMEEGLSMLKLANLAEAALAFEAVCQA-A-PEREEAWRSLGLTQAENEKDGL--AIIALNHARMLDPKDIAVHAALAVS   98 (327)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHHTTCHHH--HHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHh-C-CCCHHHHHHHHHHHHHcCCHHH--HHHHHHHHHhcCcCCHHHHHHHHHH
Confidence            3444455666667777777777766643 1 2255566666666666666433  3222222     1245678888889


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCCHH-HHHHH------------H-HH--HhcCCCCHHHHHHHHHHHhhcCCCCCCHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLDPS-IYAKL------------I-LE--LGKNPDKYMLVMTLLDELGQRDDLNLSQQ  336 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd~~-t~~~l------------i-~~--~~~~~~~~~~a~~l~~~m~~~~g~~p~~~  336 (493)
                      |.+.|++++|.+.|+++.+..  |+.. .+..+            + ..  +... |++++|.+.++++.+.  ...+..
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~  173 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLSQ--PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAP-NEYRECRTLLHAALEM--NPNDAQ  173 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTS--TTTTTC--------------------CCTTSH-HHHHHHHHHHHHHHHH--STTCHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHc-ccHHHHHHHHHHHHhh--CCCCHH
Confidence            999999999999999998754  3322 22222            0 33  5666 8999999999998875  234788


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .+..+...|.+.|++++|.+.|++..+.. +.+..+|..+...|...|++++|.+.|+++.+.. ..+..++..+...|.
T Consensus       174 ~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~  251 (327)
T 3cv0_A          174 LHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYS  251 (327)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHH
Confidence            99999999999999999999999987653 3467889999999999999999999999987753 235788999999999


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCC-----------CHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKEAGFCP-----------TYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p-----------~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      +.|++++|.+.|++..+..-..           +..+|..+..+|.+.|++++|.+++++.
T Consensus       252 ~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  312 (327)
T 3cv0_A          252 NMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQN  312 (327)
T ss_dssp             HTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCC
T ss_pred             HhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            9999999999999987543221           4788999999999999999999987654

>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=99.53  E-value=8.4e-12  Score=120.62  Aligned_cols=272  Identities=11%  Similarity=-0.051  Sum_probs=216.0

Q ss_pred             hccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC-CCc
Q 011102          176 GLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHH-ELK  249 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g-~~~  249 (493)
                      .+...|++++|++.+.+.....     .+..+...+.+.|++++|+.+|+.+.+.  -.-+...|..+...+...| +++
T Consensus        31 ~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~  108 (330)
T 3hym_B           31 RHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDL--YPSNPVSWFAVGCYYLMVGHKNE  108 (330)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTSTHHHHHHHHHHHHSCSCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhhhhHH
Confidence            3445599999999999876543     6677888999999999999999999864  1235667888888899998 744


Q ss_pred             hhhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHH
Q 011102          250 VPFKLENFVS-----LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDE  324 (493)
Q Consensus       250 ~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~  324 (493)
                        +++..+..     ..+..+|..+...|...|++++|.+.|++..+..- .+...+..+...+... |++++|.+.+++
T Consensus       109 --~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~-~~~~~A~~~~~~  184 (330)
T 3hym_B          109 --HARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK-GCHLPMLYIGLEYGLT-NNSKLAERFFSQ  184 (330)
T ss_dssp             --HHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT-TCSHHHHHHHHHHHHT-TCHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHH-hhHHHHHHHHHH
Confidence              34433432     22456899999999999999999999999988642 2356677788889999 999999999999


Q ss_pred             HhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC--------CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          325 LGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSG--------RDPTVVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       325 m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--------~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      ....  ...+...+..+...|.+.|++++|...|++..+..        ...+..+|..+...|.+.|++++|.+.+++.
T Consensus       185 al~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  262 (330)
T 3hym_B          185 ALSI--APEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQA  262 (330)
T ss_dssp             HHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHh--CCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            9875  34567889999999999999999999999987531        1344678999999999999999999999998


Q ss_pred             HHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH-HHcCCHH
Q 011102          397 EASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIF-MASGRLA  457 (493)
Q Consensus       397 ~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~-~~~g~~~  457 (493)
                      .+..- .+...+..+-..|.+.|++++|.+.|++..+.. +.+...+..+..++ ...|+.+
T Consensus       263 ~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          263 LVLIP-QNASTYSAIGYIHSLMGNFENAVDYFHTALGLR-RDDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             HHHST-TCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTC-SCCHHHHHHHHHHHHTTTTC--
T ss_pred             HhhCc-cchHHHHHHHHHHHHhccHHHHHHHHHHHHccC-CCchHHHHHHHHHHHHHhCchh
Confidence            87532 356788999999999999999999999987543 23677788888777 4555543

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.53  E-value=7.2e-12  Score=129.10  Aligned_cols=197  Identities=11%  Similarity=-0.000  Sum_probs=99.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      +|..+...+.+.|++++|.++|+++.+..  |+..+|..+...+... |++++|...++.+...  ...+...|..+...
T Consensus       239 ~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~  313 (514)
T 2gw1_A          239 SLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADR-NDSTEYYNYFDKALKL--DSNNSSVYYHRGQM  313 (514)
T ss_dssp             HHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTS-SCCTTGGGHHHHHHTT--CTTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHC-CCHHHHHHHHHHHhhc--CcCCHHHHHHHHHH
Confidence            45555555666666666666666555543  3344555555555555 5555665555555443  12234455555555


Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRA  424 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A  424 (493)
                      |.+.|++++|...|++..+.. +.+...|..+...|...|++++|.++++++.+.. ..+..++..+...|.+.|++++|
T Consensus       314 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  391 (514)
T 2gw1_A          314 NFILQNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKA  391 (514)
T ss_dssp             HHHTTCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHH
Confidence            555555555555555554432 1234455555555555555555555555544321 11234445555555555555555


Q ss_pred             HHHHHHHHHCCC-CCC----HHHHHHHHHHHHH---cCCHHHHHHHHHHHHH
Q 011102          425 IRYFSKLKEAGF-CPT----YDIYRDMIRIFMA---SGRLAKCRDVCKEAEM  468 (493)
Q Consensus       425 ~~~~~~m~~~g~-~p~----~~ty~~li~~~~~---~g~~~~A~~l~~~m~~  468 (493)
                      ...|+.+.+..- .++    ...|..+...|..   .|++++|.+.+++..+
T Consensus       392 ~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~  443 (514)
T 2gw1_A          392 LKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASK  443 (514)
T ss_dssp             HHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHH
Confidence            555555442110 011    2244555555555   5555555555555544

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.52  E-value=3.1e-12  Score=131.89  Aligned_cols=188  Identities=7%  Similarity=-0.134  Sum_probs=159.1

Q ss_pred             hcCCHHHHHHHHHHHHh-----CCCCC--------CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          275 KGGNLKLAWKLLMVAKD-----GGRML--------DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~-----~g~~p--------d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +.|++++|..+|+++.+     ..-.|        +..+|..+...+... |++++|...|+++... .  |+...+..+
T Consensus       201 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~l~~-~--~~~~~~~~l  276 (514)
T 2gw1_A          201 SPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLK-NDPLGAHEDIKKAIEL-F--PRVNSYIYM  276 (514)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHS-SCHHHHHHHHHHHHHH-C--CCHHHHHHH
T ss_pred             hhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHhh-C--ccHHHHHHH
Confidence            38999999999999988     32222        345677788889999 9999999999998876 2  348889999


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      ...|.+.|++++|.+.|++..+.. +.+...|..+...|...|++++|...+++..+... .+...+..+...|.+.|++
T Consensus       277 ~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~  354 (514)
T 2gw1_A          277 ALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELDP-ENIFPYIQLACLAYRENKF  354 (514)
T ss_dssp             HHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCS-SCSHHHHHHHHHTTTTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCh-hhHHHHHHHHHHHHHcCCH
Confidence            999999999999999999988653 34677899999999999999999999999887643 2567888999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          422 SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       422 ~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      ++|..+|+.+.+..- .+..+|..+...|.+.|++++|.+.++++.+.
T Consensus       355 ~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~  401 (514)
T 2gw1_A          355 DDCETLFSEAKRKFP-EAPEVPNFFAEILTDKNDFDKALKQYDLAIEL  401 (514)
T ss_dssp             HHHHHHHHHHHHHST-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcc-cCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            999999999986432 35678999999999999999999999998763

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.48  E-value=2.3e-10  Score=111.53  Aligned_cols=270  Identities=10%  Similarity=-0.000  Sum_probs=210.5

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHH
Q 011102          199 LSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKGF  273 (493)
Q Consensus       199 ~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~  273 (493)
                      +..+-..+.+.|++++|++.|+.+...  -..+..++..+...+...|+++.  ++..+..     ..+..+|..+...|
T Consensus         6 ~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~a~~~~~~~~~~~--A~~~~~~~~~~~~~~~~~~~~l~~~~   81 (359)
T 3ieg_A            6 HLELGKKLLAAGQLADALSQFHAAVDG--DPDNYIAYYRRATVFLAMGKSKA--ALPDLTKVIALKMDFTAARLQRGHLL   81 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHH--HHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhh--CcccHHHHHHHHHHHHHccCHHH--HHHHHHHHHHhCCCcchHHHHHHHHH
Confidence            455667889999999999999999864  22357788899999999998554  4433433     22567899999999


Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCC----CHHHHHHH------------HHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHH
Q 011102          274 VKGGNLKLAWKLLMVAKDGGRML----DPSIYAKL------------ILELGKNPDKYMLVMTLLDELGQRDDLNLSQQD  337 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~~~g~~p----d~~t~~~l------------i~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~  337 (493)
                      .+.|++++|.+.|++..+..  |    +...+..+            ...+... |++++|.++++++.+.  ...+...
T Consensus        82 ~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~  156 (359)
T 3ieg_A           82 LKQGKLDEAEDDFKKVLKSN--PSEQEEKEAESQLVKADEMQRLRSQALDAFDG-ADYTAAITFLDKILEV--CVWDAEL  156 (359)
T ss_dssp             HHHTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHH
T ss_pred             HHcCChHHHHHHHHHHHhcC--CcccChHHHHHHHHHHHHHHHHHHHHHHHHHc-cCHHHHHHHHHHHHHh--CCCchHH
Confidence            99999999999999998854  5    33344433            4677888 9999999999999875  3356788


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHH-------
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYR-------  409 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~-------  409 (493)
                      +..+...|.+.|++++|.+.|++..+.. +.+..+|..+...|...|++++|.+.|++..+..  |+ ...+.       
T Consensus       157 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~  233 (359)
T 3ieg_A          157 RELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKLD--QDHKRCFAHYKQVKK  233 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--ccchHHHHHHHHHHH
Confidence            9999999999999999999999998653 4578899999999999999999999999987643  33 23232       


Q ss_pred             -----HHHHHHHHcCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCcc-CHHHHH
Q 011102          410 -----VVIKLFVALNDISRAIRYFSKLKEAGFCPTY----DIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKL-DKQTVV  479 (493)
Q Consensus       410 -----~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~----~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~  479 (493)
                           .+...+.+.|++++|...+++..+..-. +.    ..|..+...|.+.|++++|.+.+++..+.  .| +..+|.
T Consensus       234 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~  310 (359)
T 3ieg_A          234 LNKLIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQM--EPDNVNALK  310 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CcccHHHHH
Confidence                 2256689999999999999999864422 22    23556778899999999999999999875  34 455555


Q ss_pred             HHHH
Q 011102          480 ELLQ  483 (493)
Q Consensus       480 ~Ll~  483 (493)
                      .+-.
T Consensus       311 ~~~~  314 (359)
T 3ieg_A          311 DRAE  314 (359)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4444

>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=99.45  E-value=1.1e-11  Score=122.23  Aligned_cols=257  Identities=10%  Similarity=-0.086  Sum_probs=191.7

Q ss_pred             HHHhCCChHHHHH-HHHHHHhCCCCCC--CHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHhc
Q 011102          205 ELGHMNLPERALQ-TFCWAQKQPHLFP--DDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKGFVKG  276 (493)
Q Consensus       205 ~~~~~g~~~~A~~-l~~~m~~~~g~~p--d~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~~  276 (493)
                      .+...|++++|++ .|+.......-.|  +...+..+...+.+.|+++.  ++..+..     ..+..+|..+...|.+.
T Consensus        34 ~~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~--A~~~~~~al~~~p~~~~~~~~l~~~~~~~  111 (368)
T 1fch_A           34 AHPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPN--AVLLFEAAVQQDPKHMEAWQYLGTTQAEN  111 (368)
T ss_dssp             ------------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHH--HHHHHHHHHHSCTTCHHHHHHHHHHHHHT
T ss_pred             hhHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHH--HHHHHHHHHHhCCCCHHHHHHHHHHHHHC
Confidence            3445688899998 8876553211122  34567788888999998544  4444433     23567899999999999


Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHH---------------H
Q 011102          277 GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTA---------------I  341 (493)
Q Consensus       277 g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~---------------l  341 (493)
                      |++++|.+.|+++.+.. +.+..++..+...+... |++++|.+.++.+.... - .+...+..               .
T Consensus       112 g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~  187 (368)
T 1fch_A          112 EQELLAISALRRCLELK-PDNQTALMALAVSFTNE-SLQRQACEILRDWLRYT-P-AYAHLVTPAEEGAGGAGLGPSKRI  187 (368)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHTS-T-TTGGGCC---------------CT
T ss_pred             cCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHhC-c-CcHHHHHHHHHHhhhhcccHHHHH
Confidence            99999999999998864 34678899999999999 99999999999987751 1 11111111               2


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRD-PTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      +..+.+.|++++|...|+++.+..-. ++..+|..+...|.+.|++++|.+.|+++.+.. ..+..+|..+...|.+.|+
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            44445899999999999999865322 158899999999999999999999999987753 2357889999999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          421 ISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       421 ~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      +++|...|++..+.. +.+...|..+...|.+.|++++|.+.|++..+.
T Consensus       267 ~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  314 (368)
T 1fch_A          267 SEEAVAAYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNM  314 (368)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            999999999988653 246788999999999999999999999998763

>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=99.44  E-value=4.6e-11  Score=111.13  Aligned_cols=211  Identities=11%  Similarity=-0.044  Sum_probs=176.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      ..+|..+...|...|++++|.+.|+++.+.. ..+..++..+...+... |++++|.+.++++.+.  ...+...+..+.
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~-~~~~~A~~~~~~a~~~--~~~~~~~~~~la  112 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTE-MEPKLADEEYRKALAS--DSRNARVLNNYG  112 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHH--CcCcHHHHHHHH
Confidence            4568888899999999999999999988753 33677888888899999 9999999999998775  234678899999


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      ..|.+.|++++|.++|++..+.+..| +...|..+...|...|++++|.+.|++..+.. ..+...+..+...|.+.|++
T Consensus       113 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~  191 (252)
T 2ho1_A          113 GFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREY  191 (252)
T ss_dssp             HHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCH
Confidence            99999999999999999998644455 56788889999999999999999999987753 23578889999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHH
Q 011102          422 SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVEL  481 (493)
Q Consensus       422 ~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~L  481 (493)
                      ++|..+|+...+..- .+...+..+...+.+.|++++|.++++++.+.  .|+...+..+
T Consensus       192 ~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~  248 (252)
T 2ho1_A          192 VPARQYYDLFAQGGG-QNARSLLLGIRLAKVFEDRDTAASYGLQLKRL--YPGSLEYQEF  248 (252)
T ss_dssp             HHHHHHHHHHHTTSC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTSHHHHHH
T ss_pred             HHHHHHHHHHHHhCc-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH--CCCCHHHHHH
Confidence            999999999886432 46788899999999999999999999999874  4555444433

>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=99.43  E-value=6.5e-11  Score=122.82  Aligned_cols=282  Identities=8%  Similarity=-0.049  Sum_probs=208.6

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+.+.|++++|+..|.+....+     .|..+...|.+.|++++|++.|+.+.+. . ..+..++..+..++...|+++
T Consensus        33 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~-~-p~~~~~~~~la~~~~~~g~~~  110 (537)
T 3fp2_A           33 NHFFTAKNFNEAIKYYQYAIELDPNEPVFYSNISACYISTGDLEKVIEFTTKALEI-K-PDHSKALLRRASANESLGNFT  110 (537)
T ss_dssp             HHHHHTTCCC-CHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHhccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-C-CchHHHHHHHHHHHHHcCCHH
Confidence            44556677777777777665432     6677777888888888888888887754 2 225667777777777777744


Q ss_pred             hhhhHHHhhccC---c---------------------------------------HH-----------------------
Q 011102          250 VPFKLENFVSLA---S---------------------------------------KG-----------------------  264 (493)
Q Consensus       250 ~~~~l~~~~~~~---~---------------------------------------~~-----------------------  264 (493)
                      .+..  .|..+.   +                                       ..                       
T Consensus       111 ~A~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  188 (537)
T 3fp2_A          111 DAMF--DLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSN  188 (537)
T ss_dssp             HHHH--HHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCS
T ss_pred             HHHH--HHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccc
Confidence            4332  221110   0                                       00                       


Q ss_pred             -------HHHHHHHHHHh--------cCCHHHHHHHHHHHHhCCCCCC--------HHHHHHHHHHHhcCCCCHHHHHHH
Q 011102          265 -------VLEATAKGFVK--------GGNLKLAWKLLMVAKDGGRMLD--------PSIYAKLILELGKNPDKYMLVMTL  321 (493)
Q Consensus       265 -------~~~~li~~~~~--------~g~~~~A~~l~~~m~~~g~~pd--------~~t~~~li~~~~~~~~~~~~a~~l  321 (493)
                             ....+...+..        .|++++|..+|+++.+..  |+        ..+|..+-..+... |++++|...
T Consensus       189 ~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~--p~~~~~~~~~~~~~~~~g~~~~~~-~~~~~A~~~  265 (537)
T 3fp2_A          189 YDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSAN--TVDDPLRENAALALCYTGIFHFLK-NNLLDAQVL  265 (537)
T ss_dssp             SCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHT-TCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHC--CCcchhhHHHHHHHHHHHHHHHhc-ccHHHHHHH
Confidence                   11222222221        247899999999988754  44        23456666777888 999999999


Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 011102          322 LDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNC  401 (493)
Q Consensus       322 ~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi  401 (493)
                      |++....   .|+...|..+...|.+.|++++|.+.|++..+.. +.+..+|..+...|...|++++|.+.|++..+..-
T Consensus       266 ~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~  341 (537)
T 3fp2_A          266 LQESINL---HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNP  341 (537)
T ss_dssp             HHHHHHH---CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHhc---CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCC
Confidence            9999875   3668889999999999999999999999987653 34678899999999999999999999999887532


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          402 LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       402 ~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                       -+...|..+...|.+.|++++|..+|++..+.. ..+...|..+...|...|++++|.+.|+++.+.
T Consensus       342 -~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  407 (537)
T 3fp2_A          342 -ENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRL  407 (537)
T ss_dssp             -TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHc
Confidence             245788899999999999999999999998654 235678899999999999999999999998753

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.43  E-value=1.1e-10  Score=105.91  Aligned_cols=214  Identities=10%  Similarity=-0.083  Sum_probs=177.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +..+|..+...+...|++++|.+.|+++.+.. +.+...|..+...+... |++++|.+.+++....  ...+...+..+
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~a~~~--~~~~~~~~~~l   82 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYL-KVNDKAQESFRQALSI--KPDSAEINNNY   82 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHc-CChHHHHHHHHHHHHh--CCCChHHHHHH
Confidence            34568888999999999999999999988753 23577888888999999 9999999999998775  23467889999


Q ss_pred             HHHHHHc-CCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC
Q 011102          342 MKVGIRL-QKFGVVESLFHWFTHSGRDPT-VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN  419 (493)
Q Consensus       342 i~~~~~~-g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g  419 (493)
                      ...|... |++++|.+.|+++.+.+..|+ ...|..+...|...|++++|.+.++++.+... .+...+..+...+.+.|
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~  161 (225)
T 2vq2_A           83 GWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQP-QFPPAFKELARTKMLAG  161 (225)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCchHHHHHHHHHHHcC
Confidence            9999999 999999999999987433444 67889999999999999999999999877532 34788999999999999


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHH
Q 011102          420 DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELL  482 (493)
Q Consensus       420 ~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll  482 (493)
                      ++++|..+|++..+..-..+...+..+...+...|+.++|..+++.+.+.  .|+...+..++
T Consensus       162 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~p~~~~~~~~l  222 (225)
T 2vq2_A          162 QLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN--FPYSEELQTVL  222 (225)
T ss_dssp             CHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHHHHh
Confidence            99999999999886543247778888888999999999999999998753  46555554443

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.41  E-value=2.2e-11  Score=120.19  Aligned_cols=248  Identities=8%  Similarity=-0.066  Sum_probs=192.3

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+.+.|++++|+..|.+.....     .|..+...|.+.|++++|++.|+.+... . ..+..+|..+...+.+.|+++
T Consensus        73 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-~-p~~~~~~~~l~~~~~~~g~~~  150 (365)
T 4eqf_A           73 LKRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLEL-Q-PNNLKALMALAVSYTNTSHQQ  150 (365)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc-C-CCCHHHHHHHHHHHHccccHH
Confidence            34456699999999999876543     7888999999999999999999999864 2 235778999999999999855


Q ss_pred             hhhhHHHhhccC----c-----------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHhcCCC
Q 011102          250 VPFKLENFVSLA----S-----------KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRM-LDPSIYAKLILELGKNPD  313 (493)
Q Consensus       250 ~~~~l~~~~~~~----~-----------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-pd~~t~~~li~~~~~~~~  313 (493)
                      .  ++..+....    +           ..++..+...|.+.|++++|.++|+++.+..-. ++..+|..+...|.+. |
T Consensus       151 ~--A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~~~~~-g  227 (365)
T 4eqf_A          151 D--ACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVLFHLS-G  227 (365)
T ss_dssp             H--HHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHHHHHH-T
T ss_pred             H--HHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHHHHHC-C
Confidence            4  443343321    1           123445688999999999999999999986422 2688999999999999 9


Q ss_pred             CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHH
Q 011102          314 KYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVV  393 (493)
Q Consensus       314 ~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~  393 (493)
                      ++++|.+.|++..+.  ...+..+|+.+...|.+.|++++|.+.|++..+.. +.+..+|..+...|.+.|++++|.+.|
T Consensus       228 ~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~  304 (365)
T 4eqf_A          228 EFNRAIDAFNAALTV--RPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREAVSNF  304 (365)
T ss_dssp             CHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHH
Confidence            999999999998875  33468899999999999999999999999987652 335889999999999999999999999


Q ss_pred             HHHHHCC---CC--------CCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          394 WNMEASN---CL--------FDLPAYRVVIKLFVALNDISRAIRYFSK  430 (493)
Q Consensus       394 ~~M~~~g---i~--------pd~~ty~~li~~~~~~g~~~~A~~~~~~  430 (493)
                      +++.+..   ..        .+...|..+-.++...|+.+.|.++.+.
T Consensus       305 ~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          305 LTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            9987532   11        1357889999999999999998887654

>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=99.40  E-value=2.5e-10  Score=118.34  Aligned_cols=196  Identities=12%  Similarity=0.030  Sum_probs=98.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Q 011102          266 LEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVG  345 (493)
Q Consensus       266 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~  345 (493)
                      |..+-..+...|++++|.+.|++..+..  |+..+|..+-..+... |++++|...+++....  ...+..+|..+...|
T Consensus       246 ~~~~g~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~  320 (537)
T 3fp2_A          246 LCYTGIFHFLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADK-ENSQEFFKFFQKAVDL--NPEYPPTYYHRGQMY  320 (537)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCS-SCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHh-cCHHHHHHHHHHHhcc--CCCCHHHHHHHHHHH
Confidence            4444444555555555555555555432  4444444444455555 5555555555554443  112344455555555


Q ss_pred             HHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc-------
Q 011102          346 IRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL-------  418 (493)
Q Consensus       346 ~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~-------  418 (493)
                      .+.|++++|.+.|++..+.. +.+...|..+...|...|++++|.+.++++.+.. ..+...+..+...|.+.       
T Consensus       321 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~  398 (537)
T 3fp2_A          321 FILQDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAI  398 (537)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHH
T ss_pred             HhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHH
Confidence            55555555555555544332 1123444455555555555555555555544331 11223444444444444       


Q ss_pred             -------------------------------------------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          419 -------------------------------------------NDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGR  455 (493)
Q Consensus       419 -------------------------------------------g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~  455 (493)
                                                                 |++++|...|+...+.. ..+...|..+...|.+.|+
T Consensus       399 ~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~~~~~g~  477 (537)
T 3fp2_A          399 KQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD-PRSEQAKIGLAQLKLQMEK  477 (537)
T ss_dssp             HHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcc
Confidence                                                       55555555555554332 1245666667777777777


Q ss_pred             HHHHHHHHHHHHHC
Q 011102          456 LAKCRDVCKEAEMA  469 (493)
Q Consensus       456 ~~~A~~l~~~m~~~  469 (493)
                      +++|.+.|++..+.
T Consensus       478 ~~~A~~~~~~al~~  491 (537)
T 3fp2_A          478 IDEAIELFEDSAIL  491 (537)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            77777777776653

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.40  E-value=1.1e-10  Score=112.03  Aligned_cols=258  Identities=14%  Similarity=0.056  Sum_probs=183.3

Q ss_pred             CCCHHHHHHHHhhhcccC------cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhh
Q 011102          180 HKDVAEVLDKCGRFLRKG------SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFK  253 (493)
Q Consensus       180 ~~~~~~a~~~~~~m~~~~------~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~  253 (493)
                      .|....|+..........      ..-.+..+|...|+++.|+..++.     .-.|+..++..+...+...++  ..++
T Consensus        12 ~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~-----~~~~~~~a~~~la~~~~~~~~--~~~A   84 (291)
T 3mkr_A           12 IGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP-----SSAPELQAVRMFAEYLASHSR--RDAI   84 (291)
T ss_dssp             TTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT-----TSCHHHHHHHHHHHHHHCSTT--HHHH
T ss_pred             HHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc-----cCChhHHHHHHHHHHHcCCCc--HHHH
Confidence            477777777766543332      223456788888888888876643     234566677888888887776  4444


Q ss_pred             HHHhhcc------C-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHh
Q 011102          254 LENFVSL------A-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELG  326 (493)
Q Consensus       254 l~~~~~~------~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~  326 (493)
                      +..+..+      | +...+..+-..|.+.|++++|++.|++      ..+...+..+...+.+. |++++|.+.|+.+.
T Consensus        85 ~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~-g~~~~A~~~l~~~~  157 (291)
T 3mkr_A           85 VAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKL-DRLDLARKELKKMQ  157 (291)
T ss_dssp             HHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHH
Confidence            4444331      3 445667777888999999999999987      46788888889999999 99999999999988


Q ss_pred             hcCCCCCCHHHH---HHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC
Q 011102          327 QRDDLNLSQQDC---TAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF  403 (493)
Q Consensus       327 ~~~g~~p~~~~~---~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p  403 (493)
                      +.   .|+....   ..++..+...|++++|..+|+++.+. .+.+...|+.+..++.+.|++++|.+.|++..+.. +-
T Consensus       158 ~~---~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~-~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~  232 (291)
T 3mkr_A          158 DQ---DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK-CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SG  232 (291)
T ss_dssp             HH---CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT
T ss_pred             hh---CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CC
Confidence            75   2553221   22334444558899999999999876 35688889999999999999999999999977643 23


Q ss_pred             CHHHHHHHHHHHHHcCCHHH-HHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          404 DLPAYRVVIKLFVALNDISR-AIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRD  461 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~-A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~  461 (493)
                      +..++..++..+...|+.++ +.++++++.+..  |+...   +.+...+.+.++++..
T Consensus       233 ~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~--P~~~~---~~d~~~~~~~fd~~~~  286 (291)
T 3mkr_A          233 HPETLINLVVLSQHLGKPPEVTNRYLSQLKDAH--RSHPF---IKEYRAKENDFDRLVL  286 (291)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTCHH---HHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhC--CCChH---HHHHHHHHHHHHHHHH
Confidence            56788889999999999876 578888887543  43322   3334445555555543

>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=99.40  E-value=3.4e-11  Score=116.14  Aligned_cols=247  Identities=9%  Similarity=-0.071  Sum_probs=194.4

Q ss_pred             hccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCch
Q 011102          176 GLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKV  250 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~  250 (493)
                      .+...|++++|+..+.+.....     .|..+...+.+.|++++|++.|+.+...  ...+..++..+...+...|+++.
T Consensus        30 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~la~~~~~~~~~~~  107 (327)
T 3cv0_A           30 SMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARML--DPKDIAVHAALAVSHTNEHNANA  107 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CcCCHHHHHHHHHHHHHcCCHHH
Confidence            4456789999999999776543     6777888999999999999999999864  23367788899999999998554


Q ss_pred             hhhHHHhhcc----C-cHHHHHHH--------------HH-HHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhc
Q 011102          251 PFKLENFVSL----A-SKGVLEAT--------------AK-GFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGK  310 (493)
Q Consensus       251 ~~~l~~~~~~----~-~~~~~~~l--------------i~-~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~  310 (493)
                      +.  ..+...    + +...+..+              .. .+...|++++|.+.++++.+.. +.+..++..+...+.+
T Consensus       108 A~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~  184 (327)
T 3cv0_A          108 AL--ASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNL  184 (327)
T ss_dssp             HH--HHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHH
T ss_pred             HH--HHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHH
Confidence            43  333321    1 11122222              22 3778899999999999998764 2367888999999999


Q ss_pred             CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHH
Q 011102          311 NPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREAL  390 (493)
Q Consensus       311 ~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~  390 (493)
                      . |++++|.+.+++..+.  ...+...+..+...|.+.|++++|.+.|++..+.. +.+..+|..+...|.+.|++++|.
T Consensus       185 ~-~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~  260 (327)
T 3cv0_A          185 S-NNYDSAAANLRRAVEL--RPDDAQLWNKLGATLANGNRPQEALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAA  260 (327)
T ss_dssp             T-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             h-ccHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHH
Confidence            9 9999999999998875  23467889999999999999999999999987653 346888999999999999999999


Q ss_pred             HHHHHHHHCCCCC-----------CHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          391 TVVWNMEASNCLF-----------DLPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       391 ~l~~~M~~~gi~p-----------d~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      +.+++..+.....           +..+|..+...+.+.|+.++|..+++..
T Consensus       261 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  312 (327)
T 3cv0_A          261 KQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQN  312 (327)
T ss_dssp             HHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCC
T ss_pred             HHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            9999987643221           4678999999999999999999998643

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.36  E-value=1.3e-10  Score=107.88  Aligned_cols=235  Identities=11%  Similarity=-0.011  Sum_probs=174.9

Q ss_pred             HHHHHHHHHHHHcCCCchhhhHHHhhcc----CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC--CCCC----HHHHH
Q 011102          233 RLLASTVEVLARHHELKVPFKLENFVSL----ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGG--RMLD----PSIYA  302 (493)
Q Consensus       233 ~t~~~li~~~~~~g~~~~~~~l~~~~~~----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--~~pd----~~t~~  302 (493)
                      ..|..+-..+...|+++.+...  +...    .+..+|..+...|...|++++|.+.|++..+..  ..++    ..+|.
T Consensus         6 ~~~~~~g~~~~~~~~~~~A~~~--~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~   83 (258)
T 3uq3_A            6 DKEKAEGNKFYKARQFDEAIEH--YNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFA   83 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHH--HHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHH--HHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHH
Confidence            4566777777777875443332  2211    456678888888888888888888888776632  1122    46777


Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 011102          303 KLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS  382 (493)
Q Consensus       303 ~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~  382 (493)
                      .+...+.+. |++++|...|++....   .|+.       ..+.+.|++++|.+.+++..... +.+...|..+...+..
T Consensus        84 ~l~~~~~~~-~~~~~A~~~~~~a~~~---~~~~-------~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~  151 (258)
T 3uq3_A           84 RIGNAYHKL-GDLKKTIEYYQKSLTE---HRTA-------DILTKLRNAEKELKKAEAEAYVN-PEKAEEARLEGKEYFT  151 (258)
T ss_dssp             HHHHHHHHT-TCHHHHHHHHHHHHHH---CCCH-------HHHHHHHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-ccHHHHHHHHHHHHhc---Cchh-------HHHHHHhHHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHH
Confidence            777788888 8888888888887764   2342       34666777888888888877542 2345778899999999


Q ss_pred             CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          383 EKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       383 ~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                      .|++++|.+.+++..+..- .+..+|..+...|.+.|++++|...|++..+.. ..+...|..+...|.+.|++++|.+.
T Consensus       152 ~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~  229 (258)
T 3uq3_A          152 KSDWPNAVKAYTEMIKRAP-EDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALET  229 (258)
T ss_dssp             TTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            9999999999999887532 367889999999999999999999999998654 23588899999999999999999999


Q ss_pred             HHHHHHCC----CccCHHHHHHHHH
Q 011102          463 CKEAEMAG----FKLDKQTVVELLQ  483 (493)
Q Consensus       463 ~~~m~~~g----~~pd~~t~~~Ll~  483 (493)
                      +++..+..    ..|+......++.
T Consensus       230 ~~~a~~~~~~~~~~p~~~~~~~~l~  254 (258)
T 3uq3_A          230 LDAARTKDAEVNNGSSAREIDQLYY  254 (258)
T ss_dssp             HHHHHHHHHHHHTTTTHHHHHHHHH
T ss_pred             HHHHHHhChhhcCCCchHHHHHHHH
Confidence            99987642    2366655544444

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.31  E-value=2.8e-10  Score=104.80  Aligned_cols=210  Identities=10%  Similarity=-0.022  Sum_probs=159.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      ..+|..+...+.+.|++++|..+|+++.+.. ..+...+..+...+... |++++|.+.+++..+.  ...+...+..+.
T Consensus        23 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~la   98 (243)
T 2q7f_A           23 SMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSV-NELERALAFYDKALEL--DSSAATAYYGAG   98 (243)
T ss_dssp             -------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHc--CCcchHHHHHHH
Confidence            3457778888899999999999999998753 23577888888889999 9999999999998775  234678889999


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      ..|.+.|++++|.+.|++..+.. +.+...|..+...|.+.|++++|.+.++++.+.. ..+...+..+...+.+.|+++
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~  176 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLD  176 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHH
Confidence            99999999999999999987654 3467889999999999999999999999987653 236778889999999999999


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCcc-CHHHHHHH
Q 011102          423 RAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKL-DKQTVVEL  481 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~L  481 (493)
                      +|...|++..+..- .+..+|..+...|.+.|++++|.+.+++..+.  .| +...+..+
T Consensus       177 ~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~~  233 (243)
T 2q7f_A          177 EALSQFAAVTEQDP-GHADAFYNAGVTYAYKENREKALEMLDKAIDI--QPDHMLALHAK  233 (243)
T ss_dssp             HHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhCc-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHcc--CcchHHHHHHH
Confidence            99999999886542 36788999999999999999999999999874  34 34444433

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.30  E-value=5.1e-10  Score=102.30  Aligned_cols=198  Identities=10%  Similarity=-0.035  Sum_probs=155.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +...|..+-..+.+.|++++|...|++..+.. +-+...|..+-..+.+. |++++|...+++..+.  -.-+...+..+
T Consensus         4 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~-g~~~~A~~~~~~al~~--~P~~~~a~~~l   79 (217)
T 2pl2_A            4 AEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKL-GLVNPALENGKTLVAR--TPRYLGGYMVL   79 (217)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCcHHHHHHH
Confidence            34567778888999999999999999998754 23567788888889999 9999999999998775  22356788888


Q ss_pred             HHHHHHc-----------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q 011102          342 MKVGIRL-----------QKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRV  410 (493)
Q Consensus       342 i~~~~~~-----------g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~  410 (493)
                      -..|.+.           |++++|...|++..+.. +-+...|..+-..|...|++++|++.|++..+..  .+...+..
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~  156 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSA  156 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHH
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHH
Confidence            8999999           99999999999987652 2357889999999999999999999999998877  78889999


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          411 VIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       411 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      +-..|...|++++|...|+...+..- -+...+..+...+.+.|++++|.+.|++..
T Consensus       157 la~~~~~~g~~~~A~~~~~~al~~~P-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          157 LAELYLSMGRLDEALAQYAKALEQAP-KDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHTC---------------
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            99999999999999999999986542 367888899999999999999999988754

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.30  E-value=1.1e-09  Score=101.43  Aligned_cols=217  Identities=10%  Similarity=0.002  Sum_probs=175.0

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhcc----Cc--------HHH
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSL----AS--------KGV  265 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~----~~--------~~~  265 (493)
                      .|..+-..+.+.|++++|++.|+.+.+. .  .+..+|..+...+...|+++.+.  ..+...    ++        ..+
T Consensus         7 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~-~--~~~~~~~~~~~~~~~~~~~~~A~--~~~~~a~~~~~~~~~~~~~~~~~   81 (258)
T 3uq3_A            7 KEKAEGNKFYKARQFDEAIEHYNKAWEL-H--KDITYLNNRAAAEYEKGEYETAI--STLNDAVEQGREMRADYKVISKS   81 (258)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH-S--CCTHHHHHHHHHHHHTTCHHHHH--HHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHh-h--ccHHHHHHHHHHHHHcccHHHHH--HHHHHHHHhCcccccchHHHHHH
Confidence            4556667888889999999999988876 4  67788888888888888854433  333221    11        467


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Q 011102          266 LEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVG  345 (493)
Q Consensus       266 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~  345 (493)
                      |..+...|.+.|++++|.+.|++..+..  |+..+       +.+. |++++|...++.+...  ...+...+..+...|
T Consensus        82 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~-------~~~~-~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~  149 (258)
T 3uq3_A           82 FARIGNAYHKLGDLKKTIEYYQKSLTEH--RTADI-------LTKL-RNAEKELKKAEAEAYV--NPEKAEEARLEGKEY  149 (258)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHH-------HHHH-HHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhcC--chhHH-------HHHH-hHHHHHHHHHHHHHHc--CcchHHHHHHHHHHH
Confidence            8999999999999999999999998843  56433       4455 8899999999998765  223456788889999


Q ss_pred             HHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          346 IRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAI  425 (493)
Q Consensus       346 ~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~  425 (493)
                      .+.|++++|.+.|++..+.. +.+...|..+...|.+.|++++|.+.|++..+.. ..+...|..+-..|.+.|++++|.
T Consensus       150 ~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~  227 (258)
T 3uq3_A          150 FTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASAL  227 (258)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHH
Confidence            99999999999999987653 3468899999999999999999999999987753 235788999999999999999999


Q ss_pred             HHHHHHHH
Q 011102          426 RYFSKLKE  433 (493)
Q Consensus       426 ~~~~~m~~  433 (493)
                      ..|+...+
T Consensus       228 ~~~~~a~~  235 (258)
T 3uq3_A          228 ETLDAART  235 (258)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99998774

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.23  E-value=1.4e-09  Score=102.11  Aligned_cols=222  Identities=10%  Similarity=-0.036  Sum_probs=97.2

Q ss_pred             hCCChHHHHHHHHHHHhCCCCCC--CHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHH
Q 011102          208 HMNLPERALQTFCWAQKQPHLFP--DDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKL  285 (493)
Q Consensus       208 ~~g~~~~A~~l~~~m~~~~g~~p--d~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l  285 (493)
                      ..|++++|++.|+.+.+.....+  +..+|..+...+...                               |++++|.+.
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-------------------------------~~~~~A~~~   65 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSL-------------------------------GLRALARND   65 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHT-------------------------------TCHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHc-------------------------------ccHHHHHHH
Confidence            45778899999998886511111  223344444444444                               444444444


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Q 011102          286 LMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSG  365 (493)
Q Consensus       286 ~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  365 (493)
                      |++..+.. +.+..+|..+...+... |++++|...|++....  ...+...+..+...|.+.|++++|.+.|+++.+. 
T Consensus        66 ~~~al~~~-~~~~~~~~~la~~~~~~-~~~~~A~~~~~~al~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~-  140 (275)
T 1xnf_A           66 FSQALAIR-PDMPEVFNYLGIYLTQA-GNFDAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD-  140 (275)
T ss_dssp             HHHHHHHC-CCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHcC-CCcHHHHHHHHHHHHHc-cCHHHHHHHHHHHHhc--CccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh-
Confidence            44444422 11334444444444444 4455555554444432  1112344444444444555555555555444432 


Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC--C-CHHH
Q 011102          366 RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFC--P-TYDI  442 (493)
Q Consensus       366 ~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~--p-~~~t  442 (493)
                       .|+...+...+..+...|+.++|...+.+..... .++...+ .++..+...++.++|...++...+....  | +..+
T Consensus       141 -~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  217 (275)
T 1xnf_A          141 -DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSET  217 (275)
T ss_dssp             -CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHH
T ss_pred             -CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHH
Confidence             2222222223333333444555555444433321 1121222 2333344444444444444444321110  0 1234


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          443 YRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       443 y~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |..+...|.+.|++++|.+.|++..+
T Consensus       218 ~~~la~~~~~~g~~~~A~~~~~~al~  243 (275)
T 1xnf_A          218 NFYLGKYYLSLGDLDSATALFKLAVA  243 (275)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44444445555555555555554443

>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=99.22  E-value=3.2e-08  Score=93.17  Aligned_cols=221  Identities=12%  Similarity=-0.052  Sum_probs=177.1

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHh--
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVK--  275 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~--  275 (493)
                      .+..+-..|.+.|++++|++.|+...+. +   +                               ...+..+-..|..  
T Consensus         8 a~~~lg~~~~~~~~~~~A~~~~~~a~~~-~---~-------------------------------~~a~~~lg~~~~~g~   52 (273)
T 1ouv_A            8 ELVGLGAKSYKEKDFTQAKKYFEKACDL-K---E-------------------------------NSGCFNLGVLYYQGQ   52 (273)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHT-T---C-------------------------------HHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHC-C---C-------------------------------HHHHHHHHHHHHcCC
Confidence            3444555666777777777777766642 1   1                               1233344455555  


Q ss_pred             --cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhc----CCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH--
Q 011102          276 --GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGK----NPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR--  347 (493)
Q Consensus       276 --~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~----~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~--  347 (493)
                        .+++++|.+.|++..+.+   +...+..+-..|..    . +++++|...|++..+. +   +...+..+-..|.+  
T Consensus        53 ~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~-~~~~~A~~~~~~a~~~-~---~~~a~~~lg~~~~~~~  124 (273)
T 1ouv_A           53 GVEKNLKKAASFYAKACDLN---YSNGCHLLGNLYYSGQGVS-QNTNKALQYYSKACDL-K---YAEGCASLGGIYHDGK  124 (273)
T ss_dssp             SSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSC-CCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHCS
T ss_pred             CcCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhCCCCcc-cCHHHHHHHHHHHHHc-C---CccHHHHHHHHHHcCC
Confidence              788999999999998876   77788888788887    8 9999999999998876 3   77888888889998  


Q ss_pred             --cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----
Q 011102          348 --LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS----EKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA----  417 (493)
Q Consensus       348 --~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~----  417 (493)
                        .+++++|.+.|++..+.+   +...+..+-..|..    .++.++|.+.|++..+.+   +...+..+-..|.+    
T Consensus       125 ~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~  198 (273)
T 1ouv_A          125 VVTRDFKKAVEYFTKACDLN---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGA  198 (273)
T ss_dssp             SSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSS
T ss_pred             CcccCHHHHHHHHHHHHhcC---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCC
Confidence              999999999999988765   67778888888887    899999999999988764   46778888888888    


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCC
Q 011102          418 LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA----SGRLAKCRDVCKEAEMAG  470 (493)
Q Consensus       418 ~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~m~~~g  470 (493)
                      .+++++|...|+...+.+   +...+..+-..|.+    .+++++|.+.|++..+.|
T Consensus       199 ~~~~~~A~~~~~~a~~~~---~~~a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~  252 (273)
T 1ouv_A          199 TKNFKEALARYSKACELE---NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLG  252 (273)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHT
T ss_pred             CccHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcC
Confidence            999999999999988765   36677888888888    899999999999998865

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.22  E-value=4.7e-10  Score=107.18  Aligned_cols=203  Identities=11%  Similarity=0.050  Sum_probs=113.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC-------CCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc------CCC
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDG-------GRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQR------DDL  331 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~-------g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~------~g~  331 (493)
                      +|..+...|...|++++|..+|+++.+.       .......++..+-..|... |++++|...+++....      ...
T Consensus        29 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~  107 (311)
T 3nf1_A           29 TLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQ-NKYKDAANLLNDALAIREKTLGKDH  107 (311)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            4555555666666666666666555542       1112233445555555555 6666666666554432      111


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc------CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----
Q 011102          332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS------GRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEAS-----  399 (493)
Q Consensus       332 ~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-----  399 (493)
                      ......+..+...|...|++++|.+.|++..+.      +-.| ....|..+...|...|++++|.+.++++.+.     
T Consensus       108 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~  187 (311)
T 3nf1_A          108 PAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKL  187 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence            122344555555666666666666666555432      1112 2344555556666666666666666655442     


Q ss_pred             -CCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHC-------------------------------------------
Q 011102          400 -NCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLKEA-------------------------------------------  434 (493)
Q Consensus       400 -gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~~-------------------------------------------  434 (493)
                       +-.|+ ..++..+...|.+.|++++|..+|++..+.                                           
T Consensus       188 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~  267 (311)
T 3nf1_A          188 GPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWY  267 (311)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHH
Confidence             11121 234555555566666666666666555431                                           


Q ss_pred             -----CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          435 -----GFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       435 -----g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                           .-..+..+|..+...|.+.|++++|.++|++..+
T Consensus       268 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          268 KACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 1123456788999999999999999999998764

>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=99.21  E-value=1.2e-08  Score=94.66  Aligned_cols=200  Identities=15%  Similarity=-0.018  Sum_probs=160.0

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcC
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGG  277 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g  277 (493)
                      .|..+...+...|++++|++.|+.+...   .|+                              +..+|..+...|.+.|
T Consensus        39 ~~~~~a~~~~~~~~~~~A~~~~~~al~~---~~~------------------------------~~~~~~~la~~~~~~~   85 (252)
T 2ho1_A           39 AYIQLGLGYLQRGNTEQAKVPLRKALEI---DPS------------------------------SADAHAALAVVFQTEM   85 (252)
T ss_dssp             HHHHHHHHHHHTTCTGGGHHHHHHHHHH---CTT------------------------------CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHhc---CCC------------------------------hHHHHHHHHHHHHHcC
Confidence            5666777788888888888888877653   111                              2235666777788889


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC-CHHHHHHHHHHHHHcCCHHHHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNL-SQQDCTAIMKVGIRLQKFGVVES  356 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p-~~~~~~~li~~~~~~g~~~~A~~  356 (493)
                      ++++|.+.|+++.+.. ..+...|..+...+... |++++|.++++++... +..| +...+..+...|.+.|++++|.+
T Consensus        86 ~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~-g~~~~A~~~~~~~~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~  162 (252)
T 2ho1_A           86 EPKLADEEYRKALASD-SRNARVLNNYGGFLYEQ-KRYEEAYQRLLEASQD-TLYPERSRVFENLGLVSLQMKKPAQAKE  162 (252)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHTTC-TTCTTHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHH-hHHHHHHHHHHHHHhC-ccCcccHHHHHHHHHHHHHcCCHHHHHH
Confidence            9999999999888754 23677888888889999 9999999999998773 3445 45678888899999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          357 LFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       357 l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      .|++..+.. +.+...|..+...|...|++++|.+.++++.+.. ..+...+..+...+.+.|+.++|.++++.+.+..
T Consensus       163 ~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          163 YFEKSLRLN-RNQPSVALEMADLLYKEREYVPARQYYDLFAQGG-GQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             HHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhcC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC
Confidence            999987653 3467889999999999999999999999987643 2466778888899999999999999999988653

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.20  E-value=9.2e-09  Score=93.06  Aligned_cols=200  Identities=11%  Similarity=-0.050  Sum_probs=123.1

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcC
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGG  277 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g  277 (493)
                      .|..+...+...|++++|++.|+.+.+. . ..+..                               +|..+...|...|
T Consensus        10 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~-~-~~~~~-------------------------------~~~~l~~~~~~~~   56 (225)
T 2vq2_A           10 IKTQLAMEYMRGQDYRQATASIEDALKS-D-PKNEL-------------------------------AWLVRAEIYQYLK   56 (225)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH-C-TTCHH-------------------------------HHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHh-C-ccchH-------------------------------HHHHHHHHHHHcC
Confidence            4566677788888888888888877653 1 11222                               3444555556666


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-HHHHHHHHHHHHHcCCHHHHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-QQDCTAIMKVGIRLQKFGVVES  356 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-~~~~~~li~~~~~~g~~~~A~~  356 (493)
                      ++++|.+.|+++.+.. ..+..++..+...+....|++++|...++++... +..|+ ...+..+...|.+.|++++|.+
T Consensus        57 ~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~A~~  134 (225)
T 2vq2_A           57 VNDKAQESFRQALSIK-PDSAEINNNYGWFLCGRLNRPAESMAYFDKALAD-PTYPTPYIANLNKGICSAKQGQFGLAEA  134 (225)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTS-TTCSCHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ChHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcC-cCCcchHHHHHHHHHHHHHcCCHHHHHH
Confidence            6666666666665532 1244455555555544425667777777766652 22232 4556666667777777777777


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          357 LFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       357 l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      .|++..+.. +.+...|..+...|.+.|++++|.+.++++.+..-..+...+..+...+.+.|+.++|..+++.+.+
T Consensus       135 ~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          135 YLKRSLAAQ-PQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             HHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhC-CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            777665442 2246666777777777777777777777765542213555666666666777777777777777654

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.18  E-value=1.3e-07  Score=98.45  Aligned_cols=163  Identities=10%  Similarity=0.034  Sum_probs=115.5

Q ss_pred             HHHHHHHHHhhcCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHH
Q 011102          317 LVMTLLDELGQRDDLNL-SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT--VVMYTTLIHSRLSEKKCREALTVV  393 (493)
Q Consensus       317 ~a~~l~~~m~~~~g~~p-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~  393 (493)
                      +|..+|++..+.  +.| +...|..+...+.+.|++++|..+|++..+.  .|+  ...|...+..+.+.|+.++|.++|
T Consensus       304 ~A~~~~~~Al~~--~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~  379 (530)
T 2ooe_A          304 EAANIYERAIST--LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIF  379 (530)
T ss_dssp             HHHHHHHHHTTT--TCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH--hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHH
Confidence            777777777652  233 4777888888888888888888888888764  453  357888888888888888888888


Q ss_pred             HHHHHCCCCCCHHHHHHHHH-HHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-C
Q 011102          394 WNMEASNCLFDLPAYRVVIK-LFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAG-F  471 (493)
Q Consensus       394 ~~M~~~gi~pd~~ty~~li~-~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g-~  471 (493)
                      ++..+..- .+...|..... .+...|+.++|..+|+...+.. .-+...|..+++.+.+.|+.++|..+|++....+ .
T Consensus       380 ~~Al~~~~-~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~-p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~  457 (530)
T 2ooe_A          380 KKAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  457 (530)
T ss_dssp             HHHHTCTT-CCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCS
T ss_pred             HHHHhccC-CchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCC
Confidence            88776421 12222222221 2336889999999999877532 2257888899999999999999999999988764 3


Q ss_pred             ccC--HHHHHHHHHhh
Q 011102          472 KLD--KQTVVELLQIE  485 (493)
Q Consensus       472 ~pd--~~t~~~Ll~~~  485 (493)
                      .|+  ...|...++.+
T Consensus       458 ~~~~~~~lw~~~~~~e  473 (530)
T 2ooe_A          458 PPEKSGEIWARFLAFE  473 (530)
T ss_dssp             CGGGCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHH
Confidence            343  44676666653

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.16  E-value=1.5e-09  Score=101.82  Aligned_cols=242  Identities=11%  Similarity=0.007  Sum_probs=177.5

Q ss_pred             cCCCCHHHHHHHHhhhccc---------CcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCC
Q 011102          178 DSHKDVAEVLDKCGRFLRK---------GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHEL  248 (493)
Q Consensus       178 ~~~~~~~~a~~~~~~m~~~---------~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~  248 (493)
                      ...+++++|+..+.+....         ..|..+...|...|++++|+..|+.+...   .|+                 
T Consensus        16 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~---~~~-----------------   75 (275)
T 1xnf_A           16 QPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAI---RPD-----------------   75 (275)
T ss_dssp             CCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCC-----------------
T ss_pred             CccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHc---CCC-----------------
Confidence            3457778888888866653         16777888999999999999999988754   122                 


Q ss_pred             chhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc
Q 011102          249 KVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQR  328 (493)
Q Consensus       249 ~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~  328 (493)
                                   +..+|..+...|.+.|++++|.+.|++..+.. +.+..+|..+...+.+. |++++|...|+++.+.
T Consensus        76 -------------~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~-g~~~~A~~~~~~a~~~  140 (275)
T 1xnf_A           76 -------------MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIALYYG-GRDKLAQDDLLAFYQD  140 (275)
T ss_dssp             -------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH
T ss_pred             -------------cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHHHHHHh-ccHHHHHHHHHHHHHh
Confidence                         22345566777888888999999999888753 22567888888899999 9999999999998765


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC--C-CH
Q 011102          329 DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL--F-DL  405 (493)
Q Consensus       329 ~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~--p-d~  405 (493)
                         .|+.......+..+.+.|++++|...|++..... .++...|+ ++..+...++.++|.+.+.+..+....  | +.
T Consensus       141 ---~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  215 (275)
T 1xnf_A          141 ---DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLS  215 (275)
T ss_dssp             ---CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHH
T ss_pred             ---CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CcchHHHH-HHHHHHHhcCHHHHHHHHHHHhccccccccccc
Confidence               3554555556666677899999999998776543 34444444 777788888899999999887654211  1 14


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVC  463 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~  463 (493)
                      .+|..+-..|.+.|++++|...|++..+..  |+.  +.....++...|++++|.+-+
T Consensus       216 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~--p~~--~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          216 ETNFYLGKYYLSLGDLDSATALFKLAVANN--VHN--FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--CTT--CHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhCC--chh--HHHHHHHHHHHHHHHhhHHHH
Confidence            778888999999999999999999998653  422  333455677888888887765

>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=99.16  E-value=2.2e-08  Score=111.05  Aligned_cols=247  Identities=11%  Similarity=0.098  Sum_probs=171.9

Q ss_pred             cCCCCHHHHHHHHhhhcccCcHHHHHHHHH-hCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHH
Q 011102          178 DSHKDVAEVLDKCGRFLRKGSLSFTVRELG-HMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLEN  256 (493)
Q Consensus       178 ~~~~~~~~a~~~~~~m~~~~~~~~li~~~~-~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~  256 (493)
                      ...+.+++|..+|++..   .+...+..+. +.|++++|.++.+...       +..+|..+-.++.+.|+  ..+|+..
T Consensus      1060 i~lglyEEAf~IYkKa~---~~~~A~~VLie~i~nldrAiE~Aervn-------~p~vWsqLAKAql~~G~--~kEAIds 1127 (1630)
T 1xi4_A         1060 ISNELFEEAFAIFRKFD---VNTSAVQVLIEHIGNLDRAYEFAERCN-------EPAVWSQLAKAQLQKGM--VKEAIDS 1127 (1630)
T ss_pred             HhCCCHHHHHHHHHHcC---CHHHHHHHHHHHHhhHHHHHHHHHhcC-------CHHHHHHHHHHHHhCCC--HHHHHHH
Confidence            34577777777777643   2222223222 5667777777776442       35567777777777777  5566666


Q ss_pred             hhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHH
Q 011102          257 FVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQ  336 (493)
Q Consensus       257 ~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~  336 (493)
                      |..-.+...|.-++..|.+.|++++|.+.|...++..  +++...+.+..+|++. +++++...+.    .    .++..
T Consensus      1128 YiKAdD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl-~rleele~fI----~----~~n~a 1196 (1630)
T 1xi4_A         1128 YIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKT-NRLAELEEFI----N----GPNNA 1196 (1630)
T ss_pred             HHhcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhh-cCHHHHHHHH----h----CCCHH
Confidence            7777777777778888888888888888887666544  3433344577777887 7777533332    2    24556


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .|..+-+.|...|++++|..+|...         ..|..+...|++.|++++|.+.+++.      -+..+|.-+-.+|.
T Consensus      1197 d~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~~acv 1261 (1630)
T 1xi4_A         1197 HIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACV 1261 (1630)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHHHHHh
Confidence            6667777788888888888888763         36888888888888888888888765      35577777777787


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      ..|++..|......     +..+...+..++.-|.+.|.+++|..+++.-.
T Consensus      1262 e~~Ef~LA~~cgl~-----Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL 1307 (1630)
T 1xi4_A         1262 DGKEFRLAQMCGLH-----IVVHADELEELINYYQDRGYFEELITMLEAAL 1307 (1630)
T ss_pred             hhhHHHHHHHHHHh-----hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            77877777776543     33466778899999999999999999997665

>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=99.16  E-value=5.8e-08  Score=91.39  Aligned_cols=193  Identities=10%  Similarity=-0.016  Sum_probs=167.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhc----CCCCHHHHHHHHHHHhhcCCCCCCHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGK----NPDKYMLVMTLLDELGQRDDLNLSQQD  337 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~----~~~~~~~a~~l~~~m~~~~g~~p~~~~  337 (493)
                      +..++..+-..|.+.|++++|.+.|++..+.+   +...+..+-..|..    . +++++|...|++..+. +   +...
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~-~~~~~A~~~~~~a~~~-~---~~~a   76 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVE-KNLKKAASFYAKACDL-N---YSNG   76 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSC-CCHHHHHHHHHHHHHT-T---CHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcC-CCHHHHHHHHHHHHHC-C---CHHH
Confidence            34566777888899999999999999999843   56677777778887    8 9999999999999876 4   7888


Q ss_pred             HHHHHHHHHH----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          338 CTAIMKVGIR----LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS----EKKCREALTVVWNMEASNCLFDLPAYR  409 (493)
Q Consensus       338 ~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~gi~pd~~ty~  409 (493)
                      +..+-..|..    .+++++|.+.|++..+.+   +..++..+-..|..    .++.++|++.|++..+.+   +...+.
T Consensus        77 ~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~  150 (273)
T 1ouv_A           77 CHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCT  150 (273)
T ss_dssp             HHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             HHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHH
Confidence            8999999999    999999999999998765   78889999999999    999999999999998876   567778


Q ss_pred             HHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCC
Q 011102          410 VVIKLFVA----LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA----SGRLAKCRDVCKEAEMAGF  471 (493)
Q Consensus       410 ~li~~~~~----~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~m~~~g~  471 (493)
                      .+-..|..    .++.++|...|++..+.+   +...+..+-..|..    .+++++|.+.|++..+.+-
T Consensus       151 ~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~  217 (273)
T 1ouv_A          151 ILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN  217 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC
Confidence            88888888    999999999999998764   56788888899999    9999999999999988753

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.14  E-value=2.7e-08  Score=93.20  Aligned_cols=237  Identities=11%  Similarity=-0.047  Sum_probs=171.5

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHH
Q 011102          201 FTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLK  280 (493)
Q Consensus       201 ~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~  280 (493)
                      ..-..+.+.|++++|+..|+...+.   .|+                              +..+|..+...|.+.|+++
T Consensus         8 ~~a~~~~~~~~~~~A~~~~~~~l~~---~p~------------------------------~~~~~~~l~~~~~~~~~~~   54 (272)
T 3u4t_A            8 RYADFLFKNNNYAEAIEVFNKLEAK---KYN------------------------------SPYIYNRRAVCYYELAKYD   54 (272)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHHHT---TCC------------------------------CSTTHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHh---CCC------------------------------cHHHHHHHHHHHHHHhhHH
Confidence            3455677888899999998888754   222                              1113445666777888899


Q ss_pred             HHHHHHHHHHhCCCCCC--HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          281 LAWKLLMVAKDGGRMLD--PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLF  358 (493)
Q Consensus       281 ~A~~l~~~m~~~g~~pd--~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~  358 (493)
                      +|.+.|++..+.+-.++  ..+|..+-..+... |++++|...|+...+.  ..-+...|..+...|.+.|++++|.+.|
T Consensus        55 ~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~~~-~~~~~A~~~~~~a~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~  131 (272)
T 3u4t_A           55 LAQKDIETYFSKVNATKAKSADFEYYGKILMKK-GQDSLAIQQYQAAVDR--DTTRLDMYGQIGSYFYNKGNFPLAIQYM  131 (272)
T ss_dssp             HHHHHHHHHHTTSCTTTCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--STTCTHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhccCchhHHHHHHHHHHHHHHHc-ccHHHHHHHHHHHHhc--CcccHHHHHHHHHHHHHccCHHHHHHHH
Confidence            99999998888442222  33477788888888 9999999999988765  2235578888899999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHCC
Q 011102          359 HWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND---ISRAIRYFSKLKEAG  435 (493)
Q Consensus       359 ~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~---~~~A~~~~~~m~~~g  435 (493)
                      ++..+. .+.+...|..+...+...+++++|.+.|++..+..- .+...+..+-..+...|+   .++|...|++..+..
T Consensus       132 ~~al~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~  209 (272)
T 3u4t_A          132 EKQIRP-TTTDPKVFYELGQAYYYNKEYVKADSSFVKVLELKP-NIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVC  209 (272)
T ss_dssp             GGGCCS-SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHH
T ss_pred             HHHhhc-CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc-cchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHH
Confidence            887755 234566677776344445699999999998876421 235677777778888887   788888888776321


Q ss_pred             -CCCC------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHH
Q 011102          436 -FCPT------YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQT  477 (493)
Q Consensus       436 -~~p~------~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t  477 (493)
                       -.|+      ...|..+-..|.+.|++++|.+.|++..+.  .|+...
T Consensus       210 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~  256 (272)
T 3u4t_A          210 APGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILAL--DPTNKK  256 (272)
T ss_dssp             GGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHH
T ss_pred             hcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CccHHH
Confidence             1233      257888888999999999999999999874  454443

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.12  E-value=1.3e-06  Score=89.73  Aligned_cols=145  Identities=9%  Similarity=0.018  Sum_probs=64.2

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHc-----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC---
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRL-----QKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK---  384 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g---  384 (493)
                      ++.++|...|+...+. |   +...+..+-..|...     ++.++|...|++..+.|   +...+..|-..|...|   
T Consensus       273 ~d~~~A~~~~~~a~~~-~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~  345 (490)
T 2xm6_A          273 KEPLKALEWYRKSAEQ-G---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYFRLGSEE  345 (490)
T ss_dssp             CCHHHHHHHHHHHHTT-T---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHH
T ss_pred             CCHHHHHHHHHHHHHc-C---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCcc
Confidence            4444444444444332 1   233333344444443     44445555444444332   2333444444444333   


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVA----LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA----SGRL  456 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~----~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~----~g~~  456 (493)
                      +.++|.+.|++..+.|   +...+..|-..|..    .++.++|..+|+...+.|   +...+..|-..|.+    .++.
T Consensus       346 ~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~---~~~a~~~Lg~~y~~g~g~~~d~  419 (490)
T 2xm6_A          346 EHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG---LSAAQVQLGEIYYYGLGVERDY  419 (490)
T ss_dssp             HHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCH
T ss_pred             cHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC---CHHHHHHHHHHHHcCCCCCCCH
Confidence            4444555554444432   33344444444444    445555555555544433   23444444444444    4555


Q ss_pred             HHHHHHHHHHHHCC
Q 011102          457 AKCRDVCKEAEMAG  470 (493)
Q Consensus       457 ~~A~~l~~~m~~~g  470 (493)
                      ++|.+.|++..+.|
T Consensus       420 ~~A~~~~~~A~~~~  433 (490)
T 2xm6_A          420 VQAWAWFDTASTND  433 (490)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCC
Confidence            55555555554433

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.10  E-value=7.9e-07  Score=91.40  Aligned_cols=271  Identities=11%  Similarity=0.002  Sum_probs=217.0

Q ss_pred             ccCCCCHHHHHHHHhhhcccC---cHHHHHHHHHh----CCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH----c
Q 011102          177 LDSHKDVAEVLDKCGRFLRKG---SLSFTVRELGH----MNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLAR----H  245 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~~---~~~~li~~~~~----~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~----~  245 (493)
                      .+..++.++|+..|.+..+.+   .+..+-..|..    .+++++|++.|+...+. |   +...+..+-..|..    .
T Consensus        89 ~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~-~---~~~a~~~Lg~~y~~g~g~~  164 (490)
T 2xm6_A           89 EGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQ-G---RDSGQQSMGDAYFEGDGVT  164 (490)
T ss_dssp             SSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHTSSSC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHHcCCCCC
Confidence            344789999999999877766   45556667777    88999999999999876 5   56667777777766    3


Q ss_pred             CCCchhhhHHHhhc---cCcHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhc----CCCC
Q 011102          246 HELKVPFKLENFVS---LASKGVLEATAKGFVK----GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGK----NPDK  314 (493)
Q Consensus       246 g~~~~~~~l~~~~~---~~~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~----~~~~  314 (493)
                      ++  ..+++..|..   ..+...+..|-..|.+    .++.++|.+.|++..+.|   +...+..+-..|..    . ++
T Consensus       165 ~d--~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~-~~  238 (490)
T 2xm6_A          165 RD--YVMAREWYSKAAEQGNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVT-QD  238 (490)
T ss_dssp             CC--HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSC-CC
T ss_pred             CC--HHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCC-CC
Confidence            44  5555554543   3467788888888888    899999999999999876   66777777777765    5 89


Q ss_pred             HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC-----CC
Q 011102          315 YMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR----LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE-----KK  385 (493)
Q Consensus       315 ~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~-----g~  385 (493)
                      +++|..+|+...+. +   +...+..+-..|..    .++.++|.+.|++..+.|   +...+..|-..|...     ++
T Consensus       239 ~~~A~~~~~~a~~~-~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~  311 (490)
T 2xm6_A          239 YTQSRVLFSQSAEQ-G---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKN  311 (490)
T ss_dssp             HHHHHHHHHHHHTT-T---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCC
T ss_pred             HHHHHHHHHHHHHC-C---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCC
Confidence            99999999998776 2   45677777777877    899999999999988654   566777888888877     89


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHH
Q 011102          386 CREALTVVWNMEASNCLFDLPAYRVVIKLFVALN---DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA----SGRLAK  458 (493)
Q Consensus       386 ~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g---~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~  458 (493)
                      .++|.+.|++..+.|   +...+..+-..|.+.|   +.++|.++|+...+.|   +...+..|-..|..    .+++++
T Consensus       312 ~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~  385 (490)
T 2xm6_A          312 REQAISWYTKSAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQ  385 (490)
T ss_dssp             HHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHH
T ss_pred             HHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHH
Confidence            999999999998875   4566777777777766   8899999999998874   67788888888988    899999


Q ss_pred             HHHHHHHHHHCC
Q 011102          459 CRDVCKEAEMAG  470 (493)
Q Consensus       459 A~~l~~~m~~~g  470 (493)
                      |.+.|++..+.|
T Consensus       386 A~~~~~~A~~~~  397 (490)
T 2xm6_A          386 AAIWMRKAAEQG  397 (490)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHHHHHhCC
Confidence            999999999876

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.08  E-value=6.3e-09  Score=103.98  Aligned_cols=265  Identities=11%  Similarity=-0.038  Sum_probs=182.6

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHhCCCCCCCH----HHHHHHHHHHHHcCCCchhhhHH-----Hhhcc----CcHHHHHH
Q 011102          202 TVRELGHMNLPERALQTFCWAQKQPHLFPDD----RLLASTVEVLARHHELKVPFKLE-----NFVSL----ASKGVLEA  268 (493)
Q Consensus       202 li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~----~t~~~li~~~~~~g~~~~~~~l~-----~~~~~----~~~~~~~~  268 (493)
                      +-..+.+.|++++|++.|+.+.+. .-. +.    ..|..+...+...|+++.+....     .....    ....+|..
T Consensus        54 ~g~~~~~~g~~~~A~~~~~~al~~-~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  131 (411)
T 4a1s_A           54 EGERLCNAGDCRAGVAFFQAAIQA-GTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGN  131 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH-CCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHhCcHHHHHHHHHHHHHh-ccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHH
Confidence            344566677777777777777653 111 22    35666666666667644333221     11111    12346888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHhcCCCC-----------------HHHHHHHHHHHh
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDG----GRML-DPSIYAKLILELGKNPDK-----------------YMLVMTLLDELG  326 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~----g~~p-d~~t~~~li~~~~~~~~~-----------------~~~a~~l~~~m~  326 (493)
                      +...|...|++++|.+.|++..+.    +-.+ ...++..+-..|... |+                 +++|.+.+++..
T Consensus       132 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al  210 (411)
T 4a1s_A          132 LGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAK-GKHLGQRNPGKFGDDVKEALTRAVEFYQENL  210 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH-HHHHHHHSTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHc-CcccccccchhhhhhhhHHHHHHHHHHHHHH
Confidence            889999999999999999887653    1111 234667777788888 88                 899998888754


Q ss_pred             hc----CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          327 QR----DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGR-DPT----VVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       327 ~~----~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~----~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      ..    +........+..+-..|...|++++|.+.|++..+..- .++    ..+|..+...|...|++++|.+.+++..
T Consensus       211 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  290 (411)
T 4a1s_A          211 KLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTL  290 (411)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            32    01111234778888899999999999999998764210 112    3478899999999999999999999876


Q ss_pred             HCC----CC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          398 ASN----CL-FDLPAYRVVIKLFVALNDISRAIRYFSKLKEA----GF-CPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       398 ~~g----i~-pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~----g~-~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      +..    -. ....++..+-..|...|++++|..+|++..+.    +- .....+|..+...|.+.|++++|.+.+++..
T Consensus       291 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  370 (411)
T 4a1s_A          291 ALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHL  370 (411)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            531    11 11467788888999999999999999987632    11 1124578889999999999999999999987


Q ss_pred             HC
Q 011102          468 MA  469 (493)
Q Consensus       468 ~~  469 (493)
                      +.
T Consensus       371 ~~  372 (411)
T 4a1s_A          371 QL  372 (411)
T ss_dssp             HH
T ss_pred             HH
Confidence            53

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.07  E-value=1.9e-08  Score=92.29  Aligned_cols=199  Identities=10%  Similarity=-0.047  Sum_probs=141.7

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcC
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGG  277 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g  277 (493)
                      .|..+-..+.+.|++++|+..|+.+.+.   .|+                              +..+|..+...|.+.|
T Consensus        25 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~---~~~------------------------------~~~~~~~la~~~~~~~   71 (243)
T 2q7f_A           25 TGGQQMGRGSEFGDYEKAAEAFTKAIEE---NKE------------------------------DAIPYINFANLLSSVN   71 (243)
T ss_dssp             -----------------CCTTHHHHHTT---CTT------------------------------CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhhCHHHHHHHHHHHHHh---Ccc------------------------------cHHHHHHHHHHHHHcC
Confidence            5555556666677777777777766542   121                              2345556677777888


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      ++++|.+.|++..+.. ..+..++..+...+... |++++|.+.++++.+.  ...+...+..+...|.+.|++++|.+.
T Consensus        72 ~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~  147 (243)
T 2q7f_A           72 ELERALAFYDKALELD-SSAATAYYGAGNVYVVK-EMYKEAKDMFEKALRA--GMENGDLFYMLGTVLVKLEQPKLALPY  147 (243)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--TCCSHHHHHHHHHHHHHTSCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcC-CcchHHHHHHHHHHHHh-ccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhccHHHHHHH
Confidence            8899999998887753 23567788888888888 9999999999988765  234677888888899999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          358 FHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       358 ~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      |++..+.. +.+...|..+...|.+.|++++|.+.|+++.+.. ..+..++..+...|.+.|++++|.+.|++..+..
T Consensus       148 ~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          148 LQRAVELN-ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQD-PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHhC-CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            99887653 3467788889999999999999999999877653 2356788888999999999999999999887643

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.07  E-value=7.7e-09  Score=99.33  Aligned_cols=263  Identities=11%  Similarity=-0.023  Sum_probs=180.0

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHHcCCCchhhhHHH-----hhccC----cHHHHHHHH
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHLFPD----DRLLASTVEVLARHHELKVPFKLEN-----FVSLA----SKGVLEATA  270 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~~pd----~~t~~~li~~~~~~g~~~~~~~l~~-----~~~~~----~~~~~~~li  270 (493)
                      ..+.+.|++++|+..|+.+.+. .- .+    ...+..+...+...|+++.+.....     .....    ...++..+.
T Consensus        13 ~~~~~~g~~~~A~~~~~~al~~-~~-~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~   90 (338)
T 3ro2_A           13 ERLCKSGDCRAGVSFFEAAVQV-GT-EDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLG   90 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CC-SCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHhh-Cc-ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHHH
Confidence            3556677777777777776653 11 12    2455666666666676433322211     11111    234678888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCC-CCC----HHHHHHHHHHHhcCCCC--------------------HHHHHHHHHHH
Q 011102          271 KGFVKGGNLKLAWKLLMVAKDGGR-MLD----PSIYAKLILELGKNPDK--------------------YMLVMTLLDEL  325 (493)
Q Consensus       271 ~~~~~~g~~~~A~~l~~~m~~~g~-~pd----~~t~~~li~~~~~~~~~--------------------~~~a~~l~~~m  325 (493)
                      ..|...|++++|.+.+++..+..- .++    ..++..+-..+... |+                    +++|.+.+++.
T Consensus        91 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a  169 (338)
T 3ro2_A           91 NTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAK-GKSFGCPGPQDTGEFPEDVRNALQAAVDLYEEN  169 (338)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH-HHTSSSSSCC----CCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHc-CcccccchhhhhhhhhhhHHHHHHHHHHHHHHH
Confidence            899999999999999988765210 122    33667777778888 88                    89998888875


Q ss_pred             hhc----CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          326 GQR----DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS----GRDP-TVVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       326 ~~~----~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      ...    +........+..+...|...|++++|.+.|++..+.    +..+ ...+|..+...|...|++++|.+.+++.
T Consensus       170 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  249 (338)
T 3ro2_A          170 LSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKT  249 (338)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            432    011112346778888999999999999999887532    1111 1347888999999999999999999987


Q ss_pred             HHC----CCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          397 EAS----NCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLKEA----GFC-PTYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       397 ~~~----gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~~----g~~-p~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      .+.    +-.+. ..++..+-..|...|++++|...+++..+.    +-. ....+|..+...|.+.|++++|.+.+++.
T Consensus       250 l~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  329 (338)
T 3ro2_A          250 LLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKH  329 (338)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHH
Confidence            642    11111 456778888899999999999999987632    111 12457888999999999999999999998


Q ss_pred             HHC
Q 011102          467 EMA  469 (493)
Q Consensus       467 ~~~  469 (493)
                      .+.
T Consensus       330 ~~~  332 (338)
T 3ro2_A          330 LEI  332 (338)
T ss_dssp             HHC
T ss_pred             HHH
Confidence            753

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.05  E-value=1.6e-08  Score=100.40  Aligned_cols=264  Identities=10%  Similarity=-0.072  Sum_probs=176.9

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHHcCCCchhhhHH-----HhhccC----cHHHHHHHHHH
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHLFPD--DRLLASTVEVLARHHELKVPFKLE-----NFVSLA----SKGVLEATAKG  272 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~~pd--~~t~~~li~~~~~~g~~~~~~~l~-----~~~~~~----~~~~~~~li~~  272 (493)
                      ..+.+.|++++|+..|+.......-.++  ..+|..+...+...|+++.+....     ......    ...+|..+...
T Consensus        17 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~   96 (406)
T 3sf4_A           17 ERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNT   96 (406)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            3556666777777777666643111111  234555666666666643322211     111111    23467788888


Q ss_pred             HHhcCCHHHHHHHHHHHHhCCC-CCC----HHHHHHHHHHHhcCCCC--------------------HHHHHHHHHHHhh
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGR-MLD----PSIYAKLILELGKNPDK--------------------YMLVMTLLDELGQ  327 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~-~pd----~~t~~~li~~~~~~~~~--------------------~~~a~~l~~~m~~  327 (493)
                      |...|++++|...+++..+..- .++    ..++..+-..|... |+                    +++|...+++...
T Consensus        97 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~  175 (406)
T 3sf4_A           97 LKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAK-GKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLS  175 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH-HHTCC-------CCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHc-CCcccccccchhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            9999999999999987765210 012    33667777778888 88                    8999888887543


Q ss_pred             c---CCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          328 R---DDLNL-SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSG-RDPT----VVMYTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       328 ~---~g~~p-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~----~~ty~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      .   .+-.+ ...++..+-..|...|++++|.+.|++..+.. -.++    ..+|..+...|...|++++|.+.+++..+
T Consensus       176 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  255 (406)
T 3sf4_A          176 LVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLL  255 (406)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            2   11111 23467888889999999999999998876321 0122    34788899999999999999999998764


Q ss_pred             C----CCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          399 S----NCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLKEA----GFCP-TYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       399 ~----gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~~----g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      .    +-.+. ..++..+-..|.+.|++++|...|++..+.    +-.+ ...+|..+...|...|++++|.+.+++..+
T Consensus       256 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          256 LARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2    21111 457788888899999999999999987632    1111 156788889999999999999999988754

>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=99.05  E-value=8.8e-08  Score=106.40  Aligned_cols=256  Identities=11%  Similarity=0.056  Sum_probs=186.8

Q ss_pred             hhccCCCCHHHHHHHHhhhcccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhH
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKL  254 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l  254 (493)
                      .++...|++.+|++.|.+..+...|.-++..|.+.|++++|++.|....+. .  ++....+.++.+|++.++++   ++
T Consensus      1113 KAql~~G~~kEAIdsYiKAdD~say~eVa~~~~~lGkyEEAIeyL~mArk~-~--~e~~Idt~LafaYAKl~rle---el 1186 (1630)
T 1xi4_A         1113 KAQLQKGMVKEAIDSYIKADDPSSYMEVVQAANTSGNWEELVKYLQMARKK-A--RESYVETELIFALAKTNRLA---EL 1186 (1630)
T ss_pred             HHHHhCCCHHHHHHHHHhcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-c--ccccccHHHHHHHHhhcCHH---HH
Confidence            345667888888888887766668888888888888888888888876653 2  33333445888888887643   35


Q ss_pred             HHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC
Q 011102          255 ENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS  334 (493)
Q Consensus       255 ~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~  334 (493)
                      ..|...++...|..+-+.|...|++++|..+|...         ..|..+...|++. |++++|.+.+.+.       -+
T Consensus      1187 e~fI~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkL-ge~q~AIEaarKA-------~n 1249 (1630)
T 1xi4_A         1187 EEFINGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHL-GEYQAAVDGARKA-------NS 1249 (1630)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHh-CCHHHHHHHHHHh-------CC
Confidence            55666666666777888888889999998888874         3788888888888 8888888888766       24


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKL  414 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~  414 (493)
                      ..+|.-+-.+|...|++..|......+     ..+...+..++.-|-+.|.+++|+.+++.-.... .-....|+-+-..
T Consensus      1250 ~~aWkev~~acve~~Ef~LA~~cgl~I-----iv~~deLeeli~yYe~~G~feEAI~LlE~aL~Le-raH~gmftELaiL 1323 (1630)
T 1xi4_A         1250 TRTWKEVCFACVDGKEFRLAQMCGLHI-----VVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAIL 1323 (1630)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHhh-----hcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-hhHhHHHHHHHHH
Confidence            578888888888888888888776543     3456667799999999999999999997654332 2223345444444


Q ss_pred             HHH--cCCHHHHHHHHHHHHHCCCCC------CHHHHHHHHHHHHHcCCHHHHHH
Q 011102          415 FVA--LNDISRAIRYFSKLKEAGFCP------TYDIYRDMIRIFMASGRLAKCRD  461 (493)
Q Consensus       415 ~~~--~g~~~~A~~~~~~m~~~g~~p------~~~ty~~li~~~~~~g~~~~A~~  461 (493)
                      |++  -+++.++.++|..=.  .+.|      +...|.-++-.|.+.|+++.|..
T Consensus      1324 yaKy~peklmEhlk~f~~ri--ni~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~ 1376 (1630)
T 1xi4_A         1324 YSKFKPQKMREHLELFWSRV--NIPKVLRAAEQAHLWAELVFLYDKYEEYDNAII 1376 (1630)
T ss_pred             HHhCCHHHHHHHHHHHHHhc--ccchHhHHHHHHHHHHHHHHHHHhcccHHHHHH
Confidence            444  456666776665322  2222      56779999999999999999984

>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=99.04  E-value=3.8e-08  Score=85.85  Aligned_cols=162  Identities=13%  Similarity=0.062  Sum_probs=99.9

Q ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011102          301 YAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSR  380 (493)
Q Consensus       301 ~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~  380 (493)
                      |..+...+... |++++|...++++...  ...+...+..+...|.+.|++++|.+.|++..+.. +.+...|..+...|
T Consensus        11 ~~~~~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A           11 YRDKGISHAKA-GRYSQAVMLLEQVYDA--DAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHH-TCHHHHHHHHTTTCCT--TSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh-cCHHHHHHHHHHHHHh--CccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            34444455555 6666666666655443  12345556666666666666666666666655432 23455666666666


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          381 LSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCR  460 (493)
Q Consensus       381 ~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~  460 (493)
                      ...|++++|.+.++++.+.. ..+...+..+...+.+.|++++|..++++..+.. ..+...|..+...+...|++++|.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~  164 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEAL  164 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHH
Confidence            66677777777666665542 2345566666677777777777777777766443 235666777777777777777777


Q ss_pred             HHHHHHHH
Q 011102          461 DVCKEAEM  468 (493)
Q Consensus       461 ~l~~~m~~  468 (493)
                      +.+++..+
T Consensus       165 ~~~~~~~~  172 (186)
T 3as5_A          165 PHFKKANE  172 (186)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77777654

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.03  E-value=1.5e-07  Score=90.61  Aligned_cols=184  Identities=15%  Similarity=0.035  Sum_probs=139.0

Q ss_pred             HHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-HH-HHHHHHHHHHHcCCHHHHH
Q 011102          279 LKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-QQ-DCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-~~-~~~~li~~~~~~g~~~~A~  355 (493)
                      .++|..+|++..+. +.| +...|..+...+.+. |++++|.++|++..+.   .|+ .. .|..+...+.+.|++++|.
T Consensus        80 ~~~A~~~~~rAl~~-~~p~~~~~~~~~~~~~~~~-~~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~~~~~~~A~  154 (308)
T 2ond_A           80 SDEAANIYERAIST-LLKKNMLLYFAYADYEESR-MKYEKVHSIYNRLLAI---EDIDPTLVYIQYMKFARRAEGIKSGR  154 (308)
T ss_dssp             HHHHHHHHHHHHTT-TTTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHTS---SSSCTHHHHHHHHHHHHHHHCHHHHH
T ss_pred             hHHHHHHHHHHHHH-hCcccHHHHHHHHHHHHhc-CCHHHHHHHHHHHHhc---cccCccHHHHHHHHHHHHhcCHHHHH
Confidence            38899999888873 124 455788888888888 8999999999988764   343 33 7888888888999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHH-HcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          356 SLFHWFTHSGRDPTVVMYTTLIHSR-LSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       356 ~l~~~m~~~g~~p~~~ty~~li~~~-~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      .+|++..+.. +.+...|....... ...|+.++|.++|++..+.. .-+...|..++..+.+.|+.++|..+|++..+.
T Consensus       155 ~~~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~  232 (308)
T 2ond_A          155 MIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTS  232 (308)
T ss_dssp             HHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHS
T ss_pred             HHHHHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            9999887653 23344454333332 23689999999999876642 125677888888888999999999999998876


Q ss_pred             C-CCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          435 G-FCP--TYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       435 g-~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      . +.|  ....|..++..+.+.|+.++|..+++++.+.
T Consensus       233 ~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~~~  270 (308)
T 2ond_A          233 GSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTA  270 (308)
T ss_dssp             SSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3 454  4678888888888899999999999888763

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.01  E-value=7.4e-08  Score=87.77  Aligned_cols=179  Identities=13%  Similarity=0.043  Sum_probs=149.5

Q ss_pred             CCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 011102          295 MLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYT  374 (493)
Q Consensus       295 ~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~  374 (493)
                      +++...+..+-..+.+. |++++|...|++..+.  -.-+...+..+-..|.+.|++++|...|++..+.. +-+...|.
T Consensus         2 p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~   77 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYAL-GRYDAALTLFERALKE--NPQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYM   77 (217)
T ss_dssp             --CCHHHHHHHHHHHHT-TCHHHHHHHHHHHHTT--SSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHH
Confidence            35667788888888999 9999999999998765  23467788899999999999999999999987653 34678899


Q ss_pred             HHHHHHHcC-----------CCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHH
Q 011102          375 TLIHSRLSE-----------KKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDI  442 (493)
Q Consensus       375 ~li~~~~~~-----------g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~t  442 (493)
                      .+-..|.+.           |++++|+..|++..+.  .| +...+..+-..|...|++++|...|++..+..  .+...
T Consensus        78 ~lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~  153 (217)
T 2pl2_A           78 VLSEAYVALYRQAEDRERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEI  153 (217)
T ss_dssp             HHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHH
T ss_pred             HHHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHH
Confidence            999999999           9999999999998775  34 46778888889999999999999999999777  68999


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCcc-CHHHHHHHHH
Q 011102          443 YRDMIRIFMASGRLAKCRDVCKEAEMAGFKL-DKQTVVELLQ  483 (493)
Q Consensus       443 y~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~Ll~  483 (493)
                      |..+-..|...|++++|...|++..+.  .| +...+..+-.
T Consensus       154 ~~~la~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~la~  193 (217)
T 2pl2_A          154 RSALAELYLSMGRLDEALAQYAKALEQ--APKDLDLRVRYAS  193 (217)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHH
Confidence            999999999999999999999999874  44 3444444433

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.01  E-value=1.2e-07  Score=88.60  Aligned_cols=236  Identities=9%  Similarity=-0.027  Sum_probs=171.9

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCc
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELK  249 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~  249 (493)
                      ..+...|++++|+..+.+.....     .|..+...|.+.|++++|++.|+..... +-.|+.                 
T Consensus        11 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~-~~~~~~-----------------   72 (272)
T 3u4t_A           11 DFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSK-VNATKA-----------------   72 (272)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTT-SCTTTC-----------------
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-cCchhH-----------------
Confidence            34567799999999999765543     7888888999999999999999999864 322221                 


Q ss_pred             hhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC
Q 011102          250 VPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRD  329 (493)
Q Consensus       250 ~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~  329 (493)
                                  ...+|..+...|.+.|++++|.+.|++..+.. +-+..+|..+-..|... |++++|...|++..+. 
T Consensus        73 ------------~~~~~~~lg~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~al~~-  137 (272)
T 3u4t_A           73 ------------KSADFEYYGKILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNK-GNFPLAIQYMEKQIRP-  137 (272)
T ss_dssp             ------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHT-TCHHHHHHHHGGGCCS-
T ss_pred             ------------HHHHHHHHHHHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHc-cCHHHHHHHHHHHhhc-
Confidence                        22345567777888888999999998888753 22456788888888888 9999999999888764 


Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHC-CCCCC-
Q 011102          330 DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK---CREALTVVWNMEAS-NCLFD-  404 (493)
Q Consensus       330 g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~---~~~A~~l~~~M~~~-gi~pd-  404 (493)
                       ..-+...|..+...+...+++++|.+.|++..+.. +.+...|..+...+...|+   .++|...+++..+. .-.|+ 
T Consensus       138 -~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~  215 (272)
T 3u4t_A          138 -TTTDPKVFYELGQAYYYNKEYVKADSSFVKVLELK-PNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAK  215 (272)
T ss_dssp             -SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGG
T ss_pred             -CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhccccc
Confidence             23345566666624445569999999999887652 2346777778888888887   77788888876653 12233 


Q ss_pred             -----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 011102          405 -----LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDM  446 (493)
Q Consensus       405 -----~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~l  446 (493)
                           ..+|..+-..|.+.|++++|.+.|++..+..- -|...+..+
T Consensus       216 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~l  261 (272)
T 3u4t_A          216 YKDELIEANEYIAYYYTINRDKVKADAAWKNILALDP-TNKKAIDGL  261 (272)
T ss_dssp             GHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCc-cHHHHHHHh
Confidence                 25677788889999999999999999886441 234444443

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.00  E-value=2.4e-08  Score=95.15  Aligned_cols=234  Identities=14%  Similarity=-0.042  Sum_probs=133.8

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCC------CCCCCHHHHHHHHHHHHHcCCCchhhhHH-----Hhhcc------
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQP------HLFPDDRLLASTVEVLARHHELKVPFKLE-----NFVSL------  260 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~------g~~pd~~t~~~li~~~~~~g~~~~~~~l~-----~~~~~------  260 (493)
                      .|..+...|...|++++|+.+|+.+.+..      .......++..+...+...|+++.+....     .+...      
T Consensus        29 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  108 (311)
T 3nf1_A           29 TLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDHP  108 (311)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCCh
Confidence            45666778888999999999998887520      11123345666777777777754433221     11111      


Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc-----
Q 011102          261 ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDG------GRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQR-----  328 (493)
Q Consensus       261 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~-----  328 (493)
                      ....+|..+...|...|++++|.+.|++..+.      +-.| ...++..+-..+... |++++|.+++++....     
T Consensus       109 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~-~~~~~A~~~~~~a~~~~~~~~  187 (311)
T 3nf1_A          109 AVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQ-GKYEEVEYYYQRALEIYQTKL  187 (311)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHHh
Confidence            12335777777777788888888877777653      2222 233456666667777 7788888777776542     


Q ss_pred             -CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-------CCCCC-------HHHHHHHHHHHHcCCCHHHHHHHH
Q 011102          329 -DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS-------GRDPT-------VVMYTTLIHSRLSEKKCREALTVV  393 (493)
Q Consensus       329 -~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-------g~~p~-------~~ty~~li~~~~~~g~~~~A~~l~  393 (493)
                       ........++..+...|.+.|++++|.+.|++..+.       ...+.       ...+..+...+...+.+.+|...+
T Consensus       188 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~  267 (311)
T 3nf1_A          188 GPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWY  267 (311)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHH
Confidence             111112345667777777778888888777776642       11111       111222223333334444444455


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          394 WNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       394 ~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      ...... -..+..++..+...|.+.|++++|.++|++..+
T Consensus       268 ~~~~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          268 KACKVD-SPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hhcCCC-CchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            444332 122456788899999999999999999998763

>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=99.00  E-value=6.6e-09  Score=97.40  Aligned_cols=204  Identities=14%  Similarity=0.027  Sum_probs=125.5

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhC------CCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc------C
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDG------GRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQR------D  329 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~------~  329 (493)
                      ..+|..+...|...|++++|...|++..+.      +-.| ...+|..+-..|... |++++|.+.+.+....      .
T Consensus        43 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~al~~~~~~~~~  121 (283)
T 3edt_B           43 ATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKR-GKYKEAEPLCKRALEIREKVLGK  121 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHh-ccHHHHHHHHHHHHHHHHHHcCC
Confidence            346777888888888888888888877653      2222 234566777777777 8888888888876543      0


Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc------CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC---
Q 011102          330 DLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS------GRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEAS---  399 (493)
Q Consensus       330 g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~---  399 (493)
                      .-......+..+...|...|++++|.+.|++..+.      +-.| ...++..+...|...|++++|.+.+++..+.   
T Consensus       122 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~  201 (283)
T 3edt_B          122 FHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHE  201 (283)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            11223456777777888888888888888877653      1122 3466777788888888888888888876542   


Q ss_pred             ----CCCCCHH-HHHHHHHHHHHcCCH------HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          400 ----NCLFDLP-AYRVVIKLFVALNDI------SRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       400 ----gi~pd~~-ty~~li~~~~~~g~~------~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                          ...+... .|..+-..+...+..      ..+...++.... .......+|..+...|.+.|++++|.+++++..+
T Consensus       202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          202 KEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV-DSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC-CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             hcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                1122222 222222222222222      222222211110 1112345788899999999999999999998764

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.00  E-value=1.3e-07  Score=83.10  Aligned_cols=165  Identities=11%  Similarity=0.030  Sum_probs=82.2

Q ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011102          298 PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLI  377 (493)
Q Consensus       298 ~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li  377 (493)
                      +..|..+=..|.+. |++++|++.|++..+.  -.-+...+..+...|.+.|++++|...+....... .-+...+..+-
T Consensus         5 ~~iy~~lG~~~~~~-g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~   80 (184)
T 3vtx_A            5 TTIYMDIGDKKRTK-GDFDGAIRAYKKVLKA--DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILG   80 (184)
T ss_dssp             HHHHHHHHHHHHHH-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHH
Confidence            33444444444444 4555555555444332  11233444444555555555555555555443321 22334444444


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          378 HSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLA  457 (493)
Q Consensus       378 ~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~  457 (493)
                      ..+...+++++|.+.+.+..+.. .-+...+..+-..|.+.|++++|.+.|++..+..- -+..+|..+-..|.+.|+++
T Consensus        81 ~~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p-~~~~~~~~lg~~~~~~g~~~  158 (184)
T 3vtx_A           81 SANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKP-GFIRAYQSIGLAYEGKGLRD  158 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcc-hhhhHHHHHHHHHHHCCCHH
Confidence            55555555555555555544321 12344455555555666666666666665554321 24555666666666666666


Q ss_pred             HHHHHHHHHHH
Q 011102          458 KCRDVCKEAEM  468 (493)
Q Consensus       458 ~A~~l~~~m~~  468 (493)
                      +|.+.|++..+
T Consensus       159 ~A~~~~~~al~  169 (184)
T 3vtx_A          159 EAVKYFKKALE  169 (184)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            66666666554

>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=98.99  E-value=5.8e-08  Score=84.61  Aligned_cols=164  Identities=14%  Similarity=0.027  Sum_probs=139.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      ..|..+...+...|++++|.+.|+++.+.. +.+..++..+...+... |++++|...+++..+.  ...+...+..+..
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~   84 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKT-GAVDRGTELLERSLAD--APDNVKVATVLGL   84 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHc-CCHHHHHHHHHHHHhc--CCCCHHHHHHHHH
Confidence            356778888999999999999999887643 23677888888899999 9999999999998775  2346788889999


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~  423 (493)
                      .|...|++++|.+.|++..+.. +.+...|..+...|...|++++|.+.+++..+.. ..+...+..+...+.+.|++++
T Consensus        85 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~  162 (186)
T 3as5_A           85 TYVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEE  162 (186)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHH
Confidence            9999999999999999987653 4577889999999999999999999999987753 3457889999999999999999


Q ss_pred             HHHHHHHHHH
Q 011102          424 AIRYFSKLKE  433 (493)
Q Consensus       424 A~~~~~~m~~  433 (493)
                      |...++...+
T Consensus       163 A~~~~~~~~~  172 (186)
T 3as5_A          163 ALPHFKKANE  172 (186)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999998764

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=98.95  E-value=2.8e-07  Score=81.02  Aligned_cols=167  Identities=10%  Similarity=-0.055  Sum_probs=141.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +..+|..+-..|.+.|++++|++.|++..+.. +-+..+|..+-..|.+. |++++|...+......  ..-+...+..+
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~-~~~~~a~~~~~~~~~~--~~~~~~~~~~~   79 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDI-GLPNDAIESLKKFVVL--DTTSAEAYYIL   79 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHhc--CchhHHHHHHH
Confidence            45678899999999999999999999988754 23567888888899999 9999999999998775  33456778888


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                      ...+...++++.|.+.+.+..+.. +-+...+..+-..|.+.|++++|++.|++..+.. +-+..+|..+-..|.+.|++
T Consensus        80 ~~~~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~  157 (184)
T 3vtx_A           80 GSANFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLR  157 (184)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCH
Confidence            889999999999999999887543 3467889999999999999999999999987753 23567889999999999999


Q ss_pred             HHHHHHHHHHHHC
Q 011102          422 SRAIRYFSKLKEA  434 (493)
Q Consensus       422 ~~A~~~~~~m~~~  434 (493)
                      ++|.+.|++..+.
T Consensus       158 ~~A~~~~~~al~~  170 (184)
T 3vtx_A          158 DEAVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999998763

>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=98.95  E-value=2.2e-07  Score=92.48  Aligned_cols=226  Identities=7%  Similarity=-0.038  Sum_probs=153.7

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCC
Q 011102          199 LSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGN  278 (493)
Q Consensus       199 ~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~  278 (493)
                      |+.+-..+.+.|++++|++.|+.....   .|+.                              ..+|+.+-..+.+.|+
T Consensus       100 ~~~lg~~~~~~g~~~~Al~~~~~al~l---~P~~------------------------------~~a~~~~g~~l~~~g~  146 (382)
T 2h6f_A          100 YDYFRAVLQRDERSERAFKLTRDAIEL---NAAN------------------------------YTVWHFRRVLLKSLQK  146 (382)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHH---CTTC------------------------------HHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHHh---CccC------------------------------HHHHHHHHHHHHHccc
Confidence            444556778889999999999988753   3432                              1233344445555665


Q ss_pred             -HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          279 -LKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       279 -~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                       +++|+..|++..+.. .-+...|+.+-..+.+. |++++|+..|+++...  -.-+...|..+-.++.+.|++++|+..
T Consensus       147 d~~eAl~~~~~al~l~-P~~~~a~~~~g~~~~~~-g~~~eAl~~~~kal~l--dP~~~~a~~~lg~~~~~~g~~~eAl~~  222 (382)
T 2h6f_A          147 DLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVEWL-RDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQY  222 (382)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH-TCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHH
T ss_pred             CHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHc-cCHHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcCChHHHHHH
Confidence             788888888777743 12456677777777777 7888888888877664  223567777777888888888888888


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHc-CCCHHHH-----HHHHHHHHHCCCCC-CHHHHHHHHHHHHHcC--CHHHHHHHH
Q 011102          358 FHWFTHSGRDPTVVMYTTLIHSRLS-EKKCREA-----LTVVWNMEASNCLF-DLPAYRVVIKLFVALN--DISRAIRYF  428 (493)
Q Consensus       358 ~~~m~~~g~~p~~~ty~~li~~~~~-~g~~~~A-----~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g--~~~~A~~~~  428 (493)
                      |+++.+.. .-+...|+.+-..|.+ .|..++|     ++.|++..+.  .| +...|+.+-..+.+.|  ++++|.+.+
T Consensus       223 ~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~  299 (382)
T 2h6f_A          223 VDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLLNQL  299 (382)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHHHHH
T ss_pred             HHHHHHhC-CCCHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHHHHH
Confidence            88877553 2356777877777777 5554666     4667665553  34 3556777777777777  577888877


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHcC---------CHHHHHHHHHHH
Q 011102          429 SKLKEAGFCPTYDIYRDMIRIFMASG---------RLAKCRDVCKEA  466 (493)
Q Consensus       429 ~~m~~~g~~p~~~ty~~li~~~~~~g---------~~~~A~~l~~~m  466 (493)
                      .++ + .-..+...+..+.+.|.+.|         .+++|.++++++
T Consensus       300 ~~~-~-~~p~~~~al~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l  344 (382)
T 2h6f_A          300 LDL-Q-PSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEIL  344 (382)
T ss_dssp             HHH-T-TTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHH
T ss_pred             HHh-c-cCCCCHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHH
Confidence            776 2 22345667777888887764         257888888887

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=98.93  E-value=4.4e-08  Score=97.14  Aligned_cols=281  Identities=11%  Similarity=-0.041  Sum_probs=198.8

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC---------cHHHHHHHHHhCCChHHHHHHHHHHHhC---CCCCC-CHHHHHHHHHH
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG---------SLSFTVRELGHMNLPERALQTFCWAQKQ---PHLFP-DDRLLASTVEV  241 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~---------~~~~li~~~~~~g~~~~A~~l~~~m~~~---~g~~p-d~~t~~~li~~  241 (493)
                      ..+...|+.++|+..|.+.....         .|..+-..|...|++++|+..|+.....   .+-.| ...++..+...
T Consensus        17 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~   96 (406)
T 3sf4_A           17 ERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNT   96 (406)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHH
Confidence            44566799999999998665432         4667778999999999999999876532   12222 23467778888


Q ss_pred             HHHcCCCchhhhH-----HHhhccCc----HHHHHHHHHHHHhcCC--------------------HHHHHHHHHHHHhC
Q 011102          242 LARHHELKVPFKL-----ENFVSLAS----KGVLEATAKGFVKGGN--------------------LKLAWKLLMVAKDG  292 (493)
Q Consensus       242 ~~~~g~~~~~~~l-----~~~~~~~~----~~~~~~li~~~~~~g~--------------------~~~A~~l~~~m~~~  292 (493)
                      +...|+++.+...     .......+    ..++..+...|...|+                    +++|.+.+++..+.
T Consensus        97 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~  176 (406)
T 3sf4_A           97 LKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSL  176 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence            8888985544332     11112222    3378889999999999                    99999999876542


Q ss_pred             ----CCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          293 ----GRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS----QQDCTAIMKVGIRLQKFGVVESLFHWFTH  363 (493)
Q Consensus       293 ----g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~  363 (493)
                          +-.|. ..++..+-..+... |++++|...+++......-.++    ..++..+...|...|++++|...|++..+
T Consensus       177 ~~~~~~~~~~~~~~~~la~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  255 (406)
T 3sf4_A          177 VTALGDRAAQGRAFGNLGNTHYLL-GNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLL  255 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHH-TBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHhccCcHHHHHHHHHHHHHHHHc-cCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence                21111 33567777888888 9999999999987543111122    33788888999999999999999998753


Q ss_pred             c----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          364 S----GRDPT-VVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       364 ~----g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      .    +..+. ..++..+...|...|++++|.+.+++..+.    +-.+. ..++..+-..|.+.|++++|...|++..+
T Consensus       256 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          256 LARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            2    11111 567889999999999999999999987653    11111 45778888889999999999999998652


Q ss_pred             ----CCCC-CCHHHHHHHHHHHHHcCCH
Q 011102          434 ----AGFC-PTYDIYRDMIRIFMASGRL  456 (493)
Q Consensus       434 ----~g~~-p~~~ty~~li~~~~~~g~~  456 (493)
                          .+-. ....++..+...+...|+.
T Consensus       336 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          336 ISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence                2221 1245677777788777765

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=98.89  E-value=4.1e-08  Score=97.98  Aligned_cols=256  Identities=10%  Similarity=-0.064  Sum_probs=186.4

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC---------cHHHHHHHHHhCCChHHHHHHHHHHHhCC---CCCC-CHHHHHHHHHH
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG---------SLSFTVRELGHMNLPERALQTFCWAQKQP---HLFP-DDRLLASTVEV  241 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~---------~~~~li~~~~~~g~~~~A~~l~~~m~~~~---g~~p-d~~t~~~li~~  241 (493)
                      ..+...|++++|+..|.+.....         .|..+-..|...|++++|++.|+......   +-.| ...++..+-..
T Consensus        56 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~  135 (411)
T 4a1s_A           56 ERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNLGNT  135 (411)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHHHHH
Confidence            45567799999999998765532         46677788999999999999998876421   1112 33467778888


Q ss_pred             HHHcCCCchhhhHHHhhc-------cC----cHHHHHHHHHHHHhcCC-----------------HHHHHHHHHHHHhC-
Q 011102          242 LARHHELKVPFKLENFVS-------LA----SKGVLEATAKGFVKGGN-----------------LKLAWKLLMVAKDG-  292 (493)
Q Consensus       242 ~~~~g~~~~~~~l~~~~~-------~~----~~~~~~~li~~~~~~g~-----------------~~~A~~l~~~m~~~-  292 (493)
                      +...|+++.+..  .+..       ..    ...+|..+...|...|+                 +++|.+.+++..+. 
T Consensus       136 ~~~~g~~~~A~~--~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~  213 (411)
T 4a1s_A          136 LKVMGRFDEAAI--CCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLM  213 (411)
T ss_dssp             HHHTTCHHHHHH--HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHH--HHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            888898554433  2322       11    23378889999999999                 99999999876542 


Q ss_pred             ---CCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Q 011102          293 ---GRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS----QQDCTAIMKVGIRLQKFGVVESLFHWFTHS  364 (493)
Q Consensus       293 ---g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  364 (493)
                         +-.+ ...++..+-..|... |++++|...+++..+...-..+    ...+..+...|...|++++|.+.|++..+.
T Consensus       214 ~~~~~~~~~~~~~~~la~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  292 (411)
T 4a1s_A          214 RDLGDRGAQGRACGNLGNTYYLL-GDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLAL  292 (411)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHc-CChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence               1111 224677777888899 9999999999987553100112    237788889999999999999999887642


Q ss_pred             CC-CC----CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          365 GR-DP----TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       365 g~-~p----~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      .. ..    ...+|..+...|...|++++|.+.+++..+.    +-.+ ...+|..+-..|.+.|+.++|..+|++..+
T Consensus       293 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          293 AVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            11 11    2567889999999999999999999987653    1111 134778888999999999999999998764

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.88  E-value=1.3e-06  Score=85.97  Aligned_cols=262  Identities=11%  Similarity=-0.063  Sum_probs=171.2

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCCHH----HHHHHHHHHHHcCCCchhhhHH-----HhhccCc----HHHHHHHHH
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFPDDR----LLASTVEVLARHHELKVPFKLE-----NFVSLAS----KGVLEATAK  271 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~pd~~----t~~~li~~~~~~g~~~~~~~l~-----~~~~~~~----~~~~~~li~  271 (493)
                      .+...|++++|...++....... ..+..    +++.+-..+...|+++.+....     ......+    ..+++.+-.
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            44567777778777777665421 11222    3444455566667644333221     1111112    124567778


Q ss_pred             HHHhcCCHHHHHHHHHHHHhC----CCC--CC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC-CCCC--CHHHHHHH
Q 011102          272 GFVKGGNLKLAWKLLMVAKDG----GRM--LD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRD-DLNL--SQQDCTAI  341 (493)
Q Consensus       272 ~~~~~g~~~~A~~l~~~m~~~----g~~--pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~-g~~p--~~~~~~~l  341 (493)
                      .+...|++++|.+.+++..+.    +-.  |. ..++..+-..+... |++++|...+++..... ...+  ....|..+
T Consensus       102 ~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  180 (373)
T 1hz4_A          102 ILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAW-ARLDEAEASARSGIEVLSSYQPQQQLQCLAML  180 (373)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHhhccCcHHHHHHHHHH
Confidence            888999999999999887652    222  22 33555666778888 99999999999875431 1111  24567788


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHH-----HHHHHHHcCCCHHHHHHHHHHHHHCCCCC---CHHHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYT-----TLIHSRLSEKKCREALTVVWNMEASNCLF---DLPAYRVVI  412 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~-----~li~~~~~~g~~~~A~~l~~~M~~~gi~p---d~~ty~~li  412 (493)
                      -..+...|++++|...+++.....-.++ ...+.     ..+..+...|+.++|...+++.......+   ....+..+.
T Consensus       181 a~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la  260 (373)
T 1hz4_A          181 IQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIA  260 (373)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHH
Confidence            8889999999999999998764321211 11222     23344779999999999999876543211   133567778


Q ss_pred             HHHHHcCCHHHHHHHHHHHHH----CCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          413 KLFVALNDISRAIRYFSKLKE----AGFCPTY-DIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       413 ~~~~~~g~~~~A~~~~~~m~~----~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ..+...|+.++|...++....    .|..++. ..+..+-.++...|+.++|...+++...
T Consensus       261 ~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          261 RAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            889999999999999988752    3322233 2666777888999999999999888754

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=98.87  E-value=6.4e-08  Score=92.79  Aligned_cols=258  Identities=11%  Similarity=-0.036  Sum_probs=184.8

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC---------cHHHHHHHHHhCCChHHHHHHHHHHHhCC---CCCC-CHHHHHHHHHH
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG---------SLSFTVRELGHMNLPERALQTFCWAQKQP---HLFP-DDRLLASTVEV  241 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~---------~~~~li~~~~~~g~~~~A~~l~~~m~~~~---g~~p-d~~t~~~li~~  241 (493)
                      ..+...|++++|+..+++.....         .|..+-..|...|++++|++.|+......   +-.| ...++..+...
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            34556799999999998765432         56677788999999999999998865321   1111 24467778888


Q ss_pred             HHHcCCCchhhhH-----HHhhccCc----HHHHHHHHHHHHhcCC--------------------HHHHHHHHHHHHhC
Q 011102          242 LARHHELKVPFKL-----ENFVSLAS----KGVLEATAKGFVKGGN--------------------LKLAWKLLMVAKDG  292 (493)
Q Consensus       242 ~~~~g~~~~~~~l-----~~~~~~~~----~~~~~~li~~~~~~g~--------------------~~~A~~l~~~m~~~  292 (493)
                      +...|+++.+...     .......+    ..++..+...|...|+                    +++|.+.+++..+.
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            8888986544332     11222222    2378889999999999                    99999999876542


Q ss_pred             ----CCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          293 ----GRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS----QQDCTAIMKVGIRLQKFGVVESLFHWFTH  363 (493)
Q Consensus       293 ----g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~  363 (493)
                          +-.+ ...++..+-..+... |++++|.+.+++......-..+    ...+..+...|.+.|++++|.+.|++..+
T Consensus       173 ~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  251 (338)
T 3ro2_A          173 VTALGDRAAQGRAFGNLGNTHYLL-GNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLL  251 (338)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence                1111 133567777788888 9999999999987543101112    33788888999999999999999998753


Q ss_pred             cCC-CCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          364 SGR-DPT----VVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       364 ~g~-~p~----~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      ... ..+    ..++..+...|...|++++|.+.+++..+.    +-.+ ...++..+-..|.+.|++++|...|++..+
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            210 112    567888999999999999999999987643    1111 134677888999999999999999998874

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.85  E-value=2.2e-07  Score=76.08  Aligned_cols=129  Identities=9%  Similarity=0.068  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .|..+...|.+.|++++|..+|+++.+.. +.+...|..+...+...|++++|.++++++.+.+ ..+...+..+...+.
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~   80 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYY   80 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHH
Confidence            45666777777888888888888776543 3356777777778888888888888888776643 234567777777888


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ..|++++|.++++++.+... .+...|..+...+.+.|++++|.+.++++.+
T Consensus        81 ~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           81 KQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             TTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            88888888888888775432 3567777788888888888888888888765

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=98.85  E-value=2.9e-06  Score=81.44  Aligned_cols=214  Identities=7%  Similarity=-0.061  Sum_probs=155.2

Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH-------HcCCCc-----hhhhHHHhhc-----cC-cHHHHHHHHHHHH
Q 011102          213 ERALQTFCWAQKQPHLFPDDRLLASTVEVLA-------RHHELK-----VPFKLENFVS-----LA-SKGVLEATAKGFV  274 (493)
Q Consensus       213 ~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~-------~~g~~~-----~~~~l~~~~~-----~~-~~~~~~~li~~~~  274 (493)
                      ++|+.+|+.....  ..-+...|..+...+.       +.|+++     ..++...|..     .+ +...|..+...+.
T Consensus        33 ~~a~~~~~~al~~--~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLV--LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHH--HTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--cCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            5667777776643  1224455666555554       235541     1223222221     12 4457888888999


Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCC-HH-HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHH-HcCCH
Q 011102          275 KGGNLKLAWKLLMVAKDGGRMLD-PS-IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGI-RLQKF  351 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~~g~~pd-~~-t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~-~~g~~  351 (493)
                      +.|++++|.++|++..+.  .|+ .. .|..+...+.+. |++++|..+|++..+..  ..+...|........ ..|++
T Consensus       111 ~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~a~~~~--p~~~~~~~~~a~~~~~~~~~~  185 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRA-EGIKSGRMIFKKAREDA--RTRHHVYVTAALMEYYCSKDK  185 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHH-HCHHHHHHHHHHHHTST--TCCTHHHHHHHHHHHHTSCCH
T ss_pred             hcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHh-cCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHHHcCCH
Confidence            999999999999999984  454 33 788888888888 99999999999988752  233444543333322 26999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC-CCC--CHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          352 GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN-CLF--DLPAYRVVIKLFVALNDISRAIRYF  428 (493)
Q Consensus       352 ~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g-i~p--d~~ty~~li~~~~~~g~~~~A~~~~  428 (493)
                      ++|.++|+...+.. +-+...|..++..+.+.|+.++|..+|++..+.. +.|  ....|..++..+.+.|+.++|..++
T Consensus       186 ~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~  264 (308)
T 2ond_A          186 SVAFKIFELGLKKY-GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVE  264 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999999886542 3367889999999999999999999999998863 455  4678899999999999999999999


Q ss_pred             HHHHHC
Q 011102          429 SKLKEA  434 (493)
Q Consensus       429 ~~m~~~  434 (493)
                      +++.+.
T Consensus       265 ~~a~~~  270 (308)
T 2ond_A          265 KRRFTA  270 (308)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            998753

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.85  E-value=6.3e-08  Score=99.41  Aligned_cols=198  Identities=12%  Similarity=-0.085  Sum_probs=157.5

Q ss_pred             cHHHHHHHHHHHHhcCCH-HHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNL-KLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTA  340 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~-~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~  340 (493)
                      +...|..+-..|...|++ ++|++.|++..+.. +-+...|..+-..|.+. |++++|.+.|++..+.   .|+...+..
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~-g~~~~A~~~~~~al~~---~p~~~~~~~  175 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKK-GDVTSAHTCFSGALTH---CKNKVSLQN  175 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHTT---CCCHHHHHH
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHhh---CCCHHHHHH
Confidence            345566677778888888 89999998887753 12467888888888888 8999999999988764   477788888


Q ss_pred             HHHHHHHc---------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC--------CCHHHHHHHHHHHHHCCCC-
Q 011102          341 IMKVGIRL---------QKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE--------KKCREALTVVWNMEASNCL-  402 (493)
Q Consensus       341 li~~~~~~---------g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~--------g~~~~A~~l~~~M~~~gi~-  402 (493)
                      +-..|...         |++++|.+.|++..+.. +-+...|..+-..|...        |++++|++.|++..+..-. 
T Consensus       176 lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~  254 (474)
T 4abn_A          176 LSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKA  254 (474)
T ss_dssp             HHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGG
T ss_pred             HHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCc
Confidence            88888888         99999999999887653 34578888999999888        8999999999998774210 


Q ss_pred             -CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          403 -FDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       403 -pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                       -+...|..+-..|.+.|++++|.+.|++..+..- -+...+..+...+...|++++|.+.+.++
T Consensus       255 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~a~~~l~~~~~~lg~~~eAi~~~~~~  318 (474)
T 4abn_A          255 SSNPDLHLNRATLHKYEESYGEALEGFSQAAALDP-AWPEPQQREQQLLEFLSRLTSLLESKGKT  318 (474)
T ss_dssp             GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence             2778899999999999999999999999876542 25667888888899999999988765443

>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=98.83  E-value=5.2e-07  Score=89.69  Aligned_cols=210  Identities=9%  Similarity=-0.032  Sum_probs=169.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCC-HHHHHHHHHHHhhcCCCCCCHHHHHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDK-YMLVMTLLDELGQRDDLNLSQQDCTA  340 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~-~~~a~~l~~~m~~~~g~~p~~~~~~~  340 (493)
                      ..+|+.+-..+.+.|++++|++.|++..+..  | +...|+.+-..+... |+ +++|+..|++....  -.-+...|+.
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~--P~~~~a~~~~g~~l~~~-g~d~~eAl~~~~~al~l--~P~~~~a~~~  171 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSL-QKDLHEEMNYITAIIEE--QPKNYQVWHH  171 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHH--CTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC--ccCHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHH--CCCCHHHHHH
Confidence            3467778888899999999999999998854  5 467788888889999 86 99999999999875  2346788999


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH-cC
Q 011102          341 IMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA-LN  419 (493)
Q Consensus       341 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~-~g  419 (493)
                      +-..|.+.|++++|+..|++..+.. .-+...|..+-.++.+.|++++|++.|+++.+... -+...|+.+-..+.+ .|
T Consensus       172 ~g~~~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~~l~~  249 (382)
T 2h6f_A          172 RRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTG  249 (382)
T ss_dssp             HHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcC
Confidence            9999999999999999999988653 34788999999999999999999999999987643 367889999889998 67


Q ss_pred             CHHHH-----HHHHHHHHHCCCCCCHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHCCCcc-CHHHHHHHHH
Q 011102          420 DISRA-----IRYFSKLKEAGFCPTYDIYRDMIRIFMASG--RLAKCRDVCKEAEMAGFKL-DKQTVVELLQ  483 (493)
Q Consensus       420 ~~~~A-----~~~~~~m~~~g~~p~~~ty~~li~~~~~~g--~~~~A~~l~~~m~~~g~~p-d~~t~~~Ll~  483 (493)
                      ..++|     ...|++..+..- -+...|+.+-..|.+.|  ++++|.+.+.++ +  ..| +...+..|..
T Consensus       250 ~~~eA~~~~el~~~~~Al~l~P-~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~--~~p~~~~al~~La~  317 (382)
T 2h6f_A          250 YNDRAVLEREVQYTLEMIKLVP-HNESAWNYLKGILQDRGLSKYPNLLNQLLDL-Q--PSHSSPYLIAFLVD  317 (382)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-T--TTCCCHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHccCccchHHHHHHHHHh-c--cCCCCHHHHHHHHH
Confidence            65777     478888775432 25778888888899888  689999999888 2  344 4455555544

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.81  E-value=7.4e-08  Score=90.15  Aligned_cols=224  Identities=13%  Similarity=-0.051  Sum_probs=142.3

Q ss_pred             hCCChHHHHHHHHHHHhCC------CCCCCHHHHHHHHHHHHHcCCCchhhhHH-----Hhhc------cCcHHHHHHHH
Q 011102          208 HMNLPERALQTFCWAQKQP------HLFPDDRLLASTVEVLARHHELKVPFKLE-----NFVS------LASKGVLEATA  270 (493)
Q Consensus       208 ~~g~~~~A~~l~~~m~~~~------g~~pd~~t~~~li~~~~~~g~~~~~~~l~-----~~~~------~~~~~~~~~li  270 (493)
                      ..|++++|+++|++..+..      .......++..+...+...|+++.+....     ....      .....+|..+.
T Consensus        13 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~   92 (283)
T 3edt_B           13 GLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLA   92 (283)
T ss_dssp             CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHH
Confidence            3455555555555444310      11224557888888999999865544331     1111      11334789999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhC------CCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc------CCCCCCHHH
Q 011102          271 KGFVKGGNLKLAWKLLMVAKDG------GRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQR------DDLNLSQQD  337 (493)
Q Consensus       271 ~~~~~~g~~~~A~~l~~~m~~~------g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~------~g~~p~~~~  337 (493)
                      ..|...|++++|.+.|++..+.      .-.| ...+|..+-..|... |++++|...+++....      +.......+
T Consensus        93 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           93 VLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQ-GKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            9999999999999999998764      1112 345677888889999 9999999999998653      111223567


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHc-------CCCCC-HHHHHHHHHHHHcCCCH------HHHHHHHHHHHHCCCCC
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHS-------GRDPT-VVMYTTLIHSRLSEKKC------REALTVVWNMEASNCLF  403 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~-------g~~p~-~~ty~~li~~~~~~g~~------~~A~~l~~~M~~~gi~p  403 (493)
                      +..+...|.+.|++++|.+.|++..+.       ...+. ...|..+...+...+..      .++...+..... ....
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV-DSPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC-CCHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC-CCHH
Confidence            888999999999999999999988753       11222 22333333333333322      222222222111 1112


Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          404 DLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      ...++..+-..|.+.|++++|..+|++..+
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345788888999999999999999998764

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.79  E-value=1.2e-06  Score=88.97  Aligned_cols=293  Identities=10%  Similarity=-0.074  Sum_probs=147.4

Q ss_pred             hccCCCCHHHHHHHHhhhccc-------------CcHHHHHHHHHh--CCChHHHHHHHHHHHhCCCCCCC-HHHHHHHH
Q 011102          176 GLDSHKDVAEVLDKCGRFLRK-------------GSLSFTVRELGH--MNLPERALQTFCWAQKQPHLFPD-DRLLASTV  239 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~-------------~~~~~li~~~~~--~g~~~~A~~l~~~m~~~~g~~pd-~~t~~~li  239 (493)
                      .+...|+.++|...+++...-             .+|+..-.++.+  .+++++|++.|+...+.   .|+ ...+..+.
T Consensus       103 ~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~---~p~~~~~~~~~~  179 (472)
T 4g1t_A          103 VYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK---KPKNPEFTSGLA  179 (472)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH---STTCHHHHHHHH
T ss_pred             HHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh---CCCCHHHHHHHH
Confidence            344556777776666543211             023322223333  34567777777776643   233 23333333


Q ss_pred             HHH---HHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 011102          240 EVL---ARHHELKVPFKLENFVS-----LASKGVLEATAKGFVK----GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILE  307 (493)
Q Consensus       240 ~~~---~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~  307 (493)
                      .++   ...++.+  +++..+..     ..+..++..+...+..    .|+.++|.+++++..... +.+..++..+-..
T Consensus       180 ~~~~~l~~~~~~~--~al~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~  256 (472)
T 4g1t_A          180 IASYRLDNWPPSQ--NAIDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKF  256 (472)
T ss_dssp             HHHHHHHHSCCCC--CTHHHHHHHHHHCSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHH
T ss_pred             HHHHHhcCchHHH--HHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHH
Confidence            332   2333322  22222221     1234445444444433    356677777777766643 2345566777777


Q ss_pred             HhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH-------------------cCCHHHHHHHHHHHHHcCCCC
Q 011102          308 LGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR-------------------LQKFGVVESLFHWFTHSGRDP  368 (493)
Q Consensus       308 ~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~-------------------~g~~~~A~~l~~~m~~~g~~p  368 (493)
                      |... |++++|...+++..+.  ..-+..++..+-..|..                   .+..++|...|++..+.. +.
T Consensus       257 ~~~~-~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~  332 (472)
T 4g1t_A          257 YRRK-DEPDKAIELLKKALEY--IPNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DN  332 (472)
T ss_dssp             HHHT-TCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TT
T ss_pred             HHHc-CchHHHHHHHHHHHHh--CCChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-Cc
Confidence            7777 8888888888877654  12234445444444322                   123456666666655432 23


Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHH--HHHHHHH-HHHHcCCHHHHHHHHHHHHHCC----------
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLP--AYRVVIK-LFVALNDISRAIRYFSKLKEAG----------  435 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~--ty~~li~-~~~~~g~~~~A~~~~~~m~~~g----------  435 (493)
                      +..+|..+-..|...|++++|.+.|++..+....+...  .+..+-. .+...|+.++|...|++..+..          
T Consensus       333 ~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~  412 (472)
T 4g1t_A          333 LFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMK  412 (472)
T ss_dssp             TCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHH
T ss_pred             hhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHH
Confidence            34557777888888888888888888877654333221  1222211 2346788888888877655321          


Q ss_pred             -------------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CccCHHHH
Q 011102          436 -------------FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAG-FKLDKQTV  478 (493)
Q Consensus       436 -------------~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g-~~pd~~t~  478 (493)
                                   -+.+..+|..|-..|...|++++|.+.|++..+.| ..|+..+|
T Consensus       413 ~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          413 DKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             HHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC----------------------
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence                         12245677888888888888888888888887654 34554443

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=98.77  E-value=6.5e-07  Score=91.81  Aligned_cols=184  Identities=7%  Similarity=-0.012  Sum_probs=155.5

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCH-HHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          279 LKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKY-MLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~-~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      ++++++.+++..... ..+...|..+-..+... |++ ++|.+.|++..+.  -.-+...|..+-..|.+.|++++|.+.
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~-g~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~  159 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVT-PDYSPEAEVLLSKAVKL--EPELVEAWNQLGEVYWKKGDVTSAHTC  159 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSS-SSCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhc-cccHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            677777887766543 24677888888888998 999 9999999998775  223578999999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHcC---------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc--------CC
Q 011102          358 FHWFTHSGRDPTVVMYTTLIHSRLSE---------KKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL--------ND  420 (493)
Q Consensus       358 ~~~m~~~g~~p~~~ty~~li~~~~~~---------g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~--------g~  420 (493)
                      |++..+.  .|+...|..+-..|...         |++++|.+.|++..+..- -+...|..+-.+|...        |+
T Consensus       160 ~~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~~~~g~  236 (474)
T 4abn_A          160 FSGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDV-LDGRSWYILGNAYLSLYFNTGQNPKI  236 (474)
T ss_dssp             HHHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHhhccccch
Confidence            9998866  57789999999999999         999999999999877532 3577888898999988        99


Q ss_pred             HHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          421 ISRAIRYFSKLKEAGFC--PTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       421 ~~~A~~~~~~m~~~g~~--p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      +++|...|++..+..-.  -+...|..+-..|...|++++|.+.|++..+.
T Consensus       237 ~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l  287 (474)
T 4abn_A          237 SQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL  287 (474)
T ss_dssp             HHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            99999999999865310  37889999999999999999999999998764

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.77  E-value=9.2e-07  Score=87.63  Aligned_cols=234  Identities=9%  Similarity=-0.030  Sum_probs=159.8

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHH
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAW  283 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~  283 (493)
                      ..+...|++++|++.|+.......-.+|...                           ...+|..+-..|...|++++|.
T Consensus       111 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~---------------------------~a~~~~~lg~~~~~~~~~~~A~  163 (383)
T 3ulq_A          111 MYELDQREYLSAIKFFKKAESKLIFVKDRIE---------------------------KAEFFFKMSESYYYMKQTYFSM  163 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTGGGCCCHHH---------------------------HHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhCCCHHH---------------------------HHHHHHHHHHHHHHcCCHHHHH
Confidence            4567889999999999998754111222110                           1234556666777778888888


Q ss_pred             HHHHHHHhCCC-CC-----CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC----HHHHHHHHHHHHHcCCHHH
Q 011102          284 KLLMVAKDGGR-ML-----DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS----QQDCTAIMKVGIRLQKFGV  353 (493)
Q Consensus       284 ~l~~~m~~~g~-~p-----d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~----~~~~~~li~~~~~~g~~~~  353 (493)
                      ..+++..+.-- .+     ...+++.+-..|... |++++|...|++......-..+    ..++..+-..|...|++++
T Consensus       164 ~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~  242 (383)
T 3ulq_A          164 DYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDL-KQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYED  242 (383)
T ss_dssp             HHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHH
Confidence            87777654210 01     134566677778888 8999999888876542100112    2367788888999999999


Q ss_pred             HHHHHHHHHHc----CC-CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHHcCC---H
Q 011102          354 VESLFHWFTHS----GR-DPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFDLPAYRVVIKLFVALND---I  421 (493)
Q Consensus       354 A~~l~~~m~~~----g~-~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd~~ty~~li~~~~~~g~---~  421 (493)
                      |.+.|++..+.    +. .....++..+-..|.+.|++++|.+.+++..+.    +-......+..+-..|...|+   +
T Consensus       243 A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  322 (383)
T 3ulq_A          243 AIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAI  322 (383)
T ss_dssp             HHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHH
T ss_pred             HHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHH
Confidence            99999887651    33 334677888999999999999999999886543    111122335666677788888   7


Q ss_pred             HHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          422 SRAIRYFSKLKEAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       422 ~~A~~~~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ++|..++++.   +..|+ ...+..+-..|...|++++|.+.+++..+
T Consensus       323 ~~al~~~~~~---~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          323 QGFFDFLESK---MLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHHHT---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHC---cCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7777777665   33333 34677788899999999999999988764

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.74  E-value=6.1e-07  Score=73.30  Aligned_cols=96  Identities=9%  Similarity=0.051  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKL  414 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~  414 (493)
                      ...+..+...+...|++++|..+|+++.+.+ +.+...|..+...+...|++++|.+.++++.+.. ..+...+..+...
T Consensus        35 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~  112 (136)
T 2fo7_A           35 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNA  112 (136)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            3344444444444444444444444443322 2233444445555555555555555555544332 1233444455555


Q ss_pred             HHHcCCHHHHHHHHHHHH
Q 011102          415 FVALNDISRAIRYFSKLK  432 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~  432 (493)
                      +.+.|++++|...|+++.
T Consensus       113 ~~~~~~~~~A~~~~~~~~  130 (136)
T 2fo7_A          113 YYKQGDYDEAIEYYQKAL  130 (136)
T ss_dssp             HHTTTCHHHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHH
Confidence            555555555555555544

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=98.70  E-value=2.9e-06  Score=88.04  Aligned_cols=200  Identities=15%  Similarity=0.051  Sum_probs=157.4

Q ss_pred             cHHHHHHHHHHHHh-------cCCHH-------HHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhh
Q 011102          262 SKGVLEATAKGFVK-------GGNLK-------LAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQ  327 (493)
Q Consensus       262 ~~~~~~~li~~~~~-------~g~~~-------~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~  327 (493)
                      +...|..+...+.+       .|+++       +|.++|++..+.-.+-+...|..+...+.+. |++++|..+|+...+
T Consensus       271 ~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~-g~~~~A~~~~~~al~  349 (530)
T 2ooe_A          271 HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESR-MKYEKVHSIYNRLLA  349 (530)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhc-CCHHHHHHHHHHHhC
Confidence            56678878777775       79987       8999999988632333578889999999999 999999999999987


Q ss_pred             cCCCCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH-HHHcCCCHHHHHHHHHHHHHCCCCC-
Q 011102          328 RDDLNLS--QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIH-SRLSEKKCREALTVVWNMEASNCLF-  403 (493)
Q Consensus       328 ~~g~~p~--~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~-~~~~~g~~~~A~~l~~~M~~~gi~p-  403 (493)
                      .   .|+  ...|...+..+.+.|++++|.++|++..+..- .+...|..... -+...|+.++|..+|++..+.  .| 
T Consensus       350 ~---~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~-~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~--~p~  423 (530)
T 2ooe_A          350 I---EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK--YGD  423 (530)
T ss_dssp             S---SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTT-CCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH--HTT
T ss_pred             c---cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccC-CchHHHHHHHHHHHHHcCChhHHHHHHHHHHHH--CCC
Confidence            5   343  35899999999999999999999999876421 12222222221 233689999999999987764  24 


Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          404 DLPAYRVVIKLFVALNDISRAIRYFSKLKEAG-FCP--TYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       404 d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g-~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +...|..++..+.+.|+.++|..+|++....+ ..|  ....|...+......|+.+.+.++++++.+
T Consensus       424 ~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~  491 (530)
T 2ooe_A          424 IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  491 (530)
T ss_dssp             CHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            57889999999999999999999999998763 233  256898889988999999999999998875

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.68  E-value=9.5e-06  Score=77.31  Aligned_cols=178  Identities=10%  Similarity=0.008  Sum_probs=99.4

Q ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          282 AWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDL-NLSQQDCTAIMKVGIRLQKFGVVESLFHW  360 (493)
Q Consensus       282 A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~-~p~~~~~~~li~~~~~~g~~~~A~~l~~~  360 (493)
                      |+..|++..+.+ .++..++..+-..+... |++++|++++.+.... +- .-+...+..++..|.+.|+.+.|.+.+++
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~-g~~eeAL~~l~~~i~~-~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~  161 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAIL-GDLDKSLETCVEGIDN-DEAEGTTELLLLAIEVALLNNNVSTASTIFDN  161 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHTS-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHc-CCHHHHHHHHHHHhcc-CCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            556666655544 34455544555566666 7777777777665433 21 12445566666777777777777777777


Q ss_pred             HHHcCCCC-----CHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          361 FTHSGRDP-----TVVMYTTLIHSRLS----EKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       361 m~~~g~~p-----~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      |.+.  .|     +-.+..-|..++..    .++..+|..+|+++.+.  .|+..+-..++.++.+.|++++|.+.++.+
T Consensus       162 ~~~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l  237 (310)
T 3mv2_B          162 YTNA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELL  237 (310)
T ss_dssp             HHHH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHhc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            7543  44     23444444444222    23677777777776543  244333344445667777777777777655


Q ss_pred             HHC-----CC----CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          432 KEA-----GF----CPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       432 ~~~-----g~----~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      .+.     +.    .-|..+.-.+|......|+  +|.++++++.+
T Consensus       238 ~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~  281 (310)
T 3mv2_B          238 LSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVK  281 (310)
T ss_dssp             HSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHH
T ss_pred             HHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHH
Confidence            421     10    2244555344444444555  66677777665

>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=98.68  E-value=1.3e-06  Score=93.96  Aligned_cols=159  Identities=9%  Similarity=-0.047  Sum_probs=69.2

Q ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011102          301 YAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSR  380 (493)
Q Consensus       301 ~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~  380 (493)
                      |+.+=..|.+. |++++|++.|++..+.  -.-+...|+.+-.+|.+.|++++|++.|++..+.. +-+...|+.+-..|
T Consensus        12 l~nLG~~~~~~-G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~~l   87 (723)
T 4gyw_A           12 LNNLANIKREQ-GNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTL   87 (723)
T ss_dssp             HHHHHHHHHHT-TCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            33343444444 4444444444443332  01123344444444444444444444444443321 11234444444444


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          381 LSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKC  459 (493)
Q Consensus       381 ~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A  459 (493)
                      .+.|++++|++.|++..+.  .| +...|+.+-..|.+.|++++|.+.|++..+..- -+...|..+...|...|++++|
T Consensus        88 ~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P-~~~~a~~~L~~~l~~~g~~~~A  164 (723)
T 4gyw_A           88 KEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKP-DFPDAYCNLAHCLQIVCDWTDY  164 (723)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCCTTH
T ss_pred             HHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CChHHHhhhhhHHHhcccHHHH
Confidence            4445555555444444332  12 233444444555555555555555554443221 1334445555555555555555


Q ss_pred             HHHHHHH
Q 011102          460 RDVCKEA  466 (493)
Q Consensus       460 ~~l~~~m  466 (493)
                      .+.+++.
T Consensus       165 ~~~~~ka  171 (723)
T 4gyw_A          165 DERMKKL  171 (723)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5444444

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.67  E-value=2.9e-06  Score=83.97  Aligned_cols=233  Identities=11%  Similarity=0.004  Sum_probs=159.6

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHH
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWK  284 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  284 (493)
                      .+...|++++|+..|+.......-.+|..                           ....+|..+-..|...|+++.|..
T Consensus       110 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~---------------------------~~a~~~~~lg~~y~~~~~~~~A~~  162 (378)
T 3q15_A          110 YEFDQKEYVEAIGYYREAEKELPFVSDDI---------------------------EKAEFHFKVAEAYYHMKQTHVSMY  162 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTGGGCCCHH---------------------------HHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHCCHHHHHHHHHHHHHHHhhCCChH---------------------------HHHHHHHHHHHHHHHcCCcHHHHH
Confidence            45678999999999998875411112211                           012345667777788888888888


Q ss_pred             HHHHHHhC----CC-CC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC---CCC-CCHHHHHHHHHHHHHcCCHHHH
Q 011102          285 LLMVAKDG----GR-ML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRD---DLN-LSQQDCTAIMKVGIRLQKFGVV  354 (493)
Q Consensus       285 l~~~m~~~----g~-~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~---g~~-p~~~~~~~li~~~~~~g~~~~A  354 (493)
                      .+++..+.    +- .+ ...+++.+-..|... |++++|.+.|++.....   +-. ....+++.+-..|...|++++|
T Consensus       163 ~~~~al~~~~~~~~~~~~~~~~~~~lg~~y~~~-~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A  241 (378)
T 3q15_A          163 HILQALDIYQNHPLYSIRTIQSLFVIAGNYDDF-KHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMA  241 (378)
T ss_dssp             HHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHH
Confidence            88776542    11 11 134566777778888 89999998888765420   111 1234677788889999999999


Q ss_pred             HHHHHHHHH----cCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC----CCCCHHHHHHHHHHHHHcCC---HHH
Q 011102          355 ESLFHWFTH----SGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN----CLFDLPAYRVVIKLFVALND---ISR  423 (493)
Q Consensus       355 ~~l~~~m~~----~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g----i~pd~~ty~~li~~~~~~g~---~~~  423 (493)
                      .+.|++..+    .+.+....++..+-..|.+.|+.++|.+.+++..+..    -......+..+-..|...|+   +++
T Consensus       242 ~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~  321 (378)
T 3q15_A          242 VEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHD  321 (378)
T ss_dssp             HHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHH
T ss_pred             HHHHHHHHHHHHhhCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHH
Confidence            999988765    1223336788889999999999999999999876531    22223455566666777788   777


Q ss_pred             HHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          424 AIRYFSKLKEAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       424 A~~~~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |..++++.   +..|+ ...+..+-..|...|++++|.+.|++..+
T Consensus       322 al~~~~~~---~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          322 LLSYFEKK---NLHAYIEACARSAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHT---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhC---CChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            77777662   22232 34566788889999999999999988753

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=98.66  E-value=1.2e-05  Score=81.59  Aligned_cols=292  Identities=10%  Similarity=-0.095  Sum_probs=180.5

Q ss_pred             cCCCCHHHHHHHHhhhcc-----------cC---cHHHHHHHHHhCCChHHHHHHHHHHHhC----CC-CCC-CHHHHHH
Q 011102          178 DSHKDVAEVLDKCGRFLR-----------KG---SLSFTVRELGHMNLPERALQTFCWAQKQ----PH-LFP-DDRLLAS  237 (493)
Q Consensus       178 ~~~~~~~~a~~~~~~m~~-----------~~---~~~~li~~~~~~g~~~~A~~l~~~m~~~----~g-~~p-d~~t~~~  237 (493)
                      ...|+.++|++.|.+..+           ..   +|+.+-..|...|++++|...|+.....    .+ ..+ ...++..
T Consensus        62 ~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~  141 (472)
T 4g1t_A           62 HLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCE  141 (472)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHH
Confidence            446888888888874322           11   5677777888889999998888887642    01 112 2345555


Q ss_pred             HHHHHHHcCCCchhhhHHHhhcc----C-cHHHHHHHHHH---HHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHh
Q 011102          238 TVEVLARHHELKVPFKLENFVSL----A-SKGVLEATAKG---FVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELG  309 (493)
Q Consensus       238 li~~~~~~g~~~~~~~l~~~~~~----~-~~~~~~~li~~---~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~  309 (493)
                      .-.++.+.|.-+..+++..|...    | +...+..+...   +...++.++|++.|++..+.. +.+..++..+-..+.
T Consensus       142 ~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~~~~~~~l~~~~~  220 (472)
T 4g1t_A          142 EGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDNQYLKVLLALKLH  220 (472)
T ss_dssp             HHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-CcchHHHHHHHHHHH
Confidence            55556665554455565555431    2 33344444333   445677778888888777643 123445554444443


Q ss_pred             cC---CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC---
Q 011102          310 KN---PDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE---  383 (493)
Q Consensus       310 ~~---~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~---  383 (493)
                      ..   .+++++|.+++++....  -..+...+..+-..|.+.|++++|.+.|++..+.. +-+..+|..+-..|...   
T Consensus       221 ~~~~~~~~~~~a~~~~~~al~~--~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~y~~~~~~  297 (472)
T 4g1t_A          221 KMREEGEEEGEGEKLVEEALEK--APGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLHCQIGCCYRAKVFQ  297 (472)
T ss_dssp             HCC------CHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHh--CccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHH
Confidence            32   25677888888887664  23456778888888889999999999988876542 23456677666666432   


Q ss_pred             ----------------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHH--HHHH
Q 011102          384 ----------------KKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYD--IYRD  445 (493)
Q Consensus       384 ----------------g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~--ty~~  445 (493)
                                      +..++|...+++..+... .+..++..+-..|.+.|++++|...|++..+....+...  .+..
T Consensus       298 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~  376 (472)
T 4g1t_A          298 VMNLRENGMYGKRKLLELIGHAVAHLKKADEAND-NLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLR  376 (472)
T ss_dssp             HHHC------CHHHHHHHHHHHHHHHHHHHHHCT-TTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCC-chhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHH
Confidence                            224566667766554321 233457777888899999999999999888655433221  1222


Q ss_pred             HHH-HHHHcCCHHHHHHHHHHHHHCCCccCHH
Q 011102          446 MIR-IFMASGRLAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       446 li~-~~~~~g~~~~A~~l~~~m~~~g~~pd~~  476 (493)
                      +.. .+...|+.++|.+.|++..+  +.|+..
T Consensus       377 ~~~~~~~~~~~~~~Ai~~y~kal~--i~~~~~  406 (472)
T 4g1t_A          377 YGNFQLYQMKCEDKAIHHFIEGVK--INQKSR  406 (472)
T ss_dssp             HHHHHHHTSSCHHHHHHHHHHHHH--SCCCCH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHh--cCcccH
Confidence            222 23467889999999988876  455544

>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=98.63  E-value=6.1e-06  Score=75.07  Aligned_cols=205  Identities=9%  Similarity=-0.057  Sum_probs=149.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +...|...-..+.+.|++++|.+.|++..+..-.++...+..+-..+... |++++|...|++..+.  -.-+...|..+
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~al~~--~p~~~~~~~~l   82 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNI-KKYKEAADYFDIAIKK--NYNLANAYIGK   82 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHT--TCSHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHh-hcHHHHHHHHHHHHHh--CcchHHHHHHH
Confidence            44677778888999999999999999998876446777777788888888 9999999999998764  22356678888


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCH-------HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC---HHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTV-------VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD---LPAYRVV  411 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~-------~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd---~~ty~~l  411 (493)
                      -..|.+.|++++|.+.|++..+.. +.+.       ..|..+-..+...|++++|.+.|++..+.  .|+   ...|..+
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l  159 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSL  159 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHH
Confidence            899999999999999999887642 2233       45778888888999999999999988764  565   3456666


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHH
Q 011102          412 IKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELL  482 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll  482 (493)
                      -..|...|     ..+++++...+- .+...|.....  ...+.+++|...+++..+.  .|+......++
T Consensus       160 ~~~~~~~~-----~~~~~~a~~~~~-~~~~~~~~~~~--~~~~~~~~A~~~~~~a~~l--~p~~~~~~~~l  220 (228)
T 4i17_A          160 GVLFYNNG-----ADVLRKATPLAS-SNKEKYASEKA--KADAAFKKAVDYLGEAVTL--SPNRTEIKQMQ  220 (228)
T ss_dssp             HHHHHHHH-----HHHHHHHGGGTT-TCHHHHHHHHH--HHHHHHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHHHHH-----HHHHHHHHhccc-CCHHHHHHHHH--HHHHHHHHHHHHHHHHhhc--CCCCHHHHHHH
Confidence            66665443     444555554432 24555554443  3456789999999998874  56554444443

>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=98.62  E-value=2.1e-06  Score=92.28  Aligned_cols=162  Identities=12%  Similarity=-0.036  Sum_probs=138.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      ..+|+.|-..|.+.|++++|++.|++..+..  |+ ..+|+.+-..|.+. |++++|++.|++..+.  -.-+...|..+
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~--P~~~~a~~nLg~~l~~~-g~~~eA~~~~~~Al~l--~P~~~~a~~nL   83 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVF--PEFAAAHSNLASVLQQQ-GKLQEALMHYKEAIRI--SPTFADAYSNM   83 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            4578889999999999999999999998853  54 67888898999999 9999999999998764  12347789999


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCC
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALND  420 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~  420 (493)
                      -.+|.+.|++++|++.|++..+.. +-+...|+.+-..|.+.|++++|++.|++..+.  .| +...|..+...|...|+
T Consensus        84 g~~l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~  160 (723)
T 4gyw_A           84 GNTLKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCD  160 (723)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhccc
Confidence            999999999999999999987642 336789999999999999999999999998764  35 46789999999999999


Q ss_pred             HHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLK  432 (493)
Q Consensus       421 ~~~A~~~~~~m~  432 (493)
                      +++|.+.+++..
T Consensus       161 ~~~A~~~~~kal  172 (723)
T 4gyw_A          161 WTDYDERMKKLV  172 (723)
T ss_dssp             CTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999888765

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.62  E-value=2.4e-06  Score=81.43  Aligned_cols=200  Identities=11%  Similarity=-0.010  Sum_probs=143.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC----H
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDG----GRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS----Q  335 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~----~  335 (493)
                      .|+.....|...|++++|.+.|++..+.    |-.++ ..+|+.+-..|.+. |++++|+..+++......-..+    .
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~-g~~~~A~~~~~~Al~l~~~~g~~~~~a  117 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSG-GNSVNAVDSLENAIQIFTHRGQFRRGA  117 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            3455567788899999999999877653    32222 45788888899999 9999999999876543100011    3


Q ss_pred             HHHHHHHHHHHHc-CCHHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH----
Q 011102          336 QDCTAIMKVGIRL-QKFGVVESLFHWFTHS----GRDPT-VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL----  405 (493)
Q Consensus       336 ~~~~~li~~~~~~-g~~~~A~~l~~~m~~~----g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~----  405 (493)
                      .+++.+-..|... |++++|...|++..+.    +-... ..+|+.+...|.+.|++++|+..|++..+.......    
T Consensus       118 ~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  197 (292)
T 1qqe_A          118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWS  197 (292)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGG
T ss_pred             HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHH
Confidence            5788888999996 9999999999987642    11111 356889999999999999999999998875433222    


Q ss_pred             --HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCH------HHHHHHHHHHH--HcCCHHHHHHHHHHHH
Q 011102          406 --PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTY------DIYRDMIRIFM--ASGRLAKCRDVCKEAE  467 (493)
Q Consensus       406 --~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~------~ty~~li~~~~--~~g~~~~A~~l~~~m~  467 (493)
                        ..|..+...+...|++++|...|++..+  +.|+.      ..+..++.+|.  ..+++++|.+.|+.+.
T Consensus       198 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~  267 (292)
T 1qqe_A          198 LKDYFLKKGLCQLAATDAVAAARTLQEGQS--EDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHGGGC--C---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence              2567777889999999999999998763  22332      23445666664  4567888888887764

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=98.61  E-value=3.4e-06  Score=83.48  Aligned_cols=204  Identities=12%  Similarity=0.015  Sum_probs=148.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCC-CCCC----HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-----HHHH
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGG-RMLD----PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-----QQDC  338 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g-~~pd----~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-----~~~~  338 (493)
                      .-..+...|++++|.+.|++..+.- -.+|    ..+|..+-..|... |++++|...+.+......-.++     ..++
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~-~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  187 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYM-KQTYFSMDYARQAYEIYKEHEAYNIRLLQCH  187 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHTCSTTHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCccchHHHHHHH
Confidence            4456778999999999999998741 1133    34677777888888 9999999999986543111122     3477


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CC-CCCHHHH
Q 011102          339 TAIMKVGIRLQKFGVVESLFHWFTHS----GRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NC-LFDLPAY  408 (493)
Q Consensus       339 ~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi-~pd~~ty  408 (493)
                      +.+-..|...|++++|.+.|++..+.    +-.+ ...+|+.+-..|...|++++|.+.+++..+.    +- .-...++
T Consensus       188 ~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  267 (383)
T 3ulq_A          188 SLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAY  267 (383)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHH
Confidence            88889999999999999999887632    1111 1247888999999999999999999987662    33 3345678


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHCCCccCHH
Q 011102          409 RVVIKLFVALNDISRAIRYFSKLKEA----GFCPTYDIYRDMIRIFMASGR---LAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       409 ~~li~~~~~~g~~~~A~~~~~~m~~~----g~~p~~~ty~~li~~~~~~g~---~~~A~~l~~~m~~~g~~pd~~  476 (493)
                      ..+-..|.+.|++++|...+++..+.    +-......+..+-..|...|+   +++|..++++.   +..|+..
T Consensus       268 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~---~~~~~~~  339 (383)
T 3ulq_A          268 FLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK---MLYADLE  339 (383)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT---TCHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC---cCHHHHH
Confidence            88899999999999999999987632    222223345677778888898   77777777665   4444443

>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=98.56  E-value=1.3e-05  Score=72.79  Aligned_cols=188  Identities=10%  Similarity=-0.054  Sum_probs=135.7

Q ss_pred             CHHHHHHHHHHHHHcCCCchhhhHHHhhc----c--CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHH
Q 011102          231 DDRLLASTVEVLARHHELKVPFKLENFVS----L--ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAK  303 (493)
Q Consensus       231 d~~t~~~li~~~~~~g~~~~~~~l~~~~~----~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~  303 (493)
                      |...+...-..+.+.|+++.  ++..|..    .  .+..++..+...|.+.|++++|.+.|++..+..  |+ ...|..
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~--A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~   81 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAV--AFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN--YNLANAYIG   81 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHH--HHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--CSHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHH--HHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC--cchHHHHHH
Confidence            56777778888888898544  4433332    2  455666668999999999999999999998854  54 557778


Q ss_pred             HHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC---HHHH
Q 011102          304 LILELGKNPDKYMLVMTLLDELGQRDDLNLSQ-------QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT---VVMY  373 (493)
Q Consensus       304 li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~-------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~---~~ty  373 (493)
                      +-..+... |++++|...+++..+..  .-+.       ..|..+-..+.+.|++++|.+.|++..+.  .|+   ...|
T Consensus        82 l~~~~~~~-~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~  156 (228)
T 4i17_A           82 KSAAYRDM-KNNQEYIATLTEGIKAV--PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDAL  156 (228)
T ss_dssp             HHHHHHHT-TCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHH
T ss_pred             HHHHHHHc-ccHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHH
Confidence            88889999 99999999999987751  2234       45777778889999999999999998754  565   4667


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      ..+-..|...|     ..+++++...+- .+...|.....  ...+.+++|...|++..+..
T Consensus       157 ~~l~~~~~~~~-----~~~~~~a~~~~~-~~~~~~~~~~~--~~~~~~~~A~~~~~~a~~l~  210 (228)
T 4i17_A          157 YSLGVLFYNNG-----ADVLRKATPLAS-SNKEKYASEKA--KADAAFKKAVDYLGEAVTLS  210 (228)
T ss_dssp             HHHHHHHHHHH-----HHHHHHHGGGTT-TCHHHHHHHHH--HHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHH-----HHHHHHHHhccc-CCHHHHHHHHH--HHHHHHHHHHHHHHHHhhcC
Confidence            77777775543     444555554432 33455555443  34566899999999887643

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.53  E-value=1.5e-05  Score=78.29  Aligned_cols=254  Identities=10%  Similarity=-0.062  Sum_probs=170.5

Q ss_pred             cCCCCHHHHHHHHhhhccc----C------cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCH----HHHHHHHHHHH
Q 011102          178 DSHKDVAEVLDKCGRFLRK----G------SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDD----RLLASTVEVLA  243 (493)
Q Consensus       178 ~~~~~~~~a~~~~~~m~~~----~------~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~----~t~~~li~~~~  243 (493)
                      ...|++++|...+.+....    +      .++.+-..+...|++++|.+.+++......-..+.    .++..+-..+.
T Consensus        25 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~  104 (373)
T 1hz4_A           25 INDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILF  104 (373)
T ss_dssp             HHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHH
Confidence            3468888888887754322    1      34455567888999999999998876421111222    23556667778


Q ss_pred             HcCCCchhhhHH-----Hhhcc-----C-cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC--C--CHHHHHHHHHHH
Q 011102          244 RHHELKVPFKLE-----NFVSL-----A-SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRM--L--DPSIYAKLILEL  308 (493)
Q Consensus       244 ~~g~~~~~~~l~-----~~~~~-----~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~--p--d~~t~~~li~~~  308 (493)
                      ..|+++.+....     .....     + ...++..+-..+...|++++|...+++..+..-.  +  ...+|..+-..+
T Consensus       105 ~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~  184 (373)
T 1hz4_A          105 AQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCS  184 (373)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHH
Confidence            888865443321     11111     1 2235677888899999999999999988764321  1  235677777788


Q ss_pred             hcCCCCHHHHHHHHHHHhhcC-CCCCCHHHHH----HHHHHHHHcCCHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHH
Q 011102          309 GKNPDKYMLVMTLLDELGQRD-DLNLSQQDCT----AIMKVGIRLQKFGVVESLFHWFTHSGRDP---TVVMYTTLIHSR  380 (493)
Q Consensus       309 ~~~~~~~~~a~~l~~~m~~~~-g~~p~~~~~~----~li~~~~~~g~~~~A~~l~~~m~~~g~~p---~~~ty~~li~~~  380 (493)
                      ... |++++|...+++..... ..........    .....+...|++++|...+++.......+   ....+..+...+
T Consensus       185 ~~~-g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~la~~~  263 (373)
T 1hz4_A          185 LAR-GDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQ  263 (373)
T ss_dssp             HHH-TCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHH
T ss_pred             HHc-CCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHHHHHH
Confidence            888 99999999999875431 1111112111    23345789999999999998876432211   134577888999


Q ss_pred             HcCCCHHHHHHHHHHHHHC----CCCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          381 LSEKKCREALTVVWNMEAS----NCLFDLP-AYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       381 ~~~g~~~~A~~l~~~M~~~----gi~pd~~-ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      ...|+.++|.+.+++....    |..++.. .+..+-.++...|+.++|...+++..
T Consensus       264 ~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al  320 (373)
T 1hz4_A          264 ILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  320 (373)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            9999999999999987542    3323332 56666778899999999999998876

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.46  E-value=2.4e-05  Score=79.49  Aligned_cols=338  Identities=9%  Similarity=-0.037  Sum_probs=206.1

Q ss_pred             ccccchhHHHHHhhhcCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCChhHHH---hhh---hhhhhhhhhccCCchhHH
Q 011102           96 FIWESEELEAISSLFQGR-IPQKPGRLYRERPLPLPLPHRLRPLELPTPKKRV---CLA---SSRASICKQVYKNPSFLI  168 (493)
Q Consensus        96 ~~~~~~~~~~a~~lf~~m-~~g~~p~~~t~~~l~~~~~~~~~~~~~~~~~~~~---~~a---~~~~~~~~~~~~~~~~l~  168 (493)
                      ..+..|+++.|..+|... ..|   +...+..|.          ..|...+..   .+|   ..++. ..    .+....
T Consensus        12 ~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg----------~~y~~~g~~~d~~~A~~~~~~A~-~~----~~~A~~   73 (452)
T 3e4b_A           12 EALKRGDTVTAQQNYQQLAELG---YSEAQVGLA----------DIQVGTRDPAQIKQAEATYRAAA-DT----SPRAQA   73 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC-------------------------------------------CHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHH----------HHHHccCCCCCHHHHHHHHHHHH-hC----CHHHHH
Confidence            456689999999999887 433   344444555          555444554   455   11111 11    122222


Q ss_pred             HHHHHHhhccC--CCCHHHHHHHHhhhcccC---cHHHHHHHHHhCCChHH---HHHHHHHHHhCCCCCCCHHHHHHHHH
Q 011102          169 SLARDIKGLDS--HKDVAEVLDKCGRFLRKG---SLSFTVRELGHMNLPER---ALQTFCWAQKQPHLFPDDRLLASTVE  240 (493)
Q Consensus       169 ~l~~~l~~~~~--~~~~~~a~~~~~~m~~~~---~~~~li~~~~~~g~~~~---A~~l~~~m~~~~g~~pd~~t~~~li~  240 (493)
                      .+...+.....  .++.++|+..+.+....+   .+..+-..|...+..++   +.+.+...... |.   ...+..+-.
T Consensus        74 ~Lg~~~~~~~~~~~~~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~-g~---~~a~~~Lg~  149 (452)
T 3e4b_A           74 RLGRLLAAKPGATEAEHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAA-GY---PEAGLAQVL  149 (452)
T ss_dssp             HHHHHHHTC--CCHHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHH-TC---TTHHHHHHH
T ss_pred             HHHHHHHhCCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHC-CC---HHHHHHHHH
Confidence            33332222211  247889999988776655   66666667766665444   44444444433 32   234455556


Q ss_pred             HHHHcCCCchhhh----HHHhhccCcHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcC--
Q 011102          241 VLARHHELKVPFK----LENFVSLASKGVLEATAKGFVKGG---NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKN--  311 (493)
Q Consensus       241 ~~~~~g~~~~~~~----l~~~~~~~~~~~~~~li~~~~~~g---~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~--  311 (493)
                      .+...+.++.+..    +..-....+...+..|-..|.+.|   +.++|++.|++..+.|. ++...+..+-..|...  
T Consensus       150 ~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~-~~a~~~~~Lg~~y~~g~~  228 (452)
T 3e4b_A          150 LYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGT-VTAQRVDSVARVLGDATL  228 (452)
T ss_dssp             HHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC-SCHHHHHHHHHHHTCGGG
T ss_pred             HHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHhCCCC
Confidence            6666665332221    111112234447888888999999   99999999999999883 3444334444444221  


Q ss_pred             -CCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH-H--HHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC---
Q 011102          312 -PDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV-G--IRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK---  384 (493)
Q Consensus       312 -~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~-~--~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g---  384 (493)
                       .++.++|...|+... . |   +...+..+-.. |  ...+++++|.+.|++..+.|   +...+..|-..|. .|   
T Consensus       229 ~~~d~~~A~~~~~~aa-~-g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~  299 (452)
T 3e4b_A          229 GTPDEKTAQALLEKIA-P-G---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWV  299 (452)
T ss_dssp             SSCCHHHHHHHHHHHG-G-G---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSS
T ss_pred             CCCCHHHHHHHHHHHc-C-C---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCC
Confidence             168999999999987 3 3   34455555554 3  45899999999999988776   6777777777777 45   


Q ss_pred             --CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cC
Q 011102          385 --KCREALTVVWNMEASNCLFDLPAYRVVIKLFVA----LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA----SG  454 (493)
Q Consensus       385 --~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~----~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~----~g  454 (493)
                        +.++|.+.|++.. .   -+...+..|=..|..    ..+.++|..+|+.-.+.|.. +  .+..|-..|..    ..
T Consensus       300 ~~d~~~A~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~-~--A~~~Lg~~y~~G~g~~~  372 (452)
T 3e4b_A          300 PADAKAAEAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQN-S--ADFAIAQLFSQGKGTKP  372 (452)
T ss_dssp             CCCHHHHHHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCT-T--HHHHHHHHHHSCTTBCC
T ss_pred             CCCHHHHHHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChH-H--HHHHHHHHHHhCCCCCC
Confidence              9999999999876 3   355666666666655    34999999999999887752 3  34444445543    45


Q ss_pred             CHHHHHHHHHHHHHCCCc
Q 011102          455 RLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       455 ~~~~A~~l~~~m~~~g~~  472 (493)
                      +.++|...|+...+.|..
T Consensus       373 d~~~A~~~~~~A~~~g~~  390 (452)
T 3e4b_A          373 DPLNAYVFSQLAKAQDTP  390 (452)
T ss_dssp             CHHHHHHHHHHHHTTCCH
T ss_pred             CHHHHHHHHHHHHHCCCH
Confidence            899999999998887754

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.44  E-value=8.3e-06  Score=77.67  Aligned_cols=175  Identities=9%  Similarity=-0.089  Sum_probs=132.2

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc---CCCCCC-HHHHHHHHHHHHHcCCHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQR---DDLNLS-QQDCTAIMKVGIRLQKFGV  353 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~---~g~~p~-~~~~~~li~~~~~~g~~~~  353 (493)
                      ++++|...|++.               ...|... |++++|.+.|.+....   .|-.++ ..+|+.+-..|.+.|++++
T Consensus        32 ~~~~A~~~~~~a---------------~~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~   95 (292)
T 1qqe_A           32 KFEEAADLCVQA---------------ATIYRLR-KELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVN   95 (292)
T ss_dssp             HHHHHHHHHHHH---------------HHHHHHT-TCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             cHHHHHHHHHHH---------------HHHHHHc-CCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHH
Confidence            488898888876               2346667 9999999999876442   121111 4688999999999999999


Q ss_pred             HHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHHcCCHH
Q 011102          354 VESLFHWFTHS----GRDP-TVVMYTTLIHSRLSE-KKCREALTVVWNMEAS----NCLFD-LPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       354 A~~l~~~m~~~----g~~p-~~~ty~~li~~~~~~-g~~~~A~~l~~~M~~~----gi~pd-~~ty~~li~~~~~~g~~~  422 (493)
                      |...|++..+.    |-.. -..+|+.+-..|... |++++|++.|++..+.    +-.+. ..+|+.+-..|.+.|+++
T Consensus        96 A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~  175 (292)
T 1qqe_A           96 AVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYI  175 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHH
Confidence            99999876532    2111 145788999999996 9999999999987653    11111 356888889999999999


Q ss_pred             HHHHHHHHHHHCCCCCCH------HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          423 RAIRYFSKLKEAGFCPTY------DIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~p~~------~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +|...|++..+.......      ..|..+..++...|++++|...|++..+
T Consensus       176 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~  227 (292)
T 1qqe_A          176 EASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQS  227 (292)
T ss_dssp             HHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGC
T ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            999999999865433221      2577788889999999999999999764

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=98.42  E-value=2.7e-05  Score=76.84  Aligned_cols=224  Identities=8%  Similarity=-0.039  Sum_probs=157.1

Q ss_pred             ccCCCCHHHHHHHHhhhccc-----------CcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc
Q 011102          177 LDSHKDVAEVLDKCGRFLRK-----------GSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARH  245 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~-----------~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~  245 (493)
                      +...|+.++|+..+.+....           ..+..+-..|...|+++.|+..+.......                -+.
T Consensus       111 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~----------------~~~  174 (378)
T 3q15_A          111 EFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIY----------------QNH  174 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH----------------HTS
T ss_pred             HHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH----------------HhC
Confidence            34579999999999865432           166677778899999999999998776420                000


Q ss_pred             CCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCC-CHHHHHHHHHHHhcCCCCHHHHHH
Q 011102          246 HELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDG----GRML-DPSIYAKLILELGKNPDKYMLVMT  320 (493)
Q Consensus       246 g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-d~~t~~~li~~~~~~~~~~~~a~~  320 (493)
                      +....          ....+++.+-..|...|++++|.+.|++..+.    |-.+ ...++..+-..|... |++++|.+
T Consensus       175 ~~~~~----------~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~-~~~~~A~~  243 (378)
T 3q15_A          175 PLYSI----------RTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRS-GDDQMAVE  243 (378)
T ss_dssp             TTCHH----------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH-TCHHHHHH
T ss_pred             CCchh----------hHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHC-CCHHHHHH
Confidence            10000          11235667778888889999998888877652    2111 123566677778888 99999999


Q ss_pred             HHHHHhh-----cCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc----CCCCCHHHHHHHHHHHHcCCC---HHH
Q 011102          321 LLDELGQ-----RDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS----GRDPTVVMYTTLIHSRLSEKK---CRE  388 (493)
Q Consensus       321 l~~~m~~-----~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~~~ty~~li~~~~~~g~---~~~  388 (493)
                      .+++...     . . .....++..+-..|.+.|++++|...|++..+.    +-......++.+-..|...++   ..+
T Consensus       244 ~~~~al~~~~~~~-~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~  321 (378)
T 3q15_A          244 HFQKAAKVSREKV-P-DLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHD  321 (378)
T ss_dssp             HHHHHHHHHHHHC-G-GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHH
T ss_pred             HHHHHHHHHHhhC-C-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHH
Confidence            9988765     3 1 222667888889999999999999999987653    222234556777777777888   777


Q ss_pred             HHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          389 ALTVVWNMEASNCLFDL-PAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       389 A~~l~~~M~~~gi~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      |+..+++   .+..|+. ..+..+-..|.+.|+.++|...|++..
T Consensus       322 al~~~~~---~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  363 (378)
T 3q15_A          322 LLSYFEK---KNLHAYIEACARSAAAVFESSCHFEQAAAFYRKVL  363 (378)
T ss_dssp             HHHHHHH---TTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHh---CCChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            8777776   3333333 356677788999999999999998875

>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=98.38  E-value=4.5e-05  Score=72.43  Aligned_cols=212  Identities=10%  Similarity=-0.021  Sum_probs=98.8

Q ss_pred             HHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHH---HHHHHHHHHHhcCCHHHHHHHHHHHHhCC-
Q 011102          218 TFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKG---VLEATAKGFVKGGNLKLAWKLLMVAKDGG-  293 (493)
Q Consensus       218 l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~---~~~~li~~~~~~g~~~~A~~l~~~m~~~g-  293 (493)
                      .+..+.. +...|+..+...+...+.-.    . ..+.......+..   .+...+..+.+.|++++|.+++++..+.. 
T Consensus        33 ~~s~~e~-g~~~~~~~~l~~i~~~l~~~----~-~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l~~~~  106 (293)
T 3u3w_A           33 EVSRIES-GAVYPSMDILQGIAAKLQIP----I-IHFYEVLIYSDIERKKQFKDQVIMLCKQKRYKEIYNKVWNELKKEE  106 (293)
T ss_dssp             HHHHHHT-TSCCCCHHHHHHHHHHHTCC----T-HHHHHTTTSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHC-CCCCCCHHHHHHHHHHhCcC----H-HHHhCCCCCCcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHhcccc
Confidence            3444443 24567777666666655421    1 1221111111122   23333556666777777777777666532 


Q ss_pred             CCCCHH----HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Q 011102          294 RMLDPS----IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS----QQDCTAIMKVGIRLQKFGVVESLFHWFTHSG  365 (493)
Q Consensus       294 ~~pd~~----t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  365 (493)
                      ..|+..    .+..+...+... +++++|...|++......-..+    ..+|+.+-..|...|++++|...|++..+. 
T Consensus       107 ~~~~~~~~~~~~~~l~~~~~~~-~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~-  184 (293)
T 3u3w_A          107 YHPEFQQFLQWQYYVAAYVLKK-VDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQ-  184 (293)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTS-SCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             CChHHHHHHHHHHHHHHHHHcc-cCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-
Confidence            112211    112233333333 5556666655555442111111    123444444444555555555544444310 


Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHH----HCCCCCC
Q 011102          366 RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS-NCLFDL-PAYRVVIKLFVALNDISRAIRYFSKLK----EAGFCPT  439 (493)
Q Consensus       366 ~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-gi~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~----~~g~~p~  439 (493)
                                                 +   .+. +..+.. .+|..+-..|.+.|++++|..++++..    +.+..+.
T Consensus       185 ---------------------------~---~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~  234 (293)
T 3u3w_A          185 ---------------------------L---EALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             ---------------------------H---HHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTT
T ss_pred             ---------------------------H---HhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHH
Confidence                                       0   011 111111 245556666666666666666666544    2222222


Q ss_pred             -HHHHHHHHHHHHHcC-CHHHHHHHHHHHH
Q 011102          440 -YDIYRDMIRIFMASG-RLAKCRDVCKEAE  467 (493)
Q Consensus       440 -~~ty~~li~~~~~~g-~~~~A~~l~~~m~  467 (493)
                       ..+|..+-.+|.+.| ++++|.+.+++..
T Consensus       235 ~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence             456666666677777 3577776666654

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.34  E-value=3.8e-05  Score=71.39  Aligned_cols=61  Identities=13%  Similarity=0.107  Sum_probs=47.0

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHCCCC-C-CHHHHHHHHHHHHHc----------CCHHHHHHHHHHHHHC
Q 011102          409 RVVIKLFVALNDISRAIRYFSKLKEAGFC-P-TYDIYRDMIRIFMAS----------GRLAKCRDVCKEAEMA  469 (493)
Q Consensus       409 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~-p-~~~ty~~li~~~~~~----------g~~~~A~~l~~~m~~~  469 (493)
                      ..+-..|.+.|++++|...|+...+..-. + ....+..+..+|...          |++++|.+.|++..+.
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            45567788999999999999998854311 1 245677778888766          8999999999999864

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.33  E-value=3.6e-05  Score=71.54  Aligned_cols=167  Identities=12%  Similarity=0.025  Sum_probs=124.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-HHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD----PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-QQD  337 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd----~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-~~~  337 (493)
                      ...+-.+...+.+.|++++|...|+++.+..  |+    ...+..+-..|.+. |++++|...|+...+...-.+. ...
T Consensus        15 ~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~-~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           15 PQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQN-KEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHh-CcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            3455566777888999999999999998754  43    56777777888888 9999999999998775211222 445


Q ss_pred             HHHHHHHHHH--------cCCHHHHHHHHHHHHHcCCCCC-HHHH-----------------HHHHHHHHcCCCHHHHHH
Q 011102          338 CTAIMKVGIR--------LQKFGVVESLFHWFTHSGRDPT-VVMY-----------------TTLIHSRLSEKKCREALT  391 (493)
Q Consensus       338 ~~~li~~~~~--------~g~~~~A~~l~~~m~~~g~~p~-~~ty-----------------~~li~~~~~~g~~~~A~~  391 (493)
                      +..+-.+|.+        .|++++|...|++..+..  |+ ...+                 ..+-..|.+.|++++|..
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  169 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY--PNHELVDDATQKIRELRAKLARKQYEAARLYERRELYEAAAV  169 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC--TTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            6677778888        899999999999987652  32 2223                 456778999999999999


Q ss_pred             HHHHHHHCCCC-C-CHHHHHHHHHHHHHc----------CCHHHHHHHHHHHHHC
Q 011102          392 VVWNMEASNCL-F-DLPAYRVVIKLFVAL----------NDISRAIRYFSKLKEA  434 (493)
Q Consensus       392 l~~~M~~~gi~-p-d~~ty~~li~~~~~~----------g~~~~A~~~~~~m~~~  434 (493)
                      .|++..+..-. + ....+..+..+|.+.          |++++|...|+...+.
T Consensus       170 ~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~  224 (261)
T 3qky_A          170 TYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQI  224 (261)
T ss_dssp             HHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHH
Confidence            99998765321 1 234667777777765          8999999999998854

>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=98.33  E-value=0.00014  Score=68.85  Aligned_cols=156  Identities=9%  Similarity=-0.104  Sum_probs=94.5

Q ss_pred             HHHHHHHHcCCCchhhhHHHhhcc-------Cc----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CC----HHH
Q 011102          237 STVEVLARHHELKVPFKLENFVSL-------AS----KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRM-LD----PSI  300 (493)
Q Consensus       237 ~li~~~~~~g~~~~~~~l~~~~~~-------~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-pd----~~t  300 (493)
                      ..+..+.+.|+++.+..+  +...       ++    ...+..+...+...|++++|+..|++..+.... .+    ..+
T Consensus        80 ~~i~~~~~~~~y~~a~~~--~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 3u3w_A           80 DQVIMLCKQKRYKEIYNK--VWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHH--HHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHH--HHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHH
Confidence            346677888885544433  3221       11    113455777788889999999999999984322 33    236


Q ss_pred             HHHHHHHHhcCCCCHHHHHHHHHHHhhc----CCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH----cCCCCC-H
Q 011102          301 YAKLILELGKNPDKYMLVMTLLDELGQR----DDLNLS-QQDCTAIMKVGIRLQKFGVVESLFHWFTH----SGRDPT-V  370 (493)
Q Consensus       301 ~~~li~~~~~~~~~~~~a~~l~~~m~~~----~g~~p~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~----~g~~p~-~  370 (493)
                      |+.+-..|... |++++|...|++..+.    ++..+. ..+|..+...|.+.|++++|.+.+++..+    .+..+. .
T Consensus       158 ~~~lg~~y~~~-g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~  236 (293)
T 3u3w_A          158 ENAIANIYAEN-GYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHH
T ss_pred             HHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHH
Confidence            88888899999 9999999999988642    011111 22556666667777777777776665442    111121 3


Q ss_pred             HHHHHHHHHHHcCCC-HHHHHHHHHH
Q 011102          371 VMYTTLIHSRLSEKK-CREALTVVWN  395 (493)
Q Consensus       371 ~ty~~li~~~~~~g~-~~~A~~l~~~  395 (493)
                      .+|..+-..|.+.|+ .++|.+.+++
T Consensus       237 ~~~~~lg~~~~~~g~~~~~A~~~~~~  262 (293)
T 3u3w_A          237 QLYYQRGECLRKLEYEEAEIEDAYKK  262 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCcHHHHHHHHHH
Confidence            444444455555552 3555544443

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.33  E-value=6.6e-05  Score=67.69  Aligned_cols=178  Identities=12%  Similarity=0.052  Sum_probs=116.6

Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcC----CHHHHHH
Q 011102          281 LAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQ----KFGVVES  356 (493)
Q Consensus       281 ~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g----~~~~A~~  356 (493)
                      +|.+.|++..+.|   ++..+..+-..|... +++++|...|+...+. |   +...+..|-..|.. +    +.++|.+
T Consensus         4 eA~~~~~~aa~~g---~~~a~~~lg~~~~~~-~~~~~A~~~~~~a~~~-g---~~~a~~~lg~~y~~-~g~~~~~~~A~~   74 (212)
T 3rjv_A            4 EPGSQYQQQAEAG---DRRAQYYLADTWVSS-GDYQKAEYWAQKAAAQ-G---DGDALALLAQLKIR-NPQQADYPQARQ   74 (212)
T ss_dssp             CTTHHHHHHHHTT---CHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHT-T---CHHHHHHHHHHTTS-STTSCCHHHHHH
T ss_pred             hHHHHHHHHHHCC---CHHHHHHHHHHHhcC-CCHHHHHHHHHHHHHc-C---CHHHHHHHHHHHHc-CCCCCCHHHHHH
Confidence            4566666666654   566666666666666 7777777777776654 2   45555556555655 5    6777777


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHH----cCCHHHHHHH
Q 011102          357 LFHWFTHSGRDPTVVMYTTLIHSRLS----EKKCREALTVVWNMEASNCL-FDLPAYRVVIKLFVA----LNDISRAIRY  427 (493)
Q Consensus       357 l~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~gi~-pd~~ty~~li~~~~~----~g~~~~A~~~  427 (493)
                      .|++..+.|   +..++..|-..|..    .++.++|.+.|++..+.|.. -+...+..|=..|..    .++.++|..+
T Consensus        75 ~~~~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~  151 (212)
T 3rjv_A           75 LAEKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEY  151 (212)
T ss_dssp             HHHHHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            777776543   55666666666666    67788888888877665431 014566666666766    6778888888


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHc-C-----CHHHHHHHHHHHHHCCCc
Q 011102          428 FSKLKEAGFCPTYDIYRDMIRIFMAS-G-----RLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       428 ~~~m~~~g~~p~~~ty~~li~~~~~~-g-----~~~~A~~l~~~m~~~g~~  472 (493)
                      |+.-.+.+  .+...+..|-..|... |     +.++|.+.|+...+.|..
T Consensus       152 ~~~A~~~~--~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~~  200 (212)
T 3rjv_A          152 FKGSSSLS--RTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGFD  200 (212)
T ss_dssp             HHHHHHTS--CTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHcC--CCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCCH
Confidence            88877652  2334555566666543 2     788888888888777744

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.31  E-value=3.5e-05  Score=73.35  Aligned_cols=166  Identities=13%  Similarity=-0.000  Sum_probs=124.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCC-----CH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRM-LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNL-----SQ  335 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p-----~~  335 (493)
                      +..++..+..++...|++++|++++.+-...|-. -+...+..++..+.+. |+.+.|.+.+++|.+.   .|     +.
T Consensus        99 ~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~-~r~d~A~k~l~~~~~~---~~d~~~~~d  174 (310)
T 3mv2_B           99 SPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLN-NNVSTASTIFDNYTNA---IEDTVSGDN  174 (310)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH---SCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHC-CCHHHHHHHHHHHHhc---Cccccccch
Confidence            4445567888899999999999999988766531 2556777888999999 9999999999999765   45     35


Q ss_pred             HHHHHHHHHHH--HcC--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----CC---CC
Q 011102          336 QDCTAIMKVGI--RLQ--KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS-----NC---LF  403 (493)
Q Consensus       336 ~~~~~li~~~~--~~g--~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-----gi---~p  403 (493)
                      .+...+..++.  ..|  +..+|..+|+++.+.  .|+..+-..++.++.+.|++++|.+.++.+.+.     +.   .|
T Consensus       175 ~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p  252 (310)
T 3mv2_B          175 EMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDYYSVEQKENAVL  252 (310)
T ss_dssp             HHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHS
T ss_pred             HHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccccccCCC
Confidence            56666666633  334  899999999999755  466445556666899999999999999876542     11   23


Q ss_pred             -CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          404 -DLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       404 -d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                       |..+...+|......|+  +|.++++++++..
T Consensus       253 ~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~  283 (310)
T 3mv2_B          253 YKPTFLANQITLALMQGL--DTEDLTNQLVKLD  283 (310)
T ss_dssp             SHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhC
Confidence             45666567766666787  8999999998654

>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=98.30  E-value=2.3e-05  Score=75.12  Aligned_cols=166  Identities=8%  Similarity=-0.018  Sum_probs=81.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-C----HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc---CCCCC-CH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-D----PSIYAKLILELGKNPDKYMLVMTLLDELGQR---DDLNL-SQ  335 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d----~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~---~g~~p-~~  335 (493)
                      .|+.....|...|++++|.+.|.+..+..... +    ..+|+.+-..|.+. |++++|...|++....   .|-.. -.
T Consensus        38 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~-g~~~~A~~~~~~Al~l~~~~g~~~~~a  116 (307)
T 2ifu_A           38 EYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDL-QRMPEAVQYIEKASVMYVENGTPDTAA  116 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT-TCGGGGHHHHHHHHHHHHTTTCHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            35555555666666666666666555422110 1    22455555555555 6666666666654322   01000 12


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCCH-
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHS----GRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFDL-  405 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd~-  405 (493)
                      .+++.+-..|.+ |++++|++.|++..+.    |-.. ...+|+.+-..|.+.|++++|++.|++..+.    +..++. 
T Consensus       117 ~~~~~lg~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  195 (307)
T 2ifu_A          117 MALDRAGKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCY  195 (307)
T ss_dssp             HHHHHHHHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHH
Confidence            344455555555 6666666666554321    1100 1244555566666666666666666655431    111111 


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      .++..+...+...|++++|...|++..
T Consensus       196 ~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          196 KKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            134444445555566666666666555

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.29  E-value=2.6e-05  Score=81.60  Aligned_cols=154  Identities=8%  Similarity=-0.143  Sum_probs=100.4

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          276 GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       276 ~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~  355 (493)
                      .|++++|.+.|++..+.. .-+...|..+-..+.+. |++++|.+.+++..+.  -.-+...|..+-..|.+.|++++|.
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~   77 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGM-GDTTAGEMAVQRGLAL--HPGHPEAVARLGRVRWTQQRHAEAA   77 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHH-TCHHHHHHHHHHHHTT--STTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHH
Confidence            467888888888776643 12356777777777787 8888888888887664  2235667778888888888888888


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc---CCHHHHHHHHHHHH
Q 011102          356 SLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL---NDISRAIRYFSKLK  432 (493)
Q Consensus       356 ~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~---g~~~~A~~~~~~m~  432 (493)
                      +.|++..+.. +-+...|..+-..|.+.|++++|.+.+++..+..- -+...+..+...+...   |+.++|.+.+++..
T Consensus        78 ~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al  155 (568)
T 2vsy_A           78 VLLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLP-EEPYITAQLLNWRRRLCDWRALDVLSAQVRAAV  155 (568)
T ss_dssp             HHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Confidence            8888876542 33567788888888888888888888888766421 2456777778888888   88888888888877


Q ss_pred             HCC
Q 011102          433 EAG  435 (493)
Q Consensus       433 ~~g  435 (493)
                      +.+
T Consensus       156 ~~~  158 (568)
T 2vsy_A          156 AQG  158 (568)
T ss_dssp             HHT
T ss_pred             hcC
Confidence            544

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.27  E-value=0.00039  Score=70.49  Aligned_cols=267  Identities=12%  Similarity=-0.013  Sum_probs=170.1

Q ss_pred             CHHHHHHHHhhhcccC--cHHHHHHHHHhCC-----ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCch-hhh
Q 011102          182 DVAEVLDKCGRFLRKG--SLSFTVRELGHMN-----LPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKV-PFK  253 (493)
Q Consensus       182 ~~~~a~~~~~~m~~~~--~~~~li~~~~~~g-----~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~-~~~  253 (493)
                      +..+|+..|.+..+..  .+..+-..+...|     +.++|++.|+...+. |.. +  .+..+-..|...+..+. .++
T Consensus        53 d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~~~~~~~A~~~~~~Aa~~-g~~-~--A~~~Lg~~y~~~~~~~~~~~a  128 (452)
T 3e4b_A           53 QIKQAEATYRAAADTSPRAQARLGRLLAAKPGATEAEHHEAESLLKKAFAN-GEG-N--TLIPLAMLYLQYPHSFPNVNA  128 (452)
T ss_dssp             ------------------CHHHHHHHHHTC--CCHHHHHHHHHHHHHHHHT-TCS-S--CHHHHHHHHHHCGGGCTTCCH
T ss_pred             CHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCcCHHHHHHHHHHHHHC-CCH-H--HHHHHHHHHHhCCCCCCCHHH
Confidence            4488888888655442  4444444344554     778999999998876 533 2  45556666655544222 222


Q ss_pred             HHHh---hccCcHHHHHHHHHHHHhcCCHH----HHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCC---CHHHHHHHHH
Q 011102          254 LENF---VSLASKGVLEATAKGFVKGGNLK----LAWKLLMVAKDGGRMLDPSIYAKLILELGKNPD---KYMLVMTLLD  323 (493)
Q Consensus       254 l~~~---~~~~~~~~~~~li~~~~~~g~~~----~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~---~~~~a~~l~~  323 (493)
                      +..+   ....+...+..|-..|...+.++    .+..+++....    .++..+..|-..|.+. |   +.++|++.|+
T Consensus       129 ~~~~~~a~~~g~~~a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~----~~~~a~~~Lg~~~~~~-g~~~~~~~A~~~~~  203 (452)
T 3e4b_A          129 QQQISQWQAAGYPEAGLAQVLLYRTQGTYDQHLDDVERICKAALN----TTDICYVELATVYQKK-QQPEQQAELLKQME  203 (452)
T ss_dssp             HHHHHHHHHHTCTTHHHHHHHHHHHHTCGGGGHHHHHHHHHHHTT----TCTTHHHHHHHHHHHT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHcCCCcccCHHHHHHHHHHHHc----CCHHHHHHHHHHHHHc-CCcccHHHHHHHHH
Confidence            2222   22334556777778888877544    44444444333    2333777777788887 8   9999999999


Q ss_pred             HHhhcCCCCCCHHHHHHHHHHHHHc----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-H--HcCCCHHHHHHHHHHH
Q 011102          324 ELGQRDDLNLSQQDCTAIMKVGIRL----QKFGVVESLFHWFTHSGRDPTVVMYTTLIHS-R--LSEKKCREALTVVWNM  396 (493)
Q Consensus       324 ~m~~~~g~~p~~~~~~~li~~~~~~----g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~-~--~~~g~~~~A~~l~~~M  396 (493)
                      ...+. | .++...+..+-..|...    +++++|.+.|++.. .|   +...+..|-.. |  ...++.++|.+.|++.
T Consensus       204 ~aa~~-g-~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~A  277 (452)
T 3e4b_A          204 AGVSR-G-TVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNG  277 (452)
T ss_dssp             HHHHT-T-CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHH
T ss_pred             HHHHC-C-CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence            98876 3 35555556666666554    78999999999987 33   44555555555 3  4589999999999999


Q ss_pred             HHCCCCCCHHHHHHHHHHHHHcC-----CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHH
Q 011102          397 EASNCLFDLPAYRVVIKLFVALN-----DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA----SGRLAKCRDVCKEAE  467 (493)
Q Consensus       397 ~~~gi~pd~~ty~~li~~~~~~g-----~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~m~  467 (493)
                      .+.|   +...+..|=..|. .|     +.++|.++|+.-. .   -+...+..|-..|..    ..++++|.+.|+...
T Consensus       278 a~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa  349 (452)
T 3e4b_A          278 RAAD---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAA  349 (452)
T ss_dssp             HHTT---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHH
T ss_pred             HHCC---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHH
Confidence            8877   5666776766666 55     9999999999877 3   356666667666665    349999999999988


Q ss_pred             HCCC
Q 011102          468 MAGF  471 (493)
Q Consensus       468 ~~g~  471 (493)
                      +.|.
T Consensus       350 ~~g~  353 (452)
T 3e4b_A          350 RNGQ  353 (452)
T ss_dssp             TTTC
T ss_pred             hhCh
Confidence            7764

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.25  E-value=6e-05  Score=67.67  Aligned_cols=136  Identities=10%  Similarity=0.025  Sum_probs=84.3

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHc
Q 011102          340 AIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVAL  418 (493)
Q Consensus       340 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~  418 (493)
                      .+-..|.+.|++++|...|++..+.. +-+...|..+-..|...|++++|.+.|++..+.  .| +..+|..+-..|...
T Consensus        59 ~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~  135 (208)
T 3urz_A           59 ELALAYKKNRNYDKAYLFYKELLQKA-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLT  135 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHH
Confidence            36667777788888888887776542 235677777778888888888888888877664  23 345666666665544


Q ss_pred             CC--HHHHHHHHHHHHHCCCCCCHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          419 ND--ISRAIRYFSKLKEAGFCPTYDI--YRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       419 g~--~~~A~~~~~~m~~~g~~p~~~t--y~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      |+  .+.+...++...    .|+...  +..+-.++...|++++|...|++..+  +.|+......|.++
T Consensus       136 ~~~~~~~~~~~~~~~~----~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~l~~i  199 (208)
T 3urz_A          136 AEQEKKKLETDYKKLS----SPTKMQYARYRDGLSKLFTTRYEKARNSLQKVIL--RFPSTEAQKTLDKI  199 (208)
T ss_dssp             HHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTT--TSCCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHh----CCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHH--hCCCHHHHHHHHHH
Confidence            43  334444444432    233332  23333445567788888888887764  56777666666554

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.23  E-value=0.00016  Score=65.61  Aligned_cols=183  Identities=13%  Similarity=0.014  Sum_probs=109.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH-HHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRM-LD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ-QDCTAI  341 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~-~~~~~l  341 (493)
                      .+-.+...+.+.|++++|...|+++.+..-. |. ...+..+..++.+. |++++|...|++..+...-.+.. ..+-.+
T Consensus         6 ~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~-~~~~~A~~~~~~~l~~~P~~~~~~~a~~~~   84 (225)
T 2yhc_A            6 EIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKN-ADLPLAQAAIDRFIRLNPTHPNIDYVMYMR   84 (225)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHCTTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHHCcCCCcHHHHHHHH
Confidence            3445566778888888888888888774311 11 34666677788888 88888888888877642111221 133333


Q ss_pred             HHHHHH------------------cCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 011102          342 MKVGIR------------------LQKFGVVESLFHWFTHSGRDPTV-VMYTTLIHSRLSEKKCREALTVVWNMEASNCL  402 (493)
Q Consensus       342 i~~~~~------------------~g~~~~A~~l~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~  402 (493)
                      -.+|.+                  .|++++|...|+++.+.  .|+. ..+.+.              ..+..+...   
T Consensus        85 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~--------------~~l~~~~~~---  145 (225)
T 2yhc_A           85 GLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDAT--------------KRLVFLKDR---  145 (225)
T ss_dssp             HHHHHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHH--------------HHHHHHHHH---
T ss_pred             HHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHH--------------HHHHHHHHH---
Confidence            333333                  24455555555555432  1221 111110              000000000   


Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          403 FDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPT----YDIYRDMIRIFMASGRLAKCRDVCKEAEMAG  470 (493)
Q Consensus       403 pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~----~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g  470 (493)
                       -....-.+-..|.+.|++++|...|+.+.+.-  |+    ...+..+..+|.+.|++++|.+.++.+...+
T Consensus       146 -~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~--p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          146 -LAKYEYSVAEYYTERGAWVAVVNRVEGMLRDY--PDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             -HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS--TTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             -HHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHC--cCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence             00011234556889999999999999988543  33    2568889999999999999999999887753

>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=98.23  E-value=2.5e-05  Score=74.93  Aligned_cols=187  Identities=12%  Similarity=-0.036  Sum_probs=101.6

Q ss_pred             CCChHHHHHHHHHHHhC-----CCCCCCHH----HHHHHHHHHHHcCCCchhhhH-----HHhhccCc----HHHHHHHH
Q 011102          209 MNLPERALQTFCWAQKQ-----PHLFPDDR----LLASTVEVLARHHELKVPFKL-----ENFVSLAS----KGVLEATA  270 (493)
Q Consensus       209 ~g~~~~A~~l~~~m~~~-----~g~~pd~~----t~~~li~~~~~~g~~~~~~~l-----~~~~~~~~----~~~~~~li  270 (493)
                      .|++++|.+++++..+.     .+..+|..    .|......|...|+++.+...     ..+....+    ..+|+.+.
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            45666777777665531     01123422    355555566666664332211     11111211    23567777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCC-C----HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC---CCCC-CHHHHHHH
Q 011102          271 KGFVKGGNLKLAWKLLMVAKDGGRML-D----PSIYAKLILELGKNPDKYMLVMTLLDELGQRD---DLNL-SQQDCTAI  341 (493)
Q Consensus       271 ~~~~~~g~~~~A~~l~~~m~~~g~~p-d----~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~---g~~p-~~~~~~~l  341 (493)
                      ..|.+.|++++|...|++..+.-... +    ..+++.+-..|. . |++++|+..|++.....   +-.. ...+++.+
T Consensus        84 ~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~-~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~l  161 (307)
T 2ifu_A           84 MMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLME-P-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKA  161 (307)
T ss_dssp             HHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHT-T-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-c-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHH
Confidence            77777777777777777666532111 1    123444444443 3 77777777777654420   1000 13456666


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHS----GRDPT-VVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~----g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      -..|.+.|++++|.+.|++..+.    +..++ ...|..+...+...|++++|...|++..
T Consensus       162 g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          162 SRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            77777777777777777766532    21111 1255566666666677777777777765

>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=98.22  E-value=6.6e-05  Score=67.07  Aligned_cols=126  Identities=8%  Similarity=-0.031  Sum_probs=76.1

Q ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 011102          302 AKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRL  381 (493)
Q Consensus       302 ~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~  381 (493)
                      ..+-..+... |++++|...|++..     .|+...|..+...|.+.|++++|.+.|++..+.. +.+...|..+-..|.
T Consensus        10 ~~~g~~~~~~-~~~~~A~~~~~~a~-----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~   82 (213)
T 1hh8_A           10 WNEGVLAADK-KDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   82 (213)
T ss_dssp             HHHHHHHHHT-TCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh-CCHHHHHHHHHHHc-----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHH
Confidence            3444455566 67777776666542     3456666666667777777777777776665432 334566666666677


Q ss_pred             cCCCHHHHHHHHHHHHHCCC--------------CCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          382 SEKKCREALTVVWNMEASNC--------------LFD-LPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       382 ~~g~~~~A~~l~~~M~~~gi--------------~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      ..|++++|.+.|++..+..-              .|+ ...+..+-..|.+.|++++|...|+...+.
T Consensus        83 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           83 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            77777777777766655321              111 145555666666666666666666666543

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.21  E-value=0.00012  Score=69.41  Aligned_cols=166  Identities=11%  Similarity=-0.023  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH-----HHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC--CCCCC--
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP-----SIYAKLILELGKNPDKYMLVMTLLDELGQRD--DLNLS--  334 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~-----~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~--g~~p~--  334 (493)
                      ..+...+..+...|++++|.+.+++..+..-..+.     ..+..+...+... |++++|...+++.....  ...+.  
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~al~~~~~~~~~~~~  154 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKK-VDYEYCILELKKLLNQQLTGIDVYQN  154 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTS-SCHHHHHHHHHHHHTTCCCSSCTTHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcC-CCHHHHHHHHHHHHHHHhcCCchHHH
Confidence            34556777888889999999888877764322111     1122333344555 78888888877765421  11111  


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHH---c-CCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCC
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTH---S-GRDP--TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFD  404 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~---~-g~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd  404 (493)
                      ..+|+.+-..|...|++++|...|++..+   . +..+  ...+|+.+...|.+.|++++|++.+++..+.    +....
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            34667777777777777777777776541   1 1111  1146666666677777777777666664432    11111


Q ss_pred             -HHHHHHHHHHHHHcCCHHHH-HHHHHH
Q 011102          405 -LPAYRVVIKLFVALNDISRA-IRYFSK  430 (493)
Q Consensus       405 -~~ty~~li~~~~~~g~~~~A-~~~~~~  430 (493)
                       ..+|..+-..|.+.|+.++| ...+++
T Consensus       235 ~~~~~~~lg~~y~~~g~~~~Ai~~~~~~  262 (293)
T 2qfc_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKK  262 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence             34555555666666666666 444444

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.17  E-value=0.00012  Score=58.46  Aligned_cols=95  Identities=9%  Similarity=0.055  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLF  415 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~  415 (493)
                      ..|..+...|.+.|++++|.++|+++.+.. +.+..+|..+...+.+.|++++|..+++++.+.. ..+..++..+...|
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~   87 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHH
Confidence            344444455555555555555555544331 2234444555555555555555555555544321 12334444444445


Q ss_pred             HHcCCHHHHHHHHHHHH
Q 011102          416 VALNDISRAIRYFSKLK  432 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~  432 (493)
                      .+.|++++|...|+++.
T Consensus        88 ~~~~~~~~A~~~~~~~~  104 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKAL  104 (125)
T ss_dssp             HHTTCHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHH
Confidence            55555555555555444

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.15  E-value=0.00017  Score=65.44  Aligned_cols=176  Identities=10%  Similarity=-0.028  Sum_probs=110.9

Q ss_pred             HHHHHHHHHHHHHcCCCchhhhHHHhhcc----Cc----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCH----H
Q 011102          232 DRLLASTVEVLARHHELKVPFKLENFVSL----AS----KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDP----S  299 (493)
Q Consensus       232 ~~t~~~li~~~~~~g~~~~~~~l~~~~~~----~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~----~  299 (493)
                      ...+-.+...+.+.|+++  +++..|...    |+    ...+..+...|.+.|++++|...|++..+..  |+.    .
T Consensus         4 ~~~~~~~a~~~~~~g~~~--~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~--P~~~~~~~   79 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWR--QAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN--PTHPNIDY   79 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHH--HHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCTTHHH
T ss_pred             HHHHHHHHHHHHHcCCHH--HHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC--cCCCcHHH
Confidence            344555566778888854  444444432    22    2467788899999999999999999998754  432    1


Q ss_pred             HHHHHHHHHhc------------------CCCCHHHHHHHHHHHhhcCCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          300 IYAKLILELGK------------------NPDKYMLVMTLLDELGQRDDLNLSQ-QDCTAIMKVGIRLQKFGVVESLFHW  360 (493)
Q Consensus       300 t~~~li~~~~~------------------~~~~~~~a~~l~~~m~~~~g~~p~~-~~~~~li~~~~~~g~~~~A~~l~~~  360 (493)
                      .+-.+-..+.+                  . |++++|...|+++.+.   .|+. ..+.+..    +.+      .+...
T Consensus        80 a~~~~g~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~A~~~~~~~l~~---~P~~~~a~~a~~----~l~------~~~~~  145 (225)
T 2yhc_A           80 VMYMRGLTNMALDDSALQGFFGVDRSDRDP-QQARAAFSDFSKLVRG---YPNSQYTTDATK----RLV------FLKDR  145 (225)
T ss_dssp             HHHHHHHHHHHHHC--------------CC-HHHHHHHHHHHHHHTT---CTTCTTHHHHHH----HHH------HHHHH
T ss_pred             HHHHHHHHHHhhhhhhhhhhhccchhhcCc-HHHHHHHHHHHHHHHH---CcCChhHHHHHH----HHH------HHHHH
Confidence            33333334432                  4 7899999999999875   2432 2222111    100      11111


Q ss_pred             HHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          361 FTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL----PAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       361 m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~----~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      +.        ...-.+-..|.+.|++++|...|+++.+.  .|+.    ..+..+..+|.+.|+.++|.+.++.+...+
T Consensus       146 ~~--------~~~~~~a~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~  214 (225)
T 2yhc_A          146 LA--------KYEYSVAEYYTERGAWVAVVNRVEGMLRD--YPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANS  214 (225)
T ss_dssp             HH--------HHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCC
T ss_pred             HH--------HHHHHHHHHHHHcCcHHHHHHHHHHHHHH--CcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC
Confidence            11        11234556677888888888888887764  2332    457777888888888888888888877554

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.15  E-value=0.00016  Score=68.59  Aligned_cols=167  Identities=8%  Similarity=0.010  Sum_probs=122.3

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCH----HHHHHHHHHHHHcCCHHHHHHHHHHHHHcC---CCCC--H
Q 011102          300 IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQ----QDCTAIMKVGIRLQKFGVVESLFHWFTHSG---RDPT--V  370 (493)
Q Consensus       300 t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~----~~~~~li~~~~~~g~~~~A~~l~~~m~~~g---~~p~--~  370 (493)
                      .+...+..+... |++++|.+.+.+..+.....++.    ..+..+...|...|++++|.+.|++..+..   ..+.  .
T Consensus        77 ~l~~~~~~~~~~-~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           77 QFKDQVIMLCKQ-KRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHT-TCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHh-hhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            344556677888 99999999998876652221111    223445566778899999999999876432   1222  4


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCCCC-----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCCC-
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEAS-NCLFD-----LPAYRVVIKLFVALNDISRAIRYFSKLKEA----GFCPT-  439 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~-gi~pd-----~~ty~~li~~~~~~g~~~~A~~~~~~m~~~----g~~p~-  439 (493)
                      .+|+.+-..|...|++++|...|++..+. ...|+     ..+|..+-..|.+.|++++|..++++..+.    +.... 
T Consensus       156 ~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            58999999999999999999999987631 11122     258888899999999999999999987632    21111 


Q ss_pred             HHHHHHHHHHHHHcCCHHHH-HHHHHHHH
Q 011102          440 YDIYRDMIRIFMASGRLAKC-RDVCKEAE  467 (493)
Q Consensus       440 ~~ty~~li~~~~~~g~~~~A-~~l~~~m~  467 (493)
                      ..+|..+-..|.+.|++++| ...+++..
T Consensus       236 ~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            67788999999999999999 77677654

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.14  E-value=6.6e-05  Score=78.51  Aligned_cols=134  Identities=8%  Similarity=-0.133  Sum_probs=112.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +...|..+-..|.+.|++++|.+.|++..+.. .-+...|..+-..|... |++++|.+.+++..+.  -.-+...+..+
T Consensus        22 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~--~p~~~~~~~~l   97 (568)
T 2vsy_A           22 DFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQ-QRHAEAAVLLQQASDA--APEHPGIALWL   97 (568)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHC-CCHHHHHHHHHHHHhc--CCCCHHHHHHH
Confidence            46688899999999999999999999988854 23467788888888898 9999999999998765  23457788899


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC---CCHHHHHHHHHHHHHCC
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE---KKCREALTVVWNMEASN  400 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~---g~~~~A~~l~~~M~~~g  400 (493)
                      -..|.+.|++++|.+.|++..+.. .-+...+..+...+...   |+.++|.+.+++..+.+
T Consensus        98 a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~~  158 (568)
T 2vsy_A           98 GHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQG  158 (568)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhcC
Confidence            999999999999999999987653 34577888999999999   99999999999987754

>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=98.14  E-value=0.00015  Score=61.55  Aligned_cols=128  Identities=8%  Similarity=-0.012  Sum_probs=89.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .+..+-..+...|++++|...|++..+.. +.+...|..+...+...|++++|.+.+++..+.. ..+...|..+-..+.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~   92 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHH
Confidence            45566667777888888888888766542 3356777788888888888888888888776542 234667777777888


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHHHH--HHHHHHHHcCCHHHHHHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKEAGFCPTYDIYR--DMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g~~p~~~ty~--~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      +.|++++|...|++..+..- -+...+.  .+...+.+.|++++|.+.+....
T Consensus        93 ~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            88888888888888775432 2344443  33344677788888888877654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.13  E-value=3.4e-05  Score=68.20  Aligned_cols=154  Identities=11%  Similarity=-0.012  Sum_probs=90.0

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH----cCCCC-CHHHHHHHHHHHHcCCCHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTH----SGRDP-TVVMYTTLIHSRLSEKKCR  387 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~----~g~~p-~~~ty~~li~~~~~~g~~~  387 (493)
                      |++++|.++++.+...  .......+..+-..|...|++++|...|++..+    .|..+ ...+++.+-..|...|+++
T Consensus         6 g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~   83 (203)
T 3gw4_A            6 HDYALAERQAQALLAH--PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWD   83 (203)
T ss_dssp             -CHHHHHHHHHHHHTS--TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             ccHHHHHHHHHHhcCC--hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            6666666644444322  122345566666666677777777777666543    11111 2355666667777777777


Q ss_pred             HHHHHHHHHHHC----CCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH----CCCC-CCHHHHHHHHHHHHHcCCH
Q 011102          388 EALTVVWNMEAS----NCLF--DLPAYRVVIKLFVALNDISRAIRYFSKLKE----AGFC-PTYDIYRDMIRIFMASGRL  456 (493)
Q Consensus       388 ~A~~l~~~M~~~----gi~p--d~~ty~~li~~~~~~g~~~~A~~~~~~m~~----~g~~-p~~~ty~~li~~~~~~g~~  456 (493)
                      +|.+.+++..+.    +-.|  ....+..+-..+...|++++|...+++..+    .+-. .-..++..+-..+...|++
T Consensus        84 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~  163 (203)
T 3gw4_A           84 AARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNL  163 (203)
T ss_dssp             HHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCH
Confidence            777777765432    2111  123456666677777888888777776552    1111 0123356677777788888


Q ss_pred             HHHHHHHHHHHH
Q 011102          457 AKCRDVCKEAEM  468 (493)
Q Consensus       457 ~~A~~l~~~m~~  468 (493)
                      ++|.+.+++..+
T Consensus       164 ~~A~~~~~~al~  175 (203)
T 3gw4_A          164 LEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            888887777653

>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=98.13  E-value=0.00014  Score=64.90  Aligned_cols=129  Identities=6%  Similarity=-0.140  Sum_probs=108.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      .+..+-..+.+.|++++|.+.|++.    +.|+...|..+-..+.+. |++++|...|++....  ...+...|..+-..
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~--~~~~~~~~~~lg~~   80 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTIL-KNMTEAEKAFTRSINR--DKHLAVAYFQRGML   80 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CccchHHHHHHHHH
Confidence            3456677788999999999999876    357889999999999999 9999999999998775  23467889999999


Q ss_pred             HHHcCCHHHHHHHHHHHHHcCC--------------CC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          345 GIRLQKFGVVESLFHWFTHSGR--------------DP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~--------------~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      |.+.|++++|.+.|++..+..-              .| +...|..+-..|.+.|++++|.+.|++..+..
T Consensus        81 ~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           81 YYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            9999999999999999886421              11 23778899999999999999999999987653

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.13  E-value=0.00022  Score=63.97  Aligned_cols=167  Identities=11%  Similarity=-0.030  Sum_probs=119.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHH----------------HHHHHhcCCCCHHHHHHHHHHHhhcCCC
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAK----------------LILELGKNPDKYMLVMTLLDELGQRDDL  331 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~----------------li~~~~~~~~~~~~a~~l~~~m~~~~g~  331 (493)
                      ....+.+.|++++|...|++..+..  |+ ...|..                +-..|.+. |++++|...|++..+.  -
T Consensus        10 ~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~~--~   84 (208)
T 3urz_A           10 KVSAAIEAGQNGQAVSYFRQTIALN--IDRTEMYYWTNVDKNSEISSKLATELALAYKKN-RNYDKAYLFYKELLQK--A   84 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--C
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHH--C
Confidence            3345678899999999999988743  43 334555                67778888 9999999999998775  2


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHCCCCCCHHH--
Q 011102          332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK--CREALTVVWNMEASNCLFDLPA--  407 (493)
Q Consensus       332 ~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~--~~~A~~l~~~M~~~gi~pd~~t--  407 (493)
                      .-+...+..+-..|...|++++|...|++..+.. +-+..+|..+-..|...|+  ...+...+....    .|+...  
T Consensus        85 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~a  159 (208)
T 3urz_A           85 PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS----SPTKMQYA  159 (208)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHC-------CCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh----CCCchhHH
Confidence            3467889999999999999999999999987652 3367888888888876654  344555555442    344433  


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMI  447 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li  447 (493)
                      +...-.++...|++++|...|++..+  +.|+......+.
T Consensus       160 ~~~~g~~~~~~~~~~~A~~~~~~al~--l~P~~~~~~~l~  197 (208)
T 3urz_A          160 RYRDGLSKLFTTRYEKARNSLQKVIL--RFPSTEAQKTLD  197 (208)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHTT--TSCCHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHH--hCCCHHHHHHHH
Confidence            33333445668999999999999875  458866554443

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.12  E-value=4.1e-05  Score=66.67  Aligned_cols=152  Identities=8%  Similarity=0.034  Sum_probs=68.7

Q ss_pred             HhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHcCCCH
Q 011102          308 LGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHS-RLSEKKC  386 (493)
Q Consensus       308 ~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~-~~~~g~~  386 (493)
                      +.+. |++++|...|++..+.  -.-+...+..+-..|.+.|++++|...|+...+.  .|+...+..+... +...+..
T Consensus        16 ~~~~-g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~~~~~~~~~~~~   90 (176)
T 2r5s_A           16 LLQQ-GEHAQALNVIQTLSDE--LQSRGDVKLAKADCLLETKQFELAQELLATIPLE--YQDNSYKSLIAKLELHQQAAE   90 (176)
T ss_dssp             HHHT-TCHHHHHHHHHTSCHH--HHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG--GCCHHHHHHHHHHHHHHHHTS
T ss_pred             HHHc-CCHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc--cCChHHHHHHHHHHHHhhccc
Confidence            3344 4555555555443322  1112334444444555555555555555444322  1222211111100 1111112


Q ss_pred             HHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHH
Q 011102          387 REALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCP-TYDIYRDMIRIFMASGRLAKCRDVCK  464 (493)
Q Consensus       387 ~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~  464 (493)
                      .+|.+.+++..+.  .| +...+..+-..+...|++++|...|++..+..-.+ +...+..+...|...|+.++|...|+
T Consensus        91 ~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~  168 (176)
T 2r5s_A           91 SPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYR  168 (176)
T ss_dssp             CHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHH
T ss_pred             chHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHH
Confidence            2345555554432  23 24555555556666666666666666655433211 23455556666666666666666655


Q ss_pred             HH
Q 011102          465 EA  466 (493)
Q Consensus       465 ~m  466 (493)
                      +.
T Consensus       169 ~a  170 (176)
T 2r5s_A          169 RQ  170 (176)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.11  E-value=8.8e-05  Score=70.34  Aligned_cols=154  Identities=12%  Similarity=0.037  Sum_probs=66.1

Q ss_pred             HHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH-HHHHcCC
Q 011102          306 LELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLI-HSRLSEK  384 (493)
Q Consensus       306 ~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li-~~~~~~g  384 (493)
                      ..+.+. |++++|.+.|++....  -.-+...+..+...|.+.|++++|..+|++....  .|+........ ..+.+.+
T Consensus       125 ~~~~~~-g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~~l~~~~  199 (287)
T 3qou_A          125 MQLMQE-SNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQIELLXQA  199 (287)
T ss_dssp             HHHHHT-TCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHhC-CCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHHHHHhhc
Confidence            333444 4555555555444332  1112334444444455555555555555444322  23322111111 1233344


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFC-PTYDIYRDMIRIFMASGRLAKCRDVC  463 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~-p~~~ty~~li~~~~~~g~~~~A~~l~  463 (493)
                      +.++|.+.+++..+.. .-+...+..+-..|...|++++|...|.+.....-. .+...+..+...|...|+.++|...+
T Consensus       200 ~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~a~~~~  278 (287)
T 3qou_A          200 ADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGDALASXY  278 (287)
T ss_dssp             TSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             ccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCCcHHHHH
Confidence            4444444444443321 123344444555555555555555555555432211 11344555555555555555555544


Q ss_pred             HH
Q 011102          464 KE  465 (493)
Q Consensus       464 ~~  465 (493)
                      ++
T Consensus       279 r~  280 (287)
T 3qou_A          279 RR  280 (287)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.11  E-value=2.5e-05  Score=83.75  Aligned_cols=173  Identities=9%  Similarity=-0.074  Sum_probs=137.5

Q ss_pred             HhcCCHHHHHHHHHHHH--------hCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHH
Q 011102          274 VKGGNLKLAWKLLMVAK--------DGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVG  345 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~--------~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~  345 (493)
                      ...|++++|++.|++..        +. -..+...|..+-..+.+. |++++|.+.|++..+.  -.-+...|..+-.+|
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~-g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~  477 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDL-GDVAKATRKLDDLAER--VGWRWRLVWYRAVAE  477 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHH-TCHHHHHHHHHHHHHH--HCCCHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhc-CCHHHHHHHHHHHhcc--CcchHHHHHHHHHHH
Confidence            78899999999999988        32 123456777888888999 9999999999998765  223677888899999


Q ss_pred             HHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          346 IRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAI  425 (493)
Q Consensus       346 ~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~  425 (493)
                      .+.|++++|.+.|++..+.. +-+...|..+-..|.+.|++++ ++.|++..+..- -+...|..+-.++.+.|++++|.
T Consensus       478 ~~~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~  554 (681)
T 2pzi_A          478 LLTGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTND-GVISAAFGLARARSAEGDRVGAV  554 (681)
T ss_dssp             HHHTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCC-chHHHHHHHHHHHHHcCCHHHHH
Confidence            99999999999999987652 2356888999999999999999 999999876532 25678899999999999999999


Q ss_pred             HHHHHHHHCCCCCC-HHHHHHHHHHHHHcCC
Q 011102          426 RYFSKLKEAGFCPT-YDIYRDMIRIFMASGR  455 (493)
Q Consensus       426 ~~~~~m~~~g~~p~-~~ty~~li~~~~~~g~  455 (493)
                      +.|++..+.  .|+ ...|..+..++...|+
T Consensus       555 ~~~~~al~l--~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          555 RTLDEVPPT--SRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHHTSCTT--STTHHHHHHHHHHHTC----
T ss_pred             HHHHhhccc--CcccHHHHHHHHHHHHccCC
Confidence            999987653  355 5667777777766554

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.10  E-value=5.5e-05  Score=65.85  Aligned_cols=159  Identities=13%  Similarity=0.057  Sum_probs=116.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH-H
Q 011102          267 EATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV-G  345 (493)
Q Consensus       267 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~-~  345 (493)
                      ..+...+.+.|++++|...|++..+.. +-+...+..+-..+.+. |++++|...++.....   .|+...+..+... +
T Consensus        10 ~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~-g~~~~A~~~~~~a~~~---~p~~~~~~~~~~~~~   84 (176)
T 2r5s_A           10 LKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLET-KQFELAQELLATIPLE---YQDNSYKSLIAKLEL   84 (176)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHT-TCHHHHHHHHTTCCGG---GCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHC-CCHHHHHHHHHHhhhc---cCChHHHHHHHHHHH
Confidence            345567788899999999998766532 12456777888888888 9999999999987654   2344333322111 2


Q ss_pred             HHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHH
Q 011102          346 IRLQKFGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       346 ~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~  423 (493)
                      .+.+...+|...|++..+.  .| +...+..+-..+...|++++|.+.|+++.+..-.+ +...+..+...+...|+.++
T Consensus        85 ~~~~~~~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~  162 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNA  162 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCH
T ss_pred             HhhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCc
Confidence            2333344578888887654  44 57888999999999999999999999988764332 35678889999999999999


Q ss_pred             HHHHHHHHH
Q 011102          424 AIRYFSKLK  432 (493)
Q Consensus       424 A~~~~~~m~  432 (493)
                      |...|++..
T Consensus       163 A~~~y~~al  171 (176)
T 2r5s_A          163 IASKYRRQL  171 (176)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999988764

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=98.10  E-value=0.0034  Score=66.70  Aligned_cols=168  Identities=10%  Similarity=0.005  Sum_probs=100.8

Q ss_pred             CCHHHHH-HHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC---------CCCC------------H
Q 011102          313 DKYMLVM-TLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSG---------RDPT------------V  370 (493)
Q Consensus       313 ~~~~~a~-~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g---------~~p~------------~  370 (493)
                      |+.++|. ++|+.....  +..+...|-..+...-+.|++++|.++|+.+....         -.|+            .
T Consensus       357 ~~~~~a~r~il~rAi~~--~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~  434 (679)
T 4e6h_A          357 NTDSTVITKYLKLGQQC--IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLT  434 (679)
T ss_dssp             SCCTTHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchH
Confidence            3344554 555555432  33345556666667777788888888887776431         0132            2


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHC-C-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEAS-N-CLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR  448 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~-g-i~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~  448 (493)
                      ..|...+....+.|..+.|.++|.+..+. + ..+......+.+.-.+ .++.+.|.++|+...+. +.-+...|...++
T Consensus       435 ~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife~~Lk~-~p~~~~~w~~y~~  512 (679)
T 4e6h_A          435 YVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHI-SKDTKTACKVLELGLKY-FATDGEYINKYLD  512 (679)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTT-TSCCHHHHHHHHHHHHH-HTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHh-CCCHHHHHHHHHHHHHH-CCCchHHHHHHHH
Confidence            35777777777777788888888877665 2 2233333333333222 34578888888877654 3335555667777


Q ss_pred             HHHHcCCHHHHHHHHHHHHHCCCcc--CHHHHHHHHHh
Q 011102          449 IFMASGRLAKCRDVCKEAEMAGFKL--DKQTVVELLQI  484 (493)
Q Consensus       449 ~~~~~g~~~~A~~l~~~m~~~g~~p--d~~t~~~Ll~~  484 (493)
                      -....|+.+.|..+|+......-.+  ....|...++.
T Consensus       513 fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~f  550 (679)
T 4e6h_A          513 FLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFF  550 (679)
T ss_dssp             HHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence            7777788888888888776543322  33456666665

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.02  E-value=0.00017  Score=68.25  Aligned_cols=162  Identities=11%  Similarity=-0.023  Sum_probs=128.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      ..+..+...+.+.|++++|...|++..+..  | +...+..+-..+.+. |++++|...++.....   .|+........
T Consensus       118 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~--P~~~~a~~~la~~~~~~-g~~~~A~~~l~~~~~~---~p~~~~~~~~~  191 (287)
T 3qou_A          118 ELXAQQAMQLMQESNYTDALPLLXDAWQLS--NQNGEIGLLLAETLIAL-NRSEDAEAVLXTIPLQ---DQDTRYQGLVA  191 (287)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TSCHHHHHHHHHHHHHT-TCHHHHHHHHTTSCGG---GCSHHHHHHHH
T ss_pred             hhHHHHHHHHHhCCCHHHHHHHHHHHHHhC--CcchhHHHHHHHHHHHC-CCHHHHHHHHHhCchh---hcchHHHHHHH
Confidence            345567777889999999999999988753  4 556778888889999 9999999999988654   35554333332


Q ss_pred             -HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHcCC
Q 011102          343 -KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL-FDLPAYRVVIKLFVALND  420 (493)
Q Consensus       343 -~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~-pd~~ty~~li~~~~~~g~  420 (493)
                       ..+.+.++.++|.+.|++..+.. +.+...+..+-..|...|++++|++.|.++.+..-. .+...+..+...|...|+
T Consensus       192 ~~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~  270 (287)
T 3qou_A          192 QIELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGT  270 (287)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCT
T ss_pred             HHHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCC
Confidence             34677788889999998877653 456888999999999999999999999998875322 236789999999999999


Q ss_pred             HHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLK  432 (493)
Q Consensus       421 ~~~A~~~~~~m~  432 (493)
                      .++|...|++-.
T Consensus       271 ~~~a~~~~r~al  282 (287)
T 3qou_A          271 GDALASXYRRQL  282 (287)
T ss_dssp             TCHHHHHHHHHH
T ss_pred             CCcHHHHHHHHH
Confidence            999998887654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.01  E-value=0.00033  Score=55.79  Aligned_cols=96  Identities=6%  Similarity=-0.047  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011102          299 SIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIH  378 (493)
Q Consensus       299 ~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~  378 (493)
                      ..|..+...+... |++++|.++++++...  ...+...+..+...|.+.|++++|..+|+++.+.. +.+..++..+..
T Consensus        10 ~~~~~~~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~   85 (125)
T 1na0_A           10 EAWYNLGNAYYKQ-GDYDEAIEYYQKALEL--DPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGN   85 (125)
T ss_dssp             HHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-CCHHHHHHHHHHHHHH--CcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHH
Confidence            3444445555555 5556666555555443  12244555555566666666666666666655432 234555666666


Q ss_pred             HHHcCCCHHHHHHHHHHHHH
Q 011102          379 SRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       379 ~~~~~g~~~~A~~l~~~M~~  398 (493)
                      .|...|++++|.+.|+++.+
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           86 AYYKQGDYDEAIEYYQKALE  105 (125)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHH
Confidence            66666666666666666554

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.01  E-value=5.9e-05  Score=66.58  Aligned_cols=157  Identities=10%  Similarity=-0.047  Sum_probs=109.5

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc---CCCC-CCHHHHHHHHHHHHHcC
Q 011102          274 VKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQR---DDLN-LSQQDCTAIMKVGIRLQ  349 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~---~g~~-p~~~~~~~li~~~~~~g  349 (493)
                      ...|++++|.++++..... ......++..+-..+... |++++|...+++....   .+.. .....+..+-..|...|
T Consensus         3 ~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g   80 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH-PATASGARFMLGYVYAFM-DRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAG   80 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             cccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHh-CcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcC
Confidence            4578999999965555432 123456777777788888 9999999999886551   1111 22456777888999999


Q ss_pred             CHHHHHHHHHHHHHc----CCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHHc
Q 011102          350 KFGVVESLFHWFTHS----GRDP--TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLF-DLPAYRVVIKLFVAL  418 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~----g~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~p-d~~ty~~li~~~~~~  418 (493)
                      ++++|.+.|++..+.    +-.+  ....++.+-..+...|++++|.+.+++..+.    +-.. -..++..+-..+...
T Consensus        81 ~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~  160 (203)
T 3gw4_A           81 NWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQE  160 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHC
Confidence            999999999876542    2122  2456888889999999999999999986532    2111 123457777889999


Q ss_pred             CCHHHHHHHHHHHH
Q 011102          419 NDISRAIRYFSKLK  432 (493)
Q Consensus       419 g~~~~A~~~~~~m~  432 (493)
                      |++++|.+.+++..
T Consensus       161 g~~~~A~~~~~~al  174 (203)
T 3gw4_A          161 KNLLEAQQHWLRAR  174 (203)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHH
Confidence            99999999887765

>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=97.99  E-value=0.001  Score=59.76  Aligned_cols=166  Identities=14%  Similarity=0.029  Sum_probs=122.9

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCC---CHHHHHHHHHHHhhcCCCCCCHHH
Q 011102          261 ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPD---KYMLVMTLLDELGQRDDLNLSQQD  337 (493)
Q Consensus       261 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~---~~~~a~~l~~~m~~~~g~~p~~~~  337 (493)
                      .+...+..|-..|...+++++|.+.|++..+.|   +...+..|=..|... |   +.++|.+.|+...+. |   +...
T Consensus        16 g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~~-g~~~~~~~A~~~~~~A~~~-g---~~~a   87 (212)
T 3rjv_A           16 GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIRN-PQQADYPQARQLAEKAVEA-G---SKSG   87 (212)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTSS-TTSCCHHHHHHHHHHHHHT-T---CHHH
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcC-CCCCCHHHHHHHHHHHHHC-C---CHHH
Confidence            455566677777778899999999999988876   566666665555552 3   789999999988765 3   5667


Q ss_pred             HHHHHHHHHH----cCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCCCHHHH
Q 011102          338 CTAIMKVGIR----LQKFGVVESLFHWFTHSGRD-PTVVMYTTLIHSRLS----EKKCREALTVVWNMEASNCLFDLPAY  408 (493)
Q Consensus       338 ~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~-p~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~gi~pd~~ty  408 (493)
                      +..|-..|..    .+++++|.+.|++..+.|.. .+..++..|-..|..    .++.++|.+.|++..+.+  .+...+
T Consensus        88 ~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~--~~~~a~  165 (212)
T 3rjv_A           88 EIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLS--RTGYAE  165 (212)
T ss_dssp             HHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTS--CTTHHH
T ss_pred             HHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcC--CCHHHH
Confidence            7777777776    78899999999988765432 126777888888887    788999999999987762  234456


Q ss_pred             HHHHHHHHHc-C-----CHHHHHHHHHHHHHCCC
Q 011102          409 RVVIKLFVAL-N-----DISRAIRYFSKLKEAGF  436 (493)
Q Consensus       409 ~~li~~~~~~-g-----~~~~A~~~~~~m~~~g~  436 (493)
                      ..|-..|.+. |     +.++|..+|+.-.+.|.
T Consensus       166 ~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          166 YWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            6666666553 3     89999999988887764

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.97  E-value=0.0003  Score=56.61  Aligned_cols=117  Identities=9%  Similarity=0.004  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLF  415 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~  415 (493)
                      ..+..+...+...|++++|.+.|++..+.. +.+...|..+...+...|++++|.+.+++..+.. ..+...+..+-..|
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~   90 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLAL   90 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHH
Confidence            345555556666666666666666655432 2245556666666666666666666666655432 12345555556666


Q ss_pred             HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          416 VALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGR  455 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~  455 (493)
                      .+.|++++|...|++..+..- .+...+..+...+.+.|+
T Consensus        91 ~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKALELDP-DNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHTT
T ss_pred             HHhCCHHHHHHHHHHHHhcCc-cchHHHHHHHHHHHHHhc
Confidence            666666666666666554321 244555555555555554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.95  E-value=0.00029  Score=57.11  Aligned_cols=117  Identities=9%  Similarity=-0.005  Sum_probs=67.5

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          334 SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIK  413 (493)
Q Consensus       334 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~  413 (493)
                      +...|..+...+.+.|++++|.+.|++..+.. +.+...|..+...|...|++++|.+.+++..+.. ..+...+..+-.
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~   92 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAA   92 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHH
Confidence            34456666666667777777777776665432 2255666666666666777777777766655532 124455666666


Q ss_pred             HHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          414 LFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMAS  453 (493)
Q Consensus       414 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~  453 (493)
                      .+.+.|++++|.+.|++..+..- -+...+..+...+.+.
T Consensus        93 ~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~  131 (133)
T 2lni_A           93 ALEAMKDYTKAMDVYQKALDLDS-SCKEAADGYQRCMMAQ  131 (133)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCG-GGTHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHhCC-CchHHHHHHHHHHHHh
Confidence            66666666666666666654321 1233444444444443

>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=97.94  E-value=0.00035  Score=59.16  Aligned_cols=121  Identities=13%  Similarity=-0.047  Sum_probs=57.5

Q ss_pred             HHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC
Q 011102          306 LELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK  385 (493)
Q Consensus       306 ~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~  385 (493)
                      ..+... |++++|...|+.....  ...+...+..+...|.+.|++++|.+.|++..+.. +.+...|..+...+...|+
T Consensus        21 ~~~~~~-~~~~~A~~~~~~al~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~   96 (166)
T 1a17_A           21 NDYFKA-KDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGK   96 (166)
T ss_dssp             HHHHHT-TCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHc-cCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhcc
Confidence            334444 4555555555444332  11234444555555555555555555555544331 2234455555555555666


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHH--HHHHHHHHHcCCHHHHHHHHHHH
Q 011102          386 CREALTVVWNMEASNCLFDLPAY--RVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       386 ~~~A~~l~~~M~~~gi~pd~~ty--~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      +++|.+.|++..+..- -+...+  -.....+.+.|++++|...+...
T Consensus        97 ~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           97 FRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            6666666655544321 122222  22223345556666666665543

>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=97.92  E-value=0.00034  Score=74.38  Aligned_cols=203  Identities=14%  Similarity=0.015  Sum_probs=153.8

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHH-HHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC---------CC
Q 011102          262 SKGVLEATAKGFVKGGNLKLAW-KLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRD---------DL  331 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~-~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~---------g~  331 (493)
                      ...+|-..+..+-+.|+.++|. ++|++.... ++.+...|-..+...-+. |+++.|.++|+.+....         +.
T Consensus       342 ~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~-~~~e~aR~iyek~l~~l~~~~~~~~~~~  419 (679)
T 4e6h_A          342 APEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELN-TKIPEIETTILSCIDRIHLDLAALMEDD  419 (679)
T ss_dssp             CHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHhhhhhhcc
Confidence            4456777777777889999997 999998863 344555666777778888 89999999999987530         11


Q ss_pred             CCC------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-C-CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          332 NLS------------QQDCTAIMKVGIRLQKFGVVESLFHWFTHS-G-RDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       332 ~p~------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g-~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                       |+            ..+|...+....+.|.++.|..+|....+. + ..+.+....+.|.-.+ .++.+.|.++|+...
T Consensus       420 -p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~-~~d~e~Ar~ife~~L  497 (679)
T 4e6h_A          420 -PTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHI-SKDTKTACKVLELGL  497 (679)
T ss_dssp             -TTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTT-TSCCHHHHHHHHHHH
T ss_pred             -CcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHh-CCCHHHHHHHHHHHH
Confidence             32            346888888888999999999999998765 2 3344555555554322 356999999999977


Q ss_pred             HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          398 ASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCP--TYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       398 ~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      +. +.-+...+...++.....|+.+.|..+|+........+  ....|...++--.+.|+.+.+.++.+++.+.
T Consensus       498 k~-~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~  570 (679)
T 4e6h_A          498 KY-FATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEK  570 (679)
T ss_dssp             HH-HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH
T ss_pred             HH-CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            65 33355566788888889999999999999988654321  4567999999889999999999999999875

>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=97.86  E-value=0.00016  Score=77.55  Aligned_cols=157  Identities=6%  Similarity=-0.100  Sum_probs=130.5

Q ss_pred             hcCCCCHHHHHHHHHHHh--------hcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011102          309 GKNPDKYMLVMTLLDELG--------QRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSR  380 (493)
Q Consensus       309 ~~~~~~~~~a~~l~~~m~--------~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~  380 (493)
                      ... |++++|++.+++..        +.  -..+...+..+-..|.+.|++++|.+.|++..+.. .-+...|..+-..|
T Consensus       402 ~~~-~~~~~A~~~~~~al~~~~~~~~~~--~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~  477 (681)
T 2pzi_A          402 TVL-SQPVQTLDSLRAARHGALDADGVD--FSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAE  477 (681)
T ss_dssp             TTT-CCHHHHHHHHHHHHTC-------C--CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHH
T ss_pred             ccc-cCHHHHHHHHHHhhhhcccccccc--cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHH
Confidence            556 89999999999987        32  23356778888899999999999999999987642 34678899999999


Q ss_pred             HcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          381 LSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKC  459 (493)
Q Consensus       381 ~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A  459 (493)
                      ...|++++|.+.|++..+..  | +...|..+-..|.+.|++++ .+.|++..+..- -+...|..+-.+|.+.|++++|
T Consensus       478 ~~~g~~~~A~~~~~~al~l~--P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A  553 (681)
T 2pzi_A          478 LLTGDYDSATKHFTEVLDTF--PGELAPKLALAATAELAGNTDE-HKFYQTVWSTND-GVISAAFGLARARSAEGDRVGA  553 (681)
T ss_dssp             HHHTCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCC-chHHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999987653  4 45778888899999999999 999999886543 2677899999999999999999


Q ss_pred             HHHHHHHHHCCCccCH
Q 011102          460 RDVCKEAEMAGFKLDK  475 (493)
Q Consensus       460 ~~l~~~m~~~g~~pd~  475 (493)
                      .+.|++..+  +.|+.
T Consensus       554 ~~~~~~al~--l~P~~  567 (681)
T 2pzi_A          554 VRTLDEVPP--TSRHF  567 (681)
T ss_dssp             HHHHHTSCT--TSTTH
T ss_pred             HHHHHhhcc--cCccc
Confidence            999998765  45654

>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=97.84  E-value=0.00062  Score=66.06  Aligned_cols=132  Identities=8%  Similarity=-0.046  Sum_probs=76.0

Q ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          297 DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-------------QQDCTAIMKVGIRLQKFGVVESLFHWFTH  363 (493)
Q Consensus       297 d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~  363 (493)
                      +...|..+-..|.+. |++++|...|++......-.++             ...|..+-.+|.+.|++++|...|++..+
T Consensus       146 ~a~~~~~~g~~~~~~-g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~  224 (336)
T 1p5q_A          146 QSTIVKERGTVYFKE-GKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALE  224 (336)
T ss_dssp             HHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            355677777777888 8888888888887664111110             35566666666666666666666666554


Q ss_pred             cCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH-HHHHHHH
Q 011102          364 SGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRA-IRYFSKL  431 (493)
Q Consensus       364 ~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A-~~~~~~m  431 (493)
                      .. +.+...|..+-.+|...|++++|.+.|++..+..- -+...+..+-..+.+.|+.++| ..+|+.|
T Consensus       225 ~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  291 (336)
T 1p5q_A          225 LD-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYP-NNKAAKTQLAVCQQRIRRQLAREKKLYANM  291 (336)
T ss_dssp             HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            32 22455566666666666666666666665554321 1344555555555555555555 2344444

>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=97.82  E-value=0.0002  Score=60.52  Aligned_cols=108  Identities=5%  Similarity=-0.095  Sum_probs=51.7

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLS-QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALT  391 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~  391 (493)
                      |++++|++.+......   .|+ ...+-.+-..|.+.|++++|.+.|++..+.. +-+..+|..+-..|.+.|++++|..
T Consensus        11 ~~~e~ai~~~~~a~~~---~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~   86 (150)
T 4ga2_A           11 ADVERYIASVQGSTPS---PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTDKAVE   86 (150)
T ss_dssp             HHHHHHHHHHHHHSCS---HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ChHHHHHHHHHHhccc---CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchHHHHH
Confidence            4455555555544322   111 1223344455555555555555555554331 2244555555555555555555555


Q ss_pred             HHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHH
Q 011102          392 VVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIR  426 (493)
Q Consensus       392 l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~  426 (493)
                      .|++..+.  .| +...|..+-..|.+.|+.++|.+
T Consensus        87 ~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~aa~  120 (150)
T 4ga2_A           87 CYRRSVEL--NPTQKDLVLKIAELLCKNDVTDGRAK  120 (150)
T ss_dssp             HHHHHHHH--CTTCHHHHHHHHHHHHHHCSSSSHHH
T ss_pred             HHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHH
Confidence            55554442  22 23445555555555555544433

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.81  E-value=0.00084  Score=55.48  Aligned_cols=97  Identities=13%  Similarity=-0.078  Sum_probs=61.9

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD----LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYR  444 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd----~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~  444 (493)
                      +...|..+...+...|++++|.+.|++..+.  .|+    ...|..+-..|.+.|++++|...++...+..- .+...|.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~  103 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDG-GDVKALY  103 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTS-CCHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCc-cCHHHHH
Confidence            4555666666666666666666666665543  344    45566666666777777777777776664321 2456666


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          445 DMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       445 ~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      .+..+|...|++++|.+.|++..+
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            677777777777777777777665

>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=97.81  E-value=0.00021  Score=61.84  Aligned_cols=116  Identities=7%  Similarity=0.030  Sum_probs=48.7

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHcCCCH--HHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHS-RLSEKKC--REA  389 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~-~~~~g~~--~~A  389 (493)
                      |++++|...++.....  -..+...|..+-..|...|++++|...|++..+.. +.+...|..+... |...|++  ++|
T Consensus        24 ~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A  100 (177)
T 2e2e_A           24 QNPEAQLQALQDKIRA--NPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQT  100 (177)
T ss_dssp             ---CCCCHHHHHHHHH--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHH
T ss_pred             cCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHH
Confidence            4444454444444332  11233444444445555555555555554443321 1233344444444 3444444  455


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          390 LTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       390 ~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      ...+++..+..- -+...+..+-..|...|++++|...|+...
T Consensus       101 ~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al  142 (177)
T 2e2e_A          101 RAMIDKALALDS-NEITALMLLASDAFMQANYAQAIELWQKVM  142 (177)
T ss_dssp             HHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCC-CcHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            544444443211 123334444444444444444444444444

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.79  E-value=0.001  Score=66.21  Aligned_cols=194  Identities=8%  Similarity=-0.047  Sum_probs=99.0

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCC----------------HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLD----------------PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQ  336 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd----------------~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~  336 (493)
                      +.+.|++++|++.|....+..-...                ...+..+...|.+. |++++|.+.+.......+-.++..
T Consensus        14 l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~-~~~~~a~~~~~~~~~~~~~~~~~~   92 (434)
T 4b4t_Q           14 LVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTM-GAKDKLREFIPHSTEYMMQFAKSK   92 (434)
T ss_dssp             HHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHTHHHHHTSCHHH
T ss_pred             HHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHccchH
Confidence            4556666666666666655321111                11245556666666 666766666665543211111111


Q ss_pred             ----HHHHHHHHHHHcCCHHHHHHHHHHHHH----cCCCCC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--CC--CC
Q 011102          337 ----DCTAIMKVGIRLQKFGVVESLFHWFTH----SGRDPT-VVMYTTLIHSRLSEKKCREALTVVWNMEAS--NC--LF  403 (493)
Q Consensus       337 ----~~~~li~~~~~~g~~~~A~~l~~~m~~----~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~~--gi--~p  403 (493)
                          +.+.+-..+...|+.+.|.+++.....    .+..+. ..++..|...|...|++++|..++++....  +.  .+
T Consensus        93 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~  172 (434)
T 4b4t_Q           93 TVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKP  172 (434)
T ss_dssp             HHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCST
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccch
Confidence                112222222334566666666655432    222222 345566666666677777777666665432  11  11


Q ss_pred             C-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH--CCCC-C-C--HHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          404 D-LPAYRVVIKLFVALNDISRAIRYFSKLKE--AGFC-P-T--YDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       404 d-~~ty~~li~~~~~~g~~~~A~~~~~~m~~--~g~~-p-~--~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      . ..+|..+...|...|++++|..+++....  ..+. | .  ...|..+...+...|++++|...|.+..
T Consensus       173 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          173 SLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            1 23566666667777777777776665541  1111 1 1  2344555555566667777666655553

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=97.79  E-value=0.00076  Score=54.11  Aligned_cols=91  Identities=9%  Similarity=-0.132  Sum_probs=40.7

Q ss_pred             HHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC
Q 011102          304 LILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE  383 (493)
Q Consensus       304 li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~  383 (493)
                      +...+... |++++|...|++....  ...+...+..+...|...|++++|.+.|++..+.. +.+...|..+...|.+.
T Consensus        18 ~~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   93 (131)
T 2vyi_A           18 EGNEQMKV-ENFEAAVHFYGKAIEL--NPANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALSSL   93 (131)
T ss_dssp             HHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHc-cCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHHHh
Confidence            33334444 4444444444444332  11233444444444445555555555554444321 12344444555555555


Q ss_pred             CCHHHHHHHHHHHHH
Q 011102          384 KKCREALTVVWNMEA  398 (493)
Q Consensus       384 g~~~~A~~l~~~M~~  398 (493)
                      |++++|.+.|++..+
T Consensus        94 ~~~~~A~~~~~~~~~  108 (131)
T 2vyi_A           94 NKHVEAVAYYKKALE  108 (131)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHh
Confidence            555555555555443

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.75  E-value=0.00072  Score=63.44  Aligned_cols=196  Identities=7%  Similarity=-0.094  Sum_probs=134.4

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHH-------HHHhcCCCCHHHHHHHHHHHhhcCCCCCC------------
Q 011102          275 KGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLI-------LELGKNPDKYMLVMTLLDELGQRDDLNLS------------  334 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li-------~~~~~~~~~~~~a~~l~~~m~~~~g~~p~------------  334 (493)
                      ..++.+.|.+.|.+..+..  |+ ...|..++       ..+... ++..+++..+..-.   ++.|+            
T Consensus        18 ~~~d~~~A~~~F~~a~~~d--P~~~Daw~g~~a~g~~~~~~L~~~-~r~~~a~~~~~~~l---~l~p~~l~a~~~~~g~y   91 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYD--ESACDAWIGRIRCGDTDRVTLFRA-WYSRRNFGQLSGSV---QISMSTLNARIAIGGLY   91 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHTTCCCHHHHHHH-HHTGGGTTHHHHTT---TCCGGGGCCEEECCTTT
T ss_pred             cCCCHHHHHHHHHHHHHhC--hhhhHHHHhHHHccCCcHHHHHHH-HHHHHHHHHHHHHh---cCChhhhhhhhccCCcc
Confidence            6899999999999998853  43 45666553       222222 22233333222221   22221            


Q ss_pred             ----------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC
Q 011102          335 ----------QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD  404 (493)
Q Consensus       335 ----------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd  404 (493)
                                ...+-.....+...|++++|.++|+.+...  .|+......+-..+.+.+++++|+..|+...+.   |+
T Consensus        92 ~~~~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~--~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~---~d  166 (282)
T 4f3v_A           92 GDITYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVA--GSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKW---PD  166 (282)
T ss_dssp             CCCEEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCT--TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGC---SC
T ss_pred             cccccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHcCCHHHHHHHHHHhhcc---CC
Confidence                      223345667888999999999999988754  354446666667899999999999999855432   32


Q ss_pred             H----HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHH
Q 011102          405 L----PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPT--YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTV  478 (493)
Q Consensus       405 ~----~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~  478 (493)
                      .    ..+..+=.++.+.|++++|+..|++.......|.  .......-.++.+.|+.++|..+|+++...  .|+...+
T Consensus       167 ~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~--~P~~~~~  244 (282)
T 4f3v_A          167 KFLAGAAGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT--HPEPKVA  244 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--SCCHHHH
T ss_pred             cccHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcHHHH
Confidence            2    3566667789999999999999999885444354  335566777788999999999999999874  5665555


Q ss_pred             HHHHH
Q 011102          479 VELLQ  483 (493)
Q Consensus       479 ~~Ll~  483 (493)
                      ..|..
T Consensus       245 ~aL~~  249 (282)
T 4f3v_A          245 AALKD  249 (282)
T ss_dssp             HHHHC
T ss_pred             HHHhC
Confidence            55543

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.72  E-value=0.0012  Score=52.98  Aligned_cols=95  Identities=9%  Similarity=0.059  Sum_probs=42.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC--CCC----HHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGF--CPT----YDIYRDM  446 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~--~p~----~~ty~~l  446 (493)
                      |..+...+...|++++|...|++..+.. ..+...+..+-..|...|++++|...|++..+..-  .++    ..+|..+
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l   85 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHH
Confidence            3334444444444444444444433321 12333444444444445555555554444432110  111    3444555


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Q 011102          447 IRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       447 i~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ...|.+.|++++|.+.|++..+
T Consensus        86 a~~~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           86 GNSYFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHH
Confidence            5555555555555555555544

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.72  E-value=0.0012  Score=53.91  Aligned_cols=94  Identities=10%  Similarity=-0.019  Sum_probs=44.6

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMA  452 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~  452 (493)
                      |.-.-..|.+.|++++|++.|++..+.. .-+...|..+-.+|.+.|++++|...|+...+..- .+...|..+-.+|..
T Consensus        16 ~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~   93 (126)
T 4gco_A           16 EKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDS-KFIKGYIRKAACLVA   93 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhh-hhhHHHHHHHHHHHH
Confidence            3334444444555555555554443321 12334444444555555555555555555443221 134445555555555


Q ss_pred             cCCHHHHHHHHHHHHH
Q 011102          453 SGRLAKCRDVCKEAEM  468 (493)
Q Consensus       453 ~g~~~~A~~l~~~m~~  468 (493)
                      .|++++|.+.|++..+
T Consensus        94 ~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           94 MREWSKAQRAYEDALQ  109 (126)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            5555555555555544

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.71  E-value=0.00033  Score=58.59  Aligned_cols=132  Identities=10%  Similarity=-0.048  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCC-CHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGR-DPT----VVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLF-DLP  406 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~----~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~p-d~~  406 (493)
                      ++..+-..|...|++++|.+.|++..+..- .++    ..++..+-..|...|++++|.+.+++..+.    +-.+ ...
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            455666677777777777777776543210 111    246777777888888888888888776542    1111 134


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH----CCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          407 AYRVVIKLFVALNDISRAIRYFSKLKE----AGFCP-TYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       407 ty~~li~~~~~~g~~~~A~~~~~~m~~----~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      .+..+-..+...|++++|...+++..+    .+..+ ...++..+...|...|++++|.+.+++..+
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            566677778888888888888887652    22111 135677788888899999999999888654

>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=97.69  E-value=0.0014  Score=53.03  Aligned_cols=95  Identities=14%  Similarity=0.002  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          372 MYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFM  451 (493)
Q Consensus       372 ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~  451 (493)
                      .|..+-..+.+.|++++|.+.|++..+.. ..+...|..+-.+|.+.|++++|...|++..+..- -+...|..+-.+|.
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~   83 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHH
Confidence            34445555556666666666666554432 12345566666666666666666666666554331 24555666666666


Q ss_pred             HcCCHHHHHHHHHHHHH
Q 011102          452 ASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       452 ~~g~~~~A~~l~~~m~~  468 (493)
                      ..|++++|.+.|++..+
T Consensus        84 ~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           84 AVKEYASALETLDAART  100 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHH
Confidence            66666666666666654

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=97.69  E-value=0.00094  Score=53.94  Aligned_cols=94  Identities=12%  Similarity=0.036  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      .|..+...+.+.|++++|.+.|++..+.. ..+...+..+-..+... |++++|...+++..+.  ...+...+..+...
T Consensus        18 ~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~-~~~~~A~~~~~~a~~~--~~~~~~~~~~la~~   93 (133)
T 2lni_A           18 MVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKL-LEFQLALKDCEECIQL--EPTFIKGYTRKAAA   93 (133)
T ss_dssp             HHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHh-ccHHHHHHHHHHHHHh--CCCchHHHHHHHHH
Confidence            44445555555555555555555544432 11334444444444444 5555555555544432  11233344444444


Q ss_pred             HHHcCCHHHHHHHHHHHH
Q 011102          345 GIRLQKFGVVESLFHWFT  362 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~  362 (493)
                      |.+.|++++|.+.|++..
T Consensus        94 ~~~~~~~~~A~~~~~~~~  111 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKAL  111 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            444444444444444443

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.69  E-value=0.00084  Score=53.91  Aligned_cols=110  Identities=9%  Similarity=0.051  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC--CCC----HHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNC--LFD----LPAYR  409 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi--~pd----~~ty~  409 (493)
                      ..|..+...+...|++++|...|++..+.. +.+...|..+...|...|++++|...+++..+...  .++    ..+|.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            345556666777777777777777765442 33566677777777777777777777777654321  122    55666


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          410 VVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR  448 (493)
Q Consensus       410 ~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~  448 (493)
                      .+-..|.+.|++++|.+.|+...+..  |+...+..+-.
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~  120 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAEH--RTPDVLKKCQQ  120 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhC--CCHHHHHHHHH
Confidence            77777778888888888887777543  45544444433

>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=97.68  E-value=0.0004  Score=60.05  Aligned_cols=118  Identities=6%  Similarity=-0.054  Sum_probs=52.2

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHHcCCH--HHH
Q 011102          348 LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKL-FVALNDI--SRA  424 (493)
Q Consensus       348 ~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~-~~~~g~~--~~A  424 (493)
                      .|++++|...|++..+.. +.+...|..+-..|...|++++|...|++..+..- .+...+..+-.. +...|++  ++|
T Consensus        23 ~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~l~~~~~~~~~~~A  100 (177)
T 2e2e_A           23 QQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRG-ENAELYAALATVLYYQASQHMTAQT  100 (177)
T ss_dssp             ----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTTTCCCHHH
T ss_pred             ccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhcCCcchHHH
Confidence            344455555554443321 22344455555555555555555555555443211 123334444444 4445554  555


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          425 IRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       425 ~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ...|+...+..- -+...|..+...|...|++++|.+.|++..+
T Consensus       101 ~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          101 RAMIDKALALDS-NEITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCC-CcHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            555555443321 1334444455555555555555555555444

>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=97.68  E-value=0.00099  Score=64.60  Aligned_cols=131  Identities=9%  Similarity=-0.029  Sum_probs=106.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC--------------HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD--------------PSIYAKLILELGKNPDKYMLVMTLLDELGQR  328 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd--------------~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~  328 (493)
                      ...|..+-..|.+.|++++|...|++..+..-...              ...|..+-..|.+. |++++|+..+++..+.
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~-g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKL-QAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh
Confidence            34677788888999999999999999887542211              47888888899999 9999999999998875


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHH-HHHHHHHH
Q 011102          329 DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREA-LTVVWNME  397 (493)
Q Consensus       329 ~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A-~~l~~~M~  397 (493)
                        -.-+...|..+-.+|.+.|++++|...|++..+.. +-+...+..+...+.+.|+.++| ..++..|.
T Consensus       226 --~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          226 --DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLY-PNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             --CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              23467889999999999999999999999987652 33677889999999999999988 45666664

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.67  E-value=0.0013  Score=65.57  Aligned_cols=213  Identities=9%  Similarity=-0.002  Sum_probs=138.3

Q ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHHHHH
Q 011102          204 RELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLKLAW  283 (493)
Q Consensus       204 ~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~~A~  283 (493)
                      ..+.+.|++++|++.|....+...-..+...         ..+..  .....     .....+..|...|.+.|++++|.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~---------~~~~~--~~~~~-----~~~~al~~l~~~y~~~~~~~~a~   75 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAA---------GASVD--DKRRN-----EQETSILELGQLYVTMGAKDKLR   75 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSS---------SSSBC--SHHHH-----HHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHH---------HHHHH--HHHhh-----hHHHHHHHHHHHHHHCCCHHHHH
Confidence            3567789999999999998875222111100         00000  00000     01124567888999999999999


Q ss_pred             HHHHHHHhC-CCCCCH---HHHHHHHHHHhcCCCCHHHHHHHHHHHhhc---CCCCCC-HHHHHHHHHHHHHcCCHHHHH
Q 011102          284 KLLMVAKDG-GRMLDP---SIYAKLILELGKNPDKYMLVMTLLDELGQR---DDLNLS-QQDCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       284 ~l~~~m~~~-g~~pd~---~t~~~li~~~~~~~~~~~~a~~l~~~m~~~---~g~~p~-~~~~~~li~~~~~~g~~~~A~  355 (493)
                      +.+..+... +-.++.   ......+..+....|..++|..++......   .+..+. ..++..+...|...|++++|.
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  155 (434)
T 4b4t_Q           76 EFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSL  155 (434)
T ss_dssp             HHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHH
Confidence            999877542 111222   233455666666668899999888875431   122232 457788889999999999999


Q ss_pred             HHHHHHHHc--CC--CC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----CCCCC--HHHHHHHHHHHHHcCCHHHH
Q 011102          356 SLFHWFTHS--GR--DP-TVVMYTTLIHSRLSEKKCREALTVVWNMEAS----NCLFD--LPAYRVVIKLFVALNDISRA  424 (493)
Q Consensus       356 ~l~~~m~~~--g~--~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----gi~pd--~~ty~~li~~~~~~g~~~~A  424 (493)
                      .++++....  +.  .+ .+..|..++..|...|++++|..++++....    +..+.  ...|..+...+...|++++|
T Consensus       156 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A  235 (434)
T 4b4t_Q          156 ALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTA  235 (434)
T ss_dssp             HHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHH
T ss_pred             HHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHH
Confidence            999887542  11  12 2467889999999999999999999886542    22111  24566666777888999999


Q ss_pred             HHHHHHHH
Q 011102          425 IRYFSKLK  432 (493)
Q Consensus       425 ~~~~~~m~  432 (493)
                      ...|.+..
T Consensus       236 ~~~~~~a~  243 (434)
T 4b4t_Q          236 FSYFFESF  243 (434)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88877664

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=97.65  E-value=0.0022  Score=60.06  Aligned_cols=130  Identities=15%  Similarity=0.051  Sum_probs=87.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC--HHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS--QQDCTAIM  342 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~--~~~~~~li  342 (493)
                      .+-.+...+...|++++|.++|+.+...+  |+....-.+-..+.+. ++|++|+..|+..... . .|.  ...+..+-
T Consensus       104 l~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~-~r~~dA~~~l~~a~~~-~-d~~~~~~a~~~LG  178 (282)
T 4f3v_A          104 ITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAA-ERWTDVIDQVKSAGKW-P-DKFLAGAAGVAHG  178 (282)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHT-TCHHHHHHHHTTGGGC-S-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHc-CCHHHHHHHHHHhhcc-C-CcccHHHHHHHHH
Confidence            34556677888899999999998877654  5544433444466777 8888888888755432 0 111  23566666


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPT--VVMYTTLIHSRLSEKKCREALTVVWNMEAS  399 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~M~~~  399 (493)
                      .++.+.|++++|++.|++.......|.  .......-.++.+.|+.++|..+|+++...
T Consensus       179 ~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          179 VAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            778888888888888887764332253  235566666777788888888888887764

>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=97.64  E-value=0.0026  Score=49.81  Aligned_cols=96  Identities=11%  Similarity=-0.035  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIF  450 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~  450 (493)
                      ..|..+...+...|++++|.+.|++..+.. ..+...+..+-..+.+.|++++|...+++..+..- .+...|..+...|
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~   82 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCc-ccHHHHHHHHHHH
Confidence            344555555555566666666655554431 12344555555556666666666666666554321 2455566666666


Q ss_pred             HHcCCHHHHHHHHHHHHH
Q 011102          451 MASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       451 ~~~g~~~~A~~l~~~m~~  468 (493)
                      ...|++++|.+.+++..+
T Consensus        83 ~~~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHT
T ss_pred             HHHhhHHHHHHHHHHHHH
Confidence            666666666666666654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=97.64  E-value=0.0024  Score=52.08  Aligned_cols=96  Identities=9%  Similarity=0.032  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .+...-..|.+.|++++|.+.|++..+.. +.+...|..+-.+|.+.|++++|++.|++..+..- .+...|..+-.+|.
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~   92 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDS-KFIKGYIRKAACLV   92 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhh-hhhHHHHHHHHHHH
Confidence            44555566777777777777777665432 33566677777777777777777777777655321 23556777777777


Q ss_pred             HcCCHHHHHHHHHHHHHC
Q 011102          417 ALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~  434 (493)
                      ..|++++|.+.|++..+.
T Consensus        93 ~~~~~~~A~~~~~~al~l  110 (126)
T 4gco_A           93 AMREWSKAQRAYEDALQV  110 (126)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHH
Confidence            777777777777776653

>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=97.62  E-value=0.0029  Score=59.49  Aligned_cols=191  Identities=8%  Similarity=-0.043  Sum_probs=125.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC-CHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRML-DPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-d~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      ...+..+-..+.+.|++++|...|++..+..  | +...|..+-..|.+. |++++|...+++..+.  -.-+...+..+
T Consensus         4 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~la~~~~~~-~~~~~A~~~~~~al~~--~p~~~~~~~~l   78 (281)
T 2c2l_A            4 AQELKEQGNRLFVGRKYPEAAACYGRAITRN--PLVAVYYTNRALCYLKM-QQPEQALADCRRALEL--DGQSVKAHFFL   78 (281)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            3456677888899999999999999988753  4 677888888889999 9999999999998765  23457788889


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTV-VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND  420 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~  420 (493)
                      -.+|.+.|++++|...|++..+..  |+. ..+...+....+   ..++ .-+..........+..... .+..+ ..|+
T Consensus        79 g~~~~~~g~~~~A~~~~~~al~l~--p~~~~~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~~~~i~~-~l~~l-~~~~  150 (281)
T 2c2l_A           79 GQCQLEMESYDEAIANLQRAYSLA--KEQRLNFGDDIPSALR---IAKK-KRWNSIEERRIHQESELHS-YLTRL-IAAE  150 (281)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHH--HHTTCCCCSHHHHHHH---HHHH-HHHHHHHHTCCCCCCHHHH-HHHHH-HHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC--ccchhhHHHHHHHHHH---HHHH-HHHHHHHHHHHhhhHHHHH-HHHHH-HHHH
Confidence            999999999999999998876431  110 011111111111   1111 1122233333434443333 33333 3688


Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHH-HHHHHHHHHc-CCHHHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLKEAGFCPTYDIY-RDMIRIFMAS-GRLAKCRDVCKEAEM  468 (493)
Q Consensus       421 ~~~A~~~~~~m~~~g~~p~~~ty-~~li~~~~~~-g~~~~A~~l~~~m~~  468 (493)
                      .++|.+.++...+.  .|+.... ..+-..+.+. +.+++|.++|.+..+
T Consensus       151 ~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          151 RERELEECQRNHEG--HEDDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HHHHHTTTSGGGTT--TSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHhhhcc--ccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            89998888876643  4554433 3343334444 678899999988764

>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=97.61  E-value=0.0028  Score=49.59  Aligned_cols=97  Identities=8%  Similarity=-0.045  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLF  415 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~  415 (493)
                      ..+..+...+...|++++|.+.|++..... +.+...|..+...|...|++++|...+++..+... .+...+..+-..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~   82 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCc-ccHHHHHHHHHHH
Confidence            445556666667777777777777665432 23556666667777777777777777776655421 2455666666777


Q ss_pred             HHcCCHHHHHHHHHHHHHC
Q 011102          416 VALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~~  434 (493)
                      .+.|++++|.+.|+...+.
T Consensus        83 ~~~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTT
T ss_pred             HHHhhHHHHHHHHHHHHHc
Confidence            7777777777777776643

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.61  E-value=0.0034  Score=51.17  Aligned_cols=97  Identities=12%  Similarity=0.016  Sum_probs=48.5

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          334 SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIK  413 (493)
Q Consensus       334 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~  413 (493)
                      +...|..+-..+.+.|++++|...|+...+.. +.+...|..+...|...|++++|...+++..+..- -+...+..+-.
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~   85 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFLGQ   85 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-hhHHHHHHHHH
Confidence            34445555555555555555555555544332 22344555555555555555555555555444321 13344455555


Q ss_pred             HHHHcCCHHHHHHHHHHHH
Q 011102          414 LFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       414 ~~~~~g~~~~A~~~~~~m~  432 (493)
                      .|...|++++|...|+...
T Consensus        86 ~~~~~~~~~~A~~~~~~a~  104 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRAY  104 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHH
Confidence            5555555555555555444

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.60  E-value=0.025  Score=53.80  Aligned_cols=186  Identities=8%  Similarity=-0.023  Sum_probs=136.7

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHH---HH----HHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCC
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAK---LI----LELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQK  350 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~---li----~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~  350 (493)
                      +++++++.++.+....- -+..+|+.   ++    ...... +++++++++++.+.+.  -.-+-..|+---..+.+.|.
T Consensus        84 ~~~eeL~~~~~~L~~nP-k~y~aW~~R~~iL~~~~~~l~~~-~~~~~EL~~~~~~l~~--~pkny~aW~~R~~vl~~l~~  159 (306)
T 3dra_A           84 NLYDELDWCEEIALDNE-KNYQIWNYRQLIIGQIMELNNND-FDPYREFDILEAMLSS--DPKNHHVWSYRKWLVDTFDL  159 (306)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCCHHHHHHHHHHHHHHHHTTTC-CCTHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHHHCc-ccHHHHHHHHHHHHHHHHhcccc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcc
Confidence            78889998888887542 23334543   22    222222 6788999999998875  34577788877778888888


Q ss_pred             HH--HHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC------HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          351 FG--VVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK------CREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       351 ~~--~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~------~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      ++  ++++.++++.+.. .-|-..|+---..+.+.++      ++++++.++++..... -|...|+-+-..+.+.|+..
T Consensus       160 ~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p-~n~SaW~y~~~ll~~~~~~~  237 (306)
T 3dra_A          160 HNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKCP-QNPSTWNYLLGIHERFDRSI  237 (306)
T ss_dssp             TTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCS-SCHHHHHHHHHHHHHTTCCG
T ss_pred             cChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhCC-CCccHHHHHHHHHHhcCCCh
Confidence            88  9999999998654 4577788877777777776      8899999998877543 47788888888888888744


Q ss_pred             H-HHHHHHHHHHCC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          423 R-AIRYFSKLKEAG--FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       423 ~-A~~~~~~m~~~g--~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      . +..+.+++.+.+  -..+...+..+.+.|.+.|+.++|.++++.+.+.
T Consensus       238 ~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~l~~~  287 (306)
T 3dra_A          238 TQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDLLKSK  287 (306)
T ss_dssp             GGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHhc
Confidence            4 555666665432  1347788999999999999999999999998753

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.60  E-value=0.0017  Score=57.27  Aligned_cols=131  Identities=8%  Similarity=-0.144  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-CCC--------------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGR-DPT--------------VVMYTTLIHSRLSEKKCREALTVVWNMEASNC  401 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~--------------~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi  401 (493)
                      .+..+-..+.+.|++++|.+.|++..+..- .|+              ...|..+-.+|.+.|++++|+..+++..+.. 
T Consensus        40 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-  118 (198)
T 2fbn_A           40 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID-  118 (198)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-
Confidence            445555666677777777777776654311 110              2677777888888888888888888876642 


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHH-HHHHHHHHC
Q 011102          402 LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCR-DVCKEAEMA  469 (493)
Q Consensus       402 ~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~-~l~~~m~~~  469 (493)
                      ..+...|..+-.+|...|++++|...|++..+..- -+...+..+...+...++.+++. ..+..|...
T Consensus       119 p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~  186 (198)
T 2fbn_A          119 KNNVKALYKLGVANMYFGFLEEAKENLYKAASLNP-NNLDIRNSYELCVNKLKEARKKDKLTFGGMFDK  186 (198)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHC------------
T ss_pred             cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            23566777777888888888888888888775432 25666777777777777776666 455555443

>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=97.57  E-value=0.0017  Score=53.01  Aligned_cols=108  Identities=10%  Similarity=0.042  Sum_probs=52.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC--CCCC----HHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG--FCPT----YDIYRDM  446 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g--~~p~----~~ty~~l  446 (493)
                      +.-|-..+.+.|++++|++.|++..+.. +-+...|+.+-.+|.+.|++++|.+.|+...+..  ..++    ..+|..+
T Consensus        11 ~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~l   89 (127)
T 4gcn_A           11 EKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRA   89 (127)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHH
Confidence            3344444555555555555555444321 1123444555555555555555555555443211  1111    1245555


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          447 IRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       447 i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      -.++...|++++|.+.|++..+  ..||..+...|-.
T Consensus        90 g~~~~~~~~~~~A~~~~~kal~--~~~~~~~~~~l~~  124 (127)
T 4gcn_A           90 GNAFQKQNDLSLAVQWFHRSLS--EFRDPELVKKVKE  124 (127)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH--HSCCHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHh--hCcCHHHHHHHHH
Confidence            5566666777777777766554  3455555444433

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.56  E-value=0.0012  Score=56.08  Aligned_cols=95  Identities=12%  Similarity=-0.057  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .+..+-..+.+.|++++|...|++..+.. +-+...|..+-.+|...|++++|.+.|++..+..- -+...|..+-.+|.
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P-~~~~~~~~lg~~~~  115 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGK-NDYTPVFHTGQCQL  115 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSS-SCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCC-CCcHHHHHHHHHHH
Confidence            44445555666666666666666655431 22455566666666666666666666666554321 12345555555666


Q ss_pred             HcCCHHHHHHHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKE  433 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~  433 (493)
                      +.|++++|...|+...+
T Consensus       116 ~lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          116 RLKAPLKAKECFELVIQ  132 (151)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            66666666666666554

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.56  E-value=0.0025  Score=51.99  Aligned_cols=100  Identities=9%  Similarity=-0.051  Sum_probs=86.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 011102          367 DPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDM  446 (493)
Q Consensus       367 ~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~l  446 (493)
                      ..+...|..+-..+...|++++|...|++..+..- .+...|..+-..+...|++++|...|+...+..- -+...|..+
T Consensus         6 ~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l   83 (137)
T 3q49_B            6 SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFL   83 (137)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCc-CcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-hhHHHHHHH
Confidence            45678899999999999999999999999776532 3577889999999999999999999999886542 367889999


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Q 011102          447 IRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       447 i~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      -.+|...|++++|.+.|++..+
T Consensus        84 ~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           84 GQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHH
Confidence            9999999999999999998875

>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=97.55  E-value=0.0003  Score=59.48  Aligned_cols=139  Identities=4%  Similarity=-0.146  Sum_probs=85.4

Q ss_pred             HHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          273 FVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKF  351 (493)
Q Consensus       273 ~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~  351 (493)
                      +...|++++|++.++.....  .|+ ...+-.+-..|.+. |++++|.+.|++..+.  -.-+...|..+-..|.+.|++
T Consensus         7 ~~~~~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~-~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~   81 (150)
T 4ga2_A            7 RRSKADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEA-KEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEENT   81 (150)
T ss_dssp             CCCHHHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHcChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCch
Confidence            34556777777777765442  122 22334455567777 7888888888777654  123566777777778888888


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH-HHHHHHCCCCCC-HHHHHHHHHHHHHcC
Q 011102          352 GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTV-VWNMEASNCLFD-LPAYRVVIKLFVALN  419 (493)
Q Consensus       352 ~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l-~~~M~~~gi~pd-~~ty~~li~~~~~~g  419 (493)
                      ++|...|++..+.. +-+...|..+-..|.+.|+.++|.+. +++..+.  .|+ ...|...-..+...|
T Consensus        82 ~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l--~P~~~~~~~l~~~ll~~~G  148 (150)
T 4ga2_A           82 DKAVECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKL--FPGSPAVYKLKEQLLDCEG  148 (150)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHH--STTCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHhC
Confidence            88888887766542 22466777777778888877665554 4554442  343 344554444444444

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.49  E-value=0.0035  Score=53.25  Aligned_cols=97  Identities=7%  Similarity=-0.051  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKL  414 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~  414 (493)
                      ...+..+-..|.+.|++++|.+.|++..+.. +-+...|..+-..|.+.|++++|++.|++..+..- -+...|..+-..
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~   88 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDP-KYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            4456666667777777777777777765442 23566677777777777777777777777665431 235667777777


Q ss_pred             HHHcCCHHHHHHHHHHHHH
Q 011102          415 FVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~~  433 (493)
                      |.+.|++++|...|++..+
T Consensus        89 ~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHH
Confidence            7777777777777777663

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.48  E-value=0.0045  Score=50.90  Aligned_cols=98  Identities=12%  Similarity=0.009  Sum_probs=67.1

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          334 SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT----VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYR  409 (493)
Q Consensus       334 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~----~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~  409 (493)
                      +...+..+...+.+.|++++|.+.|++..+.  .|+    ...|..+...|...|++++|.+.+++..+.. ..+...+.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  103 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALY  103 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHH
Confidence            4556666667777777777777777776643  454    5667777777777777777777777765542 12456666


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          410 VVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       410 ~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      .+-..|...|++++|...|++..+.
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            7777777778888888777777643

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.48  E-value=0.0012  Score=51.44  Aligned_cols=98  Identities=8%  Similarity=-0.020  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHH
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFC-PTYDIYRDMIRI  449 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~-p~~~ty~~li~~  449 (493)
                      ..|..+...+.+.|++++|...|++..+..- .+...|..+-..+...|++++|...|++..+..-. .+...|..+...
T Consensus         7 ~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~   85 (112)
T 2kck_A            7 EEYYLEGVLQYDAGNYTESIDLFEKAIQLDP-EESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADA   85 (112)
T ss_dssp             TGGGGHHHHHHSSCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHH
Confidence            3444555556666666666666666554321 23455556666666666666666666666543210 135566666666


Q ss_pred             HHHc-CCHHHHHHHHHHHHHC
Q 011102          450 FMAS-GRLAKCRDVCKEAEMA  469 (493)
Q Consensus       450 ~~~~-g~~~~A~~l~~~m~~~  469 (493)
                      |.+. |++++|.+.+++..+.
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           86 LRYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             HTTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHHhCCHHHHHHHHHHHhhc
Confidence            6666 6777776666666543

>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=97.47  E-value=0.0019  Score=54.33  Aligned_cols=95  Identities=5%  Similarity=-0.061  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLF  415 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~  415 (493)
                      ..+..+-..+.+.|++++|...|+...... +.+...|..+-.+|...|++++|.+.|++..+..- -+...|..+-.+|
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~~   99 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDI-XEPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCchHHHHHHHHH
Confidence            345555666777777777777777765432 23566666677777777777777777777655321 2345566666667


Q ss_pred             HHcCCHHHHHHHHHHHH
Q 011102          416 VALNDISRAIRYFSKLK  432 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~  432 (493)
                      ...|++++|...|+...
T Consensus       100 ~~~g~~~~A~~~~~~al  116 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQ  116 (148)
T ss_dssp             HHTTCHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHH
Confidence            77777777777776665

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.47  E-value=0.002  Score=56.75  Aligned_cols=123  Identities=10%  Similarity=-0.081  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CC--------------HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRM-LD--------------PSIYAKLILELGKNPDKYMLVMTLLDELGQR  328 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-pd--------------~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~  328 (493)
                      ..+..+-..+.+.|++++|.+.|++..+..-. |+              ...|..+-..|.+. |++++|+..++.....
T Consensus        39 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~-~~~~~A~~~~~~al~~  117 (198)
T 2fbn_A           39 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKN-KDYPKAIDHASKVLKI  117 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHh
Confidence            35677777888889999999999888764211 10              13444444445555 5555555555554443


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHH
Q 011102          329 DDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREAL  390 (493)
Q Consensus       329 ~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~  390 (493)
                        -..+...+..+-.+|...|++++|.+.|++..+.. +-+...+..+...+...++.+++.
T Consensus       118 --~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          118 --DKNNVKALYKLGVANMYFGFLEEAKENLYKAASLN-PNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             --STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             --CcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHHHHHHHH
Confidence              11234444455555555555555555555543321 123334444444444444443333

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=97.47  E-value=0.0018  Score=54.88  Aligned_cols=92  Identities=8%  Similarity=-0.096  Sum_probs=44.2

Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 011102          303 KLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS  382 (493)
Q Consensus       303 ~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~  382 (493)
                      .+-..+.+. |++++|...|+.....  -.-+...|..+-.+|.+.|++++|.+.|++..+.. +-+...|..+-.+|.+
T Consensus        41 ~lg~~~~~~-g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~-P~~~~~~~~lg~~~~~  116 (151)
T 3gyz_A           41 SYAYDFYNK-GRIEEAEVFFRFLCIY--DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALG-KNDYTPVFHTGQCQLR  116 (151)
T ss_dssp             HHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-SSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHH
Confidence            333444444 5555555555554443  11234445555555555555555555555544321 1133444555555555


Q ss_pred             CCCHHHHHHHHHHHHH
Q 011102          383 EKKCREALTVVWNMEA  398 (493)
Q Consensus       383 ~g~~~~A~~l~~~M~~  398 (493)
                      .|++++|.+.|++..+
T Consensus       117 lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          117 LKAPLKAKECFELVIQ  132 (151)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            5555555555555444

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=97.46  E-value=0.0022  Score=54.60  Aligned_cols=99  Identities=5%  Similarity=-0.092  Sum_probs=85.7

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIR  448 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~  448 (493)
                      +...|..+-..|.+.|++++|++.|++..+..- -+...|..+-..|.+.|++++|...|++..+..- -+...|..+-.
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSIAP-ANPIYLSNRAAAYSASGQHEKAAEDAELATVVDP-KYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-cCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence            456788888999999999999999999876532 2678889999999999999999999999986542 36888999999


Q ss_pred             HHHHcCCHHHHHHHHHHHHHC
Q 011102          449 IFMASGRLAKCRDVCKEAEMA  469 (493)
Q Consensus       449 ~~~~~g~~~~A~~l~~~m~~~  469 (493)
                      +|.+.|++++|.+.|++..+.
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~  108 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEA  108 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHh
Confidence            999999999999999998764

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=97.45  E-value=0.036  Score=52.69  Aligned_cols=165  Identities=5%  Similarity=-0.060  Sum_probs=106.8

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHH--HHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCC----
Q 011102          277 GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYM--LVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQK----  350 (493)
Q Consensus       277 g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~--~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~----  350 (493)
                      +++++++++++.+.+.. .-+-.+|+.---.+.+. +.++  ++++.++.+.+. . .-|-..|+---..+.+.|+    
T Consensus       124 ~~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l-~~~~~~~EL~~~~~~i~~-d-~~N~sAW~~R~~ll~~l~~~~~~  199 (306)
T 3dra_A          124 FDPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTF-DLHNDAKELSFVDKVIDT-D-LKNNSAWSHRFFLLFSKKHLATD  199 (306)
T ss_dssp             CCTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCTTCHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHSSGGGCCH
T ss_pred             CCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHh-cccChHHHHHHHHHHHHh-C-CCCHHHHHHHHHHHHhccccchh
Confidence            56778888888777643 23556666555555555 6666  788888887765 2 2456666655555555555    


Q ss_pred             --HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHH-HHHHHHHHHHCC--CCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          351 --FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCRE-ALTVVWNMEASN--CLFDLPAYRVVIKLFVALNDISRAI  425 (493)
Q Consensus       351 --~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~-A~~l~~~M~~~g--i~pd~~ty~~li~~~~~~g~~~~A~  425 (493)
                        ++++++.+++..... .-|...|+-+-..+.+.|+..+ +.++..+..+.+  -..+...+..+...|.+.|+.++|.
T Consensus       200 ~~~~eEl~~~~~aI~~~-p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~  278 (306)
T 3dra_A          200 NTIDEELNYVKDKIVKC-PQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESR  278 (306)
T ss_dssp             HHHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hhHHHHHHHHHHHHHhC-CCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHH
Confidence              778888887776543 4577778877777777776443 445665554432  1346677888888888888888888


Q ss_pred             HHHHHHHHCCCCCCHHHHHHH
Q 011102          426 RYFSKLKEAGFCPTYDIYRDM  446 (493)
Q Consensus       426 ~~~~~m~~~g~~p~~~ty~~l  446 (493)
                      ++++.+.+.-=+....-|+..
T Consensus       279 ~~~~~l~~~~Dpir~~yW~~~  299 (306)
T 3dra_A          279 TVYDLLKSKYNPIRSNFWDYQ  299 (306)
T ss_dssp             HHHHHHHHTTCGGGHHHHHHH
T ss_pred             HHHHHHHhccChHHHHHHHHH
Confidence            888888753212234444433

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.44  E-value=0.00079  Score=56.17  Aligned_cols=60  Identities=10%  Similarity=-0.114  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCC-CCH----HHHHHHHHHHhcCCCCHHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRM-LDP----SIYAKLILELGKNPDKYMLVMTLLDEL  325 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-pd~----~t~~~li~~~~~~~~~~~~a~~l~~~m  325 (493)
                      ++..+-..|...|++++|.+.+++..+..-. .+.    .++..+-..+... |++++|...+++.
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~a   75 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFL-GEFETASEYYKKT   75 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHc-CCHHHHHHHHHHH
Confidence            4666667777777777777777766542100 111    2344444445555 5555555555554

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.43  E-value=0.0024  Score=52.99  Aligned_cols=95  Identities=13%  Similarity=-0.015  Sum_probs=62.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFV  416 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~  416 (493)
                      .+..+-..+.+.|++++|...|++..... +.+...|..+-..|.+.|++++|...|++..+..- -+...|..+-.+|.
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~   97 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDI-NEPRFPFHAAECHL   97 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CCcHHHHHHHHHHH
Confidence            34445566677777777777777766542 23566677777777777777777777777665431 23455666666777


Q ss_pred             HcCCHHHHHHHHHHHHH
Q 011102          417 ALNDISRAIRYFSKLKE  433 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~  433 (493)
                      ..|++++|...|+...+
T Consensus        98 ~~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           98 QLGDLDGAESGFYSARA  114 (142)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            77777777777776653

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.41  E-value=0.0021  Score=49.88  Aligned_cols=89  Identities=7%  Similarity=-0.064  Sum_probs=34.6

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHc-CC
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL-FDLPAYRVVIKLFVAL-ND  420 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~-pd~~ty~~li~~~~~~-g~  420 (493)
                      ..+.+.|++++|...|++..+.. ..+...|..+-..+...|++++|.+.|++..+..-. .+...+..+-..+.+. |+
T Consensus        14 ~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~~~~~~   92 (112)
T 2kck_A           14 VLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALRYIEGK   92 (112)
T ss_dssp             HHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHTTCSSC
T ss_pred             HHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHHHHhCC
Confidence            33334444444444444433221 122333444444444444444444444443332100 0233344444444444 44


Q ss_pred             HHHHHHHHHHHH
Q 011102          421 ISRAIRYFSKLK  432 (493)
Q Consensus       421 ~~~A~~~~~~m~  432 (493)
                      +++|.+.|+...
T Consensus        93 ~~~A~~~~~~~~  104 (112)
T 2kck_A           93 EVEAEIAEARAK  104 (112)
T ss_dssp             SHHHHHHHHHHG
T ss_pred             HHHHHHHHHHHh
Confidence            444444444443

>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=97.39  E-value=0.0049  Score=51.71  Aligned_cols=90  Identities=7%  Similarity=-0.032  Sum_probs=40.5

Q ss_pred             HHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC
Q 011102          304 LILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE  383 (493)
Q Consensus       304 li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~  383 (493)
                      +-..+.+. |++++|...|+.....  -..+...|..+-.+|.+.|++++|...|++..+.. +-+...|..+-.+|...
T Consensus        27 ~g~~~~~~-g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~  102 (148)
T 2vgx_A           27 LAFNQYQS-GXYEDAHXVFQALCVL--DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQX  102 (148)
T ss_dssp             HHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHT
T ss_pred             HHHHHHHc-CChHHHHHHHHHHHHc--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHc
Confidence            33344444 4555555555544432  11234444444444555555555555555443321 12334444444455555


Q ss_pred             CCHHHHHHHHHHHH
Q 011102          384 KKCREALTVVWNME  397 (493)
Q Consensus       384 g~~~~A~~l~~~M~  397 (493)
                      |++++|.+.|+...
T Consensus       103 g~~~~A~~~~~~al  116 (148)
T 2vgx_A          103 GELAEAESGLFLAQ  116 (148)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            55555555554443

>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=97.36  E-value=0.007  Score=48.64  Aligned_cols=88  Identities=9%  Similarity=-0.005  Sum_probs=35.8

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      ..+.+.|++++|...|++..+.. +.+...|..+-.+|.+.|++++|++.+++..+..- -+...|..+-.++...|+++
T Consensus        12 ~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~   89 (126)
T 3upv_A           12 KEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDP-NFVRAYIRKATAQIAVKEYA   89 (126)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHhCHH
Confidence            33444444444444444433221 12334444444444444444444444444333211 12333444444444444444


Q ss_pred             HHHHHHHHHH
Q 011102          423 RAIRYFSKLK  432 (493)
Q Consensus       423 ~A~~~~~~m~  432 (493)
                      +|...|++..
T Consensus        90 ~A~~~~~~al   99 (126)
T 3upv_A           90 SALETLDAAR   99 (126)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            4444444433

>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=97.34  E-value=0.0056  Score=49.78  Aligned_cols=105  Identities=13%  Similarity=0.140  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--CCCC----HHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN--CLFD----LPAYRV  410 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g--i~pd----~~ty~~  410 (493)
                      .+.-+-..|.+.|++++|++.|++..+.. +-+...|+.+-.+|.+.|++++|++.+++..+..  ..++    ..+|..
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            45556667777788888888887766542 2356777777788888888888888877765421  1112    134555


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          411 VIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYR  444 (493)
Q Consensus       411 li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~  444 (493)
                      +=..+...|++++|.+.|++-.+.  .||..+..
T Consensus        89 lg~~~~~~~~~~~A~~~~~kal~~--~~~~~~~~  120 (127)
T 4gcn_A           89 AGNAFQKQNDLSLAVQWFHRSLSE--FRDPELVK  120 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--SCCHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhh--CcCHHHHH
Confidence            666677888888888888776642  35554433

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=97.34  E-value=0.0037  Score=51.79  Aligned_cols=87  Identities=6%  Similarity=-0.079  Sum_probs=37.9

Q ss_pred             HHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH
Q 011102          307 ELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC  386 (493)
Q Consensus       307 ~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~  386 (493)
                      .+.+. |++++|...|+.....  -..+...|..+-.+|.+.|++++|...|+...+.. +-+...|..+-.+|...|++
T Consensus        27 ~~~~~-g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~  102 (142)
T 2xcb_A           27 NQYQA-GKWDDAQKIFQALCML--DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQLGDL  102 (142)
T ss_dssp             HHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCH
T ss_pred             HHHHH-ccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCH
Confidence            34444 4445555444444332  11233344444444444455555555444443321 12233344444444444555


Q ss_pred             HHHHHHHHHHH
Q 011102          387 REALTVVWNME  397 (493)
Q Consensus       387 ~~A~~l~~~M~  397 (493)
                      ++|.+.|+...
T Consensus       103 ~~A~~~~~~al  113 (142)
T 2xcb_A          103 DGAESGFYSAR  113 (142)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55554444433

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.27  E-value=0.095  Score=53.43  Aligned_cols=142  Identities=6%  Similarity=0.005  Sum_probs=75.5

Q ss_pred             HHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHH------------------------
Q 011102          317 LVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVM------------------------  372 (493)
Q Consensus       317 ~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t------------------------  372 (493)
                      .+..+|+++...  ...+...|-..+.-+.+.|+++.|..+|+.....  +.+...                        
T Consensus       197 Rv~~~ye~al~~--~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~  272 (493)
T 2uy1_A          197 RMHFIHNYILDS--FYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSLYYGLVMDEEAVYGDLKRKYSMG  272 (493)
T ss_dssp             HHHHHHHHHHHH--TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHTTCTHHHHHHHHHTC--
T ss_pred             HHHHHHHHHHHc--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHHHHHhhcchhHHHHHHHHHHHhh
Confidence            345566665543  3344566666667777788888888888876655  222211                        


Q ss_pred             ----------------HHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHH--HHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          373 ----------------YTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYR--VVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       373 ----------------y~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~--~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                                      |-..+..+.+.+..+.|.++|+.....+  .+...|.  +.+...+ .++.+.|..+|+...+.
T Consensus       273 ~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~  349 (493)
T 2uy1_A          273 EAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIELGNEG--VGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLK  349 (493)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHH
T ss_pred             ccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence                            2222222233455666777777662111  1222332  2222222 23577777777766643


Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          435 GFCPTYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       435 g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      - .-+...|...++-..+.|+.+.|..+|+..
T Consensus       350 ~-~~~~~~~~~yid~e~~~~~~~~aR~l~er~  380 (493)
T 2uy1_A          350 H-PDSTLLKEEFFLFLLRIGDEENARALFKRL  380 (493)
T ss_dssp             C-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHS
T ss_pred             C-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            2 112334455566566667777777666664

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.14  E-value=0.0099  Score=47.68  Aligned_cols=59  Identities=12%  Similarity=0.044  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLKEAGFCPT----YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~----~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +..+-..+.+.|++++|...|+...+..  |+    ...+..+..+|.+.|++++|.+.|++..+
T Consensus        42 ~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           42 LYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3334444444555555555554444322  11    33344444455555555555555555543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.13  E-value=0.0009  Score=53.56  Aligned_cols=83  Identities=12%  Similarity=-0.020  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHHcC--CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          349 QKFGVVESLFHWFTHSG--RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIR  426 (493)
Q Consensus       349 g~~~~A~~l~~~m~~~g--~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~  426 (493)
                      |++++|+..|++..+.+  -+-+...|..+-..|.+.|++++|.+.|++..+..- -+...+..+-.++.+.|++++|..
T Consensus         4 g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            4 GLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFP-NHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ---CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CchHHHHHHHHHHHHcCCHHHHHH
Confidence            44444555554444322  111233444444445555555555555554443311 123344444444455555555555


Q ss_pred             HHHHHH
Q 011102          427 YFSKLK  432 (493)
Q Consensus       427 ~~~~m~  432 (493)
                      .|++..
T Consensus        83 ~~~~al   88 (117)
T 3k9i_A           83 LLLKII   88 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            554443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.12  E-value=0.0063  Score=61.62  Aligned_cols=124  Identities=7%  Similarity=-0.094  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Q 011102          298 PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS-------------QQDCTAIMKVGIRLQKFGVVESLFHWFTHS  364 (493)
Q Consensus       298 ~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  364 (493)
                      ...|..+-..+.+. |++++|...|++..+...-.++             ...|..+-.+|.+.|++++|+..|++..+.
T Consensus       268 a~~~~~~G~~~~~~-g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  346 (457)
T 1kt0_A          268 AAIVKEKGTVYFKG-GKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL  346 (457)
T ss_dssp             HHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            44566666777777 8888888888877653111111             355666666666666666666666665543


Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHH
Q 011102          365 GRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAI  425 (493)
Q Consensus       365 g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~  425 (493)
                      . +.+...|..+-.+|...|++++|...|++..+.  .| +...+..+-..+.+.|+.++|.
T Consensus       347 ~-p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          347 D-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             S-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            2 234556666666666666666666666665543  22 2234555555555555555544

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.11  E-value=0.013  Score=46.98  Aligned_cols=90  Identities=10%  Similarity=-0.047  Sum_probs=57.5

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTV---VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD----LPAYRVVIKL  414 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~---~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd----~~ty~~li~~  414 (493)
                      -..+.+.|++++|.+.|++..+..-. +.   ..+..+-..|.+.|++++|...|++..+..  |+    ...+..+-..
T Consensus         9 a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~   85 (129)
T 2xev_A            9 AFDALKNGKYDDASQLFLSFLELYPN-GVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLS   85 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCSS-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHH
Confidence            34556677777777777776653211 11   356666677777777777777777766542  22    4456666667


Q ss_pred             HHHcCCHHHHHHHHHHHHHC
Q 011102          415 FVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~~~  434 (493)
                      +.+.|++++|...|+...+.
T Consensus        86 ~~~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHH
Confidence            77777777777777777643

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.08  E-value=0.003  Score=64.40  Aligned_cols=83  Identities=11%  Similarity=-0.043  Sum_probs=39.0

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTV  392 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  392 (493)
                      |++++|.+.+++..+.  -.-+...|..+-.+|.+.|++++|.+.|++..+.. +-+...|..+-.+|.+.|++++|++.
T Consensus        20 g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA~~~   96 (477)
T 1wao_1           20 KDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAALRD   96 (477)
T ss_dssp             TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4555555555554433  11234444555555555555555555555544331 12344444445555555555555555


Q ss_pred             HHHHHH
Q 011102          393 VWNMEA  398 (493)
Q Consensus       393 ~~~M~~  398 (493)
                      |++..+
T Consensus        97 ~~~al~  102 (477)
T 1wao_1           97 YETVVK  102 (477)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            554433

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.07  E-value=0.0062  Score=49.08  Aligned_cols=88  Identities=8%  Similarity=0.012  Sum_probs=39.6

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      ..+.+.|++++|...|++..+.. +-+...|..+-..+...|++++|+..|++..+..- -+...+..+-..|.+.|+++
T Consensus        25 ~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~~~~~la~~~~~~g~~~  102 (121)
T 1hxi_A           25 LSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVSHTNEHNAN  102 (121)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHH
Confidence            34445555555555555544321 12344444444455555555555555544433211 12334444444444444555


Q ss_pred             HHHHHHHHHH
Q 011102          423 RAIRYFSKLK  432 (493)
Q Consensus       423 ~A~~~~~~m~  432 (493)
                      +|...|++..
T Consensus       103 ~A~~~~~~al  112 (121)
T 1hxi_A          103 AALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5544444443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.06  E-value=0.0038  Score=63.74  Aligned_cols=124  Identities=10%  Similarity=-0.101  Sum_probs=81.4

Q ss_pred             HHHcCCHHHHHHHHHHHHHc---CCC---C-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----C-CCCCH-HHHHH
Q 011102          345 GIRLQKFGVVESLFHWFTHS---GRD---P-TVVMYTTLIHSRLSEKKCREALTVVWNMEAS-----N-CLFDL-PAYRV  410 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~---g~~---p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-----g-i~pd~-~ty~~  410 (493)
                      +...|++++|+.++++..+.   -+-   | ...+++.|...|...|++++|+.++++..+.     | -.|++ .+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            44567778887777665432   111   2 2466788888888888888888877775431     2 12333 56777


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHH-----HCCC-CCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          411 VIKLFVALNDISRAIRYFSKLK-----EAGF-CPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       411 li~~~~~~g~~~~A~~~~~~m~-----~~g~-~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |-..|...|++++|..++++..     ..|- .|+ ..+.+.+-.++...|.+++|+.++..+.+
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8888888888888888877654     1231 122 33455666777778888888888888865

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.04  E-value=0.0013  Score=52.61  Aligned_cols=87  Identities=10%  Similarity=-0.091  Sum_probs=68.7

Q ss_pred             cCCCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011102          382 SEKKCREALTVVWNMEASNC--LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKC  459 (493)
Q Consensus       382 ~~g~~~~A~~l~~~M~~~gi--~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A  459 (493)
                      ..|++++|+..|++..+.+.  .-+...+..+-..|.+.|++++|...|++..+..-. +...|..+..+|.+.|++++|
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPN-HQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHcCCHHHH
Confidence            46889999999999887541  223467888888999999999999999999865432 578888999999999999999


Q ss_pred             HHHHHHHHHC
Q 011102          460 RDVCKEAEMA  469 (493)
Q Consensus       460 ~~l~~~m~~~  469 (493)
                      .+.+++..+.
T Consensus        81 ~~~~~~al~~   90 (117)
T 3k9i_A           81 VELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999998764

>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=97.01  E-value=0.27  Score=47.42  Aligned_cols=201  Identities=6%  Similarity=-0.046  Sum_probs=128.0

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCC-CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHH----
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPD-KYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFG----  352 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~-~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~----  352 (493)
                      .+++++++++.+.... .-+..+|+.--..+.+..+ +.++++++++.+.+.  -.-|-..|+--...+.+.|.++    
T Consensus       104 ~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~L~~--dpkNy~AW~~R~wvl~~l~~~~~~~~  180 (349)
T 3q7a_A          104 SLEDELRLMNEFAVQN-LKSYQVWHHRLLLLDRISPQDPVSEIEYIHGSLLP--DPKNYHTWAYLHWLYSHFSTLGRISE  180 (349)
T ss_dssp             CHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHHHCCSCCHHHHHHHHHHTSS--CTTCHHHHHHHHHHHHHHHHTTCCCH
T ss_pred             hHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhccccccch
Confidence            4788888888888754 2244556643333322212 567888888888765  2346667776555555555555    


Q ss_pred             ----HHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC-------HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          353 ----VVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK-------CREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       353 ----~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~-------~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~  421 (493)
                          ++++.++++.+.. .-|...|+-.-..+.+.++       ++++++.++++..... -|...|+-+-..+.+.|+-
T Consensus       181 ~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P-~n~SaW~Ylr~Ll~~~~~~  258 (349)
T 3q7a_A          181 AQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIP-HNVSAWNYLRGFLKHFSLP  258 (349)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCC
T ss_pred             hhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCCC
Confidence                8888888887653 4577888888888877776       6888888888776432 3566777666666665542


Q ss_pred             --------------------HHHHHHHHHHHHCC-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHH
Q 011102          422 --------------------SRAIRYFSKLKEAG-----FCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQ  476 (493)
Q Consensus       422 --------------------~~A~~~~~~m~~~g-----~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~  476 (493)
                                          .....+..++...+     -.+.......|.+.|...|+.++|.++++.+.+.-=+....
T Consensus       259 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~~dpir~~  338 (349)
T 3q7a_A          259 LVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLPVPLALEYLADSFIEQNRVDDAAKVFEKLSSEYDQMRAG  338 (349)
T ss_dssp             SGGGHHHHGGGTC--------------CCCCC-CCCSSCCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCGGGHH
T ss_pred             cccccccccccccccccccchhHHHHHHHHHhcccccccCCCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhhChHHHH
Confidence                                33344444443222     13678888999999999999999999999986542233344


Q ss_pred             HHHHHHH
Q 011102          477 TVVELLQ  483 (493)
Q Consensus       477 t~~~Ll~  483 (493)
                      -|+...+
T Consensus       339 yw~~~~~  345 (349)
T 3q7a_A          339 YWEFRRR  345 (349)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.98  E-value=0.022  Score=48.07  Aligned_cols=62  Identities=13%  Similarity=0.098  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ..|..+-.+|.+.|++++|...++...+.. .-+...|..+-.+|...|++++|.+.|++..+
T Consensus        64 ~~~~nla~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           64 PLYANMSQCYLNIGDLHEAEETSSEVLKRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence            456666666777777777777777666543 12456666677777777777777777776655

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=96.94  E-value=0.011  Score=47.53  Aligned_cols=93  Identities=9%  Similarity=-0.141  Sum_probs=58.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMAS  453 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~  453 (493)
                      ..+-..+.+.|++++|...|++..+..- -+...|..+-..+...|++++|...|++..+..- -+...|..+-.+|.+.
T Consensus        21 ~~~g~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P-~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           21 MEEGLSMLKLANLAEAALAFEAVCQKEP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVSHTNE   98 (121)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHc
Confidence            3444556667777777777776655321 2455566666666777777777777776664432 1455666666677777


Q ss_pred             CCHHHHHHHHHHHHH
Q 011102          454 GRLAKCRDVCKEAEM  468 (493)
Q Consensus       454 g~~~~A~~l~~~m~~  468 (493)
                      |++++|.+.+++..+
T Consensus        99 g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           99 HNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHH
Confidence            777777777776654

>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=96.91  E-value=0.017  Score=54.19  Aligned_cols=98  Identities=12%  Similarity=0.008  Sum_probs=82.4

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011102          334 SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIK  413 (493)
Q Consensus       334 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~  413 (493)
                      +...+..+-..+.+.|++++|...|++..+.. +-+...|..+-..|.+.|++++|.+.+++..+.. .-+...+..+-.
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            45677788889999999999999999987652 2378889999999999999999999999887642 235678888889


Q ss_pred             HHHHcCCHHHHHHHHHHHHH
Q 011102          414 LFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       414 ~~~~~g~~~~A~~~~~~m~~  433 (493)
                      +|.+.|++++|...|+...+
T Consensus        81 ~~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           81 CQLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999998764

>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=96.86  E-value=0.011  Score=59.87  Aligned_cols=129  Identities=12%  Similarity=0.029  Sum_probs=102.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC----------------HHHHHHHHHHHhcCCCCHHHHHHHHHHHh
Q 011102          263 KGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD----------------PSIYAKLILELGKNPDKYMLVMTLLDELG  326 (493)
Q Consensus       263 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd----------------~~t~~~li~~~~~~~~~~~~a~~l~~~m~  326 (493)
                      ...|..+-..|.+.|++++|...|++..+..  |+                ...|..+-.+|.+. |++++|+..+++..
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~-g~~~~A~~~~~~al  344 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWL--EMEYGLSEKESKASESFLLAAFLNLAMCYLKL-REYTKAVECCDKAL  344 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--TTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccCChHHHHHHHHHHHHHHHHHHHHHHHh-cCHHHHHHHHHHHH
Confidence            3468888899999999999999999988743  33                57888888899999 99999999999987


Q ss_pred             hcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcCCCHHHHHH-HHHHHHH
Q 011102          327 QRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLSEKKCREALT-VVWNMEA  398 (493)
Q Consensus       327 ~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~~g~~~~A~~-l~~~M~~  398 (493)
                      ..  -.-+...|..+-.+|.+.|++++|...|++..+.  .| +...|..+-..+.+.++.++|.+ ++..|..
T Consensus       345 ~~--~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f~  414 (457)
T 1kt0_A          345 GL--DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMCQKKAKEHNERDRRIYANMFK  414 (457)
T ss_dssp             HH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             hc--CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            75  2346788999999999999999999999998754  34 45678888888888888887764 4555543

>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=96.85  E-value=0.0056  Score=62.39  Aligned_cols=122  Identities=11%  Similarity=-0.012  Sum_probs=89.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHc
Q 011102          269 TAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRL  348 (493)
Q Consensus       269 li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~  348 (493)
                      +-..+.+.|++++|.+.|++..+.. .-+..+|..+-..|.+. |++++|.+.+++..+.  -.-+...|..+-.+|.+.
T Consensus        12 lg~~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~-g~~~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~   87 (477)
T 1wao_1           12 QANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRT-ECYGYALGDATRAIEL--DKKYIKGYYRRAASNMAL   87 (477)
T ss_dssp             SSSSTTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHh-cCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHc
Confidence            3345778899999999999998853 22477888899999999 9999999999998875  234677889999999999


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH--HHcCCCHHHHHHHHHH
Q 011102          349 QKFGVVESLFHWFTHSGRDPTVVMYTTLIHS--RLSEKKCREALTVVWN  395 (493)
Q Consensus       349 g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~--~~~~g~~~~A~~l~~~  395 (493)
                      |++++|.+.|++..+.. +-+...+..+-.+  +.+.|++++|++++++
T Consensus        88 g~~~eA~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~  135 (477)
T 1wao_1           88 GKFRAALRDYETVVKVK-PHDKDAKMKYQECNKIVKQKAFERAIAGDEH  135 (477)
T ss_dssp             TCHHHHHHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHHHCCC------
T ss_pred             CCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            99999999999987642 1122334444444  7777888888888775

>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=96.82  E-value=0.015  Score=57.12  Aligned_cols=90  Identities=9%  Similarity=0.032  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRI  449 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~  449 (493)
                      ...|+.+-.+|.+.|++++|++.+++..+..- -+...|..+-.+|.+.|++++|...|++..+..- -+...+..+-..
T Consensus       273 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P-~~~~~~~~l~~~  350 (370)
T 1ihg_A          273 LSCVLNIGACKLKMSDWQGAVDSCLEALEIDP-SNTKALYRRAQGWQGLKEYDQALADLKKAQEIAP-EDKAIQAELLKV  350 (370)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCHHHHHHHHHHHHHhCc-hhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            45566666667777777777777776665321 2455666666677777777777777776664321 145555566666


Q ss_pred             HHHcCCHHHHHH
Q 011102          450 FMASGRLAKCRD  461 (493)
Q Consensus       450 ~~~~g~~~~A~~  461 (493)
                      +.+.++.+++.+
T Consensus       351 ~~~~~~~~~a~k  362 (370)
T 1ihg_A          351 KQKIKAQKDKEK  362 (370)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666666555543

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=96.80  E-value=0.0075  Score=61.50  Aligned_cols=125  Identities=10%  Similarity=-0.026  Sum_probs=93.0

Q ss_pred             HhcCCCCHHHHHHHHHHHhhc--CCCC---CC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-----cCC-CCC-HHHHH
Q 011102          308 LGKNPDKYMLVMTLLDELGQR--DDLN---LS-QQDCTAIMKVGIRLQKFGVVESLFHWFTH-----SGR-DPT-VVMYT  374 (493)
Q Consensus       308 ~~~~~~~~~~a~~l~~~m~~~--~g~~---p~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~-----~g~-~p~-~~ty~  374 (493)
                      +-.. |++++|+.++++....  .-+.   |+ ..+++.|...|...|++++|+.++++..+     .|- .|+ ..+|+
T Consensus       319 ~~~q-g~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          319 ARSE-GLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHTT-TCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHhC-CCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            4456 9999999998876432  0122   22 45789999999999999999999988653     222 233 47799


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHH-----CCC-CCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          375 TLIHSRLSEKKCREALTVVWNMEA-----SNC-LFDL-PAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       375 ~li~~~~~~g~~~~A~~l~~~M~~-----~gi-~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      .|-..|...|++++|+.++++..+     .|- .|++ .+.+.+-.++...|.+++|+.+|..+.+
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999998653     232 1333 3456666778888999999999999874

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.78  E-value=0.025  Score=46.73  Aligned_cols=113  Identities=12%  Similarity=-0.008  Sum_probs=75.9

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHH
Q 011102          349 QKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA----LNDISRA  424 (493)
Q Consensus       349 g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~----~g~~~~A  424 (493)
                      +++++|.+.|++..+.| .++..    |-..|...+.+++|.+.|++..+.|   +...+..|=..|..    .++.++|
T Consensus         9 ~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A   80 (138)
T 1klx_A            9 KDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             cCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHH
Confidence            45677777777776666 33333    4455555566777777777776654   45566666666666    6778888


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCc
Q 011102          425 IRYFSKLKEAGFCPTYDIYRDMIRIFMA----SGRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       425 ~~~~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~m~~~g~~  472 (493)
                      .++|+.-.+.|   +...+..|-..|..    .++.++|.+.|++..+.|..
T Consensus        81 ~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~  129 (138)
T 1klx_A           81 AQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGSE  129 (138)
T ss_dssp             HHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCCH
Confidence            88887777664   45566667677777    77888888888887777643

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.60  E-value=0.086  Score=56.87  Aligned_cols=150  Identities=15%  Similarity=0.071  Sum_probs=89.0

Q ss_pred             CCCCHHHHHH-HHhhhcc-cCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHH
Q 011102          179 SHKDVAEVLD-KCGRFLR-KGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLEN  256 (493)
Q Consensus       179 ~~~~~~~a~~-~~~~m~~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~  256 (493)
                      ..+++++|.+ .+ .+.+ .+....++..+.+.|.+++|+++.+.-..             -.......|+++  +++..
T Consensus       611 ~~~~~~~a~~~~l-~~i~~~~~~~~~~~~l~~~~~~~~a~~~~~~~~~-------------~f~~~l~~~~~~--~A~~~  674 (814)
T 3mkq_A          611 LRGEIEEAIENVL-PNVEGKDSLTKIARFLEGQEYYEEALNISPDQDQ-------------KFELALKVGQLT--LARDL  674 (814)
T ss_dssp             HTTCHHHHHHHTG-GGCCCHHHHHHHHHHHHHTTCHHHHHHHCCCHHH-------------HHHHHHHHTCHH--HHHHH
T ss_pred             HhCCHHHHHHHHH-hcCCchHHHHHHHHHHHhCCChHHheecCCCcch-------------heehhhhcCCHH--HHHHH
Confidence            3577788777 44 2333 44557777788888888888876632211             012234456643  34444


Q ss_pred             hhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHH
Q 011102          257 FVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQ  336 (493)
Q Consensus       257 ~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~  336 (493)
                      ...+.+...|..|-..+.+.|+++.|.+.|..+.+         |..+...+... ++.+...++-+..... |      
T Consensus       675 ~~~~~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~-~~~~~~~~~~~~a~~~-~------  737 (814)
T 3mkq_A          675 LTDESAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSF-NNKEGLVTLAKDAETT-G------  737 (814)
T ss_dssp             HTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHT-TCHHHHHHHHHHHHHT-T------
T ss_pred             HHhhCcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHc-CCHHHHHHHHHHHHHc-C------
Confidence            66666777888888888888888888888887654         34444444445 5666555554444443 2      


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWF  361 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m  361 (493)
                      -++....+|.+.|++++|.++|.++
T Consensus       738 ~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          738 KFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             chHHHHHHHHHcCCHHHHHHHHHHc
Confidence            1344444555566666666555443

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=96.48  E-value=0.21  Score=50.85  Aligned_cols=187  Identities=11%  Similarity=0.078  Sum_probs=123.9

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC--------CCCC
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRD--------DLNL  333 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~--------g~~p  333 (493)
                      ...+|-..+.-+.+.|+++.|..+|++....   |...........+.+. +   +.   ++.+....        +..+
T Consensus       212 ~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~---P~~~~l~~~y~~~~e~-~---~~---~~~l~~~~~~~~~~~~~~~~  281 (493)
T 2uy1_A          212 AEEVYFFYSEYLIGIGQKEKAKKVVERGIEM---SDGMFLSLYYGLVMDE-E---AV---YGDLKRKYSMGEAESAEKVF  281 (493)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHTTC-T---HH---HHHHHHHTC----------C
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC---CCcHHHHHHHHhhcch-h---HH---HHHHHHHHHhhccchhhhhc
Confidence            4557777778888999999999999999987   4433222211112122 2   11   22222110        0001


Q ss_pred             ---CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHH--HHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHH
Q 011102          334 ---SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYT--TLIHSRLSEKKCREALTVVWNMEASNCLFD-LPA  407 (493)
Q Consensus       334 ---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~--~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~t  407 (493)
                         ....|-..+..+.+.+.++.|..+|+.....+  .+...|-  +.+...+ .++.+.|.++|+...+.-  |+ ...
T Consensus       282 ~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~--~~~~v~i~~A~lE~~~-~~d~~~ar~ife~al~~~--~~~~~~  356 (493)
T 2uy1_A          282 SKELDLLRINHLNYVLKKRGLELFRKLFIELGNEG--VGPHVFIYCAFIEYYA-TGSRATPYNIFSSGLLKH--PDSTLL  356 (493)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSC--CCHHHHHHHHHHHHHH-HCCSHHHHHHHHHHHHHC--TTCHHH
T ss_pred             ccccHHHHHHHHHHHHHcCCHHHHHHHHHHhhCCC--CChHHHHHHHHHHHHH-CCChHHHHHHHHHHHHHC--CCCHHH
Confidence               12456667777777889999999999882222  2333343  4444333 236999999999977642  33 344


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      +...++...+.|+.+.|..+|+...     -....|...++--...|+.+.+.++++++.+
T Consensus       357 ~~~yid~e~~~~~~~~aR~l~er~~-----k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          357 KEEFFLFLLRIGDEENARALFKRLE-----KTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHSC-----CBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5667777888999999999999973     2577899998888888999999999888864

>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=96.44  E-value=0.029  Score=54.95  Aligned_cols=137  Identities=9%  Similarity=-0.065  Sum_probs=77.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      .|..+-..+.+.|++++|++.|++..+.-  ++.          ... ...+++.+       .  -..+...|..+-.+
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~--~~~----------~~~-~~~~~~~~-------~--~~~~~~~~~nla~~  282 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYV--EGS----------RAA-AEDADGAK-------L--QPVALSCVLNIGAC  282 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHH--HHH----------HHH-SCHHHHGG-------G--HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHh--hcC----------ccc-cChHHHHH-------H--HHHHHHHHHHHHHH
Confidence            57778888899999999999998876510  000          000 01111110       0  00123455566666


Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~  423 (493)
                      |.+.|++++|++.+++..+.. +-+...|..+-.+|...|++++|++.|++..+.  .| +...+..+-..+.+.++.++
T Consensus       283 ~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~  359 (370)
T 1ihg_A          283 KLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKD  359 (370)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHH
Confidence            666666666666666665432 224566666666666777777777776665543  23 34455555555555666655


Q ss_pred             HHH
Q 011102          424 AIR  426 (493)
Q Consensus       424 A~~  426 (493)
                      +.+
T Consensus       360 a~k  362 (370)
T 1ihg_A          360 KEK  362 (370)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.43  E-value=0.0091  Score=57.75  Aligned_cols=147  Identities=13%  Similarity=-0.058  Sum_probs=76.7

Q ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011102          298 PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLI  377 (493)
Q Consensus       298 ~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li  377 (493)
                      ...+..+-..+.+. |++++|...|++....   .|+...       +...|+.+++...+   .       ...|+.+-
T Consensus       179 a~~~~~~g~~~~~~-g~~~~A~~~y~~Al~~---~p~~~~-------~~~~~~~~~~~~~l---~-------~~~~~nla  237 (338)
T 2if4_A          179 ADRRKMDGNSLFKE-EKLEEAMQQYEMAIAY---MGDDFM-------FQLYGKYQDMALAV---K-------NPCHLNIA  237 (338)
T ss_dssp             HHHHHHHHHHTCSS-SCCHHHHHHHHHHHHH---SCHHHH-------HTCCHHHHHHHHHH---H-------THHHHHHH
T ss_pred             HHHHHHHHHHHHhc-CCHHHHHHHHHHHHHH---hccchh-------hhhcccHHHHHHHH---H-------HHHHHHHH
Confidence            45566667777888 9999999999987654   244331       12223333333222   1       13677777


Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHH-HHHcCC
Q 011102          378 HSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPT-YDIYRDMIRI-FMASGR  455 (493)
Q Consensus       378 ~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~li~~-~~~~g~  455 (493)
                      .+|.+.|++++|+..+++..+.. .-+...|..+-.+|...|++++|...|++..+.  .|+ ...+..+... ....+.
T Consensus       238 ~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~  314 (338)
T 2if4_A          238 ACLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKAL  314 (338)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------------------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHH
Confidence            88888888888888888776542 135667777888888888888888888877532  232 3334444433 233456


Q ss_pred             HHHHHHHHHHHHH
Q 011102          456 LAKCRDVCKEAEM  468 (493)
Q Consensus       456 ~~~A~~l~~~m~~  468 (493)
                      .+++.++|..|..
T Consensus       315 ~~~a~~~~~~~l~  327 (338)
T 2if4_A          315 YQKQKEMYKGIFK  327 (338)
T ss_dssp             -------------
T ss_pred             HHHHHHHHHHhhC
Confidence            6677777777754

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=96.32  E-value=0.064  Score=45.07  Aligned_cols=96  Identities=9%  Similarity=-0.052  Sum_probs=59.0

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHc-------C----------CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHS-------G----------RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN  400 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~-------g----------~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g  400 (493)
                      +...-..+.+.|++++|...|.+..+.       .          -+-+...|..+-.+|.+.|++++|+..+++..+..
T Consensus        14 ~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~   93 (162)
T 3rkv_A           14 LRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVLKRE   93 (162)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcC
Confidence            344445555666666666666554432       0          01223566777777777777777777777766542


Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          401 CLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       401 i~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                       .-+...|..+-.+|...|++++|...|+...+.
T Consensus        94 -p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           94 -ETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence             224566777777777777777777777776643

>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=96.25  E-value=0.17  Score=42.78  Aligned_cols=77  Identities=13%  Similarity=0.067  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHC-----CCCCC-HHHH----HHHHHHHHHcCCHHHHHHHHHHHHH-----CCC
Q 011102          407 AYRVVIKLFVALNDISRAIRYFSKLKEA-----GFCPT-YDIY----RDMIRIFMASGRLAKCRDVCKEAEM-----AGF  471 (493)
Q Consensus       407 ty~~li~~~~~~g~~~~A~~~~~~m~~~-----g~~p~-~~ty----~~li~~~~~~g~~~~A~~l~~~m~~-----~g~  471 (493)
                      .|+.+-.++.+.|++++|...+++-.+.     .+.|+ ...|    ...-.++...|++++|++.|++..+     .|+
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~  138 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGE  138 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHH
Confidence            5555555566666666666666655542     12343 3455    6666677777777777777777753     466


Q ss_pred             ccCHHHHHHHHH
Q 011102          472 KLDKQTVVELLQ  483 (493)
Q Consensus       472 ~pd~~t~~~Ll~  483 (493)
                      .+........+.
T Consensus       139 ~~~~~~~~~~~~  150 (159)
T 2hr2_A          139 TPGKERMMEVAI  150 (159)
T ss_dssp             CTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666555554444

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=96.17  E-value=0.0059  Score=47.47  Aligned_cols=63  Identities=13%  Similarity=0.055  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      ...|..+-..+.+.|++++|.+.|++..+.. ..+...|..+-.+|.+.|++++|...|++..+
T Consensus         4 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            4 FEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            3445555555555566666666665554431 12344555555556666666666666665553

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.16  E-value=0.087  Score=43.31  Aligned_cols=111  Identities=9%  Similarity=-0.028  Sum_probs=58.9

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH----cCCHH
Q 011102          277 GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR----LQKFG  352 (493)
Q Consensus       277 g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~----~g~~~  352 (493)
                      ++.++|.+.|++..+.| .|+..     +..+...++.+++|.+.|++..+. |   +...+..|-..|..    .++++
T Consensus         9 ~d~~~A~~~~~~aa~~g-~~~a~-----lg~~y~~g~~~~~A~~~~~~Aa~~-g---~~~a~~~Lg~~y~~G~g~~~d~~   78 (138)
T 1klx_A            9 KDLKKAIQYYVKACELN-EMFGC-----LSLVSNSQINKQKLFQYLSKACEL-N---SGNGCRFLGDFYENGKYVKKDLR   78 (138)
T ss_dssp             HHHHHHHHHHHHHHHTT-CTTHH-----HHHHTCTTSCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHCSSSCCCHH
T ss_pred             cCHHHHHHHHHHHHcCC-CHhhh-----HHHHHHcCCCHHHHHHHHHHHHcC-C---CHHHHHHHHHHHHcCCCCCccHH
Confidence            34566677776666665 22222     222222325566666666666554 2   44555555555555    55666


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCC
Q 011102          353 VVESLFHWFTHSGRDPTVVMYTTLIHSRLS----EKKCREALTVVWNMEASN  400 (493)
Q Consensus       353 ~A~~l~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~g  400 (493)
                      +|.+.|++-.+.|   +...+..|-..|..    .++.++|.+.|++..+.|
T Consensus        79 ~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           79 KAAQYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            6666666555443   34444555555554    455555555555555544

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=96.06  E-value=0.015  Score=56.18  Aligned_cols=146  Identities=10%  Similarity=-0.041  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      ..|..+-..+.+.|++++|...|++..+..  |+...       +... ++..++...+   .        ...|..+-.
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~-------~~~~-~~~~~~~~~l---~--------~~~~~nla~  238 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAYM--GDDFM-------FQLY-GKYQDMALAV---K--------NPCHLNIAA  238 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHHS--CHHHH-------HTCC-HHHHHHHHHH---H--------THHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHh--ccchh-------hhhc-ccHHHHHHHH---H--------HHHHHHHHH
Confidence            346677788889999999999999877642  44332       2233 4445444322   1        126777888


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHH-HHHcCCH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL-PAYRVVIKL-FVALNDI  421 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~-~ty~~li~~-~~~~g~~  421 (493)
                      +|.+.|++++|...|++..+.. +-+...|..+-.+|...|++++|.+.|++..+.  .|+. ..+..+-.. ....+..
T Consensus       239 ~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l--~p~~~~a~~~L~~l~~~~~~~~  315 (338)
T 2if4_A          239 CLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQKY--APDDKAIRRELRALAEQEKALY  315 (338)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-------------------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHH
Confidence            8889999999999998877542 346788888999999999999999999887643  3443 333333333 2345677


Q ss_pred             HHHHHHHHHHHH
Q 011102          422 SRAIRYFSKLKE  433 (493)
Q Consensus       422 ~~A~~~~~~m~~  433 (493)
                      +.+..+|..|..
T Consensus       316 ~~a~~~~~~~l~  327 (338)
T 2if4_A          316 QKQKEMYKGIFK  327 (338)
T ss_dssp             ------------
T ss_pred             HHHHHHHHHhhC
Confidence            788888888864

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.01  E-value=0.041  Score=43.20  Aligned_cols=62  Identities=13%  Similarity=-0.007  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      ...|..+-..|...|++++|.+.|++..+..- .+...|..+-..|.+.|++++|...|+...
T Consensus        19 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A           19 MLLRFTLGKTYAEHEQFDAALPHLRAALDFDP-TYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44444444445555555555555544443211 123344444444555555555555554443

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.98  E-value=0.11  Score=56.08  Aligned_cols=98  Identities=12%  Similarity=0.137  Sum_probs=52.0

Q ss_pred             HhcCCHHHHHH-HHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          274 VKGGNLKLAWK-LLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFG  352 (493)
Q Consensus       274 ~~~g~~~~A~~-l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~  352 (493)
                      ...+++++|.+ ++..+      ++......++..+.+. |.+++|+++.+.-..             -.......|+++
T Consensus       610 ~~~~~~~~a~~~~l~~i------~~~~~~~~~~~~l~~~-~~~~~a~~~~~~~~~-------------~f~~~l~~~~~~  669 (814)
T 3mkq_A          610 TLRGEIEEAIENVLPNV------EGKDSLTKIARFLEGQ-EYYEEALNISPDQDQ-------------KFELALKVGQLT  669 (814)
T ss_dssp             HHTTCHHHHHHHTGGGC------CCHHHHHHHHHHHHHT-TCHHHHHHHCCCHHH-------------HHHHHHHHTCHH
T ss_pred             HHhCCHHHHHHHHHhcC------CchHHHHHHHHHHHhC-CChHHheecCCCcch-------------heehhhhcCCHH
Confidence            34566666665 44211      1112224555555555 666666655421111             122334566666


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          353 VVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       353 ~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      +|+++.+.+      .+...|..|-..+.+.|+++.|.+.|..+.
T Consensus       670 ~A~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~  708 (814)
T 3mkq_A          670 LARDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAH  708 (814)
T ss_dssp             HHHHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHcc
Confidence            666665433      345566666666666777777766666654

>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=95.95  E-value=0.3  Score=41.26  Aligned_cols=108  Identities=11%  Similarity=-0.014  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC--------H-----HHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----
Q 011102          338 CTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT--------V-----VMYTTLIHSRLSEKKCREALTVVWNMEAS-----  399 (493)
Q Consensus       338 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--------~-----~ty~~li~~~~~~g~~~~A~~l~~~M~~~-----  399 (493)
                      +...-..+.+.|++++|...|++..+.  .|+        .     ..|+.+-.++.+.|++++|+..+++..+.     
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l--~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~   91 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEI--SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG   91 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH--HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccc
Confidence            334445566777777777777766543  222        2     37788888888888888888888776653     


Q ss_pred             CCCCCH-HHH----HHHHHHHHHcCCHHHHHHHHHHHH-----HCCCCCCHHHHHHHH
Q 011102          400 NCLFDL-PAY----RVVIKLFVALNDISRAIRYFSKLK-----EAGFCPTYDIYRDMI  447 (493)
Q Consensus       400 gi~pd~-~ty----~~li~~~~~~g~~~~A~~~~~~m~-----~~g~~p~~~ty~~li  447 (493)
                      .+.||. ..|    ...=.++...|++++|...|++..     ..|+.+......-.|
T Consensus        92 e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~~~~~  149 (159)
T 2hr2_A           92 ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVA  149 (159)
T ss_dssp             CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHH
Confidence            235654 355    666677888888888888888765     355555544444333

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=95.89  E-value=0.0079  Score=46.72  Aligned_cols=23  Identities=9%  Similarity=0.154  Sum_probs=8.9

Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHH
Q 011102          373 YTTLIHSRLSEKKCREALTVVWN  395 (493)
Q Consensus       373 y~~li~~~~~~g~~~~A~~l~~~  395 (493)
                      |..+-.+|.+.|++++|++.+++
T Consensus        41 ~~~lg~~~~~~g~~~~A~~~~~~   63 (111)
T 2l6j_A           41 YSNKAMALIKLGEYTQAIQMCQQ   63 (111)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHH
Confidence            33333333333333333333333

>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=95.86  E-value=1.3  Score=42.26  Aligned_cols=192  Identities=11%  Similarity=0.044  Sum_probs=129.8

Q ss_pred             hcCCH-HHHHHHHHHHHhCCCCCCHH-HHHH---HHHHHhcCC------CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          275 KGGNL-KLAWKLLMVAKDGGRMLDPS-IYAK---LILELGKNP------DKYMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       275 ~~g~~-~~A~~l~~~m~~~g~~pd~~-t~~~---li~~~~~~~------~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      +.|.+ ++|+++++.+....  |+-. .|+.   ++....+..      ..+++++.+++.+...  -.-+..+|+---.
T Consensus        41 ~~~e~s~eaL~~t~~~L~~n--P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~--~PKny~aW~hR~w  116 (331)
T 3dss_A           41 QAGELDESVLELTSQILGAN--PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV--NPKSYGTWHHRCW  116 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTC--TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            44554 47889998888754  5443 3542   333333210      1167888888888765  3346778887777


Q ss_pred             HHHHcCC--HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc--
Q 011102          344 VGIRLQK--FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKK-CREALTVVWNMEASNCLFDLPAYRVVIKLFVAL--  418 (493)
Q Consensus       344 ~~~~~g~--~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~-~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~--  418 (493)
                      .+.+.|+  +++++++++.+.+.. +.|-.+|+----.+...|. ++++++.++++.+... -|...|+..-..+.+.  
T Consensus       117 lL~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p-~N~SAW~~R~~ll~~l~~  194 (331)
T 3dss_A          117 LLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHP  194 (331)
T ss_dssp             HHHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHHSC
T ss_pred             HHhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHhhh
Confidence            7777774  889999999887653 4577888877777777787 5899999998887654 4666676655554444  


Q ss_pred             ------------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc-----------CCHHHHHHHHHHHHHCCCccCH
Q 011102          419 ------------NDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMAS-----------GRLAKCRDVCKEAEMAGFKLDK  475 (493)
Q Consensus       419 ------------g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~-----------g~~~~A~~l~~~m~~~g~~pd~  475 (493)
                                  +.++++.+++......... |...|+-+-..+.+.           +.++++++.++++.+  +.||.
T Consensus       195 ~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~-d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle--~~pd~  271 (331)
T 3dss_A          195 QPDSGPQGRLPENVLLKELELVQNAFFTDPN-DQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQE--LEPEN  271 (331)
T ss_dssp             CC------CCCHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHH--HCTTC
T ss_pred             ccccccccccchHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHh--hCccc
Confidence                        4578888888888765432 677777555555544           457888888888876  45554

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=95.84  E-value=0.12  Score=38.05  Aligned_cols=25  Identities=20%  Similarity=0.323  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      +..+-..+.+.|++++|...|++..
T Consensus        46 ~~~l~~~~~~~~~~~~A~~~~~~a~   70 (91)
T 1na3_A           46 WYNLGNAYYKQGDYDEAIEYYQKAL   70 (91)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            3333334444444444444444433

>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=95.81  E-value=1.4  Score=42.30  Aligned_cols=184  Identities=10%  Similarity=-0.089  Sum_probs=134.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCC-CHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPD-KYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~-~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      .++.+-....+.+..++|+++++++....  |+ ..+|+.--..+... + .+++++++++.+...  -.-+...|+---
T Consensus        56 ~~~~~r~~~~~~e~se~AL~lt~~~L~~n--P~~ytaWn~R~~iL~~l-~~~l~eEL~~~~~~L~~--nPKny~aW~hR~  130 (349)
T 3q7a_A           56 AMDYFRAIAAKEEKSERALELTEIIVRMN--PAHYTVWQYRFSLLTSL-NKSLEDELRLMNEFAVQ--NLKSYQVWHHRL  130 (349)
T ss_dssp             HHHHHHHHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHT--TCCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHhC--chhHHHHHHHHHHHHHh-hhhHHHHHHHHHHHHHh--CCCcHHHHHHHH
Confidence            34555555566677789999999998854  54 34566655555566 5 599999999999875  345677888777


Q ss_pred             HHHHHc-C-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHH--------HHHHHHHHHHHCCCCCCHHHHHHHH
Q 011102          343 KVGIRL-Q-KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCR--------EALTVVWNMEASNCLFDLPAYRVVI  412 (493)
Q Consensus       343 ~~~~~~-g-~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~--------~A~~l~~~M~~~gi~pd~~ty~~li  412 (493)
                      ..+.+. + +.++++++++.+.+.. ..|-.+|+--.-.+.+.|.++        ++++.++++.+... -|...|+---
T Consensus       131 wlL~~l~~~~~~~EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~  208 (349)
T 3q7a_A          131 LLLDRISPQDPVSEIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRW  208 (349)
T ss_dssp             HHHHHHCCSCCHHHHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             HHHHHhcCCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHH
Confidence            777776 7 8899999999998543 457778876555555555555        89999999988654 4777888777


Q ss_pred             HHHHHcCC-------HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          413 KLFVALND-------ISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRL  456 (493)
Q Consensus       413 ~~~~~~g~-------~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~  456 (493)
                      ..+.+.+.       ++++++.+++....... |...|+-+-..+.+.|+.
T Consensus       209 ~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~-n~SaW~Ylr~Ll~~~~~~  258 (349)
T 3q7a_A          209 YLRVSRPGAETSSRSLQDELIYILKSIHLIPH-NVSAWNYLRGFLKHFSLP  258 (349)
T ss_dssp             HHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCC
T ss_pred             HHHHhccccccchHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCCC
Confidence            77777776       78999999988866543 778888777777776654

>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=95.74  E-value=0.51  Score=48.92  Aligned_cols=129  Identities=6%  Similarity=-0.030  Sum_probs=78.7

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC--CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC-CHHHHHHH
Q 011102          351 FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK--KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN-DISRAIRY  427 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g--~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g-~~~~A~~~  427 (493)
                      ++++++.++.+.+.. +-+..+|+----.+.+.|  +++++++.++++.+... -|...|+.---.+.+.| ..+++.+.
T Consensus        89 ~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~~~~~~el~~~~k~l~~d~-~N~~aW~~R~~~l~~l~~~~~~el~~  166 (567)
T 1dce_A           89 VKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAF  166 (567)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccccHHHHHHHHHHHHhhcc-ccccHHHHHHHHHHHcCCChHHHHHH
Confidence            566666666665432 335556666555566666  55777777777666543 25556665555555666 67777777


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHc--------------CCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          428 FSKLKEAGFCPTYDIYRDMIRIFMAS--------------GRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       428 ~~~m~~~g~~p~~~ty~~li~~~~~~--------------g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      ++++.+.... |...|+..-..+.+.              +.+++|.+.+++..... .-|...|..+--
T Consensus       167 ~~~~I~~~p~-n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~-P~~~saW~y~~~  234 (567)
T 1dce_A          167 TDSLITRNFS-NYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRW  234 (567)
T ss_dssp             HHTTTTTTCC-CHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHC-SSCSHHHHHHHH
T ss_pred             HHHHHHHCCC-CccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhC-CCCccHHHHHHH
Confidence            7777665543 666666666555552              55788888888887642 225556655443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=95.70  E-value=0.12  Score=40.35  Aligned_cols=79  Identities=9%  Similarity=-0.126  Sum_probs=51.4

Q ss_pred             HHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 011102          317 LVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNM  396 (493)
Q Consensus       317 ~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M  396 (493)
                      +|.+.|++..+.  -.-+...+..+-..|.+.|++++|...|++..+.. +.+...|..+-..|...|++++|...|++.
T Consensus         3 ~a~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            3 AITERLEAMLAQ--GTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             CHHHHHHHHHTT--TCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            345555555443  12345666777777777777777777777766542 234566777777777777777777777765


Q ss_pred             HH
Q 011102          397 EA  398 (493)
Q Consensus       397 ~~  398 (493)
                      .+
T Consensus        80 l~   81 (115)
T 2kat_A           80 LA   81 (115)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.53  E-value=0.78  Score=37.30  Aligned_cols=138  Identities=13%  Similarity=0.051  Sum_probs=76.8

Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          276 GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVE  355 (493)
Q Consensus       276 ~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~  355 (493)
                      .|.+++..++..+....   -+..-||.+|.-.... -+-+...++++.+..-.++              ..+|++....
T Consensus        20 dG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~-a~C~y~v~vLd~IGkiFDi--------------s~C~NlKrVi   81 (172)
T 1wy6_A           20 DGYIDEGVKIVLEITKS---STKSEYNWFICNLLES-IDCRYMFQVLDKIGSYFDL--------------DKCQNLKSVV   81 (172)
T ss_dssp             TTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHH-CCHHHHHHHHHHHGGGSCG--------------GGCSCTHHHH
T ss_pred             hhhHHHHHHHHHHHcCC---CCccccceeeeecchh-hchhHHHHHHHHHhhhcCc--------------HhhhcHHHHH
Confidence            46677777777776664   3556666666666666 5566666666666543221              1334444444


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          356 SLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       356 ~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      ..+-.+-     .+....+.-++.+...|+-+.-.++..++.. +.+|+....-.+-.||.+.|+..+|.+++.+.-+.|
T Consensus        82 ~C~~~~n-----~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG  155 (172)
T 1wy6_A           82 ECGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKG  155 (172)
T ss_dssp             HHHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHhc-----chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhh
Confidence            4443332     2223345555566666666666666666322 334555555566666666666666666666666665


Q ss_pred             CC
Q 011102          436 FC  437 (493)
Q Consensus       436 ~~  437 (493)
                      ++
T Consensus       156 ~k  157 (172)
T 1wy6_A          156 EK  157 (172)
T ss_dssp             CH
T ss_pred             hH
Confidence            53

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=95.52  E-value=0.19  Score=36.85  Aligned_cols=64  Identities=5%  Similarity=-0.044  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS  399 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~  399 (493)
                      ...+..+-..|.+.|++++|...|++..+.. +.+...|..+-..|.+.|++++|.+.|++..+.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            3455556666777777777777777665432 235566677777777777777777777776553

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.44  E-value=0.082  Score=40.52  Aligned_cols=62  Identities=11%  Similarity=-0.003  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      ...+..+-..|.+.|++++|.+.|++..+.. +-+...|..+-.+|...|++++|.+.|++..
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4455555566666666666666666655432 1234455666666666666666666666543

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=95.36  E-value=0.1  Score=39.90  Aligned_cols=63  Identities=16%  Similarity=0.154  Sum_probs=39.7

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      +...|..+-..|.+.|++++|.+.|++..+..- -+...|..+-.+|.+.|++++|.+.|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDP-DYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            455666666677777777777777776655421 134456666666677777777776666554

>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=95.30  E-value=0.13  Score=51.34  Aligned_cols=87  Identities=15%  Similarity=0.111  Sum_probs=62.2

Q ss_pred             cCCCHHHHHHHHHHHHHC--C-CCC---C-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-----CC-CCCC-HHHHHHHH
Q 011102          382 SEKKCREALTVVWNMEAS--N-CLF---D-LPAYRVVIKLFVALNDISRAIRYFSKLKE-----AG-FCPT-YDIYRDMI  447 (493)
Q Consensus       382 ~~g~~~~A~~l~~~M~~~--g-i~p---d-~~ty~~li~~~~~~g~~~~A~~~~~~m~~-----~g-~~p~-~~ty~~li  447 (493)
                      ..|++++|+.++++..+.  . +-|   + ..+++.|-..|...|++++|..++++..+     .| -.|+ ..+|+.|-
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            347788888888875542  1 222   2 35788888888889999998888887652     22 1233 35688888


Q ss_pred             HHHHHcCCHHHHHHHHHHHHH
Q 011102          448 RIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       448 ~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      ..|...|++++|+.++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            889999999999988887753

>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=95.27  E-value=0.098  Score=52.26  Aligned_cols=92  Identities=13%  Similarity=0.034  Sum_probs=65.9

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHC--C-CCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-----CC-CCCC-HHH
Q 011102          377 IHSRLSEKKCREALTVVWNMEAS--N-CLFD----LPAYRVVIKLFVALNDISRAIRYFSKLKE-----AG-FCPT-YDI  442 (493)
Q Consensus       377 i~~~~~~g~~~~A~~l~~~M~~~--g-i~pd----~~ty~~li~~~~~~g~~~~A~~~~~~m~~-----~g-~~p~-~~t  442 (493)
                      +..+.+.|++++|++++++..+.  . +-|+    ..+++.|...|...|++++|..++++..+     .| -.|+ ..+
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            44566778888888888877643  1 2222    35788888888889999999888887652     12 2233 356


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          443 YRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       443 y~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |+.|-..|...|++++|+.++++..+
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            88888889999999999988887753

>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=95.20  E-value=0.77  Score=47.52  Aligned_cols=175  Identities=9%  Similarity=-0.043  Sum_probs=127.9

Q ss_pred             hcCCHHHHHHHHHHHHhCCCCCCH-HHHHHHHHHHhcCCCC----------HHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          275 KGGNLKLAWKLLMVAKDGGRMLDP-SIYAKLILELGKNPDK----------YMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       275 ~~g~~~~A~~l~~~m~~~g~~pd~-~t~~~li~~~~~~~~~----------~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      ....-++|++.++++....  |+- ..|+.-=..+... ++          ++++++.++.+.+.  -.-+..+|+---.
T Consensus        41 ~~~~~eeal~~~~~~l~~n--P~~~taW~~R~~~l~~l-~~~~~~~~~~~~~~~eL~~~~~~l~~--~pK~y~aW~hR~w  115 (567)
T 1dce_A           41 AGELDESVLELTSQILGAN--PDFATLWNCRREVLQHL-ETEKSPEESAALVKAELGFLESCLRV--NPKSYGTWHHRCW  115 (567)
T ss_dssp             TTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHH-HTTSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHC--chhHHHHHHHHHHHHhc-ccccchhhhhhhHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            3445578899999998854  543 4455433333333 33          89999999998875  3456778888888


Q ss_pred             HHHHcC--CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc--
Q 011102          344 VGIRLQ--KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK-KCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL--  418 (493)
Q Consensus       344 ~~~~~g--~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g-~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~--  418 (493)
                      .+.+.|  +++++++.++++.+.. ..|..+|+---..+.+.| ..+++++.++++.+... -|...|+..-..+.+.  
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 LLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQLHP  193 (567)
T ss_dssp             HHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHHSC
T ss_pred             HHHHcccccHHHHHHHHHHHHhhc-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCC-CCccHHHHHHHHHHhhcc
Confidence            888889  7799999999998754 457888998888888888 89999999999887654 3677777766666553  


Q ss_pred             ------------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          419 ------------NDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLA  457 (493)
Q Consensus       419 ------------g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~  457 (493)
                                  +.+++|.++++......- -|...|+.+-..+.+.++.+
T Consensus       194 ~~~~~~~~~~~~~~~~eel~~~~~ai~~~P-~~~saW~y~~~ll~~~~~~~  243 (567)
T 1dce_A          194 QPDSGPQGRLPENVLLKELELVQNAFFTDP-NDQSAWFYHRWLLGRAEPHD  243 (567)
T ss_dssp             CCCSSSCCSSCHHHHHHHHHHHHHHHHHCS-SCSHHHHHHHHHHSCCCCCS
T ss_pred             cccccccccccHHHHHHHHHHHHHHHhhCC-CCccHHHHHHHHHhcCCCcc
Confidence                        567899999988875442 26777887777777766643

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=95.09  E-value=0.82  Score=37.20  Aligned_cols=137  Identities=6%  Similarity=-0.083  Sum_probs=89.0

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTV  392 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  392 (493)
                      |.+++..++..+....    -+..-||-+|--....-+-+-..++++.+-+   -.|.          ...|++.....-
T Consensus        21 G~v~qGveii~k~~~s----sni~E~NW~ICNiiD~a~C~y~v~vLd~IGk---iFDi----------s~C~NlKrVi~C   83 (172)
T 1wy6_A           21 GYIDEGVKIVLEITKS----STKSEYNWFICNLLESIDCRYMFQVLDKIGS---YFDL----------DKCQNLKSVVEC   83 (172)
T ss_dssp             TCHHHHHHHHHHHHHH----SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGG---GSCG----------GGCSCTHHHHHH
T ss_pred             hhHHHHHHHHHHHcCC----CCccccceeeeecchhhchhHHHHHHHHHhh---hcCc----------HhhhcHHHHHHH
Confidence            6666666666666554    2444555555444444444444444444421   2222          123333333333


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCc
Q 011102          393 VWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       393 ~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~  472 (493)
                      +-.+-     -+..-+...++.+..+|+-|+-.+++.++.. ..+|+....-.+-.||.+.|+..+|.+++.+..++|++
T Consensus        84 ~~~~n-----~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           84 GVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHhc-----chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            33221     2445567788889999999999999999643 44578888889999999999999999999999999986

>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=94.86  E-value=0.092  Score=52.48  Aligned_cols=91  Identities=11%  Similarity=-0.083  Sum_probs=61.4

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHc---CCCC----CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----C-CCCCH-HH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHS---GRDP----TVVMYTTLIHSRLSEKKCREALTVVWNMEAS-----N-CLFDL-PA  407 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~---g~~p----~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-----g-i~pd~-~t  407 (493)
                      +..+.+.|++++|+.++++..+.   -+.|    ...+++.|...|...|++++|+.++++..+-     | -.|++ .+
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            44455667777887777776532   1112    2456778888888888888888888776431     2 22333 56


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      |+.|-..|...|++++|..++++..
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            7788888888888888888887654

>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=94.80  E-value=0.16  Score=50.67  Aligned_cols=85  Identities=9%  Similarity=0.039  Sum_probs=62.5

Q ss_pred             cCCHHHHHHHHHHHHH---cCCCC---C-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-----C-CCCCH-HHHHHHHH
Q 011102          348 LQKFGVVESLFHWFTH---SGRDP---T-VVMYTTLIHSRLSEKKCREALTVVWNMEAS-----N-CLFDL-PAYRVVIK  413 (493)
Q Consensus       348 ~g~~~~A~~l~~~m~~---~g~~p---~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~~-----g-i~pd~-~ty~~li~  413 (493)
                      .|++++|+.++++..+   .-+.|   + ..+++.|..+|...|++++|+.++++..+-     | -.|++ .+|+.|-.
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~  390 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGR  390 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHH
Confidence            4678888888877653   21222   2 477888999999999999999888886531     2 22443 56888888


Q ss_pred             HHHHcCCHHHHHHHHHHHH
Q 011102          414 LFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       414 ~~~~~g~~~~A~~~~~~m~  432 (493)
                      .|...|++++|..++++..
T Consensus       391 ~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          391 LYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhccCHHHHHHHHHHHH
Confidence            8999999999999888754

>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=94.59  E-value=3.3  Score=39.48  Aligned_cols=181  Identities=8%  Similarity=-0.107  Sum_probs=102.2

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCC--CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCC-HHHHH
Q 011102          279 LKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPD--KYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQK-FGVVE  355 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~--~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~-~~~A~  355 (493)
                      +++++.+++.+.... +-+..+|+.---.+.+. +  .+++++++++.+.+.  -.-|-..|+---..+.+.|. +++++
T Consensus        90 l~~EL~~~~~~L~~~-PKny~aW~hR~wlL~~l-~~~~~~~EL~~~~k~l~~--dprNy~AW~~R~~vl~~l~~~~~eel  165 (331)
T 3dss_A           90 VKAELGFLESCLRVN-PKSYGTWHHRCWLLSRL-PEPNWARELELCARFLEA--DERNFHCWDYRRFVAAQAAVAPAEEL  165 (331)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHC-SSCCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHhcc-CcccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhCcCHHHHH
Confidence            456666666666532 22455565544444444 3  467777777777665  23456666666666666666 47777


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHcC--------------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc---
Q 011102          356 SLFHWFTHSGRDPTVVMYTTLIHSRLSE--------------KKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL---  418 (493)
Q Consensus       356 ~l~~~m~~~g~~p~~~ty~~li~~~~~~--------------g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~---  418 (493)
                      +.++++.+.. .-|...|+-.-..+.+.              +.++++++.+....... +-|...|+-+--.+.+.   
T Consensus       166 ~~~~~~I~~~-p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~-P~d~SaW~Y~r~ll~~~~~~  243 (331)
T 3dss_A          166 AFTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD-PNDQSAWFYHRWLLGAGSGR  243 (331)
T ss_dssp             HHHHHHHHHC-SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHSSSCG
T ss_pred             HHHHHHHHHC-CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccCc
Confidence            7777776543 34555565544444333              34667777777765432 12444554333333333   


Q ss_pred             --------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHH-----HHHHcCCHHHHHHHHHHHHH
Q 011102          419 --------NDISRAIRYFSKLKEAGFCPTYDIYRDMIR-----IFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       419 --------g~~~~A~~~~~~m~~~g~~p~~~ty~~li~-----~~~~~g~~~~A~~l~~~m~~  468 (493)
                              +.++++.+.++++.+..  ||. .|+.+-.     +....|..+++...++++.+
T Consensus       244 ~~~~~~~~~~l~~el~~~~elle~~--pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~  303 (331)
T 3dss_A          244 CELSVEKSTVLQSELESCKELQELE--PEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKA  303 (331)
T ss_dssp             GGCCHHHHHHHHHHHHHHHHHHHHC--TTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHHHHHHHHhhC--ccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHH
Confidence                    45778888888887543  443 3432222     22235667777777777765

>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=94.11  E-value=0.14  Score=43.16  Aligned_cols=86  Identities=13%  Similarity=-0.024  Sum_probs=47.1

Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH----------HHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC----------REALTVVWNMEASNCLF-DLPAYRVVIK  413 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~----------~~A~~l~~~M~~~gi~p-d~~ty~~li~  413 (493)
                      ..+.+.+++|.+.++...+.. +-+...|+.+-.++...+++          ++|+..|++..+.  .| +..+|..+=.
T Consensus        12 ~~r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~   88 (158)
T 1zu2_A           12 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGN   88 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHH
Confidence            345666777777777765542 33566666666666666554          3555555554443  23 2344555555


Q ss_pred             HHHHcC-----------CHHHHHHHHHHHHH
Q 011102          414 LFVALN-----------DISRAIRYFSKLKE  433 (493)
Q Consensus       414 ~~~~~g-----------~~~~A~~~~~~m~~  433 (493)
                      +|...|           ++++|.+.|++..+
T Consensus        89 ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~  119 (158)
T 1zu2_A           89 AYTSFAFLTPDETEAKHNFDLATQFFQQAVD  119 (158)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcccCcchhhhhccHHHHHHHHHHHHH
Confidence            555443           45555555554443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=93.93  E-value=2.2  Score=36.46  Aligned_cols=128  Identities=9%  Similarity=0.033  Sum_probs=76.6

Q ss_pred             HHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH
Q 011102          307 ELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC  386 (493)
Q Consensus       307 ~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~  386 (493)
                      -..+. |+++.|.++.+++       -+...|..|-+...+.|+++-|++.|....      |   |..|.--|.-.|+.
T Consensus        14 LAL~l-g~l~~A~e~a~~l-------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~------D---~~~L~~Ly~~tg~~   76 (177)
T 3mkq_B           14 LALEY-GNLDAALDEAKKL-------NDSITWERLIQEALAQGNASLAEMIYQTQH------S---FDKLSFLYLVTGDV   76 (177)
T ss_dssp             HHHHT-TCHHHHHHHHHHH-------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTT------C---HHHHHHHHHHHTCH
T ss_pred             HHHhc-CCHHHHHHHHHHh-------CCHHHHHHHHHHHHHcCChHHHHHHHHHhC------C---HHHHHHHHHHhCCH
Confidence            34455 7777777776554       356777777777777777777777777655      2   34444445556666


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          387 REALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEA  466 (493)
Q Consensus       387 ~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m  466 (493)
                      ++-.++-+.....|-      ++.....+.-.|+++++.++|.+.   |-.|....      .....|..+.|.++.+++
T Consensus        77 e~L~kla~iA~~~g~------~n~af~~~l~lGdv~~~i~lL~~~---~r~~eA~~------~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           77 NKLSKMQNIAQTRED------FGSMLLNTFYNNSTKERSSIFAEG---GSLPLAYA------VAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHHHHT---TCHHHHHH------HHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCcc------HHHHHHHHHHcCCHHHHHHHHHHC---CChHHHHH------HHHHcCcHHHHHHHHHHh
Confidence            666555554444432      556666666778888888777443   22221111      112246667777776655

>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=93.64  E-value=3.3  Score=40.01  Aligned_cols=74  Identities=8%  Similarity=-0.012  Sum_probs=49.6

Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHH
Q 011102          402 LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVV  479 (493)
Q Consensus       402 ~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~  479 (493)
                      ..+..+|.++-..+...|++++|...+++....+  |+...|..+-..+.-.|++++|.+.+++...  +.|...||.
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~Alr--L~P~~~t~~  347 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFN--LRPGANTLY  347 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HSCSHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh--cCCCcChHH
Confidence            3456666666666666677777777777777654  6666666666667777777777777776655  456555553

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=93.33  E-value=1  Score=37.57  Aligned_cols=79  Identities=11%  Similarity=-0.035  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          388 EALTVVWNMEASNCLFDLPAYRVVIKLFVALN---DISRAIRYFSKLKEAGFCP--TYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       388 ~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g---~~~~A~~~~~~m~~~g~~p--~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                      .+.+-|.+..+.|. ++..+--.+--++++.+   +++++..+|++..+.. .|  +...+-.|--+|.+.|++++|.+.
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            33344444333333 34444444444444444   4445555555554432 12  122333344444555555555555


Q ss_pred             HHHHHH
Q 011102          463 CKEAEM  468 (493)
Q Consensus       463 ~~~m~~  468 (493)
                      ++.+.+
T Consensus        94 ~~~lL~   99 (152)
T 1pc2_A           94 VRGLLQ   99 (152)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            555554

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=93.31  E-value=0.51  Score=35.33  Aligned_cols=54  Identities=9%  Similarity=-0.090  Sum_probs=28.3

Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVV-MYTTLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~-ty~~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      .+.+.|++++|.+.|++..+.. +.+.. .|..+-..|...|++++|.+.|++..+
T Consensus         9 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A            9 ELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4445556666666665554431 12334 555555555555555555555555544

>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=93.00  E-value=0.3  Score=41.14  Aligned_cols=95  Identities=12%  Similarity=-0.038  Sum_probs=52.4

Q ss_pred             CHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCC----------HHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHc
Q 011102          314 KYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQK----------FGVVESLFHWFTHSGRDP-TVVMYTTLIHSRLS  382 (493)
Q Consensus       314 ~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~----------~~~A~~l~~~m~~~g~~p-~~~ty~~li~~~~~  382 (493)
                      .+++|.+.++...+.  -.-+...|+.+-.++...++          +++|+..|++..+.  .| +...|+.+-.+|..
T Consensus        17 ~feeA~~~~~~Ai~l--~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~ay~~   92 (158)
T 1zu2_A           17 LFEQIRQDAENTYKS--NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNAYTS   92 (158)
T ss_dssp             HHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHHHHH
Confidence            445555555544433  11234444444444444443          34666666665543  33 45566666666666


Q ss_pred             C-----------CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011102          383 E-----------KKCREALTVVWNMEASNCLFDLPAYRVVIKL  414 (493)
Q Consensus       383 ~-----------g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~  414 (493)
                      .           |++++|++.|++..+.  .|+...|...+..
T Consensus        93 lg~l~P~~~~a~g~~~eA~~~~~kAl~l--~P~~~~y~~al~~  133 (158)
T 1zu2_A           93 FAFLTPDETEAKHNFDLATQFFQQAVDE--QPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             hcccCcchhhhhccHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            5           3778888888776653  5666666555443

>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=92.19  E-value=2.7  Score=40.57  Aligned_cols=74  Identities=9%  Similarity=-0.203  Sum_probs=54.9

Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHH
Q 011102          332 NLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYR  409 (493)
Q Consensus       332 ~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~  409 (493)
                      ..+...|.++-..+...|++++|...+++....+  |+...|..+-..+.-.|+.++|.+.+++....  .|...||.
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL--~P~~~t~~  347 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNL--RPGANTLY  347 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SCSHHHHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCcChHH
Confidence            4567777777666667788888888888887764  77777777777788888888888888776553  46666654

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=91.42  E-value=0.76  Score=34.29  Aligned_cols=57  Identities=16%  Similarity=0.214  Sum_probs=36.6

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          377 IHSRLSEKKCREALTVVWNMEASNCLFDLP-AYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       377 i~~~~~~g~~~~A~~l~~~M~~~gi~pd~~-ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      ...+.+.|++++|.+.|++..+..- -+.. .|..+-..|.+.|++++|...|++..+.
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~   64 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTEP-VGKDEAYYLMGNAYRKLGDWQKALNNYQSAIEL   64 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCS-STHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3456667777777777777665421 2334 5666666677777777777777776644

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=90.42  E-value=7.7  Score=33.09  Aligned_cols=98  Identities=10%  Similarity=0.083  Sum_probs=49.1

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          274 VKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGV  353 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~  353 (493)
                      .+.|+++.|.++.+++      -+...|..|-...... |+++-|.+.|.....          +..+.--|.-.|+.+.
T Consensus        16 L~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~-gn~~lAe~cy~~~~D----------~~~L~~Ly~~tg~~e~   78 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKL------NDSITWERLIQEALAQ-GNASLAEMIYQTQHS----------FDKLSFLYLVTGDVNK   78 (177)
T ss_dssp             HHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHT-TCHHHHHHHHHHTTC----------HHHHHHHHHHHTCHHH
T ss_pred             HhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHc-CChHHHHHHHHHhCC----------HHHHHHHHHHhCCHHH
Confidence            3456666666655544      2455566666666665 666666666655532          2333334444455544


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHH
Q 011102          354 VESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVW  394 (493)
Q Consensus       354 A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~  394 (493)
                      -.++-+.-...|-      +|.-...+.-.|+++++.++|.
T Consensus        79 L~kla~iA~~~g~------~n~af~~~l~lGdv~~~i~lL~  113 (177)
T 3mkq_B           79 LSKMQNIAQTRED------FGSMLLNTFYNNSTKERSSIFA  113 (177)
T ss_dssp             HHHHHHHHHHTTC------HHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHCcc------HHHHHHHHHHcCCHHHHHHHHH
Confidence            4433333232221      3444444555566666666554

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.99  E-value=7.8  Score=38.53  Aligned_cols=230  Identities=11%  Similarity=0.063  Sum_probs=137.0

Q ss_pred             cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHH----HHHcCCCchhhhHHHhhccC------------
Q 011102          198 SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEV----LARHHELKVPFKLENFVSLA------------  261 (493)
Q Consensus       198 ~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~----~~~~g~~~~~~~l~~~~~~~------------  261 (493)
                      ....++..|...|+++...+.+..+.+..|..+...  ..+|+.    +......+....+.......            
T Consensus        58 ~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai--~~~V~~~~~~l~~~~~~d~~~~~~~i~~l~~vte~kiflE~e  135 (445)
T 4b4t_P           58 VLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSI--QYMIQKVMEYLKSSKSLDLNTRISVIETIRVVTENKIFVEVE  135 (445)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHH--HHHHHHHHHHHHHHCTTHHHHHHHHHHCCSSSSSCCCCCCHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHH--HHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHhccchHHHHH
Confidence            456788899999999999888887776656544443  334433    33334333222222221111            


Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHh--CCCCCC---HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc---CCCCC
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKD--GGRMLD---PSIYAKLILELGKNPDKYMLVMTLLDELGQR---DDLNL  333 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~--~g~~pd---~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~---~g~~p  333 (493)
                      .......|...|-..|++.+|.+++.++..  .|....   ...|-..+..|... +++..|..++......   ....|
T Consensus       136 rarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~-~d~~~a~~~~~ki~~~~~~~~~~~  214 (445)
T 4b4t_P          136 RARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILK-GDYSQATVLSRKILKKTFKNPKYE  214 (445)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHSSCCH
T ss_pred             HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHhhcccCCcH
Confidence            222456788999999999999999999864  232222   23456677788888 9999999999886431   01222


Q ss_pred             C--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-CCCCCHHHH-----HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH
Q 011102          334 S--QQDCTAIMKVGIRLQKFGVVESLFHWFTHS-GRDPTVVMY-----TTLIHSRLSEKKCREALTVVWNMEASNCLFDL  405 (493)
Q Consensus       334 ~--~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~ty-----~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~  405 (493)
                      +  ...|...+..+...+++.+|.+.|.+..+. ...-|...+     .+++.... .+....-.+++.......-.++.
T Consensus       215 ~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~iL-a~~~~~~~~ll~~~~~~~~~~~l  293 (445)
T 4b4t_P          215 SLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFLVL-SPYGNLQNDLIHKIQNDNNLKKL  293 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHH-SSCSSTTHHHHHSHHHHSSCHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHhhccccccc
Confidence            2  235677788888899999999888877531 111222222     22222222 22222222333333332223677


Q ss_pred             HHHHHHHHHHHHcC--CHHHHHHHHHHH
Q 011102          406 PAYRVVIKLFVALN--DISRAIRYFSKL  431 (493)
Q Consensus       406 ~ty~~li~~~~~~g--~~~~A~~~~~~m  431 (493)
                      ..|..++.+|....  +++.+.+.|...
T Consensus       294 ~~~~~L~k~f~~~~L~~~~~~~~~~~~~  321 (445)
T 4b4t_P          294 ESQESLVKLFTTNELMRWPIVQKTYEPV  321 (445)
T ss_dssp             HHHHHHHHHHHHCCSSSHHHHHHHTCSS
T ss_pred             HHHHHHHHHHHhchHhhhHHHHHHHHHH
Confidence            88999999997753  566666666543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=89.58  E-value=2.3  Score=32.46  Aligned_cols=65  Identities=12%  Similarity=-0.001  Sum_probs=33.5

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC------CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKKCREALTVVWNMEAS------NCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~------gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      +..-+-.|-..+.+.|++..|...|++..+.      +-.+....+..+-.+|.+.|+++.|..++++..+
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            3344455555566666666666666554332      0112334455555555555555555555555543

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=88.99  E-value=2.7  Score=32.06  Aligned_cols=71  Identities=14%  Similarity=0.064  Sum_probs=49.5

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc------CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH
Q 011102          333 LSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS------GRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL  405 (493)
Q Consensus       333 p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~  405 (493)
                      .+...+-.|-..+.+.|+++.|...|+...+.      +-.+....|..|..+|.+.|++++|...+++..+.  .|+.
T Consensus         3 Lsa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l--~P~~   79 (104)
T 2v5f_A            3 LTAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL--DPEH   79 (104)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTC
T ss_pred             CCHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc--CCCC
Confidence            45556667777777888888888877765432      11345667788888888888888888888887653  4553

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=88.01  E-value=4.4  Score=33.69  Aligned_cols=80  Identities=11%  Similarity=0.050  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHHCCCCC-C-HHHHHHHHHHHHHcCCHHHHHH
Q 011102          352 GVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK---KCREALTVVWNMEASNCLF-D-LPAYRVVIKLFVALNDISRAIR  426 (493)
Q Consensus       352 ~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g---~~~~A~~l~~~M~~~gi~p-d-~~ty~~li~~~~~~g~~~~A~~  426 (493)
                      ..+.+-|.+..+.|. ++..+.-.+--++++..   +.+++..+|++..+.. .| + ...+=.|--+|.+.|++++|.+
T Consensus        15 ~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~   92 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHH
Confidence            344444544444333 55555555555666655   4456666666655543 12 1 1122223334466666777776


Q ss_pred             HHHHHHH
Q 011102          427 YFSKLKE  433 (493)
Q Consensus       427 ~~~~m~~  433 (493)
                      +++.+.+
T Consensus        93 y~~~lL~   99 (152)
T 1pc2_A           93 YVRGLLQ   99 (152)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            6666664

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.89  E-value=16  Score=36.30  Aligned_cols=94  Identities=7%  Similarity=0.125  Sum_probs=50.2

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCC---HHHHHHHHHHHHcCCCHHHHHHHHHHHHH----CCCCCCH--HH
Q 011102          339 TAIMKVGIRLQKFGVVESLFHWFTHS--GRDPT---VVMYTTLIHSRLSEKKCREALTVVWNMEA----SNCLFDL--PA  407 (493)
Q Consensus       339 ~~li~~~~~~g~~~~A~~l~~~m~~~--g~~p~---~~ty~~li~~~~~~g~~~~A~~l~~~M~~----~gi~pd~--~t  407 (493)
                      ..|...|-..|++.+|.+++.++...  |....   +..|...++.|...+++.+|..++.....    ....|+.  .-
T Consensus       141 ~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~  220 (445)
T 4b4t_P          141 KDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEY  220 (445)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHH
Confidence            45556666666666666666666432  22111   23455556666666666666666665532    1222221  23


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          408 YRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       408 y~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      |...+..+...+++.+|.+.|.+..
T Consensus       221 ~~~~~~~~~~e~~y~~a~~~y~e~~  245 (445)
T 4b4t_P          221 YNLLVKISLHKREYLEVAQYLQEIY  245 (445)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            4555555556666666666555544

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=86.34  E-value=5.4  Score=30.48  Aligned_cols=62  Identities=19%  Similarity=0.236  Sum_probs=42.4

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIR  448 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~  448 (493)
                      +.-++.+-++.+....+.|+.....+.+.+|.+.+++..|.++|+..+ +.|-  ...+|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~--~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGP--HKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTT--CTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcC--chhhHHHHHH
Confidence            455666666666667777777777777888888888888888877776 3332  2345666654

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=86.26  E-value=5.6  Score=29.76  Aligned_cols=63  Identities=11%  Similarity=-0.063  Sum_probs=31.8

Q ss_pred             CHHHHHHHHHHHHcCCC---HHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          369 TVVMYTTLIHSRLSEKK---CREALTVVWNMEASNCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       369 ~~~ty~~li~~~~~~g~---~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      |...+..+-.++...++   .++|..++++..+.  .|+ ......+=..+.+.|++++|...|+.+.+
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~--dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~   71 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQL--EPYNEAALSLIANDHFISFRFQEAIDTWVLLLD   71 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44445555555543333   46666666655442  233 23333333445566666666666666654

>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=84.78  E-value=7.6  Score=36.06  Aligned_cols=88  Identities=8%  Similarity=-0.051  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHcCCCCC---HHHHHHHHHHHHcC-----CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc-CCHH
Q 011102          352 GVVESLFHWFTHSGRDPT---VVMYTTLIHSRLSE-----KKCREALTVVWNMEASNCLFDLPAYRVVIKLFVAL-NDIS  422 (493)
Q Consensus       352 ~~A~~l~~~m~~~g~~p~---~~ty~~li~~~~~~-----g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~-g~~~  422 (493)
                      ..|...+++..+.  .|+   -..|.+|...|.+.     |+.++|.+.|++..+.+-.-+..++...-+.++.. |+.+
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            3444444444332  454   34566666666663     66777777776665532111245555555666663 6667


Q ss_pred             HHHHHHHHHHHCCCC--CCHH
Q 011102          423 RAIRYFSKLKEAGFC--PTYD  441 (493)
Q Consensus       423 ~A~~~~~~m~~~g~~--p~~~  441 (493)
                      +|.+++++-......  |+..
T Consensus       258 ~a~~~L~kAL~a~p~~~P~~~  278 (301)
T 3u64_A          258 GFDEALDRALAIDPESVPHNK  278 (301)
T ss_dssp             HHHHHHHHHHHCCGGGCSSCH
T ss_pred             HHHHHHHHHHcCCCCCCCChh
Confidence            777776666655544  5543

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=84.49  E-value=4.5  Score=39.47  Aligned_cols=57  Identities=9%  Similarity=0.193  Sum_probs=25.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      ..++..+...|+.++|...+..+.... .-+...|..+|.++.+.|+..+|.+.|+..
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~  231 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRV  231 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            334444444455555544444443221 124444555555555555555555444443

>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=84.31  E-value=5.1  Score=37.21  Aligned_cols=93  Identities=9%  Similarity=-0.116  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHhhcCCCCCC---HHHHHHHHHHHHH-----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcC-CCH
Q 011102          316 MLVMTLLDELGQRDDLNLS---QQDCTAIMKVGIR-----LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSE-KKC  386 (493)
Q Consensus       316 ~~a~~l~~~m~~~~g~~p~---~~~~~~li~~~~~-----~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~-g~~  386 (493)
                      ..|..++++..+   +.|+   -..|+.+...|.+     -|+.++|.+.|++-.+..-.-+..++...-..+++. |+.
T Consensus       180 ~~A~a~lerAle---LDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~  256 (301)
T 3u64_A          180 HAAVMMLERACD---LWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHH---HCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHH---hCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCH
Confidence            455555555544   3455   5578888888888     488899999998877653222477778888888885 888


Q ss_pred             HHHHHHHHHHHHCCCC--CCHHHHHHH
Q 011102          387 REALTVVWNMEASNCL--FDLPAYRVV  411 (493)
Q Consensus       387 ~~A~~l~~~M~~~gi~--pd~~ty~~l  411 (493)
                      ++|.+.+++.......  |+....|.+
T Consensus       257 ~~a~~~L~kAL~a~p~~~P~~~lan~~  283 (301)
T 3u64_A          257 AGFDEALDRALAIDPESVPHNKLLVIL  283 (301)
T ss_dssp             HHHHHHHHHHHHCCGGGCSSCHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCChhHHHHH
Confidence            9999999988887666  765544443

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=83.94  E-value=12  Score=39.67  Aligned_cols=52  Identities=10%  Similarity=0.123  Sum_probs=37.2

Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          415 FVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE  467 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~  467 (493)
                      |...|+++.|+++-+.-...- .-+..||..|..+|...|+++.|+-.++.+.
T Consensus       347 Ll~K~~~elAL~~Ak~AV~~a-PseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          347 LLNRGDYELALGVSNTSTELA-LDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HhccCcHHHHHHHHHHHHhcC-chhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            556778888888777765432 1246778888888888888888887777763

>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=83.20  E-value=6  Score=38.56  Aligned_cols=125  Identities=18%  Similarity=0.068  Sum_probs=80.7

Q ss_pred             cHHHHHHHHHHHH---hcCCHHHHHHHHHHHHhC--C-CCCCHHHHHHHHHHHhcCCCCHHHH-HHHHHHHhhcCCCCCC
Q 011102          262 SKGVLEATAKGFV---KGGNLKLAWKLLMVAKDG--G-RMLDPSIYAKLILELGKNPDKYMLV-MTLLDELGQRDDLNLS  334 (493)
Q Consensus       262 ~~~~~~~li~~~~---~~g~~~~A~~l~~~m~~~--g-~~pd~~t~~~li~~~~~~~~~~~~a-~~l~~~m~~~~g~~p~  334 (493)
                      |...|..++..-.   ..|+.+.|.+.+++....  | .-++..           . ..|-.. ..-++++..       
T Consensus       111 D~~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG~~L~~~~-----------~-~~w~~~~r~~l~~~~~-------  171 (388)
T 2ff4_A          111 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLR-----------D-FQFVEPFATALVEDKV-------  171 (388)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGT-----------T-STTHHHHHHHHHHHHH-------
T ss_pred             hHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCCC-----------c-hhHHHHHHHHHHHHHH-------
Confidence            3444555554332   357888888888877652  3 111110           0 122211 222222221       


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCCCCHHH
Q 011102          335 QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEA-----SNCLFDLPA  407 (493)
Q Consensus       335 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~-----~gi~pd~~t  407 (493)
                       .....++..+...|+.++|...+..+.... +-+...|-.+|.+|.+.|+..+|++.|++..+     .|+.|...+
T Consensus       172 -~a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          172 -LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             -HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             -HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence             134557778888999999998888876432 45788999999999999999999999988754     499998766

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=81.70  E-value=5.6  Score=31.85  Aligned_cols=23  Identities=4%  Similarity=-0.191  Sum_probs=12.5

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Q 011102          446 MIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       446 li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      |--++.+.|++++|.+.++.+.+
T Consensus        80 LAvg~yklg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           80 LAVGNYRLKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHH
Confidence            44445555555555555555554

---

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	493
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.54
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.36
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.13
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.03
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.78
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.59
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.57
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.41
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.31
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.31
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.27
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.91
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.85
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.82
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	97.72
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	97.72
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	97.64
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.59
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.58
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.56
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.54
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.43
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	97.42
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.38
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	97.34
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	97.33
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.19
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.14
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.08
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.07
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.02
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.82
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	96.82
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.71
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	96.64
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.57
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	96.37
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	96.24
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	96.2
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	95.97
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.85
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.83
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.75
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	95.71
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	95.68
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	95.29
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	95.18
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	94.82
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.67
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	93.43
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	93.37
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	92.8
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	89.42
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	89.24
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	88.37
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	88.3
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	86.77
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	83.08
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	82.04
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	80.19

>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=99.54  E-value=2e-11  Score=117.77  Aligned_cols=298  Identities=9%  Similarity=-0.055  Sum_probs=219.3

Q ss_pred             hccCCCCHHHHHHHHhhhcccC-----cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCch
Q 011102          176 GLDSHKDVAEVLDKCGRFLRKG-----SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKV  250 (493)
Q Consensus       176 ~~~~~~~~~~a~~~~~~m~~~~-----~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~  250 (493)
                      .+...|+.++|+..+.+....+     .|..+...|.+.|++++|++.+....+. . ..+...+..........+....
T Consensus        42 ~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~~  119 (388)
T d1w3ba_          42 IHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEAIEHYRHALRL-K-PDFIDGYINLAAALVAAGDMEG  119 (388)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHHHSCSSH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHhhhhcccccccccccccccc-c-cccccccccccccccccccccc
Confidence            3455688888888888665432     6677777888888888888888887764 2 1222222222222222222211


Q ss_pred             hhhHH--------------------------------Hh----hc-cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC
Q 011102          251 PFKLE--------------------------------NF----VS-LASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGG  293 (493)
Q Consensus       251 ~~~l~--------------------------------~~----~~-~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  293 (493)
                      .....                                .+    .. ..+...+..+...+...|++++|...+++..+..
T Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~  199 (388)
T d1w3ba_         120 AVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD  199 (388)
T ss_dssp             HHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC
T ss_pred             cccccccccccccccccccccccccccccchhhhhHHHHHHhhccCcchhHHHHhhcccccccCcHHHHHHHHHHHHHhC
Confidence            11000                                00    00 1123456777888899999999999999888743


Q ss_pred             CCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 011102          294 RMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMY  373 (493)
Q Consensus       294 ~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty  373 (493)
                       +-+..+|..+-..+... |++++|...+......  ...+...+..+-..|.+.|++++|.+.|++..+.. +-+..+|
T Consensus       200 -p~~~~~~~~l~~~~~~~-~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~  274 (388)
T d1w3ba_         200 -PNFLDAYINLGNVLKEA-RIFDRAVAAYLRALSL--SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAY  274 (388)
T ss_dssp             -TTCHHHHHHHHHHHHTT-TCTTHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHH
T ss_pred             -cccHHHHHHHhhhhhcc-ccHHHHHHHHHHhHHH--hhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHH
Confidence             12456788888889999 9999999999998775  23567788888999999999999999999987652 3457889


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHc
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMAS  453 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~  453 (493)
                      ..+...|...|++++|.+.++..... ...+...+..+...+.+.|++++|...|++..+..- -+..+|..+-..|.+.
T Consensus       275 ~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~  352 (388)
T d1w3ba_         275 CNLANALKEKGSVAEAEDCYNTALRL-CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFP-EFAAAHSNLASVLQQQ  352 (388)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCT-TCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHhhhcc-CCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHc
Confidence            99999999999999999999987764 345678888999999999999999999999875431 2567788999999999


Q ss_pred             CCHHHHHHHHHHHHHCCCccC-HHHHHHHHHh
Q 011102          454 GRLAKCRDVCKEAEMAGFKLD-KQTVVELLQI  484 (493)
Q Consensus       454 g~~~~A~~l~~~m~~~g~~pd-~~t~~~Ll~~  484 (493)
                      |++++|.+.|++..+  +.|+ ...|..|-.+
T Consensus       353 g~~~~A~~~~~~al~--l~P~~~~a~~~lg~~  382 (388)
T d1w3ba_         353 GKLQEALMHYKEAIR--ISPTFADAYSNMGNT  382 (388)
T ss_dssp             TCCHHHHHHHHHHHT--TCTTCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH--hCCCCHHHHHHHHHH
Confidence            999999999999876  4665 4566655544

>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=99.36  E-value=8.7e-10  Score=105.87  Aligned_cols=268  Identities=9%  Similarity=-0.022  Sum_probs=200.5

Q ss_pred             hhccCCCCHHHHHHHHhhhcccC---------------------------------------cHHHHHHHHHhCCChHHH
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKG---------------------------------------SLSFTVRELGHMNLPERA  215 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~---------------------------------------~~~~li~~~~~~g~~~~A  215 (493)
                      ..+.+.|++++|+..+.......                                       ............+....+
T Consensus        75 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (388)
T d1w3ba_          75 NVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEA  154 (388)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHH
T ss_pred             HHhhhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhh
Confidence            44566799999999998655432                                       112223344445555555


Q ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011102          216 LQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKGFVKGGNLKLAWKLLMVAK  290 (493)
Q Consensus       216 ~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~  290 (493)
                      ...+......  ..-+...+..+...+...|..+.+  ...+..     ..+..+|..+...+...|++++|...|++..
T Consensus       155 ~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A--~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  230 (388)
T d1w3ba_         155 KACYLKAIET--QPNFAVAWSNLGCVFNAQGEIWLA--IHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRAL  230 (388)
T ss_dssp             HHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHH--HHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHH
T ss_pred             HHHHHHhhcc--CcchhHHHHhhcccccccCcHHHH--HHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhH
Confidence            5555555432  122445566666667777774433  332322     2355688999999999999999999999988


Q ss_pred             hCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCH
Q 011102          291 DGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTV  370 (493)
Q Consensus       291 ~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~  370 (493)
                      ..+ ..+...+..+-..+.+. |++++|...|++..+.  -.-+..+|..+...|.+.|++++|.+.|+...... +.+.
T Consensus       231 ~~~-~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~  305 (388)
T d1w3ba_         231 SLS-PNHAVVHGNLACVYYEQ-GLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLC-PTHA  305 (388)
T ss_dssp             HHC-TTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC-TTCH
T ss_pred             HHh-hhHHHHHHHHHHHHHHC-CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccC-Cccc
Confidence            754 24566777788888999 9999999999998764  23457788999999999999999999999877543 5678


Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCP-TYDIYRDMIR  448 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p-~~~ty~~li~  448 (493)
                      ..+..+...+.+.|++++|++.|++..+.  .|+ ..++..+-..|.+.|++++|...|++..+.  .| +...|..+..
T Consensus       306 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~lg~  381 (388)
T d1w3ba_         306 DSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGN  381 (388)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTTCHHHHHHHHH
T ss_pred             hhhhHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            88999999999999999999999997664  454 567888889999999999999999998754  35 4678888988


Q ss_pred             HHHHcCC
Q 011102          449 IFMASGR  455 (493)
Q Consensus       449 ~~~~~g~  455 (493)
                      .|.+.||
T Consensus       382 ~~~~~~D  388 (388)
T d1w3ba_         382 TLKEMQD  388 (388)
T ss_dssp             HHHHTCC
T ss_pred             HHHHcCC
Confidence            8888775

>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=99.13  E-value=3e-08  Score=93.41  Aligned_cols=245  Identities=11%  Similarity=-0.020  Sum_probs=162.1

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCC-CHHHHHHHHHHHHHcCCCchhhhHHHhhc-----cCcHHHHHHHHHHHHhcCC
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFP-DDRLLASTVEVLARHHELKVPFKLENFVS-----LASKGVLEATAKGFVKGGN  278 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~p-d~~t~~~li~~~~~~g~~~~~~~l~~~~~-----~~~~~~~~~li~~~~~~g~  278 (493)
                      .+.+.|++++|+..|+.+.+.   .| +..+|..+..++...|+++.  ++..+..     ..+...|..+...|...|+
T Consensus        28 ~~~~~g~~~~A~~~~~~al~~---~P~~~~a~~~lg~~~~~~~~~~~--A~~~~~~al~~~p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          28 RRLQEGDLPNAVLLFEAAVQQ---DPKHMEAWQYLGTTQAENEQELL--AISALRRCLELKPDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHS---CTTCHHHHHHHHHHHHHTTCHHH--HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCChHH--HHHHHHhhhcccccccccccccccccccccc
Confidence            355677777777777776653   23 35566666666777676433  3322322     1245567778888888999


Q ss_pred             HHHHHHHHHHHHhCCCCCCHH----------------HHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHH
Q 011102          279 LKLAWKLLMVAKDGGRMLDPS----------------IYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIM  342 (493)
Q Consensus       279 ~~~A~~l~~~m~~~g~~pd~~----------------t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li  342 (493)
                      +++|.+.+++.....  |+..                .....+..+... +.+.+|.+.|........-..+...+..+-
T Consensus       103 ~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~~al~~~p~~~~~~~~~~l~  179 (323)
T d1fcha_         103 QRQACEILRDWLRYT--PAYAHLVTPAEEGAGGAGLGPSKRILGSLLSD-SLFLEVKELFLAAVRLDPTSIDPDVQCGLG  179 (323)
T ss_dssp             HHHHHHHHHHHHHTS--TTTGGGCC---------------CTTHHHHHH-HHHHHHHHHHHHHHHHSTTSCCHHHHHHHH
T ss_pred             ccccccchhhHHHhc--cchHHHHHhhhhhhhhcccccchhhHHHHHHh-hHHHHHHHHHHHHHHHhhcccccccchhhH
Confidence            999999998887643  2211                011122223334 566778878777655423345677788888


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDI  421 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~  421 (493)
                      ..+...|++++|...|++..... +-+...|..+-..|.+.|++++|.+.|++..+.  .| +..+|..+-..|.+.|++
T Consensus       180 ~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~  256 (323)
T d1fcha_         180 VLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL--QPGYIRSRYNLGISCINLGAH  256 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHH--hhccHHHHHHHHHHHHHCCCH
Confidence            88889999999999998876542 235778888888999999999999999987764  34 456788888889999999


Q ss_pred             HHHHHHHHHHHHC----------CCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011102          422 SRAIRYFSKLKEA----------GFCPTYDIYRDMIRIFMASGRLAKCR  460 (493)
Q Consensus       422 ~~A~~~~~~m~~~----------g~~p~~~ty~~li~~~~~~g~~~~A~  460 (493)
                      ++|...|++..+.          ........|..+=.++...|+.+.+.
T Consensus       257 ~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~  305 (323)
T d1fcha_         257 REAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYG  305 (323)
T ss_dssp             HHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHH
T ss_pred             HHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            9999999876631          11122334566666666666665443

>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=99.03  E-value=7.8e-08  Score=90.46  Aligned_cols=222  Identities=10%  Similarity=-0.074  Sum_probs=167.3

Q ss_pred             HHHHcCCCchhhhHHHhhc----c-CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCH
Q 011102          241 VLARHHELKVPFKLENFVS----L-ASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKY  315 (493)
Q Consensus       241 ~~~~~g~~~~~~~l~~~~~----~-~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~  315 (493)
                      .+.+.|++  .+|+..|..    - .+..+|..+...|...|++++|...|++..+.. +-+...|..+...|... |++
T Consensus        28 ~~~~~g~~--~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~-~~~  103 (323)
T d1fcha_          28 RRLQEGDL--PNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNE-SLQ  103 (323)
T ss_dssp             HHHHTTCH--HHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT-TCH
T ss_pred             HHHHcCCH--HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-ccccccccccccccccc-ccc
Confidence            45677774  444444443    2 256689999999999999999999999988743 12466788888889999 999


Q ss_pred             HHHHHHHHHHhhcCCCC-------------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHH
Q 011102          316 MLVMTLLDELGQRDDLN-------------LSQQDCTAIMKVGIRLQKFGVVESLFHWFTHS-GRDPTVVMYTTLIHSRL  381 (493)
Q Consensus       316 ~~a~~l~~~m~~~~g~~-------------p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~ty~~li~~~~  381 (493)
                      ++|.+.++.......-.             .+.......+..+.+.+...+|.+.|.+..+. .-..+...+..+-..+.
T Consensus       104 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~  183 (323)
T d1fcha_         104 RQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFN  183 (323)
T ss_dssp             HHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHH
T ss_pred             cccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHH
Confidence            99999999876531100             01111222334455667788899999887643 23456788899999999


Q ss_pred             cCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          382 SEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRD  461 (493)
Q Consensus       382 ~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~  461 (493)
                      ..|++++|...|++.....- -+...|..+-..|.+.|++++|.+.|+...+..- -+...|..+-.+|.+.|++++|.+
T Consensus       184 ~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~  261 (323)
T d1fcha_         184 LSGEYDKAVDCFTAALSVRP-NDYLLWNKLGATLANGNQSEEAVAAYRRALELQP-GYIRSRYNLGISCINLGAHREAVE  261 (323)
T ss_dssp             HTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHhhhhccccccccccc-ccccchhhhhhcccccccchhHHHHHHHHHHHhh-ccHHHHHHHHHHHHHCCCHHHHHH
Confidence            99999999999999776432 2467888899999999999999999999886431 257789999999999999999999


Q ss_pred             HHHHHHH
Q 011102          462 VCKEAEM  468 (493)
Q Consensus       462 l~~~m~~  468 (493)
                      .|++..+
T Consensus       262 ~~~~al~  268 (323)
T d1fcha_         262 HFLEALN  268 (323)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998865

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.78  E-value=9.7e-07  Score=82.64  Aligned_cols=188  Identities=15%  Similarity=0.000  Sum_probs=146.9

Q ss_pred             CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011102          277 GNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVES  356 (493)
Q Consensus       277 g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~  356 (493)
                      +..++|..+|++..+...+-+...|........+. |+++.|..+|+.+... ........|...+..+.+.|+++.|.+
T Consensus        78 ~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~-~~~~~a~~i~~~~l~~-~~~~~~~~w~~~~~~~~~~~~~~~ar~  155 (308)
T d2onda1          78 LFSDEAANIYERAISTLLKKNMLLYFAYADYEESR-MKYEKVHSIYNRLLAI-EDIDPTLVYIQYMKFARRAEGIKSGRM  155 (308)
T ss_dssp             HHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHTS-SSSCTHHHHHHHHHHHHHHHCHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhc-ccHHHHHHHHHHHHHH-hcCChHHHHHHHHHHHHHcCChHHHHH
Confidence            44688899999988765556677788888888888 9999999999998765 222335678999999999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHH-HHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          357 LFHWFTHSGRDPTVVMYTTLIH-SRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       357 l~~~m~~~g~~p~~~ty~~li~-~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      +|+...+.+.. +...|..... -+...|+.+.|..+|+.+.+. ..-+...|...++.+.+.|+++.|..+|++.....
T Consensus       156 i~~~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~  233 (308)
T d2onda1         156 IFKKAREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  233 (308)
T ss_dssp             HHHHHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC
Confidence            99998865432 2333333332 344568999999999998875 23356789999999999999999999999987543


Q ss_pred             -CCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          436 -FCPT--YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       436 -~~p~--~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                       ..|+  ...|...+.--...|+.+.+.++++++.+
T Consensus       234 ~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~  269 (308)
T d2onda1         234 SLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFT  269 (308)
T ss_dssp             SSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence             4443  56799888888889999999999998865

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.59  E-value=3e-05  Score=72.12  Aligned_cols=261  Identities=10%  Similarity=-0.057  Sum_probs=166.8

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCC---HHHHHHHHHHHHHcCCCchhhhHHHhhc-------cC----cHHHHHHHH
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFPD---DRLLASTVEVLARHHELKVPFKLENFVS-------LA----SKGVLEATA  270 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~pd---~~t~~~li~~~~~~g~~~~~~~l~~~~~-------~~----~~~~~~~li  270 (493)
                      .+...|++++|+++|+.......-.++   ...+..+-..+...|+++.+.  ..+..       ..    ...++..+.
T Consensus        21 ~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~--~~~~~a~~~~~~~~~~~~~~~~~~~~~   98 (366)
T d1hz4a_          21 VAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSL--ALMQQTEQMARQHDVWHYALWSLIQQS   98 (366)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHH--HHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHH--HHHHHHHHHHHhhcchHHHHHHHHHHH
Confidence            455667777777777766543111111   123445555666666643322  22221       11    122456677


Q ss_pred             HHHHhcCCHHHHHHHHHHHHh----CCCCC--CH-HHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC---CCCCCHHHHHH
Q 011102          271 KGFVKGGNLKLAWKLLMVAKD----GGRML--DP-SIYAKLILELGKNPDKYMLVMTLLDELGQRD---DLNLSQQDCTA  340 (493)
Q Consensus       271 ~~~~~~g~~~~A~~l~~~m~~----~g~~p--d~-~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~---g~~p~~~~~~~  340 (493)
                      ..+...|++..|...+.+...    .+...  .. ..+..+-..+... |+++.+...+.......   +.......+..
T Consensus        99 ~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  177 (366)
T d1hz4a_          99 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAW-ARLDEAEASARSGIEVLSSYQPQQQLQCLAM  177 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHTTTSCGGGGHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHh-cchhhhHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence            778888999999888876643    22221  12 2344455667777 89999998888765431   22233456666


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHc----CCCC--CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC---CCHHHHHHH
Q 011102          341 IMKVGIRLQKFGVVESLFHWFTHS----GRDP--TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL---FDLPAYRVV  411 (493)
Q Consensus       341 li~~~~~~g~~~~A~~l~~~m~~~----g~~p--~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~---pd~~ty~~l  411 (493)
                      +...+...|+...+...+.+....    +..+  ....+..+...+...|+.++|...+.+.......   .....+..+
T Consensus       178 ~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l  257 (366)
T d1hz4a_         178 LIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNI  257 (366)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHH
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHH
Confidence            777788889999988888765431    1111  1234666777888899999999998876543221   224556667


Q ss_pred             HHHHHHcCCHHHHHHHHHHHH----HCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          412 IKLFVALNDISRAIRYFSKLK----EAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~----~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      -..+...|++++|...++...    ..+..|+ ..+|..+-..|.+.|++++|.+.+++..+
T Consensus       258 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         258 ARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            788999999999999998775    3344443 35677788889999999999999887643

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.57  E-value=4.8e-06  Score=77.72  Aligned_cols=170  Identities=9%  Similarity=0.015  Sum_probs=131.7

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTV  392 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  392 (493)
                      +..++|..+|+...+. ...-+...|...+..+.+.|+++.|..+|+.+.+.........|...+..+.+.|+.++|.++
T Consensus        78 ~~~~~a~~i~~ral~~-~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i  156 (308)
T d2onda1          78 LFSDEAANIYERAIST-LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMI  156 (308)
T ss_dssp             HHHHHHHHHHHHHHTT-TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHH-cCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHH
Confidence            3457888999988765 344566788888999999999999999999998654333456799999999999999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHH-HHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-
Q 011102          393 VWNMEASNCLFDLPAYRVVIK-LFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAG-  470 (493)
Q Consensus       393 ~~~M~~~gi~pd~~ty~~li~-~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g-  470 (493)
                      |+.+.+.+.. +...|..... -+...|+.+.|..+|+.+.+. ..-+...|...++.+.+.|+++.|..+|++..+.. 
T Consensus       157 ~~~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~  234 (308)
T d2onda1         157 FKKAREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGS  234 (308)
T ss_dssp             HHHHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSS
T ss_pred             HHHHHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC
Confidence            9998876432 2233333332 234568999999999999865 33467889999999999999999999999987754 


Q ss_pred             CccC--HHHHHHHHHhh
Q 011102          471 FKLD--KQTVVELLQIE  485 (493)
Q Consensus       471 ~~pd--~~t~~~Ll~~~  485 (493)
                      ..|+  ...|...++.+
T Consensus       235 ~~~~~~~~iw~~~~~fE  251 (308)
T d2onda1         235 LPPEKSGEIWARFLAFE  251 (308)
T ss_dssp             SCGGGCHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHH
Confidence            5554  45787777763

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=98.41  E-value=9.7e-05  Score=68.42  Aligned_cols=284  Identities=11%  Similarity=-0.015  Sum_probs=186.2

Q ss_pred             ccCCCCHHHHHHHHhhhccc---C-------cHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCH----HHHHHHHHHH
Q 011102          177 LDSHKDVAEVLDKCGRFLRK---G-------SLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDD----RLLASTVEVL  242 (493)
Q Consensus       177 ~~~~~~~~~a~~~~~~m~~~---~-------~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~----~t~~~li~~~  242 (493)
                      +...|+.++|+..+++....   +       .++.+-..|...|++++|+..|+.......-.++.    .++..+...+
T Consensus        22 ~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  101 (366)
T d1hz4a_          22 AINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEIL  101 (366)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHH
Confidence            34679999999999865432   1       34556678889999999999999876421111222    2345556666


Q ss_pred             HHcCCCchhhhH-----HHhhccC------cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC----CCCCHHHHHHHHHH
Q 011102          243 ARHHELKVPFKL-----ENFVSLA------SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGG----RMLDPSIYAKLILE  307 (493)
Q Consensus       243 ~~~g~~~~~~~l-----~~~~~~~------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g----~~pd~~t~~~li~~  307 (493)
                      ...|++..+...     .......      ...++..+-..+...|+++.+...+.......    ......++......
T Consensus       102 ~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  181 (366)
T d1hz4a_         102 FAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQC  181 (366)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHH
Confidence            777774433322     1111111      12356677788899999999999998887633    22334455555666


Q ss_pred             HhcCCCCHHHHHHHHHHHhhc---CCCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC---CCHHHHHHHHHH
Q 011102          308 LGKNPDKYMLVMTLLDELGQR---DDLNL--SQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRD---PTVVMYTTLIHS  379 (493)
Q Consensus       308 ~~~~~~~~~~a~~l~~~m~~~---~g~~p--~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~---p~~~ty~~li~~  379 (493)
                      +... +...++...+.+....   .+..+  ....+..+...+...|++++|...+.........   .....+..+...
T Consensus       182 ~~~~-~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~  260 (366)
T d1hz4a_         182 SLAR-GDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARA  260 (366)
T ss_dssp             HHHH-TCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHH
T ss_pred             HHhh-hhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHH
Confidence            7777 8888888887765432   11111  1234566677888999999999999876543222   234567778899


Q ss_pred             HHcCCCHHHHHHHHHHHHH----CCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHH----CCCCC----CHHHHHHH
Q 011102          380 RLSEKKCREALTVVWNMEA----SNCLFDL-PAYRVVIKLFVALNDISRAIRYFSKLKE----AGFCP----TYDIYRDM  446 (493)
Q Consensus       380 ~~~~g~~~~A~~l~~~M~~----~gi~pd~-~ty~~li~~~~~~g~~~~A~~~~~~m~~----~g~~p----~~~ty~~l  446 (493)
                      +...|++++|.+.+++...    .+..|+. .++..+-..|.+.|++++|.+.+++..+    .|...    ....+..+
T Consensus       261 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~~~~~~~~~~~~~~~~~~~~  340 (366)
T d1hz4a_         261 QILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIEGEAMAQQ  340 (366)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHHTTHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhhcCcHHHHHHHHHHHHHH
Confidence            9999999999999998753    3555543 4667777889999999999999987642    33321    12334556


Q ss_pred             HHHHHHcCCHHHHHH
Q 011102          447 IRIFMASGRLAKCRD  461 (493)
Q Consensus       447 i~~~~~~g~~~~A~~  461 (493)
                      +..+...++.+++.+
T Consensus       341 ~~~l~~~~~l~e~e~  355 (366)
T d1hz4a_         341 LRQLIQLNTLPELEQ  355 (366)
T ss_dssp             HHHHHHTTCSCHHHH
T ss_pred             HHHHHhcCCChHHHH
Confidence            666666777666544

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.31  E-value=4.3e-05  Score=71.36  Aligned_cols=196  Identities=9%  Similarity=-0.036  Sum_probs=108.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      .|+-+-..+.+.+..++|+++++++.+..  |+ ...|+..-..+...++++++|+..++...+.  -.-+..+|+.+-.
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~ln--P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~--~p~~~~a~~~~~~  120 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIELN--AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEE--QPKNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHH--HHhhhhHHHHHhH
Confidence            45555555666666677777777666632  33 3345555555555523466777666666543  1234556666666


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCC---
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALND---  420 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~---  420 (493)
                      .+.+.|++++|++.|+++.+.. +-+...|+.+...+.+.|++++|++.++.+.+... -+...|+.+-..+.+.+.   
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l~~~~~~~~  198 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGYND  198 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHHHHccccch
Confidence            6666777777777776665431 23466666666666667777777777766665432 234455544444444333   


Q ss_pred             ---HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          421 ---ISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       421 ---~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                         +++|...+....+..- -|...|+.+-..+. ....+++.+.++...+
T Consensus       199 ~~~~~~ai~~~~~al~~~P-~~~~~~~~l~~ll~-~~~~~~~~~~~~~~~~  247 (315)
T d2h6fa1         199 RAVLEREVQYTLEMIKLVP-HNESAWNYLKGILQ-DRGLSKYPNLLNQLLD  247 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHT-TTCGGGCHHHHHHHHH
T ss_pred             hhhhHHhHHHHHHHHHhCC-CchHHHHHHHHHHH-hcChHHHHHHHHHHHH
Confidence               4566666665554331 24555554444333 2334555555555544

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.31  E-value=1.6e-05  Score=71.41  Aligned_cols=200  Identities=10%  Similarity=-0.024  Sum_probs=133.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHH
Q 011102          264 GVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMK  343 (493)
Q Consensus       264 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~  343 (493)
                      .+|..+-..|.+.|++++|.+.|++..+.. +-++.+|+.+-.++.+. |++++|+..|++..+. . .-+...+..+-.
T Consensus        38 ~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~-g~~~~A~~~~~~al~~-~-p~~~~a~~~lg~  113 (259)
T d1xnfa_          38 QLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQA-GNFDAAYEAFDSVLEL-D-PTYNYAHLNRGI  113 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH-C-TTCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHH-HHHHHhhhhhhHHHHH-H-hhhhhhHHHHHH
Confidence            356667788899999999999999998743 23567888888899999 9999999999998875 1 224567888888


Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC----
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN----  419 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g----  419 (493)
                      .|...|++++|.+.|+...+.. +.+......+..++.+.+..+.+..+........-.+  ..++ ++..+....    
T Consensus       114 ~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~~~~~  189 (259)
T d1xnfa_         114 ALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQ--WGWN-IVEFYLGNISEQT  189 (259)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCS--THHH-HHHHHTTSSCHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhh--hhhh-HHHHHHHHHHHHH
Confidence            9999999999999999887653 2345555555556666666666666666655542222  1222 222222111    


Q ss_pred             CHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCH
Q 011102          420 DISRAIRYFSKLKEAGFCPT-YDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDK  475 (493)
Q Consensus       420 ~~~~A~~~~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~  475 (493)
                      ..+.+...+.....  ..|+ ..+|..+-..|...|++++|.+.|+...+.  .|+.
T Consensus       190 ~~~~~~~~~~~~~~--~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~  242 (259)
T d1xnfa_         190 LMERLKADATDNTS--LAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVHN  242 (259)
T ss_dssp             HHHHHHHHCCSHHH--HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCTT
T ss_pred             HHHHHHHHHHHhhh--cCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc--CCCC
Confidence            12222222211111  1122 245677888899999999999999998764  4543

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=0.00019  Score=66.82  Aligned_cols=229  Identities=7%  Similarity=-0.013  Sum_probs=124.7

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHH-HHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcC
Q 011102          199 LSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDR-LLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGG  277 (493)
Q Consensus       199 ~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~-t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g  277 (493)
                      |+.+-..+.+.+..++|+++++.+.+.   .|+.. .|+..-.++...|                              +
T Consensus        46 ~~~~~~~~~~~e~~~~Al~~~~~ai~l---nP~~~~a~~~r~~~l~~l~------------------------------~   92 (315)
T d2h6fa1          46 YDYFRAVLQRDERSERAFKLTRDAIEL---NAANYTVWHFRRVLLKSLQ------------------------------K   92 (315)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTT------------------------------C
T ss_pred             HHHHHHHHHhCCchHHHHHHHHHHHHH---CCCChHHHHHHHHHHHHhC------------------------------c
Confidence            344444677788999999999999854   55443 3443333333322                              2


Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESL  357 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l  357 (493)
                      ++++|++.++...+.. +-+..+|+.+-..+.+. |++++|++.++.+.+.  -.-+...|+.+...+.+.|++++|++.
T Consensus        93 ~~~eal~~~~~al~~~-p~~~~a~~~~~~~~~~l-~~~~eAl~~~~kal~~--dp~n~~a~~~~~~~~~~~~~~~~Al~~  168 (315)
T d2h6fa1          93 DLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVEWL-RDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQY  168 (315)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHH-TCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHH
T ss_pred             CHHHHHHHHHHHHHHH-HhhhhHHHHHhHHHHhh-ccHHHHHHHHhhhhhh--hhcchHHHHHHHHHHHHHHhhHHHHHH
Confidence            3566666666655532 12345566555556666 6666677666666554  223456666666667777777777777


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHcCCC------HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011102          358 FHWFTHSGRDPTVVMYTTLIHSRLSEKK------CREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKL  431 (493)
Q Consensus       358 ~~~m~~~g~~p~~~ty~~li~~~~~~g~------~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m  431 (493)
                      |++..+.. +-+...|+.+-..+.+.+.      +++|++.+....+..- -|...|+.+-..+. ....+++.+.++..
T Consensus       169 ~~~al~~~-p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P-~~~~~~~~l~~ll~-~~~~~~~~~~~~~~  245 (315)
T d2h6fa1         169 VDQLLKED-VRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVP-HNESAWNYLKGILQ-DRGLSKYPNLLNQL  245 (315)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHT-TTCGGGCHHHHHHH
T ss_pred             HHHHHHHC-CccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhCC-CchHHHHHHHHHHH-hcChHHHHHHHHHH
Confidence            76665542 2245556555444444433      4566666666554321 23444554433333 33345666666655


Q ss_pred             HHCCCC-CCHHHHHHHHHHHHHc--C-------CHHHHHHHHHHHH
Q 011102          432 KEAGFC-PTYDIYRDMIRIFMAS--G-------RLAKCRDVCKEAE  467 (493)
Q Consensus       432 ~~~g~~-p~~~ty~~li~~~~~~--g-------~~~~A~~l~~~m~  467 (493)
                      .+.... .+...+..++..|...  +       .+++|.++++.+.
T Consensus       246 ~~l~~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~~~ka~~l~~~l~  291 (315)
T d2h6fa1         246 LDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDILNKALELCEILA  291 (315)
T ss_dssp             HHHTTTCCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCcCCHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence            432211 2344555566655432  2       2445555555544

>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=97.91  E-value=0.00027  Score=64.65  Aligned_cols=215  Identities=13%  Similarity=0.052  Sum_probs=142.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhC----CCCCC-HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhc----CCCCCCH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDG----GRMLD-PSIYAKLILELGKNPDKYMLVMTLLDELGQR----DDLNLSQ  335 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~pd-~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~----~g~~p~~  335 (493)
                      .|.-..+.|...|++++|.+.|.+..+.    +-.++ ..+|+.+-..|.+. |++++|.+.++.....    +......
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~-~~~~~A~~~~~~a~~~~~~~~~~~~~~  117 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSG-GNSVNAVDSLENAIQIFTHRGQFRRGA  117 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh-CCcHHHHHHHHHhhHHhhhcccchhHH
Confidence            4666778888999999999999887652    21122 34677888888888 9999999999875432    1111123


Q ss_pred             HHHHHHHHHHHH-cCCHHHHHHHHHHHHH----cCCCC-CHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-----CC
Q 011102          336 QDCTAIMKVGIR-LQKFGVVESLFHWFTH----SGRDP-TVVMYTTLIHSRLSEKKCREALTVVWNMEASNCL-----FD  404 (493)
Q Consensus       336 ~~~~~li~~~~~-~g~~~~A~~l~~~m~~----~g~~p-~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~-----pd  404 (493)
                      .++..+...|-. .|++++|.+.|++..+    .+..+ -..+|..+...|...|++++|.+.|++.......     ..
T Consensus       118 ~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~  197 (290)
T d1qqea_         118 NFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWS  197 (290)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGG
T ss_pred             HHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhh
Confidence            455566666644 5999999999987642    22222 1355788899999999999999999997764221     12


Q ss_pred             H-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC-CC---HHHHHHHHHHHHH--cCCHHHHHHHHHHHHHCCCccCHHH
Q 011102          405 L-PAYRVVIKLFVALNDISRAIRYFSKLKEAGFC-PT---YDIYRDMIRIFMA--SGRLAKCRDVCKEAEMAGFKLDKQT  477 (493)
Q Consensus       405 ~-~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~-p~---~~ty~~li~~~~~--~g~~~~A~~l~~~m~~~g~~pd~~t  477 (493)
                      . ..|...+..+...|+.+.|...|+...+.... ++   ......++.++-.  .+.+++|...|+++.    +.|..-
T Consensus       198 ~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~----~lD~~~  273 (290)
T d1qqea_         198 LKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM----RLDKWK  273 (290)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS----CCCHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh----hcCHHH
Confidence            1 12334455667889999999999988744211 12   2345667777655  346888888887654    345544


Q ss_pred             HHHHHHh
Q 011102          478 VVELLQI  484 (493)
Q Consensus       478 ~~~Ll~~  484 (493)
                      ...|.++
T Consensus       274 ~~~L~~~  280 (290)
T d1qqea_         274 ITILNKI  280 (290)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4445543

>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=97.85  E-value=0.00031  Score=60.09  Aligned_cols=79  Identities=11%  Similarity=0.030  Sum_probs=40.1

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTV  392 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  392 (493)
                      |++++|++.|.++     ..|+..+|..+-..|.+.|++++|++.|++-.+.. +-+...|+.+-.+|.+.|+.++|++.
T Consensus        19 ~d~~~Al~~~~~i-----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~~~   92 (192)
T d1hh8a_          19 KDWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAIKD   92 (192)
T ss_dssp             TCHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CCHHHHHHHHHhc-----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHHHH
Confidence            5555555555432     12344455555555555555555555555544332 22344555555555555555555555


Q ss_pred             HHHHH
Q 011102          393 VWNME  397 (493)
Q Consensus       393 ~~~M~  397 (493)
                      |++..
T Consensus        93 ~~kAl   97 (192)
T d1hh8a_          93 LKEAL   97 (192)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55543

>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=97.82  E-value=3.8e-05  Score=72.02  Aligned_cols=255  Identities=9%  Similarity=-0.097  Sum_probs=156.3

Q ss_pred             HhCCChHHHHHHHHHHHhCCCCCCCHHH-HHH---HHHHHHHcCCCc-----hhhhHHHhhc-----cCcHHHHHHHHHH
Q 011102          207 GHMNLPERALQTFCWAQKQPHLFPDDRL-LAS---TVEVLARHHELK-----VPFKLENFVS-----LASKGVLEATAKG  272 (493)
Q Consensus       207 ~~~g~~~~A~~l~~~m~~~~g~~pd~~t-~~~---li~~~~~~g~~~-----~~~~l~~~~~-----~~~~~~~~~li~~  272 (493)
                      .+.+..++|+++++.....   .||..+ |+.   ++..+...+...     ..+++..+..     ..+...|..+..+
T Consensus        40 ~~~~~~~~al~~~~~~l~~---~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~  116 (334)
T d1dcea1          40 QAGELDESVLELTSQILGA---NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWL  116 (334)
T ss_dssp             HTTCCSHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hcccccHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHH
Confidence            3334457888888877643   455443 332   233333333211     1223322222     2245566666666


Q ss_pred             HHhcC--CHHHHHHHHHHHHhCCCCCCHHHHHHHH-HHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcC
Q 011102          273 FVKGG--NLKLAWKLLMVAKDGGRMLDPSIYAKLI-LELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQ  349 (493)
Q Consensus       273 ~~~~g--~~~~A~~l~~~m~~~g~~pd~~t~~~li-~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g  349 (493)
                      +...+  ++++|...++++.+.. .++...+...+ ..+... +.+++|+..++..... . .-+...|+.+-..+.+.|
T Consensus       117 ~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~-~~~~~Al~~~~~~i~~-~-p~~~~a~~~l~~~~~~~~  192 (334)
T d1dcea1         117 LSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAA-VAPAEELAFTDSLITR-N-FSNYSSWHYRSCLLPQLH  192 (334)
T ss_dssp             HHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTC-CCHHHHHHHHHTTTTT-T-CCCHHHHHHHHHHHHHHS
T ss_pred             HHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhc-cccHHHHHHHHHHHHc-C-CCCHHHHHHHHHHHHHhc
Confidence            66654  4788888888887743 23455554444 444555 8888898888887665 1 245677888888888888


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Q 011102          350 KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFS  429 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~  429 (493)
                      ++++|...+....+.  .|+   ...+...+...+..+++...+....... .++...+..+...+...|+.++|...+.
T Consensus       193 ~~~~A~~~~~~~~~~--~~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~  266 (334)
T d1dcea1         193 PQPDSGPQGRLPENV--LLK---ELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELESCKELQ  266 (334)
T ss_dssp             CCCCSSSCCSSCHHH--HHH---HHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHhHHh--HHH---HHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHHHHHHH
Confidence            888776555433321  111   1123333455566667777777665543 2344456666777788889999999888


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHH
Q 011102          430 KLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQT  477 (493)
Q Consensus       430 ~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t  477 (493)
                      +..+... -+..+|..+...|.+.|++++|.+.+++..+  +.|+..-
T Consensus       267 ~~~~~~p-~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~--ldP~~~~  311 (334)
T d1dcea1         267 ELEPENK-WCLLTIILLMRALDPLLYEKETLQYFSTLKA--VDPMRAA  311 (334)
T ss_dssp             HHCTTCH-HHHHHHHHHHHHHCTGGGHHHHHHHHHHHHH--HCGGGHH
T ss_pred             HHHhhCc-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--HCcccHH
Confidence            7765432 2556778888889999999999999999877  4665443

>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=97.72  E-value=0.00053  Score=58.60  Aligned_cols=127  Identities=5%  Similarity=-0.179  Sum_probs=96.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcC
Q 011102          270 AKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQ  349 (493)
Q Consensus       270 i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g  349 (493)
                      -..+...|+++.|++.|.++    ..|+..+|..+=..|... |++++|++.|++..+.  -.-+...|..+-.+|.+.|
T Consensus        12 g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~-g~~~~A~~~~~kAl~l--dp~~~~a~~~~g~~~~~~g   84 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTIL-KNMTEAEKAFTRSINR--DKHLAVAYFQRGMLYYQTE   84 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHc-CCchhHHHHHHHHHHH--hhhhhhhHHHHHHHHHhhc
Confidence            34567889999999999865    347888888888899999 9999999999998775  2346778889999999999


Q ss_pred             CHHHHHHHHHHHHHcC------------CC--CC-HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC
Q 011102          350 KFGVVESLFHWFTHSG------------RD--PT-VVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF  403 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g------------~~--p~-~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p  403 (493)
                      ++++|.+.|++-....            ..  .+ ..++..+-.+|.+.|++++|.+.+....+....+
T Consensus        85 ~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~  153 (192)
T d1hh8a_          85 KYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  153 (192)
T ss_dssp             CHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             cHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            9999999998875421            11  11 2445556667778888888888877766554433

>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=97.72  E-value=0.0024  Score=57.98  Aligned_cols=206  Identities=12%  Similarity=0.026  Sum_probs=123.9

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCC
Q 011102          199 LSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGN  278 (493)
Q Consensus       199 ~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~  278 (493)
                      |.-.-..|...|++++|++.|....+-                +.+.++  ...         ...+|+.+-..|.+.|+
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~----------------~~~~~~--~~~---------~a~~~~~~g~~y~~~~~   92 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADY----------------QKKAGN--EDE---------AGNTYVEAYKCFKSGGN   92 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHH----------------HHHTTC--HHH---------HHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHH----------------HHHcCC--CHH---------HHHHHHHHHHHHHHhCC
Confidence            334456777888888888888776532                111111  000         12345556666777777


Q ss_pred             HHHHHHHHHHHHh----CCCC-CCHHHHHHHHHHHh-cCCCCHHHHHHHHHHHhhc---CCCCC-CHHHHHHHHHHHHHc
Q 011102          279 LKLAWKLLMVAKD----GGRM-LDPSIYAKLILELG-KNPDKYMLVMTLLDELGQR---DDLNL-SQQDCTAIMKVGIRL  348 (493)
Q Consensus       279 ~~~A~~l~~~m~~----~g~~-pd~~t~~~li~~~~-~~~~~~~~a~~l~~~m~~~---~g~~p-~~~~~~~li~~~~~~  348 (493)
                      +++|.+.+++..+    .|.. ....++..+...|- .. |++++|.+.+++....   .+-.+ -..+|..+...|.+.
T Consensus        93 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~  171 (290)
T d1qqea_          93 SVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDL-HDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALD  171 (290)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT-CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHH-HHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHc
Confidence            7777777765543    1110 11233444444553 45 8999999999876432   11111 134577888999999


Q ss_pred             CCHHHHHHHHHHHHHcCCCC-----CH-HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC-CC---HHHHHHHHHHHHH-
Q 011102          349 QKFGVVESLFHWFTHSGRDP-----TV-VMYTTLIHSRLSEKKCREALTVVWNMEASNCL-FD---LPAYRVVIKLFVA-  417 (493)
Q Consensus       349 g~~~~A~~l~~~m~~~g~~p-----~~-~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~-pd---~~ty~~li~~~~~-  417 (493)
                      |++++|.+.|++........     .. ..|..++..+...|+.+.|...+++..+.... ++   ......++.++-. 
T Consensus       172 g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~  251 (290)
T d1qqea_         172 GQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEG  251 (290)
T ss_dssp             TCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTT
T ss_pred             ChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhc
Confidence            99999999999987542221     11 22344555667789999999999988764311 12   2345667777655 


Q ss_pred             -cCCHHHHHHHHHHHH
Q 011102          418 -LNDISRAIRYFSKLK  432 (493)
Q Consensus       418 -~g~~~~A~~~~~~m~  432 (493)
                       .+.+++|...|+.+.
T Consensus       252 d~e~~~eai~~y~~~~  267 (290)
T d1qqea_         252 DSEQLSEHCKEFDNFM  267 (290)
T ss_dssp             CTTTHHHHHHHHTTSS
T ss_pred             CHHHHHHHHHHHHHHh
Confidence             345888888886554

>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=97.64  E-value=0.0033  Score=55.39  Aligned_cols=165  Identities=12%  Similarity=0.005  Sum_probs=102.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHH
Q 011102          262 SKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAI  341 (493)
Q Consensus       262 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~l  341 (493)
                      +..+|+.+-..|.+.|++++|++.|++..+..- -+..+|..+-..+... |++++|...|+...+. . ..+......+
T Consensus        70 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~-g~~~~A~~~~~~al~~-~-p~~~~~~~~~  145 (259)
T d1xnfa_          70 MPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP-TYNYAHLNRGIALYYG-GRDKLAQDDLLAFYQD-D-PNDPFRSLWL  145 (259)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH-C-TTCHHHHHHH
T ss_pred             CHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHh-hhhhhHHHHHHHHHHH-hhHHHHHHHHHHHHhh-c-cccHHHHHHH
Confidence            445677788888899999999999999888531 2355677777888888 9999999999988765 1 2344444444


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH----HHHHHHHHHHHHCCCCCC-HHHHHHHHHHHH
Q 011102          342 MKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC----REALTVVWNMEASNCLFD-LPAYRVVIKLFV  416 (493)
Q Consensus       342 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~----~~A~~l~~~M~~~gi~pd-~~ty~~li~~~~  416 (493)
                      ..++.+.+..+.+..+........  ++...++ ++..+......    +.+...+.....  ..|+ ..+|..+-..|.
T Consensus       146 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~lg~~~~  220 (259)
T d1xnfa_         146 YLAEQKLDEKQAKEVLKQHFEKSD--KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTS--LAEHLSETNFYLGKYYL  220 (259)
T ss_dssp             HHHHHHHCHHHHHHHHHHHHHHSC--CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHH--HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHHHHhhccc--hhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhh--cCcccHHHHHHHHHHHH
Confidence            455566666666666666655432  2222222 22222222222    222222111111  1122 235666777889


Q ss_pred             HcCCHHHHHHHHHHHHHCC
Q 011102          417 ALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       417 ~~g~~~~A~~~~~~m~~~g  435 (493)
                      ..|++++|.+.|+......
T Consensus       221 ~~g~~~~A~~~~~~al~~~  239 (259)
T d1xnfa_         221 SLGDLDSATALFKLAVANN  239 (259)
T ss_dssp             HTTCHHHHHHHHHHHHTTC
T ss_pred             HCCCHHHHHHHHHHHHHcC
Confidence            9999999999999887543

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.59  E-value=0.023  Score=52.35  Aligned_cols=262  Identities=8%  Similarity=0.002  Sum_probs=165.5

Q ss_pred             hhccCCCCHHHHHHHHhhhcccCcHHHHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhH
Q 011102          175 KGLDSHKDVAEVLDKCGRFLRKGSLSFTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKL  254 (493)
Q Consensus       175 ~~~~~~~~~~~a~~~~~~m~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l  254 (493)
                      ..+-+.|..+.|...+..   -+.|.-++..|.+.+++..|.+++....       +..+|.-+..+|.+......+...
T Consensus        22 ~~c~~~~lye~A~~lY~~---~~d~~rl~~~~v~l~~~~~avd~~~k~~-------~~~~~k~~~~~l~~~~e~~la~i~   91 (336)
T d1b89a_          22 DRCYDEKMYDAAKLLYNN---VSNFGRLASTLVHLGEYQAAVDGARKAN-------STRTWKEVCFACVDGKEFRLAQMC   91 (336)
T ss_dssp             -------CTTTHHHHHHH---TTCHHHHHHHHHTTTCHHHHHHHHHHHT-------CHHHHHHHHHHHHHTTCHHHHHHT
T ss_pred             HHHHHCCCHHHHHHHHHh---CCCHHHHHHHHHhhccHHHHHHHHHHcC-------CHHHHHHHHHHHHhCcHHHHHHHH
Confidence            334466777888888764   3678889999999999999999887542       567899999999887764433221


Q ss_pred             HHhhccCcHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC
Q 011102          255 ENFVSLASKGVLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLS  334 (493)
Q Consensus       255 ~~~~~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~  334 (493)
                       .........-...++..|-..|.+++...+++..... -..+...++-++..|++. + .++..+.+......  +.+.
T Consensus        92 -~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~-~-~~kl~e~l~~~s~~--y~~~  165 (336)
T d1b89a_          92 -GLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKF-K-PQKMREHLELFWSR--VNIP  165 (336)
T ss_dssp             -TTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTT-C-HHHHHHHHHHHSTT--SCHH
T ss_pred             -HHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHh-C-hHHHHHHHHhcccc--CCHH
Confidence             2222334445567899999999999999999976542 346778899999999998 4 34444444443221  2221


Q ss_pred             HH--------HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHH
Q 011102          335 QQ--------DCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLP  406 (493)
Q Consensus       335 ~~--------~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~  406 (493)
                      ..        .|.-++-.|.+.|.+++|..+.-+   .  .+++......+..+.+..+.+...+++....+.  .|+..
T Consensus       166 k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~---~--~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~--~p~~i  238 (336)
T d1b89a_         166 KVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMN---H--PTDAWKEGQFKDIITKVANVELYYRAIQFYLEF--KPLLL  238 (336)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHH---S--TTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHH--CGGGH
T ss_pred             HHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHH---c--chhhhhHHHHHHHHHccCChHHHHHHHHHHHHc--CHHHH
Confidence            11        245566666677776666544321   1  233333344555566666666655555543331  24322


Q ss_pred             H-----------HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011102          407 A-----------YRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDV  462 (493)
Q Consensus       407 t-----------y~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l  462 (493)
                      .           -.-++.-+-+.+++.....+++...+.|.   ....++|.+.|...++++.-.+.
T Consensus       239 ~~lL~~v~~~~d~~r~V~~~~k~~~l~li~p~Le~v~~~n~---~~vn~al~~lyie~~d~~~l~~~  302 (336)
T d1b89a_         239 NDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNN---KSVNESLNNLFITEEDYQALRTS  302 (336)
T ss_dssp             HHHHHHHGGGCCHHHHHHHHHHTTCTTTTHHHHHHHHTTCC---HHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHhccCCCHHHHHHHHHhcCCcHHHHHHHHHHHHcCh---HHHHHHHHHHHhCcchhHHHHHH
Confidence            1           24456667777888888888877666553   46899999999999997654433

>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=97.58  E-value=0.00091  Score=54.97  Aligned_cols=91  Identities=10%  Similarity=0.031  Sum_probs=63.6

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      +.|.+.|++++|...|++..+.. +-+...|..+-..|...|++++|.+.|+...+.. .-+...|..+..+|...|+++
T Consensus        18 n~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~   95 (159)
T d1a17a_          18 NDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFR   95 (159)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHH
Confidence            45667777777777777766543 3466777777777777778888877777776543 224467777777777788888


Q ss_pred             HHHHHHHHHHHCC
Q 011102          423 RAIRYFSKLKEAG  435 (493)
Q Consensus       423 ~A~~~~~~m~~~g  435 (493)
                      +|...|++.....
T Consensus        96 eA~~~~~~a~~~~  108 (159)
T d1a17a_          96 AALRDYETVVKVK  108 (159)
T ss_dssp             HHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHcC
Confidence            8877777776543

>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=97.56  E-value=0.00095  Score=51.81  Aligned_cols=88  Identities=13%  Similarity=-0.002  Sum_probs=48.5

Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          379 SRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAK  458 (493)
Q Consensus       379 ~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~  458 (493)
                      .+.+.|++++|+.+|++..+.. +-+...|..+-.+|.+.|++++|...++...+..- .+...|..+-.++...|++++
T Consensus        12 ~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~g~~~~~~~~~~~   89 (117)
T d1elwa_          12 KALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAALEFLNRFEE   89 (117)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhcc-chhhHHHHHHHHHHHccCHHH
Confidence            3445555555555555554431 12344455555556666666666666666554432 255556666666666666666


Q ss_pred             HHHHHHHHHH
Q 011102          459 CRDVCKEAEM  468 (493)
Q Consensus       459 A~~l~~~m~~  468 (493)
                      |.+.|++..+
T Consensus        90 A~~~~~~a~~   99 (117)
T d1elwa_          90 AKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHHH
Confidence            6666666554

>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=97.54  E-value=0.00083  Score=57.08  Aligned_cols=98  Identities=12%  Similarity=-0.015  Sum_probs=82.8

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHH
Q 011102          333 LSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVV  411 (493)
Q Consensus       333 p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~l  411 (493)
                      |+...+-..-+.|.+.|++++|+..|++..+.. +-+...|+.+-.+|.+.|++++|+..|+...+.  .| +..+|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            566667777889999999999999999876553 457788999999999999999999999998653  45 46788889


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Q 011102          412 IKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       412 i~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      -.+|.+.|++++|...|+...+
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999998763

>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=97.43  E-value=0.0023  Score=49.52  Aligned_cols=89  Identities=9%  Similarity=-0.033  Sum_probs=50.5

Q ss_pred             HHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHH
Q 011102          343 KVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDIS  422 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~  422 (493)
                      +.+.+.|++++|+.+|++..+.. +-+...|+.+-.+|...|++++|+..+....+... .+...|..+-.++...|+++
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKP-DWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhcc-chhhHHHHHHHHHHHccCHH
Confidence            34555566666666666654331 23445566666666666666666666666554332 34455666666666666666


Q ss_pred             HHHHHHHHHHH
Q 011102          423 RAIRYFSKLKE  433 (493)
Q Consensus       423 ~A~~~~~~m~~  433 (493)
                      +|...|+...+
T Consensus        89 ~A~~~~~~a~~   99 (117)
T d1elwa_          89 EAKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHH
Confidence            66666666553

>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=97.42  E-value=0.0021  Score=52.66  Aligned_cols=91  Identities=11%  Similarity=-0.029  Sum_probs=79.1

Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          377 IHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRL  456 (493)
Q Consensus       377 i~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~  456 (493)
                      -..|.+.|++++|+..|++..+..- -+...|..+-..|.+.|++++|...|+...+..- -+...|..+..+|...|++
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p-~~~~a~~~~g~~~~~~g~~   94 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASNMALGKF   94 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHhhhccccch-hhhhhhhhhHHHHHhccccchHHHHHHHHHHHcc-cchHHHHHHHHHHHHcCCH
Confidence            4567899999999999999887642 3677888899999999999999999999986653 3668999999999999999


Q ss_pred             HHHHHHHHHHHHC
Q 011102          457 AKCRDVCKEAEMA  469 (493)
Q Consensus       457 ~~A~~l~~~m~~~  469 (493)
                      ++|.+.+++..+.
T Consensus        95 ~eA~~~~~~a~~~  107 (159)
T d1a17a_          95 RAALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            9999999999874

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=0.00045  Score=54.35  Aligned_cols=93  Identities=10%  Similarity=0.073  Sum_probs=40.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCH---HHHHHHHHHHHHCCCCCCH-HHHHHHHHHH
Q 011102          340 AIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKC---REALTVVWNMEASNCLFDL-PAYRVVIKLF  415 (493)
Q Consensus       340 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~---~~A~~l~~~M~~~gi~pd~-~ty~~li~~~  415 (493)
                      .+++.+...+++++|++.|++....+ +.+..++..+-.++.+.++.   ++|..++++.....-.|+. .+|..+=.+|
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            34444555555555555555544332 23444444444444443322   2345555444433222221 1333344444


Q ss_pred             HHcCCHHHHHHHHHHHHH
Q 011102          416 VALNDISRAIRYFSKLKE  433 (493)
Q Consensus       416 ~~~g~~~~A~~~~~~m~~  433 (493)
                      .+.|++++|.+.|+...+
T Consensus        83 ~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHH
Confidence            455555555555554443

>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=97.34  E-value=0.0022  Score=54.29  Aligned_cols=98  Identities=13%  Similarity=-0.071  Sum_probs=84.2

Q ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHH
Q 011102          296 LDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYT  374 (493)
Q Consensus       296 pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~  374 (493)
                      |+...+.-.-..|.+. |++++|+..|.+....  -.-+...|+.+-.+|.+.|++++|...|+...+.  .| +..+|.
T Consensus         2 ~~a~~l~~~Gn~~~~~-g~~~~Ai~~~~kal~~--~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~   76 (201)
T d2c2la1           2 PSAQELKEQGNRLFVG-RKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHF   76 (201)
T ss_dssp             CCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHH
T ss_pred             hhHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHH
Confidence            6666777777889999 9999999999987765  2356788999999999999999999999998743  45 578899


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHH
Q 011102          375 TLIHSRLSEKKCREALTVVWNMEA  398 (493)
Q Consensus       375 ~li~~~~~~g~~~~A~~l~~~M~~  398 (493)
                      .+-.+|.+.|++++|+..|++..+
T Consensus        77 ~lg~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          77 FLGQCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999999999999999998764

>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=97.33  E-value=0.00056  Score=63.66  Aligned_cols=259  Identities=11%  Similarity=-0.016  Sum_probs=172.6

Q ss_pred             CCCCHHHHHHHHhhhcccC-----cHHH---HHHHHHh-------CCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Q 011102          179 SHKDVAEVLDKCGRFLRKG-----SLSF---TVRELGH-------MNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLA  243 (493)
Q Consensus       179 ~~~~~~~a~~~~~~m~~~~-----~~~~---li~~~~~-------~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~  243 (493)
                      .....++|++++.+....+     .|+.   ++..+..       .|+.++|+.+|+...+. . .-+...|..+..++.
T Consensus        41 ~~~~~~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~-~-pk~~~~~~~~~~~~~  118 (334)
T d1dcea1          41 AGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV-N-PKSYGTWHHRCWLLS  118 (334)
T ss_dssp             TTCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHH
T ss_pred             cccccHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHh-C-CCcHHHHHHhhHHHH
Confidence            3344478888888665432     3332   2333333       44578999999998754 1 225667788888888


Q ss_pred             HcCCCchhhhHHHhhcc-----CcHHHHHHH-HHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHH
Q 011102          244 RHHELKVPFKLENFVSL-----ASKGVLEAT-AKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYML  317 (493)
Q Consensus       244 ~~g~~~~~~~l~~~~~~-----~~~~~~~~l-i~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~  317 (493)
                      ..++.+..+++..+...     .+...|... -..+...+..++|+..++...+... -+...|+.+-..+.+. |++++
T Consensus       119 ~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~~~~~-~~~~~  196 (334)
T d1dcea1         119 RLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLLPQL-HPQPD  196 (334)
T ss_dssp             TCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHHHHH-SCCCC
T ss_pred             HhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHh-cCHHH
Confidence            88877677776655442     244455444 4677778999999999998887652 3567788777777777 77776


Q ss_pred             HHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011102          318 VMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNME  397 (493)
Q Consensus       318 a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~  397 (493)
                      |...+......   .|   ....+...+...+..+++...+....... .++...+..+...+...|+.++|...+.+..
T Consensus       197 A~~~~~~~~~~---~~---~~~~~~~~~~~l~~~~~a~~~~~~~l~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  269 (334)
T d1dcea1         197 SGPQGRLPENV---LL---KELELVQNAFFTDPNDQSAWFYHRWLLGR-AEPLFRCELSVEKSTVLQSELESCKELQELE  269 (334)
T ss_dssp             SSSCCSSCHHH---HH---HHHHHHHHHHHHCSSCSHHHHHHHHHHSC-CCCSSSCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHhHHh---HH---HHHHHHHHHHHhcchhHHHHHHHHHHHhC-cchhhHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            65444432221   01   11233445667788888888888776543 3455667777888888899999999998766


Q ss_pred             HCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHH
Q 011102          398 ASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPT-YDIYRDMIRIFM  451 (493)
Q Consensus       398 ~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~-~~ty~~li~~~~  451 (493)
                      +... -+..+|..+-..|.+.|+.++|.+.|+...+.  .|+ ..-|+.|-..+.
T Consensus       270 ~~~p-~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         270 PENK-WCLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             TTCH-HHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHH
T ss_pred             hhCc-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHHHHHHHHHHh
Confidence            5431 24467777888899999999999999998864  364 345565554444

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.19  E-value=0.0019  Score=50.56  Aligned_cols=107  Identities=9%  Similarity=-0.061  Sum_probs=75.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH---HHHHHHHHHHHHCCCCCC-HHHHHHHHHH
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDI---SRAIRYFSKLKEAGFCPT-YDIYRDMIRI  449 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~---~~A~~~~~~m~~~g~~p~-~~ty~~li~~  449 (493)
                      ..|++.+...+++++|.+.|+.....+- .+..++..+-.++.+.++.   ++|..+|++....+-.|+ ..+|..+-.+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p-~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            4567778888888888888888776432 3556777777777765544   468888888776554343 2366677788


Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          450 FMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       450 ~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      |.+.|++++|.+.|++..+  +.|+..-...+..
T Consensus        82 y~~~g~~~~A~~~~~~aL~--~~P~~~~A~~l~~  113 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQ--TEPQNNQAKELER  113 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHH--hCcCCHHHHHHHH
Confidence            8888888888888888877  5676665555554

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.14  E-value=0.004  Score=52.21  Aligned_cols=128  Identities=9%  Similarity=-0.005  Sum_probs=84.5

Q ss_pred             CHHHHHHHH---HHHHHcCCHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHH
Q 011102          334 SQQDCTAIM---KVGIRLQKFGVVESLFHWFTHS--GRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAY  408 (493)
Q Consensus       334 ~~~~~~~li---~~~~~~g~~~~A~~l~~~m~~~--g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty  408 (493)
                      |...|-.++   ......|++++|.+.|..-...  |-...         .+ ..+.+  +...-..+...    ....+
T Consensus         7 D~~~f~~~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~---------~~-~~~~w--~~~~r~~l~~~----~~~a~   70 (179)
T d2ff4a2           7 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLD---------DL-RDFQF--VEPFATALVED----KVLAH   70 (179)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTG---------GG-TTSTT--HHHHHHHHHHH----HHHHH
T ss_pred             cHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccc---------cC-cchHH--HHHHHHHHHHH----HHHHH
Confidence            444444444   4667788888888888887642  21100         00 00111  11111111111    23467


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-----HCCCccCHHHH
Q 011102          409 RVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAE-----MAGFKLDKQTV  478 (493)
Q Consensus       409 ~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~-----~~g~~pd~~t~  478 (493)
                      ..+...+.+.|++++|...++.+.+..- -+...|..++.+|.+.|+.++|++.|+++.     +.|+.|...|-
T Consensus        71 ~~la~~~~~~g~~~~Al~~~~~al~~~P-~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~  144 (179)
T d2ff4a2          71 TAKAEAEIACGRASAVIAELEALTFEHP-YREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  144 (179)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHHCCCchHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHH
Confidence            7788889999999999999999886543 378889999999999999999999999874     36999988763

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.08  E-value=0.0023  Score=49.05  Aligned_cols=85  Identities=8%  Similarity=0.034  Sum_probs=41.9

Q ss_pred             HHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          344 VGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISR  423 (493)
Q Consensus       344 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~  423 (493)
                      .+.+.|++++|...|++..+.. +-+...|..+-..+.+.|++++|+..|+...+.. +-+...|..+-..|...|++++
T Consensus        25 ~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~~  102 (112)
T d1hxia_          25 SMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNANA  102 (112)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHHH
Confidence            3445555555555555554331 1134555555555555555555555555544321 1123444445555555555555


Q ss_pred             HHHHHHH
Q 011102          424 AIRYFSK  430 (493)
Q Consensus       424 A~~~~~~  430 (493)
                      |.+.|++
T Consensus       103 A~~~l~~  109 (112)
T d1hxia_         103 ALASLRA  109 (112)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5555544

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.07  E-value=0.01  Score=48.12  Aligned_cols=76  Identities=12%  Similarity=0.056  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          406 PAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       406 ~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      .+|+.+-.+|.+.|++++|.+.++...+.. +-+..+|..+..+|...|++++|...|+...+  +.|+.......+..
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~--l~P~n~~~~~~l~~  143 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAAS--LNPNNLDIRNSYEL  143 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH--HSTTCHHHHHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHH
Confidence            467778888899999999999999887654 23778899999999999999999999988876  45655544444443

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.02  E-value=0.0029  Score=48.46  Aligned_cols=86  Identities=9%  Similarity=-0.109  Sum_probs=52.5

Q ss_pred             HHHHcCCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCH
Q 011102          378 HSRLSEKKCREALTVVWNMEASNCLF-DLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRL  456 (493)
Q Consensus       378 ~~~~~~g~~~~A~~l~~~M~~~gi~p-d~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~  456 (493)
                      ..+.+.|++++|...|++..+..  | +...|..+-..+.+.|++++|...|+...+..- -+...|..+...|...|++
T Consensus        24 ~~~~~~g~~~~A~~~~~~al~~~--p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~a~~~la~~y~~~g~~  100 (112)
T d1hxia_          24 LSMLKLANLAEAALAFEAVCQKE--PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDP-KDIAVHAALAVSHTNEHNA  100 (112)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHhhhcccc--cccchhhhhhhhhhhhhhhHHHhhccccccccccc-ccccchHHHHHHHHHCCCH
Confidence            34556666666666666655432  3 355666666666666666666666666654331 2456666666666666666


Q ss_pred             HHHHHHHHHH
Q 011102          457 AKCRDVCKEA  466 (493)
Q Consensus       457 ~~A~~l~~~m  466 (493)
                      ++|.+.+++.
T Consensus       101 ~~A~~~l~~~  110 (112)
T d1hxia_         101 NAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            6666666653

>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=96.82  E-value=0.012  Score=48.62  Aligned_cols=97  Identities=11%  Similarity=-0.023  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCC-------------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCC
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHSG-RDPT-------------VVMYTTLIHSRLSEKKCREALTVVWNMEASNCL  402 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~-------------~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~  402 (493)
                      .+...-+.|.+.|++++|...|.+..+.- ..+.             ..+|+.+-.+|.+.|++++|+..++...+.. +
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p   93 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-S   93 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-c
Confidence            34444567888999999999998876431 1111             2345556666667777777777776655542 1


Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          403 FDLPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       403 pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      -+...|..+-.+|...|++++|...|+...+.
T Consensus        94 ~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          94 NNEKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            25556666666677777777777777766653

>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=96.82  E-value=0.014  Score=48.68  Aligned_cols=71  Identities=14%  Similarity=0.025  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-----CCCCCCHHH
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEA-----SNCLFDLPA  407 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~-----~gi~pd~~t  407 (493)
                      ..+..+...+.+.|++++|...++...+.. +-+...|..++.+|.+.|+..+|++.|+++.+     .|+.|...+
T Consensus        68 ~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          68 LAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            345566667777777777777777665432 33666677777777777777777777776532     466666544

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=96.71  E-value=0.086  Score=48.38  Aligned_cols=252  Identities=10%  Similarity=-0.013  Sum_probs=142.2

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCCchhhhHHHhhccCcHHHHHHHHHHHHhcCCHH
Q 011102          201 FTVRELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHELKVPFKLENFVSLASKGVLEATAKGFVKGGNLK  280 (493)
Q Consensus       201 ~li~~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~~~~~~l~~~~~~~~~~~~~~li~~~~~~g~~~  280 (493)
                      .+..-|-+.|.++.|..+|..+..          |..++..+.+.++  ...++.......+..+|.-+...+.+.....
T Consensus        19 ~i~~~c~~~~lye~A~~lY~~~~d----------~~rl~~~~v~l~~--~~~avd~~~k~~~~~~~k~~~~~l~~~~e~~   86 (336)
T d1b89a_          19 QVGDRCYDEKMYDAAKLLYNNVSN----------FGRLASTLVHLGE--YQAAVDGARKANSTRTWKEVCFACVDGKEFR   86 (336)
T ss_dssp             ----------CTTTHHHHHHHTTC----------HHHHHHHHHTTTC--HHHHHHHHHHHTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHhCCC----------HHHHHHHHHhhcc--HHHHHHHHHHcCCHHHHHHHHHHHHhCcHHH
Confidence            445566688889999999887653          4667777777776  3344444555667778988999988887775


Q ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011102          281 LAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHW  360 (493)
Q Consensus       281 ~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~  360 (493)
                      .|     .+...+...++.....++..|-.. |.+++...+++.....  -..+...++-++..|++.+. ++   +.+.
T Consensus        87 la-----~i~~~~~~~~~d~l~~~v~~ye~~-~~~e~Li~~Le~~~~~--~~~~~~~~~~L~~lyak~~~-~k---l~e~  154 (336)
T d1b89a_          87 LA-----QMCGLHIVVHADELEELINYYQDR-GYFEELITMLEAALGL--ERAHMGMFTELAILYSKFKP-QK---MREH  154 (336)
T ss_dssp             HH-----HHTTTTTTTCHHHHHHHHHHHHHT-TCHHHHHHHHHHHTTS--TTCCHHHHHHHHHHHHTTCH-HH---HHHH
T ss_pred             HH-----HHHHHHhhcCHHHHHHHHHHHHHc-CChHHHHHHHHHHHcC--CccchHHHHHHHHHHHHhCh-HH---HHHH
Confidence            54     333444556777778899999999 9999999999987543  34677788999999998653 33   3333


Q ss_pred             HHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHC--------CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          361 FTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEAS--------NCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       361 m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~--------gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                      ++.....-|   .--++..|-+.+.+.++.-++..|.+.        .-.++..-....+..+.+.++.+...++.....
T Consensus       155 l~~~s~~y~---~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL  231 (336)
T d1b89a_         155 LELFWSRVN---IPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYL  231 (336)
T ss_dssp             HHHHSTTSC---HHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH
T ss_pred             HHhccccCC---HHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCChHHHHHHHHHHH
Confidence            433211222   123344444444454444444433210        011233234455666777777776666666555


Q ss_pred             HCCCCCCHHH-----------HHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHHh
Q 011102          433 EAGFCPTYDI-----------YRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQI  484 (493)
Q Consensus       433 ~~g~~p~~~t-----------y~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~~  484 (493)
                      +.  .|+...           -.-+++-+-+.+++......++.....|.   ....++|.++
T Consensus       232 ~~--~p~~i~~lL~~v~~~~d~~r~V~~~~k~~~l~li~p~Le~v~~~n~---~~vn~al~~l  289 (336)
T d1b89a_         232 EF--KPLLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNN---KSVNESLNNL  289 (336)
T ss_dssp             HH--CGGGHHHHHHHHGGGCCHHHHHHHHHHTTCTTTTHHHHHHHHTTCC---HHHHHHHHHH
T ss_pred             Hc--CHHHHHHHHHHhccCCCHHHHHHHHHhcCCcHHHHHHHHHHHHcCh---HHHHHHHHHH
Confidence            42  243220           12234444445555555555555444442   3455555553

>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=96.64  E-value=0.055  Score=44.31  Aligned_cols=95  Identities=9%  Similarity=-0.057  Sum_probs=70.3

Q ss_pred             HHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCC-------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC
Q 011102          303 KLILELGKNPDKYMLVMTLLDELGQRDDLNLS-------------QQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT  369 (493)
Q Consensus       303 ~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~-------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~  369 (493)
                      ..=..+.+. |++++|...|.+........+.             ..+|+-+-.+|.+.|++++|+..++...+.. +-+
T Consensus        18 ~~G~~~~~~-~~~~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~y~k~~~~~~A~~~~~~al~~~-p~~   95 (170)
T d1p5qa1          18 ERGTVYFKE-GKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD-SNN   95 (170)
T ss_dssp             HHHHHHHHH-TCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTC
T ss_pred             HHHHHHHHc-CCHHHHHHHHHHHHHHhhhccccchHHHhhhchhHHHHHHHHHHHHHhhhhcccccchhhhhhhcc-ccc
Confidence            334467777 8899999999877654221111             2356667778888999999999998877652 337


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC
Q 011102          370 VVMYTTLIHSRLSEKKCREALTVVWNMEAS  399 (493)
Q Consensus       370 ~~ty~~li~~~~~~g~~~~A~~l~~~M~~~  399 (493)
                      +.+|..+-.+|...|++++|...|++..+.
T Consensus        96 ~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          96 EKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            888888888999999999999999988764

>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=96.57  E-value=0.027  Score=43.83  Aligned_cols=88  Identities=9%  Similarity=0.071  Sum_probs=38.5

Q ss_pred             HHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC--CCCC----HHHHHHHHHHHHH
Q 011102          379 SRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG--FCPT----YDIYRDMIRIFMA  452 (493)
Q Consensus       379 ~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g--~~p~----~~ty~~li~~~~~  452 (493)
                      .|.+.|++++|++.|.+..+.+- -+...|..+-.+|.+.|++++|...++...+..  ....    ..+|..+-..+..
T Consensus        13 ~~~~~~~y~~Ai~~y~~al~~~p-~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~~~~   91 (128)
T d1elra_          13 DAYKKKDFDTALKHYDKAKELDP-TNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFK   91 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444444444443321 233444444444555555555555554443210  0000    1234444445555


Q ss_pred             cCCHHHHHHHHHHHH
Q 011102          453 SGRLAKCRDVCKEAE  467 (493)
Q Consensus       453 ~g~~~~A~~l~~~m~  467 (493)
                      .+++++|.+.|+.-.
T Consensus        92 ~~~~~~A~~~~~kal  106 (128)
T d1elra_          92 EEKYKDAIHFYNKSL  106 (128)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHH
Confidence            555555555555544

>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=96.37  E-value=0.062  Score=43.06  Aligned_cols=64  Identities=9%  Similarity=-0.061  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 011102          371 VMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAG  435 (493)
Q Consensus       371 ~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g  435 (493)
                      .+|+.+..+|.+.|++++|++.+++..+.. +-+..+|..+-.++...|++++|...|+...+..
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~  131 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASLN  131 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            467778888888888888888888876643 2366788888888888888888888888877543

>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=96.24  E-value=0.018  Score=44.86  Aligned_cols=92  Identities=8%  Similarity=0.041  Sum_probs=59.4

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCC--CC---CC-HHHHHHHHHH
Q 011102          341 IMKVGIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASN--CL---FD-LPAYRVVIKL  414 (493)
Q Consensus       341 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~g--i~---pd-~~ty~~li~~  414 (493)
                      +-+.|.+.|++++|++.|.+..+.. +.+...|..+-.+|.+.|++++|++.++++.+..  ..   ++ ..+|..+=..
T Consensus        10 ~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~~   88 (128)
T d1elra_          10 LGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGNS   88 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHH
Confidence            4456677777777777777766542 2356677777777777777777777777765421  10   11 1355556666


Q ss_pred             HHHcCCHHHHHHHHHHHHH
Q 011102          415 FVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       415 ~~~~g~~~~A~~~~~~m~~  433 (493)
                      +...+++++|...|+.-..
T Consensus        89 ~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          89 YFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHh
Confidence            7777778888877776553

>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=96.20  E-value=0.049  Score=44.41  Aligned_cols=61  Identities=8%  Similarity=-0.075  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          407 AYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       407 ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      .|..+-.+|.+.|++++|+..++...+..- -+...|..+-.+|.+.|++++|.+.|+...+
T Consensus        79 ~~~nla~~~~~~~~~~~Ai~~~~~al~~~p-~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          79 CVLNIGACKLKMSDWQGAVDSCLEALEIDP-SNTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchhhhhhhhhhhhhh-hhhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            444455556666666666666666554332 2455566666666666666666666666655

>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=95.97  E-value=0.052  Score=44.25  Aligned_cols=112  Identities=10%  Similarity=0.051  Sum_probs=84.8

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHc--------------CCC-CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 011102          337 DCTAIMKVGIRLQKFGVVESLFHWFTHS--------------GRD-PTVVMYTTLIHSRLSEKKCREALTVVWNMEASNC  401 (493)
Q Consensus       337 ~~~~li~~~~~~g~~~~A~~l~~~m~~~--------------g~~-p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi  401 (493)
                      .+......+.+.|++++|++.|.+..+.              ... .+...|+.+-.+|.+.|++++|+..+++..+.. 
T Consensus        29 ~~~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-  107 (169)
T d1ihga1          29 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-  107 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhhhhhhhhhhhHHHHHhChhhHHHHHHHHHHHHhhcccchhhhhhhhhhhhh-
Confidence            4556677888999999999999876431              111 244567778889999999999999999988753 


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          402 LFDLPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIF  450 (493)
Q Consensus       402 ~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~  450 (493)
                      +-+...|..+-.+|.+.|++++|...|+...+..- -|...+..+-...
T Consensus       108 p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p-~n~~~~~~l~~~~  155 (169)
T d1ihga1         108 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAP-EDKAIQAELLKVK  155 (169)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHH
Confidence            24567899999999999999999999999986532 2445555554443

>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=95.85  E-value=0.14  Score=41.61  Aligned_cols=97  Identities=10%  Similarity=-0.030  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCCCH-----------HHHHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Q 011102          336 QDCTAIMKVGIRLQKFGVVESLFHWFTH---SGRDPTV-----------VMYTTLIHSRLSEKKCREALTVVWNMEASNC  401 (493)
Q Consensus       336 ~~~~~li~~~~~~g~~~~A~~l~~~m~~---~g~~p~~-----------~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi  401 (493)
                      ..+.-.-..+.+.|++++|...|++...   .....+.           ..|+-+-.+|.+.|++++|+..+++..+.. 
T Consensus        16 ~~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-   94 (168)
T d1kt1a1          16 AIVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD-   94 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc-
Confidence            3455566778888888888888877542   1111111           223344455566666666666666655432 


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          402 LFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       402 ~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      +.+..+|..+-.+|...|++++|...|+...+
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            23445555556666666666666666666554

>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=95.83  E-value=0.0075  Score=53.93  Aligned_cols=119  Identities=9%  Similarity=-0.027  Sum_probs=56.6

Q ss_pred             HcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHHcCCHHHHH
Q 011102          347 RLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDL-PAYRVVIKLFVALNDISRAI  425 (493)
Q Consensus       347 ~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~-~ty~~li~~~~~~g~~~~A~  425 (493)
                      +.|++++|+..|++-.+.. +-|...+..+...|+..|++++|.+.++...+.  .|+. ..+..+-..+...+..+++.
T Consensus         8 ~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l--~P~~~~~~~~l~~ll~a~~~~~~a~   84 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKL--FPEYLPGASQLRHLVKAAQARKDFA   84 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHhccccHHHH
Confidence            4466666666666655432 335566666666667777777776666665543  2332 22222222222222221111


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          426 RYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       426 ~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                      .-...-...+-.++...+......+.+.|+.++|.+++++..+
T Consensus        85 ~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e  127 (264)
T d1zbpa1          85 QGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEE  127 (264)
T ss_dssp             TSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            1100000001111223333344556667777777777776654

>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=95.75  E-value=0.14  Score=40.88  Aligned_cols=90  Identities=11%  Similarity=-0.009  Sum_probs=53.1

Q ss_pred             HHHcCCCHHHHHHHHHHHHHC-CCCCC----------HHHHHHHHHHHHHcCCHHHHHHHHHHHHH-----CCCCCC---
Q 011102          379 SRLSEKKCREALTVVWNMEAS-NCLFD----------LPAYRVVIKLFVALNDISRAIRYFSKLKE-----AGFCPT---  439 (493)
Q Consensus       379 ~~~~~g~~~~A~~l~~~M~~~-gi~pd----------~~ty~~li~~~~~~g~~~~A~~~~~~m~~-----~g~~p~---  439 (493)
                      .+.+.|++++|++.|++..+. .-.|+          ...|+.+-.+|.+.|++++|...+++..+     ....++   
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~   97 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGK   97 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccc
Confidence            334445566666655554431 00111          34566666777777777777777766542     112222   


Q ss_pred             --HHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          440 --YDIYRDMIRIFMASGRLAKCRDVCKEAEM  468 (493)
Q Consensus       440 --~~ty~~li~~~~~~g~~~~A~~l~~~m~~  468 (493)
                        ...|+.+-.+|...|++++|.+.|++..+
T Consensus        98 ~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          98 LWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence              12456667788888888888888888653

>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=95.71  E-value=0.15  Score=41.43  Aligned_cols=105  Identities=10%  Similarity=-0.076  Sum_probs=77.2

Q ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHhhcC--CCCCC-----------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Q 011102          299 SIYAKLILELGKNPDKYMLVMTLLDELGQRD--DLNLS-----------QQDCTAIMKVGIRLQKFGVVESLFHWFTHSG  365 (493)
Q Consensus       299 ~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~--g~~p~-----------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  365 (493)
                      ..+.-.-..+.+. |++.+|...|.+.....  ....+           ...|+-+-.+|.+.|++++|+..++...+..
T Consensus        16 ~~~~e~G~~~~~~-~~~~~A~~~Y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~   94 (168)
T d1kt1a1          16 AIVKEKGTVYFKG-GKYVQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD   94 (168)
T ss_dssp             HHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHc-CCHHHHHHHHHHHHHHHHHhhccchhhhhhcchhHHHHHHhHHHHHHHhhhcccchhhhhhhhhcc
Confidence            3445555678888 99999999998765321  11111           2245556678889999999999999887643


Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHH
Q 011102          366 RDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPA  407 (493)
Q Consensus       366 ~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~t  407 (493)
                       +.+..+|..+..+|...|++++|.+.|.+..+.  .|+...
T Consensus        95 -p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~  133 (168)
T d1kt1a1          95 -SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKA  133 (168)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHH
T ss_pred             -cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHH
Confidence             567888999999999999999999999998874  455433

>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=95.68  E-value=0.012  Score=52.57  Aligned_cols=117  Identities=10%  Similarity=-0.022  Sum_probs=67.4

Q ss_pred             CCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHcCCCHHHHHH
Q 011102          313 DKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDPT-VVMYTTLIHSRLSEKKCREALT  391 (493)
Q Consensus       313 ~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~ty~~li~~~~~~g~~~~A~~  391 (493)
                      |++++|++.+++..+.  -.-|...+..+...|+..|++++|.+.|+...+.  .|+ ...+..+...+...+..+++..
T Consensus        10 G~l~eAl~~l~~al~~--~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l--~P~~~~~~~~l~~ll~a~~~~~~a~~   85 (264)
T d1zbpa1          10 GQLQQALELLIEAIKA--SPKDASLRSSFIELLCIDGDFERADEQLMQSIKL--FPEYLPGASQLRHLVKAAQARKDFAQ   85 (264)
T ss_dssp             TCHHHHHHHHHHHHHT--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHhccccHHHHH
Confidence            7788888888877664  3346677788888888888888888888877654  443 3334333333332222222211


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          392 VVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       392 l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      -...-...+-.++...+......+.+.|+.++|..+++...+
T Consensus        86 ~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e  127 (264)
T d1zbpa1          86 GAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEE  127 (264)
T ss_dssp             SCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHh
Confidence            111000011112233344445567778888888888887764

>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=95.29  E-value=0.38  Score=36.61  Aligned_cols=140  Identities=13%  Similarity=0.064  Sum_probs=87.8

Q ss_pred             HhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011102          274 VKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGV  353 (493)
Q Consensus       274 ~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~  353 (493)
                      .-.|.+++..+++.+....   -+..-||.+|.-.... -+-+...+.++.+....++.              +++++..
T Consensus        13 ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt-~dC~~v~~~Ld~IG~~FDls--------------~C~Nlk~   74 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLES-IDCRYMFQVLDKIGSYFDLD--------------KCQNLKS   74 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHH-CCHHHHHHHHHHHGGGSCGG--------------GCSCTHH
T ss_pred             HHhhhHHhHHHHHHHHccc---CCccccceeeeecccc-cchHHHHHHHHHHhhhcCch--------------hhhcHHH
Confidence            4458888889998888775   3677788888877777 67777888888776542222              2333333


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 011102          354 VESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLKE  433 (493)
Q Consensus       354 A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~~  433 (493)
                      ....|-.+-     .+...++.-++.+...|+-+.-.++.+++.+ +-+|+....-.+-.+|.+-|...++-+++.+.-+
T Consensus        75 vv~C~~~~n-----~~se~vdlALd~lv~~~kkd~Ld~i~~~l~k-n~~i~~~~llkia~A~kkig~~re~nell~~ACe  148 (161)
T d1wy6a1          75 VVECGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACK  148 (161)
T ss_dssp             HHHHHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhc-----chHHHHHHHHHHHHHhccHHHHHHHHHHHHh-cCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence            333333221     2223345556666677777777777776544 3345555666666777777777777777777766


Q ss_pred             CCCC
Q 011102          434 AGFC  437 (493)
Q Consensus       434 ~g~~  437 (493)
                      .|++
T Consensus       149 ~G~K  152 (161)
T d1wy6a1         149 KGEK  152 (161)
T ss_dssp             TTCH
T ss_pred             HhHH
Confidence            6654

>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=95.18  E-value=0.22  Score=39.71  Aligned_cols=96  Identities=13%  Similarity=-0.013  Sum_probs=66.8

Q ss_pred             HHHHH--HHHHHHcCCHHHHHHHHHHHHHc-CCCCC----------HHHHHHHHHHHHcCCCHHHHHHHHHHHHHC----
Q 011102          337 DCTAI--MKVGIRLQKFGVVESLFHWFTHS-GRDPT----------VVMYTTLIHSRLSEKKCREALTVVWNMEAS----  399 (493)
Q Consensus       337 ~~~~l--i~~~~~~g~~~~A~~l~~~m~~~-g~~p~----------~~ty~~li~~~~~~g~~~~A~~l~~~M~~~----  399 (493)
                      +|..+  ...+.+.|++++|++.|++-.+. .-.|+          ..+|+.+-.+|...|++++|.+-+++..+.    
T Consensus         9 a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~   88 (156)
T d2hr2a1           9 AYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRR   88 (156)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhccccc
Confidence            45544  44556778888888888876542 11121          467888888999999999998888876542    


Q ss_pred             -CCCCCH-----HHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 011102          400 -NCLFDL-----PAYRVVIKLFVALNDISRAIRYFSKLK  432 (493)
Q Consensus       400 -gi~pd~-----~ty~~li~~~~~~g~~~~A~~~~~~m~  432 (493)
                       ...++.     ..|+.+=.+|.+.|++++|...|++..
T Consensus        89 ~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al  127 (156)
T d2hr2a1          89 GELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVV  127 (156)
T ss_dssp             CCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence             222222     245666788999999999999998765

>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=94.82  E-value=1  Score=38.59  Aligned_cols=221  Identities=12%  Similarity=-0.035  Sum_probs=125.6

Q ss_pred             HHHHHHHHHHHcCCCchhhhHHHhhc---cCcHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHH
Q 011102          234 LLASTVEVLARHHELKVPFKLENFVS---LASKGVLEATAKGFVK----GGNLKLAWKLLMVAKDGGRMLDPSIYAKLIL  306 (493)
Q Consensus       234 t~~~li~~~~~~g~~~~~~~l~~~~~---~~~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~  306 (493)
                      .+..|=..+-+.++  ..+++..|..   ..+...+-.|-..|..    ..+...|...+....+.+   +......+-.
T Consensus         4 ~~~~lG~~~~~~~d--~~~A~~~~~kAa~~g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~~l~~   78 (265)
T d1ouva_           4 ELVGLGAKSYKEKD--FTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLGN   78 (265)
T ss_dssp             HHHHHHHHHHHTTC--HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCC--HHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhhcccc
Confidence            33444344445555  4444444433   2344444445555554    457777777777777665   3333333322


Q ss_pred             HHh----cCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011102          307 ELG----KNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR----LQKFGVVESLFHWFTHSGRDPTVVMYTTLIH  378 (493)
Q Consensus       307 ~~~----~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~  378 (493)
                      .+.    .. ...+.|...++..... |.   ......+...+..    ......|...+.....   ..+...+..|..
T Consensus        79 ~~~~~~~~~-~~~~~a~~~~~~a~~~-g~---~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~L~~  150 (265)
T d1ouva_          79 LYYSGQGVS-QNTNKALQYYSKACDL-KY---AEGCASLGGIYHDGKVVTRDFKKAVEYFTKACD---LNDGDGCTILGS  150 (265)
T ss_dssp             HHHHTSSSC-CCHHHHHHHHHHHHHT-TC---HHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH---TTCHHHHHHHHH
T ss_pred             ccccccccc-hhhHHHHHHHhhhhhh-hh---hhHHHhhcccccCCCcccchhHHHHHHhhhhhc---ccccchhhhhhh
Confidence            222    23 5667777777776554 32   2222222222222    3345666666666543   345666777777


Q ss_pred             HHHc----CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011102          379 SRLS----EKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA----LNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIF  450 (493)
Q Consensus       379 ~~~~----~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~----~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~  450 (493)
                      .|..    ..+...+...++...+.|   +......+=..|..    ..+.++|..+|+.-.+.|   +...+..|-..|
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y  224 (265)
T d1ouva_         151 LYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAMQ  224 (265)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHH
T ss_pred             hhccCCCcccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHHHH
Confidence            7765    456677777777776654   33333333333333    568899999998888776   344555555555


Q ss_pred             HH----cCCHHHHHHHHHHHHHCCCcc
Q 011102          451 MA----SGRLAKCRDVCKEAEMAGFKL  473 (493)
Q Consensus       451 ~~----~g~~~~A~~l~~~m~~~g~~p  473 (493)
                      .+    ..+.++|.+.|++..+.|-.+
T Consensus       225 ~~G~g~~~n~~~A~~~~~kAa~~g~~~  251 (265)
T d1ouva_         225 YNGEGVTRNEKQAIENFKKGCKLGAKG  251 (265)
T ss_dssp             HTTSSSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             HcCCCCccCHHHHHHHHHHHHHCcCHH
Confidence            54    337888999999988888654

>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=94.67  E-value=0.63  Score=35.36  Aligned_cols=67  Identities=10%  Similarity=0.002  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCc
Q 011102          405 LPAYRVVIKLFVALNDISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       405 ~~ty~~li~~~~~~g~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~  472 (493)
                      ..-++..++.+.++|+-+.-.++++++.+. -+|+....-.+-.+|.+.|...++.+++.+..++|++
T Consensus        86 se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          86 NEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            344667788899999999999999997763 4578888888999999999999999999999999976

>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=93.43  E-value=0.3  Score=38.41  Aligned_cols=43  Identities=21%  Similarity=0.331  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 011102          421 ISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGF  471 (493)
Q Consensus       421 ~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~  471 (493)
                      +++|.+.|+...+.  .|+..+|..-+..+      .+|.+++.+..+.|+
T Consensus       102 ~~~A~~~~~kal~l--~P~~~~~~~~L~~~------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         102 FDLATQFFQQAVDE--QPDNTHYLKSLEMT------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHHHHHHHHHHHH--CTTCHHHHHHHHHH------HTHHHHHHHHHHSSS
T ss_pred             HHHhhhhhhccccc--CCCHHHHHHHHHHH------HHHHHHHHHHHHHhc
Confidence            46677777666643  36655555444333      456677777666654

>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=93.37  E-value=0.22  Score=39.29  Aligned_cols=77  Identities=9%  Similarity=-0.078  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCC-----------CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC
Q 011102          351 FGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEK-----------KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN  419 (493)
Q Consensus       351 ~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g-----------~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g  419 (493)
                      +++|...|++..+.. +-+..+|+.+-.+|...|           .+++|.+.|+...+  +.|+...|..-+..+    
T Consensus        57 ~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~----  129 (145)
T d1zu2a1          57 IQEAITKFEEALLID-PKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMT----  129 (145)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHH----
T ss_pred             HHHHHHHHHHHHHhc-chhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHH----
Confidence            345555555554331 234455555555554433           24667777776654  357766666555544    


Q ss_pred             CHHHHHHHHHHHHHCCC
Q 011102          420 DISRAIRYFSKLKEAGF  436 (493)
Q Consensus       420 ~~~~A~~~~~~m~~~g~  436 (493)
                        ..|.+++.+..+.|+
T Consensus       130 --~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         130 --AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             --HTHHHHHHHHHHSSS
T ss_pred             --HHHHHHHHHHHHHhc
Confidence              355666666665553

>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=92.80  E-value=2.5  Score=35.99  Aligned_cols=215  Identities=10%  Similarity=-0.092  Sum_probs=123.6

Q ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCC--chhhhHHHhhc---cCcHHHHHHHHHHHH----h
Q 011102          205 ELGHMNLPERALQTFCWAQKQPHLFPDDRLLASTVEVLARHHEL--KVPFKLENFVS---LASKGVLEATAKGFV----K  275 (493)
Q Consensus       205 ~~~~~g~~~~A~~l~~~m~~~~g~~pd~~t~~~li~~~~~~g~~--~~~~~l~~~~~---~~~~~~~~~li~~~~----~  275 (493)
                      .+-+.|+.++|++.|+...+. |   |...+-.|-..+-.-..+  +...+...+..   ..+......|...+.    .
T Consensus        11 ~~~~~~d~~~A~~~~~kAa~~-g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~~a~~~l~~~~~~~~~~   86 (265)
T d1ouva_          11 KSYKEKDFTQAKKYFEKACDL-K---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLGNLYYSGQGV   86 (265)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSS
T ss_pred             HHHHCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccccchhhcccccccccccc
Confidence            334566777777777766654 4   333333333333321111  12222221211   122233333333333    3


Q ss_pred             cCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH----hcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH----
Q 011102          276 GGNLKLAWKLLMVAKDGGRMLDPSIYAKLILEL----GKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR----  347 (493)
Q Consensus       276 ~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~----~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~----  347 (493)
                      ..+.+.|...++...+.|..   .....+...+    ... .....+...+......    .+...+..|...|..    
T Consensus        87 ~~~~~~a~~~~~~a~~~g~~---~a~~~l~~~~~~~~~~~-~~~~~a~~~~~~~~~~----~~~~~~~~L~~~~~~~~~~  158 (265)
T d1ouva_          87 SQNTNKALQYYSKACDLKYA---EGCASLGGIYHDGKVVT-RDFKKAVEYFTKACDL----NDGDGCTILGSLYDAGRGT  158 (265)
T ss_dssp             CCCHHHHHHHHHHHHHTTCH---HHHHHHHHHHHHCSSSC-CCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSS
T ss_pred             chhhHHHHHHHhhhhhhhhh---hHHHhhcccccCCCccc-chhHHHHHHhhhhhcc----cccchhhhhhhhhccCCCc
Confidence            56788899999988887732   2222222222    223 5677777777776554    456777777777775    


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----CCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cC
Q 011102          348 LQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS----EKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA----LN  419 (493)
Q Consensus       348 ~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~----~g  419 (493)
                      ..+...+...++...+.|   +..++.-|-..|..    ..+.++|...|....+.|   +...+..|-..|.+    ..
T Consensus       159 ~~~~~~~~~~~~~a~~~g---~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y~~G~g~~~  232 (265)
T d1ouva_         159 PKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAMQYNGEGVTR  232 (265)
T ss_dssp             CCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHTTSSSSC
T ss_pred             ccccccchhhhhcccccc---ccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHHHHHcCCCCcc
Confidence            455677788887776654   44554444444443    568999999999988876   34455555555554    34


Q ss_pred             CHHHHHHHHHHHHHCCCC
Q 011102          420 DISRAIRYFSKLKEAGFC  437 (493)
Q Consensus       420 ~~~~A~~~~~~m~~~g~~  437 (493)
                      +.++|.++|+.-.+.|-.
T Consensus       233 n~~~A~~~~~kAa~~g~~  250 (265)
T d1ouva_         233 NEKQAIENFKKGCKLGAK  250 (265)
T ss_dssp             CSTTHHHHHHHHHHHTCH
T ss_pred             CHHHHHHHHHHHHHCcCH
Confidence            788899999888777644

>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=89.42  E-value=2.5  Score=29.88  Aligned_cols=17  Identities=18%  Similarity=0.112  Sum_probs=6.9

Q ss_pred             HHHHHcCCHHHHHHHHH
Q 011102          343 KVGIRLQKFGVVESLFH  359 (493)
Q Consensus       343 ~~~~~~g~~~~A~~l~~  359 (493)
                      ..+.+.|++++|...|+
T Consensus        13 ~~~~~~g~y~~A~~~~~   29 (95)
T d1tjca_          13 KVAYTEADYYHTELWME   29 (95)
T ss_dssp             HHHHHTTCHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHH
Confidence            33334444444444443

>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=89.24  E-value=1.6  Score=30.95  Aligned_cols=61  Identities=13%  Similarity=0.022  Sum_probs=33.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHC-----CCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 011102          374 TTLIHSRLSEKKCREALTVVWNMEAS-----NCLFD-LPAYRVVIKLFVALNDISRAIRYFSKLKEA  434 (493)
Q Consensus       374 ~~li~~~~~~g~~~~A~~l~~~M~~~-----gi~pd-~~ty~~li~~~~~~g~~~~A~~~~~~m~~~  434 (493)
                      --+-..+.+.|++++|...|++..+.     ...++ ..+++.+-.+|.+.|++++|...+++..+.
T Consensus         9 ~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_           9 FELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            34445556666666666666654321     11222 345666666666666666666666666543

>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=88.37  E-value=0.63  Score=44.81  Aligned_cols=114  Identities=11%  Similarity=-0.074  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC-CHHHHHHH
Q 011102          298 PSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIRLQKFGVVESLFHWFTHSGRDP-TVVMYTTL  376 (493)
Q Consensus       298 ~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~ty~~l  376 (493)
                      ...+..+-..+.+. |+.++|...+...... .  + ...+..+-+.+...|++++|...|++..+.  .| +...|+.|
T Consensus       120 ~~~~~~lg~~~~~~-~~~~~A~~~~~~al~~-~--~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~L  192 (497)
T d1ya0a1         120 RVKSSQLGIISNKQ-THTSAIVKPQSSSCSY-I--C-QHCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQL  192 (497)
T ss_dssp             ------------------------CCHHHHH-H--H-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHH
T ss_pred             HHHHHHhHHHHHhC-CCHHHHHHHHHHHhCC-C--H-HHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHH
Confidence            34455555566666 7777877766654432 1  1 245667788888999999999999887654  44 45789999


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcC
Q 011102          377 IHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVALN  419 (493)
Q Consensus       377 i~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g  419 (493)
                      -..|...|+..+|...|.+..... .|-..++..|...|.+..
T Consensus       193 g~~~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         193 AILASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHhh
Confidence            999999999999999998877654 366778888877776544

>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=88.30  E-value=0.67  Score=44.62  Aligned_cols=111  Identities=7%  Similarity=-0.190  Sum_probs=50.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q 011102          265 VLEATAKGFVKGGNLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKV  344 (493)
Q Consensus       265 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~  344 (493)
                      .+..+-..+.+.|+.++|...+....+..  | ..++..+-+.+... +++++|...|.+..+.  ..-+...|+.|-..
T Consensus       122 ~~~~lg~~~~~~~~~~~A~~~~~~al~~~--~-~~~~~~LG~l~~~~-~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~  195 (497)
T d1ya0a1         122 KSSQLGIISNKQTHTSAIVKPQSSSCSYI--C-QHCLVHLGDIARYR-NQTSQAESYYRHAAQL--VPSNGQPYNQLAIL  195 (497)
T ss_dssp             ---------------------CCHHHHHH--H-HHHHHHHHHHHHHT-TCHHHHHHHHHHHHHH--CTTBSHHHHHHHHH
T ss_pred             HHHHhHHHHHhCCCHHHHHHHHHHHhCCC--H-HHHHHHHHHHHHHc-ccHHHHHHHHHHHHHH--CCCchHHHHHHHHH
Confidence            44455555556666666665555443311  0 12344444555555 6777777777766553  12234567777777


Q ss_pred             HHHcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 011102          345 GIRLQKFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLS  382 (493)
Q Consensus       345 ~~~~g~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~  382 (493)
                      |...|+..+|...|.+-.... .|-..+++.|...+.+
T Consensus       196 ~~~~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~~~  232 (497)
T d1ya0a1         196 ASSKGDHLTTIFYYCRSIAVK-FPFPAASTNLQKALSK  232 (497)
T ss_dssp             HHHTTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHH
Confidence            777777777777776655433 4556666666655543

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=86.77  E-value=4.9  Score=30.14  Aligned_cols=112  Identities=12%  Similarity=-0.007  Sum_probs=62.0

Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHH
Q 011102          350 KFGVVESLFHWFTHSGRDPTVVMYTTLIHSRLSEKKCREALTVVWNMEASNCLFDLPAYRVVIKLFVA----LNDISRAI  425 (493)
Q Consensus       350 ~~~~A~~l~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~----~g~~~~A~  425 (493)
                      ++++|.+.|.+-.+.|..   ..+..|.  .....+.++|.+.+++..+.|.   ...+..|=..|..    ..+.++|.
T Consensus         8 d~~~A~~~~~kaa~~g~~---~a~~~l~--~~~~~~~~~a~~~~~~aa~~g~---~~a~~~Lg~~y~~g~~~~~d~~~A~   79 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEM---FGCLSLV--SNSQINKQKLFQYLSKACELNS---GNGCRFLGDFYENGKYVKKDLRKAA   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCT---THHHHHH--TCTTSCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCh---hhhhhhc--cccccCHHHHHHHHhhhhcccc---hhhhhhHHHhhhhccccchhhHHHH
Confidence            455666666665555421   1122221  2234566777777777666553   3333333333332    34677888


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCc
Q 011102          426 RYFSKLKEAGFCPTYDIYRDMIRIFMA----SGRLAKCRDVCKEAEMAGFK  472 (493)
Q Consensus       426 ~~~~~m~~~g~~p~~~ty~~li~~~~~----~g~~~~A~~l~~~m~~~g~~  472 (493)
                      ++|+.-.+.|.   ......|-..|..    ..+.++|.++|+...+.|..
T Consensus        80 ~~~~~aa~~g~---~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~~  127 (133)
T d1klxa_          80 QYYSKACGLND---QDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGSE  127 (133)
T ss_dssp             HHHHHHHHTTC---HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHhhhhccCc---chHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCCH
Confidence            88887777663   3333444444444    35788888888887777643

>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=83.08  E-value=4.2  Score=29.03  Aligned_cols=62  Identities=21%  Similarity=0.297  Sum_probs=36.0

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HCCCCCCHHHHHHHHH
Q 011102          385 KCREALTVVWNMEASNCLFDLPAYRVVIKLFVALNDISRAIRYFSKLK-EAGFCPTYDIYRDMIR  448 (493)
Q Consensus       385 ~~~~A~~l~~~M~~~gi~pd~~ty~~li~~~~~~g~~~~A~~~~~~m~-~~g~~p~~~ty~~li~  448 (493)
                      +.-++.+-++.+....+.|+.....+.+.||.+.+++..|.++|+..+ +.|  ++...|..+++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~--~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--CcHHHHHHHHH
Confidence            444555555555555666666666666666666666666666666665 222  23345555543

>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=82.04  E-value=3.9  Score=29.22  Aligned_cols=63  Identities=13%  Similarity=0.059  Sum_probs=46.4

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCccCHHHHHHHHH
Q 011102          420 DISRAIRYFSKLKEAGFCPTYDIYRDMIRIFMASGRLAKCRDVCKEAEMAGFKLDKQTVVELLQ  483 (493)
Q Consensus       420 ~~~~A~~~~~~m~~~g~~p~~~ty~~li~~~~~~g~~~~A~~l~~~m~~~g~~pd~~t~~~Ll~  483 (493)
                      +.-++.+-++.+....+.|+...-.+-+++|-|.+++..|.++|+-.+.+ +.++..+|..+++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K-~~~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-AGPHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-TTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-hcCcHHHHHHHHH
Confidence            45566777777777788888888888888888888888888888777643 3344567777766

>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=80.19  E-value=9.5  Score=28.38  Aligned_cols=78  Identities=10%  Similarity=0.010  Sum_probs=36.7

Q ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHH----cCCHHH
Q 011102          278 NLKLAWKLLMVAKDGGRMLDPSIYAKLILELGKNPDKYMLVMTLLDELGQRDDLNLSQQDCTAIMKVGIR----LQKFGV  353 (493)
Q Consensus       278 ~~~~A~~l~~~m~~~g~~pd~~t~~~li~~~~~~~~~~~~a~~l~~~m~~~~g~~p~~~~~~~li~~~~~----~g~~~~  353 (493)
                      ++++|.++|++..+.|-   ...+..|.  .... .+.++|..+++...+. |   +...+..|-..|..    ..+.++
T Consensus         8 d~~~A~~~~~kaa~~g~---~~a~~~l~--~~~~-~~~~~a~~~~~~aa~~-g---~~~a~~~Lg~~y~~g~~~~~d~~~   77 (133)
T d1klxa_           8 DLKKAIQYYVKACELNE---MFGCLSLV--SNSQ-INKQKLFQYLSKACEL-N---SGNGCRFLGDFYENGKYVKKDLRK   77 (133)
T ss_dssp             HHHHHHHHHHHHHHTTC---TTHHHHHH--TCTT-SCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHCSSSCCCHHH
T ss_pred             CHHHHHHHHHHHHHCCC---hhhhhhhc--cccc-cCHHHHHHHHhhhhcc-c---chhhhhhHHHhhhhccccchhhHH
Confidence            46677777777766662   22222221  1222 4566666666665554 2   23333333333322    233455


Q ss_pred             HHHHHHHHHHcC
Q 011102          354 VESLFHWFTHSG  365 (493)
Q Consensus       354 A~~l~~~m~~~g  365 (493)
                      |.+.|+.-.+.|
T Consensus        78 A~~~~~~aa~~g   89 (133)
T d1klxa_          78 AAQYYSKACGLN   89 (133)
T ss_dssp             HHHHHHHHHHTT
T ss_pred             HHHHHhhhhccC
Confidence            555555544433