Citrus Sinensis ID: 040365

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510----
Protein Sequence
MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW
Secondary Structure (PSIPRED)
ccccccEEHHHHHHHHHcccccHHHHHHHHHHHHcccccccEEHHHHHHHHcccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHcccccccEEEHHHHHHHHHHccccHHHHHHHHHHHHcccccccEEHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEHHHHHHHHcccccHHHHHHHHccccccccEEHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHccccHHHHHHHHHHHcHHccccccccccHHHHHHHHcccccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccHHHHHHHHHHHHccccccccEEEEEEccEEEEEEccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHcHHHHHHHHHHcccccccEEEEcccccccHHHHHHHHHHHHcccEEEEEccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccEHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHcHcHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccEEEEEEccEEEEEEEcccccccHHHHHHHHHHHHHHHHHccccccccEEEEcccHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccEEcccHHHHHHHHHHHcccEEEEEcccccEEcccccEcccccc
Coil and Loop (DISEMBL)
MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMgnvnlkpdsftlssvlpiFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCarvedshrlfCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAkikprhvsfssimpacahlttlhlgkqlhgciirngfddNMFIASSLLDMYAKCGNIRLARcifdkmdlhDIVSWTAVIMGNALHGNAHDAISLFEQmekdgvkpnSVAFVAVLTACSHAGLIDKAWSYFNSmtkdygiapsfEHYAAVADLLGRAGKLQEAYEFIsnmhagptENVWLTLLSACRVHKNVELAGKVAEKIfmidpnnmgaYVILSNTYAAARRWKDAASLRVFMrnkgmkktpacswievkNKAYAfvagdkshpfYHRINEALKELLERMeqegyvpdtkEVLHDVEEEQKKNLLYYHSERLAIVFGIictpdgttiRIIKNLRVCGDCHTAIKFISKIVQREiivrdnsrfhhfedgkcscgdyw
Flexible Loop (DISEMBL)
MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFmrnkgmkktpacswieVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVrdnsrfhhfedgkcscgdyw
Low Complexity Region (SEG)
MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW
Disordered region (IsUnstruct)
*****LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCG***
Disordered Region (DISOPRED)
*PVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW
Disordered Region (DISEMBL)
MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW
Disordered Region (DISPRO)
***SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW
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	514	2.2.26 [Sep-21-2011]
Q9LW63	715	Putative pentatricopeptid	yes	no	0.922	0.662	0.673	0.0
Q9LNU6	760	Pentatricopeptide repeat-	no	no	0.994	0.672	0.424	1e-140
Q9LIQ7	633	Pentatricopeptide repeat-	no	no	0.998	0.810	0.441	1e-134
Q9LTV8	694	Pentatricopeptide repeat-	no	no	0.998	0.739	0.443	1e-134
Q9SY02	781	Pentatricopeptide repeat-	no	no	0.992	0.653	0.439	1e-132
Q9SN39	871	Pentatricopeptide repeat-	no	no	1.0	0.590	0.427	1e-131
Q9LN01	741	Pentatricopeptide repeat-	no	no	1.0	0.693	0.443	1e-130
Q9S7F4	825	Putative pentatricopeptid	no	no	1.0	0.623	0.434	1e-130
Q9SMZ2	990	Pentatricopeptide repeat-	no	no	0.968	0.503	0.411	1e-129
Q3E6Q1	809	Pentatricopeptide repeat-	no	no	0.990	0.629	0.433	1e-129

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

 Score =  756 bits (1952), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/514 (67%), Positives = 426/514 (82%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D+VS+NT+I G A++G+YE+AL +VR+MG  +LKPDSFTLSSVLPIF++YVDVIKG
Sbjct: 202 MPRKDVVSYNTIIAGYAQSGMYEDALRMVREMGTTDLKPDSFTLSSVLPIFSEYVDVIKG 261

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHGY IR G+D++V IGSSL++MYAK AR+EDS R+F  L  +D ISWNS++AG VQN
Sbjct: 262 KEIHGYVIRKGIDSDVYIGSSLVDMYAKSARIEDSERVFSRLYCRDGISWNSLVAGYVQN 321

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G ++E L+ FRQM+ AK+KP  V+FSS++PACAHL TLHLGKQLHG ++R GF  N+FIA
Sbjct: 322 GRYNEALRLFRQMVTAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIA 381

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           S+L+DMY+KCGNI+ AR IFD+M++ D VSWTA+IMG+ALHG+ H+A+SLFE+M++ GVK
Sbjct: 382 SALVDMYSKCGNIKAARKIFDRMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVK 441

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN VAFVAVLTACSH GL+D+AW YFNSMTK YG+    EHYAAVADLLGRAGKL+EAY 
Sbjct: 442 PNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQELEHYAAVADLLGRAGKLEEAYN 501

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FIS M   PT +VW TLLS+C VHKN+ELA KVAEKIF +D  NMGAYV++ N YA+  R
Sbjct: 502 FISKMCVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTVDSENMGAYVLMCNMYASNGR 561

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WK+ A LR+ MR KG++K PACSWIE+KNK + FV+GD+SHP   +INE LK ++E+ME+
Sbjct: 562 WKEMAKLRLRMRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSMDKINEFLKAVMEQMEK 621

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYV DT  VLHDV+EE K+ LL+ HSERLA+ FGII T  GTTIR+ KN+R+C DCH A
Sbjct: 622 EGYVADTSGVLHDVDEEHKRELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVA 681

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           IKFISKI +REIIVRDNSRFHHF  G CSCGDYW
Sbjct: 682 IKFISKITEREIIVRDNSRFHHFNRGNCSCGDYW 715

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LNU6|PPR53_ARATH Pentatricopeptide repeat-containing protein At1g20230 OS=Arabidopsis thaliana GN=PCMP-H21 PE=2 SV=2

 Score =  499 bits (1285), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 232/546 (42%), Positives = 345/546 (63%), Gaps = 35/546 (6%)

Query: 4   SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEI 63
           +++VSWN ++ G  R+G ++EA+ + +++ ++   PD  T+SSVLP   D   +  G+ I
Sbjct: 215 ANIVSWNGILSGFNRSGYHKEAVVMFQKIHHLGFCPDQVTVSSVLPSVGDSEMLNMGRLI 274

Query: 64  HGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDA---------------- 107
           HGY I+ GL  + C+ S++I+MY K   V     LF    + +A                
Sbjct: 275 HGYVIKQGLLKDKCVISAMIDMYGKSGHVYGIISLFNQFEMMEAGVCNAYITGLSRNGLV 334

Query: 108 -------------------ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSI 148
                              +SW SIIAGC QNG   E L+ FR+M +A +KP HV+  S+
Sbjct: 335 DKALEMFELFKEQTMELNVVSWTSIIAGCAQNGKDIEALELFREMQVAGVKPNHVTIPSM 394

Query: 149 MPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDI 208
           +PAC ++  L  G+  HG  +R    DN+ + S+L+DMYAKCG I L++ +F+ M   ++
Sbjct: 395 LPACGNIAALGHGRSTHGFAVRVHLLDNVHVGSALIDMYAKCGRINLSQIVFNMMPTKNL 454

Query: 209 VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNS 268
           V W +++ G ++HG A + +S+FE + +  +KP+ ++F ++L+AC   GL D+ W YF  
Sbjct: 455 VCWNSLMNGFSMHGKAKEVMSIFESLMRTRLKPDFISFTSLLSACGQVGLTDEGWKYFKM 514

Query: 269 MTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVE 328
           M+++YGI P  EHY+ + +LLGRAGKLQEAY+ I  M   P   VW  LL++CR+  NV+
Sbjct: 515 MSEEYGIKPRLEHYSCMVNLLGRAGKLQEAYDLIKEMPFEPDSCVWGALLNSCRLQNNVD 574

Query: 329 LAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVK 388
           LA   AEK+F ++P N G YV+LSN YAA   W +  S+R  M + G+KK P CSWI+VK
Sbjct: 575 LAEIAAEKLFHLEPENPGTYVLLSNIYAAKGMWTEVDSIRNKMESLGLKKNPGCSWIQVK 634

Query: 389 NKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSE 448
           N+ Y  +AGDKSHP   +I E + E+ + M + G+ P+    LHDVEE++++ +L+ HSE
Sbjct: 635 NRVYTLLAGDKSHPQIDQITEKMDEISKEMRKSGHRPNLDFALHDVEEQEQEQMLWGHSE 694

Query: 449 RLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKC 508
           +LA+VFG++ TPDGT +++IKNLR+CGDCH  IKFIS    REI +RD +RFHHF+DG C
Sbjct: 695 KLAVVFGLLNTPDGTPLQVIKNLRICGDCHAVIKFISSYAGREIFIRDTNRFHHFKDGIC 754

Query: 509 SCGDYW 514
           SCGD+W
Sbjct: 755 SCGDFW 760

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LIQ7|PP252_ARATH Pentatricopeptide repeat-containing protein At3g24000, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H87 PE=2 SV=1

 Score =  478 bits (1230), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 227/514 (44%), Positives = 333/514 (64%), Gaps = 1/514 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D V+W T+I G +++    +AL    QM      P+ FTLSSV+   A       G
Sbjct: 121 MPQRDFVTWTTLISGYSQHDRPCDALLFFNQMLRFGYSPNEFTLSSVIKAAAAERRGCCG 180

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
            ++HG+ ++ G D+NV +GS+L+++Y +   ++D+  +F  L  ++ +SWN++IAG  + 
Sbjct: 181 HQLHGFCVKCGFDSNVHVGSALLDLYTRYGLMDDAQLVFDALESRNDVSWNALIAGHARR 240

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
              ++ L+ F+ ML    +P H S++S+  AC+    L  GK +H  +I++G     F  
Sbjct: 241 SGTEKALELFQGMLRDGFRPSHFSYASLFGACSSTGFLEQGKWVHAYMIKSGEKLVAFAG 300

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           ++LLDMYAK G+I  AR IFD++   D+VSW +++   A HG   +A+  FE+M + G++
Sbjct: 301 NTLLDMYAKSGSIHDARKIFDRLAKRDVVSWNSLLTAYAQHGFGKEAVWWFEEMRRVGIR 360

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN ++F++VLTACSH+GL+D+ W Y+  M KD GI P   HY  V DLLGRAG L  A  
Sbjct: 361 PNEISFLSVLTACSHSGLLDEGWHYYELMKKD-GIVPEAWHYVTVVDLLGRAGDLNRALR 419

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FI  M   PT  +W  LL+ACR+HKN EL    AE +F +DP++ G +VIL N YA+  R
Sbjct: 420 FIEEMPIEPTAAIWKALLNACRMHKNTELGAYAAEHVFELDPDDPGPHVILYNIYASGGR 479

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           W DAA +R  M+  G+KK PACSW+E++N  + FVA D+ HP    I    +E+L ++++
Sbjct: 480 WNDAARVRKKMKESGVKKEPACSWVEIENAIHMFVANDERHPQREEIARKWEEVLAKIKE 539

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
            GYVPDT  V+  V++++++  L YHSE++A+ F ++ TP G+TI I KN+RVCGDCHTA
Sbjct: 540 LGYVPDTSHVIVHVDQQEREVNLQYHSEKIALAFALLNTPPGSTIHIKKNIRVCGDCHTA 599

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           IK  SK+V REIIVRD +RFHHF+DG CSC DYW
Sbjct: 600 IKLASKVVGREIIVRDTNRFHHFKDGNCSCKDYW 633

Arabidopsis thaliana (taxid: 3702)

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

 Score =  478 bits (1229), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 228/514 (44%), Positives = 329/514 (64%), Gaps = 1/514 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           +P   +VSW  ++   A+NG   EAL I  QM  +++KPD   L SVL  F    D+ +G
Sbjct: 182 LPERTIVSWTAIVSAYAQNGEPMEALEIFSQMRKMDVKPDWVALVSVLNAFTCLQDLKQG 241

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           + IH   ++ GL+    +  SL  MYAKC +V  +  LF  +   + I WN++I+G  +N
Sbjct: 242 RSIHASVVKMGLEIEPDLLISLNTMYAKCGQVATAKILFDKMKSPNLILWNAMISGYAKN 301

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G   E +  F +M+   ++P  +S +S + ACA + +L   + ++  + R+ + D++FI+
Sbjct: 302 GYAREAIDMFHEMINKDVRPDTISITSAISACAQVGSLEQARSMYEYVGRSDYRDDVFIS 361

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           S+L+DM+AKCG++  AR +FD+    D+V W+A+I+G  LHG A +AISL+  ME+ GV 
Sbjct: 362 SALIDMFAKCGSVEGARLVFDRTLDRDVVVWSAMIVGYGLHGRAREAISLYRAMERGGVH 421

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN V F+ +L AC+H+G++ + W +FN M  D+ I P  +HYA V DLLGRAG L +AYE
Sbjct: 422 PNDVTFLGLLMACNHSGMVREGWWFFNRMA-DHKINPQQQHYACVIDLLGRAGHLDQAYE 480

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
            I  M   P   VW  LLSAC+ H++VEL    A+++F IDP+N G YV LSN YAAAR 
Sbjct: 481 VIKCMPVQPGVTVWGALLSACKKHRHVELGEYAAQQLFSIDPSNTGHYVQLSNLYAAARL 540

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           W   A +RV M+ KG+ K   CSW+EV+ +  AF  GDKSHP Y  I   ++ +  R+++
Sbjct: 541 WDRVAEVRVRMKEKGLNKDVGCSWVEVRGRLEAFRVGDKSHPRYEEIERQVEWIESRLKE 600

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
            G+V +    LHD+ +E+ +  L  HSER+AI +G+I TP GT +RI KNLR C +CH A
Sbjct: 601 GGFVANKDASLHDLNDEEAEETLCSHSERIAIAYGLISTPQGTPLRITKNLRACVNCHAA 660

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
            K ISK+V REI+VRD +RFHHF+DG CSCGDYW
Sbjct: 661 TKLISKLVDREIVVRDTNRFHHFKDGVCSCGDYW 694

Arabidopsis thaliana (taxid: 3702)

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

 Score =  473 bits (1217), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 238/541 (43%), Positives = 336/541 (62%), Gaps = 31/541 (5%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           M V D+VSWNT+I G A++G  +EA    RQ+ + +   D FT ++++  +     V + 
Sbjct: 245 MNVRDVVSWNTIITGYAQSGKIDEA----RQLFDESPVQDVFTWTAMVSGYIQNRMVEEA 300

Query: 61  KEIH----------------GYAIRHGLDA-----------NVCIGSSLINMYAKCARVE 93
           +E+                 GY     ++            NV   +++I  YA+C ++ 
Sbjct: 301 RELFDKMPERNEVSWNAMLAGYVQGERMEMAKELFDVMPCRNVSTWNTMITGYAQCGKIS 360

Query: 94  DSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACA 153
           ++  LF  +P +D +SW ++IAG  Q+G   E L+ F QM     +    SFSS +  CA
Sbjct: 361 EAKNLFDKMPKRDPVSWAAMIAGYSQSGHSFEALRLFVQMEREGGRLNRSSFSSALSTCA 420

Query: 154 HLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTA 213
            +  L LGKQLHG +++ G++   F+ ++LL MY KCG+I  A  +F +M   DIVSW  
Sbjct: 421 DVVALELGKQLHGRLVKGGYETGCFVGNALLLMYCKCGSIEEANDLFKEMAGKDIVSWNT 480

Query: 214 VIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDY 273
           +I G + HG    A+  FE M+++G+KP+    VAVL+ACSH GL+DK   YF +MT+DY
Sbjct: 481 MIAGYSRHGFGEVALRFFESMKREGLKPDDATMVAVLSACSHTGLVDKGRQYFYTMTQDY 540

Query: 274 GIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKV 333
           G+ P+ +HYA + DLLGRAG L++A+  + NM   P   +W TLL A RVH N ELA   
Sbjct: 541 GVMPNSQHYACMVDLLGRAGLLEDAHNLMKNMPFEPDAAIWGTLLGASRVHGNTELAETA 600

Query: 334 AEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYA 393
           A+KIF ++P N G YV+LSN YA++ RW D   LRV MR+KG+KK P  SWIE++NK + 
Sbjct: 601 ADKIFAMEPENSGMYVLLSNLYASSGRWGDVGKLRVRMRDKGVKKVPGYSWIEIQNKTHT 660

Query: 394 FVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIV 453
           F  GD+ HP    I   L+EL  RM++ GYV  T  VLHDVEEE+K+ ++ YHSERLA+ 
Sbjct: 661 FSVGDEFHPEKDEIFAFLEELDLRMKKAGYVSKTSVVLHDVEEEEKERMVRYHSERLAVA 720

Query: 454 FGIICTPDGTTIRIIKNLRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDY 513
           +GI+    G  IR+IKNLRVC DCH AIK++++I  R II+RDN+RFHHF+DG CSCGDY
Sbjct: 721 YGIMRVSSGRPIRVIKNLRVCEDCHNAIKYMARITGRLIILRDNNRFHHFKDGSCSCGDY 780

Query: 514 W 514
           W
Sbjct: 781 W 781

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SN39|PP320_ARATH Pentatricopeptide repeat-containing protein At4g18750, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H45 PE=2 SV=1

 Score =  469 bits (1208), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 220/515 (42%), Positives = 331/515 (64%), Gaps = 1/515 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           M    +VS+ ++I G AR GL  EA+ +  +M    + PD +T+++VL   A Y  + +G
Sbjct: 357 MSDRSVVSYTSMIAGYAREGLAGEAVKLFEEMEEEGISPDVYTVTAVLNCCARYRLLDEG 416

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           K +H +   + L  ++ + ++L++MYAKC  ++++  +F  + VKD ISWN+II G  +N
Sbjct: 417 KRVHEWIKENDLGFDIFVSNALMDMYAKCGSMQEAELVFSEMRVKDIISWNTIIGGYSKN 476

Query: 121 GLFDEGLKFFRQMLIAK-IKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFI 179
              +E L  F  +L  K   P   + + ++PACA L+    G+++HG I+RNG+  +  +
Sbjct: 477 CYANEALSLFNLLLEEKRFSPDERTVACVLPACASLSAFDKGREIHGYIMRNGYFSDRHV 536

Query: 180 ASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV 239
           A+SL+DMYAKCG + LA  +FD +   D+VSWT +I G  +HG   +AI+LF QM + G+
Sbjct: 537 ANSLVDMYAKCGALLLAHMLFDDIASKDLVSWTVMIAGYGMHGFGKEAIALFNQMRQAGI 596

Query: 240 KPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAY 299
           + + ++FV++L ACSH+GL+D+ W +FN M  +  I P+ EHYA + D+L R G L +AY
Sbjct: 597 EADEISFVSLLYACSHSGLVDEGWRFFNIMRHECKIEPTVEHYACIVDMLARTGDLIKAY 656

Query: 300 EFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR 359
            FI NM   P   +W  LL  CR+H +V+LA KVAEK+F ++P N G YV+++N YA A 
Sbjct: 657 RFIENMPIPPDATIWGALLCGCRIHHDVKLAEKVAEKVFELEPENTGYYVLMANIYAEAE 716

Query: 360 RWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERME 419
           +W+    LR  +  +G++K P CSWIE+K +   FVAGD S+P    I   L+++  RM 
Sbjct: 717 KWEQVKRLRKRIGQRGLRKNPGCSWIEIKGRVNIFVAGDSSNPETENIEAFLRKVRARMI 776

Query: 420 QEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHT 479
           +EGY P TK  L D EE +K+  L  HSE+LA+  GII +  G  IR+ KNLRVCGDCH 
Sbjct: 777 EEGYSPLTKYALIDAEEMEKEEALCGHSEKLAMALGIISSGHGKIIRVTKNLRVCGDCHE 836

Query: 480 AIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             KF+SK+ +REI++RD++RFH F+DG CSC  +W
Sbjct: 837 MAKFMSKLTRREIVLRDSNRFHQFKDGHCSCRGFW 871

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LN01|PPR21_ARATH Pentatricopeptide repeat-containing protein At1g08070 OS=Arabidopsis thaliana GN=PCMP-H12 PE=2 SV=1

 Score =  465 bits (1197), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 229/516 (44%), Positives = 328/516 (63%), Gaps = 2/516 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           +PV D+VSWN +I G A  G Y+EAL + + M   N++PD  T+ +V+   A    +  G
Sbjct: 226 IPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELG 285

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           +++H +   HG  +N+ I ++LI++Y+KC  +E +  LF  LP KD ISWN++I G    
Sbjct: 286 RQVHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHM 345

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIR--NGFDDNMF 178
            L+ E L  F++ML +   P  V+  SI+PACAHL  + +G+ +H  I +   G  +   
Sbjct: 346 NLYKEALLLFQEMLRSGETPNDVTMLSILPACAHLGAIDIGRWIHVYIDKRLKGVTNASS 405

Query: 179 IASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG 238
           + +SL+DMYAKCG+I  A  +F+ +    + SW A+I G A+HG A  +  LF +M K G
Sbjct: 406 LRTSLIDMYAKCGDIEAAHQVFNSILHKSLSSWNAMIFGFAMHGRADASFDLFSRMRKIG 465

Query: 239 VKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA 298
           ++P+ + FV +L+ACSH+G++D     F +MT+DY + P  EHY  + DLLG +G  +EA
Sbjct: 466 IQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDYKMTPKLEHYGCMIDLLGHSGLFKEA 525

Query: 299 YEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA 358
            E I+ M   P   +W +LL AC++H NVEL    AE +  I+P N G+YV+LSN YA+A
Sbjct: 526 EEMINMMEMEPDGVIWCSLLKACKMHGNVELGESFAENLIKIEPENPGSYVLLSNIYASA 585

Query: 359 RRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERM 418
            RW + A  R  + +KGMKK P CS IE+ +  + F+ GDK HP    I   L+E+   +
Sbjct: 586 GRWNEVAKTRALLNDKGMKKVPGCSSIEIDSVVHEFIIGDKFHPRNREIYGMLEEMEVLL 645

Query: 419 EQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCH 478
           E+ G+VPDT EVL ++EEE K+  L +HSE+LAI FG+I T  GT + I+KNLRVC +CH
Sbjct: 646 EKAGFVPDTSEVLQEMEEEWKEGALRHHSEKLAIAFGLISTKPGTKLTIVKNLRVCRNCH 705

Query: 479 TAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
            A K ISKI +REII RD +RFHHF DG CSC DYW
Sbjct: 706 EATKLISKIYKREIIARDRTRFHHFRDGVCSCNDYW 741

Arabidopsis thaliana (taxid: 3702)

>sp|Q9S7F4|PP206_ARATH Putative pentatricopeptide repeat-containing protein At2g01510 OS=Arabidopsis thaliana GN=PCMP-H36 PE=3 SV=1

 Score =  464 bits (1193), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 224/515 (43%), Positives = 331/515 (64%), Gaps = 1/515 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D VS+N VI   ++   YE +L+  R+M  +     +F  +++L I A+   +  G
Sbjct: 311 MPELDFVSYNVVISSYSQADQYEASLHFFREMQCMGFDRRNFPFATMLSIAANLSSLQMG 370

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           +++H  A+    D+ + +G+SL++MYAKC   E++  +F  LP +  +SW ++I+G VQ 
Sbjct: 371 RQLHCQALLATADSILHVGNSLVDMYAKCEMFEEAELIFKSLPQRTTVSWTALISGYVQK 430

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           GL   GLK F +M  + ++    +F++++ A A   +L LGKQLH  IIR+G  +N+F  
Sbjct: 431 GLHGAGLKLFTKMRGSNLRADQSTFATVLKASASFASLLLGKQLHAFIIRSGNLENVFSG 490

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           S L+DMYAKCG+I+ A  +F++M   + VSW A+I  +A +G+   AI  F +M + G++
Sbjct: 491 SGLVDMYAKCGSIKDAVQVFEEMPDRNAVSWNALISAHADNGDGEAAIGAFAKMIESGLQ 550

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           P+SV+ + VLTACSH G +++   YF +M+  YGI P  +HYA + DLLGR G+  EA +
Sbjct: 551 PDSVSILGVLTACSHCGFVEQGTEYFQAMSPIYGITPKKKHYACMLDLLGRNGRFAEAEK 610

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDP-NNMGAYVILSNTYAAAR 359
            +  M   P E +W ++L+ACR+HKN  LA + AEK+F ++   +  AYV +SN YAAA 
Sbjct: 611 LMDEMPFEPDEIMWSSVLNACRIHKNQSLAERAAEKLFSMEKLRDAAAYVSMSNIYAAAG 670

Query: 360 RWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERME 419
            W+    ++  MR +G+KK PA SW+EV +K + F + D++HP    I   + EL   +E
Sbjct: 671 EWEKVRDVKKAMRERGIKKVPAYSWVEVNHKIHVFSSNDQTHPNGDEIVRKINELTAEIE 730

Query: 420 QEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHT 479
           +EGY PDT  V+ DV+E+ K   L YHSERLA+ F +I TP+G  I ++KNLR C DCH 
Sbjct: 731 REGYKPDTSSVVQDVDEQMKIESLKYHSERLAVAFALISTPEGCPIVVMKNLRACRDCHA 790

Query: 480 AIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           AIK ISKIV+REI VRD SRFHHF +G CSCGDYW
Sbjct: 791 AIKLISKIVKREITVRDTSRFHHFSEGVCSCGDYW 825

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SMZ2|PP347_ARATH Pentatricopeptide repeat-containing protein At4g33170 OS=Arabidopsis thaliana GN=PCMP-H53 PE=3 SV=1

 Score =  462 bits (1190), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 210/510 (41%), Positives = 329/510 (64%)

Query: 5   DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIH 64
           DLV+WN ++ G  ++    + L +   M     + D FTL++V         + +GK++H
Sbjct: 481 DLVAWNAMMAGYTQSHDGHKTLKLFALMHKQGERSDDFTLATVFKTCGFLFAINQGKQVH 540

Query: 65  GYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFD 124
            YAI+ G D ++ + S +++MY KC  +  +   F  +PV D ++W ++I+GC++NG  +
Sbjct: 541 AYAIKSGYDLDLWVSSGILDMYVKCGDMSAAQFAFDSIPVPDDVAWTTMISGCIENGEEE 600

Query: 125 EGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL 184
                F QM +  + P   + +++  A + LT L  G+Q+H   ++    ++ F+ +SL+
Sbjct: 601 RAFHVFSQMRLMGVLPDEFTIATLAKASSCLTALEQGRQIHANALKLNCTNDPFVGTSLV 660

Query: 185 DMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV 244
           DMYAKCG+I  A C+F ++++ +I +W A+++G A HG   + + LF+QM+  G+KP+ V
Sbjct: 661 DMYAKCGSIDDAYCLFKRIEMMNITAWNAMLVGLAQHGEGKETLQLFKQMKSLGIKPDKV 720

Query: 245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN 304
            F+ VL+ACSH+GL+ +A+ +  SM  DYGI P  EHY+ +AD LGRAG +++A   I +
Sbjct: 721 TFIGVLSACSHSGLVSEAYKHMRSMHGDYGIKPEIEHYSCLADALGRAGLVKQAENLIES 780

Query: 305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDA 364
           M    + +++ TLL+ACRV  + E   +VA K+  ++P +  AYV+LSN YAAA +W + 
Sbjct: 781 MSMEASASMYRTLLAACRVQGDTETGKRVATKLLELEPLDSSAYVLLSNMYAAASKWDEM 840

Query: 365 ASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYV 424
              R  M+   +KK P  SWIEVKNK + FV  D+S+     I   +K+++  ++QEGYV
Sbjct: 841 KLARTMMKGHKVKKDPGFSWIEVKNKIHIFVVDDRSNRQTELIYRKVKDMIRDIKQEGYV 900

Query: 425 PDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFI 484
           P+T   L DVEEE+K+  LYYHSE+LA+ FG++ TP  T IR+IKNLRVCGDCH A+K+I
Sbjct: 901 PETDFTLVDVEEEEKERALYYHSEKLAVAFGLLSTPPSTPIRVIKNLRVCGDCHNAMKYI 960

Query: 485 SKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           +K+  REI++RD +RFH F+DG CSCGDYW
Sbjct: 961 AKVYNREIVLRDANRFHRFKDGICSCGDYW 990

Arabidopsis thaliana (taxid: 3702)

>sp|Q3E6Q1|PPR32_ARATH Pentatricopeptide repeat-containing protein At1g11290 OS=Arabidopsis thaliana GN=PCMP-H40 PE=2 SV=1

 Score =  462 bits (1188), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 221/510 (43%), Positives = 331/510 (64%), Gaps = 1/510 (0%)

Query: 5   DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIH 64
           ++VSWN++I    +N   +EA+ I ++M +  +KP   ++   L   AD  D+ +G+ IH
Sbjct: 301 NVVSWNSMIDAYVQNENPKEAMLIFQKMLDEGVKPTDVSVMGALHACADLGDLERGRFIH 360

Query: 65  GYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFD 124
             ++  GLD NV + +SLI+MY KC  V+ +  +F  L  +  +SWN++I G  QNG   
Sbjct: 361 KLSVELGLDRNVSVVNSLISMYCKCKEVDTAASMFGKLQSRTLVSWNAMILGFAQNGRPI 420

Query: 125 EGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL 184
           + L +F QM    +KP   ++ S++ A A L+  H  K +HG ++R+  D N+F+ ++L+
Sbjct: 421 DALNYFSQMRSRTVKPDTFTYVSVITAIAELSITHHAKWIHGVVMRSCLDKNVFVTTALV 480

Query: 185 DMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV 244
           DMYAKCG I +AR IFD M    + +W A+I G   HG    A+ LFE+M+K  +KPN V
Sbjct: 481 DMYAKCGAIMIARLIFDMMSERHVTTWNAMIDGYGTHGFGKAALELFEEMQKGTIKPNGV 540

Query: 245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN 304
            F++V++ACSH+GL++     F  M ++Y I  S +HY A+ DLLGRAG+L EA++FI  
Sbjct: 541 TFLSVISACSHSGLVEAGLKCFYMMKENYSIELSMDHYGAMVDLLGRAGRLNEAWDFIMQ 600

Query: 305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDA 364
           M   P  NV+  +L AC++HKNV  A K AE++F ++P++ G +V+L+N Y AA  W+  
Sbjct: 601 MPVKPAVNVYGAMLGACQIHKNVNFAEKAAERLFELNPDDGGYHVLLANIYRAASMWEKV 660

Query: 365 ASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYV 424
             +RV M  +G++KTP CS +E+KN+ ++F +G  +HP   +I   L++L+  +++ GYV
Sbjct: 661 GQVRVSMLRQGLRKTPGCSMVEIKNEVHSFFSGSTAHPDSKKIYAFLEKLICHIKEAGYV 720

Query: 425 PDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFI 484
           PDT  VL  VE + K+ LL  HSE+LAI FG++ T  GTTI + KNLRVC DCH A K+I
Sbjct: 721 PDTNLVL-GVENDVKEQLLSTHSEKLAISFGLLNTTAGTTIHVRKNLRVCADCHNATKYI 779

Query: 485 SKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           S +  REI+VRD  RFHHF++G CSCGDYW
Sbjct: 780 SLVTGREIVVRDMQRFHHFKNGACSCGDYW 809

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	514
359481040	709	PREDICTED: putative pentatricopeptide re	0.943	0.684	0.766	0.0
449508565	712	PREDICTED: LOW QUALITY PROTEIN: putative	0.929	0.671	0.729	0.0
307136183	773	hypothetical protein [Cucumis melo subsp	0.992	0.659	0.735	0.0
449433569	705	PREDICTED: putative pentatricopeptide re	0.986	0.719	0.721	0.0
147780302	679	hypothetical protein VITISV_032008 [Viti	0.846	0.640	0.760	0.0
356511287	674	PREDICTED: putative pentatricopeptide re	1.0	0.762	0.715	0.0
357521373	701	Pentatricopeptide repeat-containing prot	1.0	0.733	0.703	0.0
297831082	679	pentatricopeptide repeat-containing prot	0.992	0.751	0.675	0.0
334185563	715	pentatricopeptide repeat-containing prot	0.922	0.662	0.673	0.0
357116318	646	PREDICTED: putative pentatricopeptide re	0.972	0.773	0.616	0.0

>gi|359481040|ref|XP_002266469.2| PREDICTED: putative pentatricopeptide repeat-containing protein At3g23330-like [Vitis vinifera]

 Score =  839 bits (2167), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/514 (76%), Positives = 457/514 (88%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D+VSWNTVI G A+NG++E+AL +VR+MGN +L+PDSFTLSSVLPIFA+YV+++KG
Sbjct: 196 MPKRDIVSWNTVISGNAQNGMHEDALMMVREMGNADLRPDSFTLSSVLPIFAEYVNLLKG 255

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHGYAIR+G DA+V IGSSLI+MYAKC RV+DS R+F +LP  D ISWNSIIAGCVQN
Sbjct: 256 KEIHGYAIRNGYDADVFIGSSLIDMYAKCTRVDDSCRVFYMLPQHDGISWNSIIAGCVQN 315

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G+FDEGLKFF+QMLIAKIKP HVSFSSIMPACAHLTTLHLGKQLHG IIR+ FD N+FIA
Sbjct: 316 GMFDEGLKFFQQMLIAKIKPNHVSFSSIMPACAHLTTLHLGKQLHGYIIRSRFDGNVFIA 375

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           S+L+DMYAKCGNIR AR IFDKM+L+D+VSWTA+IMG ALHG+A+DAISLF++ME +GVK
Sbjct: 376 SALVDMYAKCGNIRTARWIFDKMELYDMVSWTAMIMGYALHGHAYDAISLFKRMEVEGVK 435

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN VAF+AVLTACSHAGL+D+AW YFNSMT+DY I P  EHYAAVADLLGR G+L+EAYE
Sbjct: 436 PNYVAFMAVLTACSHAGLVDEAWKYFNSMTQDYRIIPGLEHYAAVADLLGRVGRLEEAYE 495

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FIS+MH  PT +VW TLL+ACRVHKN+ELA KV++K+F +DP N+GAYV+LSN Y+AA R
Sbjct: 496 FISDMHIEPTGSVWSTLLAACRVHKNIELAEKVSKKLFTVDPQNIGAYVLLSNIYSAAGR 555

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WKDA  LR+ MR+KGMKK PACSWIE+KNK +AFVAGDKSHP+Y RINEALK LLE+ME+
Sbjct: 556 WKDARKLRIAMRDKGMKKKPACSWIEIKNKVHAFVAGDKSHPYYDRINEALKVLLEQMER 615

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYV DT EVLHDVEEEQK+ LL  HSERLAI FGII TP GTTIR+ KNLRVC DCHTA
Sbjct: 616 EGYVLDTTEVLHDVEEEQKRYLLCSHSERLAITFGIISTPAGTTIRVTKNLRVCVDCHTA 675

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
            KFISKIV REI+VRDNSRFHHF+DGKCSCGD+W
Sbjct: 676 TKFISKIVGREIVVRDNSRFHHFKDGKCSCGDFW 709

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449508565|ref|XP_004163348.1| PREDICTED: LOW QUALITY PROTEIN: putative pentatricopeptide repeat-containing protein At3g23330-like [Cucumis sativus]

 Score =  808 bits (2087), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/514 (72%), Positives = 437/514 (85%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  DLVSWNT+I G ARNGLYEE L ++R+MG  NLKPDSFTLSSVLP+ A+ VD+ +G
Sbjct: 199 MPEKDLVSWNTIIAGNARNGLYEETLRMIREMGGANLKPDSFTLSSVLPLIAENVDISRG 258

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHG +IR GLDA++ + SSLI+MYAKC RV DS R+F LL  +D ISWNSIIAGCVQN
Sbjct: 259 KEIHGCSIRQGLDADIYVASSLIDMYAKCTRVADSCRVFTLLTERDGISWNSIIAGCVQN 318

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           GLFDEGL+FFRQML+AKIKP+  SFSSIMPACAHLTTLHLGKQLHG I RNGFD+N+FIA
Sbjct: 319 GLFDEGLRFFRQMLMAKIKPKSYSFSSIMPACAHLTTLHLGKQLHGYITRNGFDENIFIA 378

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           SSL+DMYAKCGNIR A+ IFD+M L D+VSWTA+IMG ALHG A DAI LFEQME +G+K
Sbjct: 379 SSLVDMYAKCGNIRTAKQIFDRMRLRDMVSWTAMIMGCALHGQAPDAIELFEQMETEGIK 438

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN VAF+AVLTACSH GL+D+AW YFNSMT+D+GIAP  EHYAAV+DLLGRAG+L+EAY+
Sbjct: 439 PNHVAFMAVLTACSHGGLVDEAWKYFNSMTRDFGIAPGVEHYAAVSDLLGRAGRLEEAYD 498

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FI  MH GPT ++W TLLSACRVH N+++A KVA +I  +DPNN GAY++L+N Y+AARR
Sbjct: 499 FICGMHIGPTGSIWATLLSACRVHXNIDMAEKVANRILEVDPNNTGAYILLANIYSAARR 558

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WK+AA  R  MR  G++KTPACSWIEVKNK YAF+AGD+SHP Y +I EA++ L+E ME+
Sbjct: 559 WKEAAKWRASMRRIGIRKTPACSWIEVKNKVYAFMAGDESHPCYEKIREAMEVLVELMEK 618

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYVPDT EV HDVEEEQKK L+  HSERLAIVFGII TP G TIR+ KNLRVC DCHTA
Sbjct: 619 EGYVPDTSEVHHDVEEEQKKYLVCSHSERLAIVFGIINTPAGMTIRVTKNLRVCTDCHTA 678

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
            KFISKIV REI+VRDNSRFHHF++G CSCGDYW
Sbjct: 679 TKFISKIVGREIVVRDNSRFHHFKNGTCSCGDYW 712

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136183|gb|ADN34022.1| hypothetical protein [Cucumis melo subsp. melo]

 Score =  808 bits (2086), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/514 (73%), Positives = 437/514 (85%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  DLVSWNT+I G ARNGLY E L +VR+MG  NLKPDSFTLSSVLP+ A+ VD+ KG
Sbjct: 260 MPEKDLVSWNTIIAGNARNGLYGETLTMVREMGGANLKPDSFTLSSVLPLIAENVDISKG 319

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHG +IR GLDA V + SSLI+MYAKC RV DS+R+F LL  +D ISWNSIIAGCVQN
Sbjct: 320 KEIHGCSIRQGLDAEVYVASSLIDMYAKCTRVVDSYRVFTLLTERDGISWNSIIAGCVQN 379

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           GLFDEGLKFFRQML+AKIKP+  SFSSIMPACAHLTTLHLGKQLHG I RNGFD+N+FIA
Sbjct: 380 GLFDEGLKFFRQMLMAKIKPKSYSFSSIMPACAHLTTLHLGKQLHGYITRNGFDENIFIA 439

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           SSL+DMYAKCGNIR AR IFD+M L D+VSWTA+IMG ALHG+A DAI LFEQM+ +G++
Sbjct: 440 SSLVDMYAKCGNIRTARQIFDRMRLRDMVSWTAMIMGCALHGHALDAIELFEQMKTEGIE 499

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN VAF+AVLTACSHAGL+D+AW YFNSMT D+GIAP  EHYAAV+DLLGRAG+L+EAY+
Sbjct: 500 PNYVAFMAVLTACSHAGLVDEAWKYFNSMTLDFGIAPGVEHYAAVSDLLGRAGRLEEAYD 559

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FI  M  GPT +VW TLLSACRVHKNV++A KVA +I  +DP N GAY++L+N Y+AARR
Sbjct: 560 FICGMPIGPTGSVWATLLSACRVHKNVDMAEKVANRILEVDPKNTGAYILLANIYSAARR 619

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WK+AA  R  +R  G++KTPACSWIEV+NK YAF+AGD+SHP Y +I EA++ L+E ME+
Sbjct: 620 WKEAAKWRASLRRTGIRKTPACSWIEVRNKVYAFMAGDESHPCYEKIREAMEVLMELMEK 679

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYVPDT EV HDVEEEQKK L+  HSERLAIVFGII TP GTTIR+ KNLRVC DCHTA
Sbjct: 680 EGYVPDTSEVHHDVEEEQKKYLVCSHSERLAIVFGIINTPAGTTIRVTKNLRVCTDCHTA 739

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
            KFISKIV REI+VRDNSRFHHF++G CSCGDYW
Sbjct: 740 TKFISKIVGREIVVRDNSRFHHFKNGTCSCGDYW 773

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433569|ref|XP_004134570.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g23330-like [Cucumis sativus]

 Score =  793 bits (2047), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 371/514 (72%), Positives = 432/514 (84%), Gaps = 7/514 (1%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  DLVSWNT+I G ARNGLYEE L ++R+MG  NLKPDSFTLSSVLP+ A+ VD+ +G
Sbjct: 199 MPEKDLVSWNTIIAGNARNGLYEETLRMIREMGGANLKPDSFTLSSVLPLIAENVDISRG 258

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHG +IR GLDA++ + SSLI+MYAKC RV DS R+F LL  +D ISWNSIIAGCVQN
Sbjct: 259 KEIHGCSIRQGLDADIYVASSLIDMYAKCTRVADSCRVFTLLTERDGISWNSIIAGCVQN 318

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           GLFDEGL+FFRQML+AKIKP+  SFSSIMPACAHLTTLHLGKQLHG I RNGFD+N+FIA
Sbjct: 319 GLFDEGLRFFRQMLMAKIKPKSYSFSSIMPACAHLTTLHLGKQLHGYITRNGFDENIFIA 378

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           SSL+DMYAKCGNIR A+ IFD+M L D+VSWTA+IMG ALHG A DAI LFEQME +G+K
Sbjct: 379 SSLVDMYAKCGNIRTAKQIFDRMRLRDMVSWTAMIMGCALHGQAPDAIELFEQMETEGIK 438

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
                  AVLTACSH GL+D+AW YFNSMT+D+GIAP  EHYAAV+DLLGRAG+L+EAY+
Sbjct: 439 -------AVLTACSHGGLVDEAWKYFNSMTRDFGIAPGVEHYAAVSDLLGRAGRLEEAYD 491

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FI  MH GPT ++W TLLSACRVHKN+++A KVA +I  +DPNN GAY++L+N Y+AARR
Sbjct: 492 FICGMHIGPTGSIWATLLSACRVHKNIDMAEKVANRILEVDPNNTGAYILLANIYSAARR 551

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WK+AA  R  MR  G++KTPACSWIEVKNK YAF+AGD+SHP Y +I EA++ L+E ME+
Sbjct: 552 WKEAAKWRASMRRIGIRKTPACSWIEVKNKVYAFMAGDESHPCYEKIREAMEVLVELMEK 611

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYVPDT EV HDVEEEQKK L+  HSERLAIVFGII TP G TIR+ KNLRVC DCHTA
Sbjct: 612 EGYVPDTSEVHHDVEEEQKKYLVCSHSERLAIVFGIINTPAGMTIRVTKNLRVCTDCHTA 671

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
            KFISKIV REI+VRDNSRFHHF++G CSCGDYW
Sbjct: 672 TKFISKIVGREIVVRDNSRFHHFKNGTCSCGDYW 705

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780302|emb|CAN70248.1| hypothetical protein VITISV_032008 [Vitis vinifera]

 Score =  789 bits (2038), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 375/493 (76%), Positives = 436/493 (88%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D+VSWNTVI G A+NG++E+AL +VR+MGN +L+PDSFTLSSVLPIFA+YV+++KG
Sbjct: 156 MPKRDIVSWNTVISGNAQNGMHEDALMMVREMGNADLRPDSFTLSSVLPIFAEYVNLLKG 215

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHGYAIR+G DA+V IGSSLI+MYAKC RV+DS R+F +LP  D ISWNSIIAGCVQN
Sbjct: 216 KEIHGYAIRNGYDADVFIGSSLIDMYAKCTRVDDSCRVFYMLPQHDGISWNSIIAGCVQN 275

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G+FDEGLKFF+QMLIAKIKP HVSFSSIMPACAHLTTLHLGKQLHG IIR+ FD N+FIA
Sbjct: 276 GMFDEGLKFFQQMLIAKIKPNHVSFSSIMPACAHLTTLHLGKQLHGYIIRSRFDGNVFIA 335

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           S+L+DMYAKCGNIR AR IFDKM+L+D+VSWTA+IMG ALHG+A+DAISLF++ME +GVK
Sbjct: 336 SALVDMYAKCGNIRTARWIFDKMELYDMVSWTAMIMGYALHGHAYDAISLFKRMEVEGVK 395

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN VAF+AVLTACSHAGL+D+AW YFNSMT+DY I P  EHYAAVADLLGR G+L+EAYE
Sbjct: 396 PNYVAFMAVLTACSHAGLVDEAWKYFNSMTQDYRIIPGLEHYAAVADLLGRVGRLEEAYE 455

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FIS+MH  PT +VW TLL+ACRVHKN+ELA KV++K+F +DP N+GAYV+LSN Y+AA R
Sbjct: 456 FISDMHIEPTGSVWSTLLAACRVHKNIELAEKVSKKLFTVDPQNIGAYVLLSNIYSAAGR 515

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WKDA  LR+ MR+KGMKK PACSWIE+KNK +AFVAGDKSHP+Y RINEALK LLE+ME+
Sbjct: 516 WKDARKLRIAMRDKGMKKKPACSWIEIKNKVHAFVAGDKSHPYYDRINEALKVLLEQMER 575

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYV DT EVLHDVEEEQK+ LL  HSERLAI FGII TP GTTIR+ KNLRVC DCHTA
Sbjct: 576 EGYVLDTTEVLHDVEEEQKRYLLCSHSERLAITFGIISTPAGTTIRVTKNLRVCVDCHTA 635

Query: 481 IKFISKIVQREII 493
            KFISKIV REI+
Sbjct: 636 TKFISKIVGREIV 648

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356511287|ref|XP_003524358.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g23330-like [Glycine max]

 Score =  780 bits (2013), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 369/516 (71%), Positives = 437/516 (84%), Gaps = 2/516 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MPV D+VSWNTVI G A+NG+YEEALN+V++MG  NL+PDSFTLSS+LPIF ++ +V KG
Sbjct: 159 MPVRDVVSWNTVIAGNAQNGMYEEALNMVKEMGKENLRPDSFTLSSILPIFTEHANVTKG 218

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHGYAIRHG D +V IGSSLI+MYAKC +VE S   F LL  +DAISWNSIIAGCVQN
Sbjct: 219 KEIHGYAIRHGFDKDVFIGSSLIDMYAKCTQVELSVCAFHLLSNRDAISWNSIIAGCVQN 278

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G FD+GL FFR+ML  K+KP  VSFSS++PACAHLT L+LGKQLH  IIR GFDDN FIA
Sbjct: 279 GRFDQGLGFFRRMLKEKVKPMQVSFSSVIPACAHLTALNLGKQLHAYIIRLGFDDNKFIA 338

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDL--HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG 238
           SSLLDMYAKCGNI++AR IF+K+++   D+VSWTA+IMG A+HG+A DA+SLFE+M  DG
Sbjct: 339 SSLLDMYAKCGNIKMARYIFNKIEMCDRDMVSWTAIIMGCAMHGHALDAVSLFEEMLVDG 398

Query: 239 VKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA 298
           VKP  VAF+AVLTACSHAGL+D+ W YFNSM +D+G+AP  EHYAAVADLLGRAG+L+EA
Sbjct: 399 VKPCYVAFMAVLTACSHAGLVDEGWKYFNSMQRDFGVAPGLEHYAAVADLLGRAGRLEEA 458

Query: 299 YEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA 358
           Y+FISNM   PT +VW TLL+ACR HKN+ELA KV  KI ++DP NMGA+VI+SN Y+AA
Sbjct: 459 YDFISNMGEEPTGSVWSTLLAACRAHKNIELAEKVVNKILLVDPGNMGAHVIMSNIYSAA 518

Query: 359 RRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERM 418
           +RW+DAA LRV MR  G+KKTPACSWIEV NK + F+AGDKSHP+Y +INEAL  LLE+M
Sbjct: 519 QRWRDAAKLRVRMRKTGLKKTPACSWIEVGNKVHTFLAGDKSHPYYDKINEALNILLEQM 578

Query: 419 EQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCH 478
           E+EGYV DT EVLHDV+EE K++LL  HSERLAI FGII T  GTTIR+IKN+RVC DCH
Sbjct: 579 EKEGYVLDTNEVLHDVDEEHKRDLLRTHSERLAIAFGIISTTSGTTIRVIKNIRVCVDCH 638

Query: 479 TAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           TAIKF++KIV REIIVRDNSRFHHF++G CSCGDYW
Sbjct: 639 TAIKFMAKIVGREIIVRDNSRFHHFKNGSCSCGDYW 674

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357521373|ref|XP_003630975.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355524997|gb|AET05451.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  772 bits (1994), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/516 (70%), Positives = 436/516 (84%), Gaps = 2/516 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMG-NVNLKPDSFTLSSVLPIFADYVDVIK 59
           MPV D+VSWNTVI G A+NG+Y EAL++VR+MG N  LKPDSFTLSS+LPIFA++VDV K
Sbjct: 186 MPVRDVVSWNTVIAGFAQNGMYVEALDMVREMGKNGKLKPDSFTLSSILPIFAEHVDVNK 245

Query: 60  GKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQ 119
           GKEIHGYA+R+G D +V IGSSLI+MYAKC R+E S R F +LP KDAISWNSIIAGCVQ
Sbjct: 246 GKEIHGYAVRNGFDGDVFIGSSLIDMYAKCNRLECSLRAFYILPRKDAISWNSIIAGCVQ 305

Query: 120 NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFI 179
           NG FD GL FFR+ML   +KP  VSFSS++PACAHLT L LG+QLHGCI+R GFDDN FI
Sbjct: 306 NGEFDRGLGFFRRMLKENVKPMAVSFSSVIPACAHLTALSLGRQLHGCIVRLGFDDNEFI 365

Query: 180 ASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV 239
           ASSL+DMYAKCGNI++AR +FD++D  D+V+WTA+IMG A+HG+A DA+SLFE M +DGV
Sbjct: 366 ASSLVDMYAKCGNIKMARYVFDRIDKRDMVAWTAIIMGCAMHGHALDAVSLFENMLEDGV 425

Query: 240 KPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAY 299
           +P  VAF+AVLTACSHAGL+D+ W YFNSM +D+GIAP  EHYAAVADLLGRAG+L+EAY
Sbjct: 426 RPCYVAFMAVLTACSHAGLVDEGWRYFNSMERDFGIAPGLEHYAAVADLLGRAGRLEEAY 485

Query: 300 EFISNMHA-GPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA 358
           +FISNM    PT +VW  LL+ACR HK+VELA KV +K+  +D  NMGAYV++SN Y+AA
Sbjct: 486 DFISNMRGVQPTGSVWSILLAACRAHKSVELAEKVLDKLLSVDSENMGAYVLMSNIYSAA 545

Query: 359 RRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERM 418
           +RWKDAA LR+ MR KG+KKTPACSWIEV N+ + F+AGDKSHP+Y +IN+AL  LLE+M
Sbjct: 546 QRWKDAARLRIHMRKKGLKKTPACSWIEVGNQVHTFMAGDKSHPYYDKINKALDVLLEQM 605

Query: 419 EQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCH 478
           E+EGYV DT +VLHDV+EE K+ LL+ HSERLAI +GII T  GTTIR+IKN+RVC DCH
Sbjct: 606 EKEGYVIDTNQVLHDVDEELKRELLHNHSERLAIAYGIISTTAGTTIRVIKNIRVCADCH 665

Query: 479 TAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           TAIKFI+KIV REI VRDNSRFHHF++G CSCGDYW
Sbjct: 666 TAIKFITKIVGREITVRDNSRFHHFKNGSCSCGDYW 701

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297831082|ref|XP_002883423.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297329263|gb|EFH59682.1| pentatricopeptide repeat-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  759 bits (1960), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 347/514 (67%), Positives = 429/514 (83%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D+VS+NTVI G A++G+YE+AL +VR+MG  +LKPD+FTLSSVLPIF++YVDV+KG
Sbjct: 166 MPRKDVVSYNTVIAGYAQSGMYEDALRMVREMGTSDLKPDAFTLSSVLPIFSEYVDVLKG 225

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHGY IR G+D++V IGSSL++MYAK AR+EDS R+F  L  +D+ISWNS++AG VQN
Sbjct: 226 KEIHGYVIRKGIDSDVYIGSSLVDMYAKSARIEDSERVFSHLYRRDSISWNSLVAGYVQN 285

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G ++E L+ FRQM+ AK++P  V+FSS++PACAHL TLHLGKQLHG ++R GF  N+FIA
Sbjct: 286 GRYNEALRLFRQMVSAKVRPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGRNIFIA 345

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           S+L+DMY+KCGNI+ AR IFD+M+LHD VSWTA+IMG+ALHG+ H+A+SLFE+M++ GVK
Sbjct: 346 SALVDMYSKCGNIQAARKIFDRMNLHDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVK 405

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN VAFVAVLTACSH GL+D+AW YFNSMTK YG+    EHYAAVADLLGRAGKL+EAY+
Sbjct: 406 PNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQELEHYAAVADLLGRAGKLEEAYD 465

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FIS M   PT +VW TLLS+C VHKN+ELA KVAEKIF ID  NMGAYV++ N YA+  R
Sbjct: 466 FISKMRVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTIDSENMGAYVLMCNMYASNGR 525

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WK+ A LR+ +R KG++K PACSWIE+KNK + FV+GD+SHP   RINE LK ++E+ME+
Sbjct: 526 WKEMAKLRLRVRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSMDRINEFLKAVMEQMEK 585

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYV DT  VLHDV+EE K+ LL+ HSERLA+ FGII T  GTTIR+ KN+R+C DCH A
Sbjct: 586 EGYVADTSGVLHDVDEEHKRELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVA 645

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           IKFISKI +REIIVRDNSRFHHF  G CSCGDYW
Sbjct: 646 IKFISKITEREIIVRDNSRFHHFNRGSCSCGDYW 679

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334185563|ref|NP_188975.3| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|75274454|sp|Q9LW63.1|PP251_ARATH RecName: Full=Putative pentatricopeptide repeat-containing protein At3g23330 gi|11994318|dbj|BAB02277.1| unnamed protein product [Arabidopsis thaliana] gi|332643232|gb|AEE76753.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  756 bits (1952), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/514 (67%), Positives = 426/514 (82%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D+VS+NT+I G A++G+YE+AL +VR+MG  +LKPDSFTLSSVLPIF++YVDVIKG
Sbjct: 202 MPRKDVVSYNTIIAGYAQSGMYEDALRMVREMGTTDLKPDSFTLSSVLPIFSEYVDVIKG 261

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           KEIHGY IR G+D++V IGSSL++MYAK AR+EDS R+F  L  +D ISWNS++AG VQN
Sbjct: 262 KEIHGYVIRKGIDSDVYIGSSLVDMYAKSARIEDSERVFSRLYCRDGISWNSLVAGYVQN 321

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G ++E L+ FRQM+ AK+KP  V+FSS++PACAHL TLHLGKQLHG ++R GF  N+FIA
Sbjct: 322 GRYNEALRLFRQMVTAKVKPGAVAFSSVIPACAHLATLHLGKQLHGYVLRGGFGSNIFIA 381

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           S+L+DMY+KCGNI+ AR IFD+M++ D VSWTA+IMG+ALHG+ H+A+SLFE+M++ GVK
Sbjct: 382 SALVDMYSKCGNIKAARKIFDRMNVLDEVSWTAIIMGHALHGHGHEAVSLFEEMKRQGVK 441

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN VAFVAVLTACSH GL+D+AW YFNSMTK YG+    EHYAAVADLLGRAGKL+EAY 
Sbjct: 442 PNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQELEHYAAVADLLGRAGKLEEAYN 501

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FIS M   PT +VW TLLS+C VHKN+ELA KVAEKIF +D  NMGAYV++ N YA+  R
Sbjct: 502 FISKMCVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTVDSENMGAYVLMCNMYASNGR 561

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           WK+ A LR+ MR KG++K PACSWIE+KNK + FV+GD+SHP   +INE LK ++E+ME+
Sbjct: 562 WKEMAKLRLRMRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSMDKINEFLKAVMEQMEK 621

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           EGYV DT  VLHDV+EE K+ LL+ HSERLA+ FGII T  GTTIR+ KN+R+C DCH A
Sbjct: 622 EGYVADTSGVLHDVDEEHKRELLFGHSERLAVAFGIINTEPGTTIRVTKNIRICTDCHVA 681

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           IKFISKI +REIIVRDNSRFHHF  G CSCGDYW
Sbjct: 682 IKFISKITEREIIVRDNSRFHHFNRGNCSCGDYW 715

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357116318|ref|XP_003559929.1| PREDICTED: putative pentatricopeptide repeat-containing protein At3g23330-like [Brachypodium distachyon]

 Score =  674 bits (1738), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 317/514 (61%), Positives = 402/514 (78%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D+VSWNT+++G A +G + EAL +VR+M     KPDSFTLSSVLPIFA+  DV +G
Sbjct: 133 MPEKDVVSWNTLVLGCAESGRHGEALGLVREMWRDGCKPDSFTLSSVLPIFAEGADVRRG 192

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
            E+HG+A R+G   +V +GSSLI+MYA C R + S ++F  LPV+DAI WNS++AGC QN
Sbjct: 193 MELHGFATRNGFHDDVFVGSSLIDMYANCTRTDYSVKVFDNLPVRDAILWNSMLAGCAQN 252

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G  DE L  FR+ML + IKP  V+FSS++PAC +L +L LGKQLH  +IR GFD N+FI+
Sbjct: 253 GSVDEALGLFRRMLHSGIKPMPVTFSSLIPACGNLASLLLGKQLHAYVIRGGFDGNVFIS 312

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           SSL+DMY KCGN+ +AR IFD++   DIVSWTA+IMG+ALHG A +A+ LF++ME   +K
Sbjct: 313 SSLIDMYCKCGNVSIARRIFDRIQSPDIVSWTAMIMGHALHGPAREALVLFDRMELGNLK 372

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN + F+AVLTACSHAGL+DK W YFNSM+  YGI PS EH+AA+AD LGR GKL+EAY 
Sbjct: 373 PNHITFLAVLTACSHAGLVDKGWKYFNSMSDHYGIVPSLEHHAALADTLGRPGKLEEAYN 432

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
           FIS M   PT +VW TLL AC+VHKN  LA +VA+KIF ++P +MG+++ILSNTY+++ R
Sbjct: 433 FISGMKIKPTASVWSTLLRACKVHKNTVLAEEVAKKIFDLEPRSMGSHIILSNTYSSSGR 492

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
           W +AA LR  MR KGM+K PACSWIEVKNK + FVA DKSHP+Y RI +AL    E+M +
Sbjct: 493 WNEAAHLRKSMRKKGMQKEPACSWIEVKNKQHVFVAHDKSHPWYERIIDALNVFSEQMVR 552

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
           +GYVP+T +V  D+EEEQK ++L  HSE+LAIVFGII TP GTTIR++KNLRVC DCHT 
Sbjct: 553 QGYVPNTDDVFQDIEEEQKNSVLCGHSEKLAIVFGIISTPPGTTIRVMKNLRVCVDCHTV 612

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
            KFISKIV REI++RD +RFHHF+DG CSCGD+W
Sbjct: 613 TKFISKIVGREIVMRDANRFHHFKDGICSCGDFW 646

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	514
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.998	0.692	0.446	7.1e-126
TAIR|locus:2140235	781	AT4G02750 [Arabidopsis thalian	0.982	0.646	0.446	1.3e-122
TAIR|locus:2124137	871	DOT4 "DEFECTIVELY ORGANIZED TR	0.990	0.584	0.429	2.5e-120
TAIR|locus:2078653	825	AT3G02010 [Arabidopsis thalian	1.0	0.623	0.434	4.6e-120
TAIR|locus:2115130	691	AT4G37170 "AT4G37170" [Arabido	1.0	0.743	0.427	1.4e-119
TAIR|locus:2202074	809	CRR22 "CHLORORESPIRATORY REDUC	0.990	0.629	0.433	1.6e-118
TAIR|locus:2125899	990	AT4G33170 [Arabidopsis thalian	0.992	0.515	0.411	3.3e-118
TAIR|locus:2149664	588	MEF1 "mitochondrial RNA editin	0.996	0.870	0.432	1.4e-117
TAIR|locus:2148101	850	AT5G16860 "AT5G16860" [Arabido	0.988	0.597	0.437	3e-117
TAIR|locus:2118964	823	EMB2758 "embryo defective 2758	0.998	0.623	0.425	1e-116

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

 Score = 1213 (432.1 bits), Expect = 7.1e-126, Sum P(2) = 7.1e-126
 Identities = 231/517 (44%), Positives = 330/517 (63%)

Query:     1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
             +PV D+VSWN +I G A  G Y+EAL + + M   N++PD  T+ +V+   A    +  G
Sbjct:   226 IPVKDVVSWNAMISGYAETGNYKEALELFKDMMKTNVRPDESTMVTVVSACAQSGSIELG 285

Query:    61 KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
             +++H +   HG  +N+ I ++LI++Y+KC  +E +  LF  LP KD ISWN++I G    
Sbjct:   286 RQVHLWIDDHGFGSNLKIVNALIDLYSKCGELETACGLFERLPYKDVISWNTLIGGYTHM 345

Query:   121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN--GFDDNMF 178
              L+ E L  F++ML +   P  V+  SI+PACAHL  + +G+ +H  I +   G  +   
Sbjct:   346 NLYKEALLLFQEMLRSGETPNDVTMLSILPACAHLGAIDIGRWIHVYIDKRLKGVTNASS 405

Query:   179 IASSLLDMYAKCGNIRLARCIFDKMDLH-DIVSWTAVIMGNALHGNAHDAISLFEQMEKD 237
             + +SL+DMYAKCG+I  A  +F+ + LH  + SW A+I G A+HG A  +  LF +M K 
Sbjct:   406 LRTSLIDMYAKCGDIEAAHQVFNSI-LHKSLSSWNAMIFGFAMHGRADASFDLFSRMRKI 464

Query:   238 GVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQE 297
             G++P+ + FV +L+ACSH+G++D     F +MT+DY + P  EHY  + DLLG +G  +E
Sbjct:   465 GIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDYKMTPKLEHYGCMIDLLGHSGLFKE 524

Query:   298 AYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA 357
             A E I+ M   P   +W +LL AC++H NVEL    AE +  I+P N G+YV+LSN YA+
Sbjct:   525 AEEMINMMEMEPDGVIWCSLLKACKMHGNVELGESFAENLIKIEPENPGSYVLLSNIYAS 584

Query:   358 ARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLER 417
             A RW + A  R  + +KGMKK P CS IE+ +  + F+ GDK HP    I   L+E+   
Sbjct:   585 AGRWNEVAKTRALLNDKGMKKVPGCSSIEIDSVVHEFIIGDKFHPRNREIYGMLEEMEVL 644

Query:   418 MEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDC 477
             +E+ G+VPDT EVL ++EEE K+  L +HSE+LAI FG+I T  GT + I+KNLRVC +C
Sbjct:   645 LEKAGFVPDTSEVLQEMEEEWKEGALRHHSEKLAIAFGLISTKPGTKLTIVKNLRVCRNC 704

Query:   478 HTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             H A K ISKI +REII RD +RFHHF DG CSC DYW
Sbjct:   705 HEATKLISKIYKREIIARDRTRFHHFRDGVCSCNDYW 741

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

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

 Score = 1169 (416.6 bits), Expect = 1.3e-122, Sum P(2) = 1.3e-122
 Identities = 229/513 (44%), Positives = 324/513 (63%)

Query:     2 PVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGK 61
             PV D+ +W  ++ G  +N + EEA  +  +M   N      + +++L  +     +   K
Sbjct:   277 PVQDVFTWTAMVSGYIQNRMVEEARELFDKMPERN----EVSWNAMLAGYVQGERMEMAK 332

Query:    62 EIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNG 121
             E+           NV   +++I  YA+C ++ ++  LF  +P +D +SW ++IAG  Q+G
Sbjct:   333 ELFDVMPCR----NVSTWNTMITGYAQCGKISEAKNLFDKMPKRDPVSWAAMIAGYSQSG 388

Query:   122 LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIAS 181
                E L+ F QM     +    SFSS +  CA +  L LGKQLHG +++ G++   F+ +
Sbjct:   389 HSFEALRLFVQMEREGGRLNRSSFSSALSTCADVVALELGKQLHGRLVKGGYETGCFVGN 448

Query:   182 SLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP 241
             +LL MY KCG+I  A  +F +M   DIVSW  +I G + HG    A+  FE M+++G+KP
Sbjct:   449 ALLLMYCKCGSIEEANDLFKEMAGKDIVSWNTMIAGYSRHGFGEVALRFFESMKREGLKP 508

Query:   242 NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEF 301
             +    VAVL+ACSH GL+DK   YF +MT+DYG+ P+ +HYA + DLLGRAG L++A+  
Sbjct:   509 DDATMVAVLSACSHTGLVDKGRQYFYTMTQDYGVMPNSQHYACMVDLLGRAGLLEDAHNL 568

Query:   302 ISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRW 361
             + NM   P   +W TLL A RVH N ELA   A+KIF ++P N G YV+LSN YA++ RW
Sbjct:   569 MKNMPFEPDAAIWGTLLGASRVHGNTELAETAADKIFAMEPENSGMYVLLSNLYASSGRW 628

Query:   362 KDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQE 421
              D   LRV MR+KG+KK P  SWIE++NK + F  GD+ HP    I   L+EL  RM++ 
Sbjct:   629 GDVGKLRVRMRDKGVKKVPGYSWIEIQNKTHTFSVGDEFHPEKDEIFAFLEELDLRMKKA 688

Query:   422 GYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAI 481
             GYV  T  VLHDVEEE+K+ ++ YHSERLA+ +GI+    G  IR+IKNLRVC DCH AI
Sbjct:   689 GYVSKTSVVLHDVEEEEKERMVRYHSERLAVAYGIMRVSSGRPIRVIKNLRVCEDCHNAI 748

Query:   482 KFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             K++++I  R II+RDN+RFHHF+DG CSCGDYW
Sbjct:   749 KYMARITGRLIILRDNNRFHHFKDGSCSCGDYW 781

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2124137 DOT4 "DEFECTIVELY ORGANIZED TRIBUTARIES 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 1184 (421.8 bits), Expect = 2.5e-120, P = 2.5e-120
 Identities = 219/510 (42%), Positives = 330/510 (64%)

Query:     6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHG 65
             +VS+ ++I G AR GL  EA+ +  +M    + PD +T+++VL   A Y  + +GK +H 
Sbjct:   362 VVSYTSMIAGYAREGLAGEAVKLFEEMEEEGISPDVYTVTAVLNCCARYRLLDEGKRVHE 421

Query:    66 YAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDE 125
             +   + L  ++ + ++L++MYAKC  ++++  +F  + VKD ISWN+II G  +N   +E
Sbjct:   422 WIKENDLGFDIFVSNALMDMYAKCGSMQEAELVFSEMRVKDIISWNTIIGGYSKNCYANE 481

Query:   126 GLKFFRQMLIAK-IKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL 184
              L  F  +L  K   P   + + ++PACA L+    G+++HG I+RNG+  +  +A+SL+
Sbjct:   482 ALSLFNLLLEEKRFSPDERTVACVLPACASLSAFDKGREIHGYIMRNGYFSDRHVANSLV 541

Query:   185 DMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV 244
             DMYAKCG + LA  +FD +   D+VSWT +I G  +HG   +AI+LF QM + G++ + +
Sbjct:   542 DMYAKCGALLLAHMLFDDIASKDLVSWTVMIAGYGMHGFGKEAIALFNQMRQAGIEADEI 601

Query:   245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN 304
             +FV++L ACSH+GL+D+ W +FN M  +  I P+ EHYA + D+L R G L +AY FI N
Sbjct:   602 SFVSLLYACSHSGLVDEGWRFFNIMRHECKIEPTVEHYACIVDMLARTGDLIKAYRFIEN 661

Query:   305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDA 364
             M   P   +W  LL  CR+H +V+LA KVAEK+F ++P N G YV+++N YA A +W+  
Sbjct:   662 MPIPPDATIWGALLCGCRIHHDVKLAEKVAEKVFELEPENTGYYVLMANIYAEAEKWEQV 721

Query:   365 ASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYV 424
               LR  +  +G++K P CSWIE+K +   FVAGD S+P    I   L+++  RM +EGY 
Sbjct:   722 KRLRKRIGQRGLRKNPGCSWIEIKGRVNIFVAGDSSNPETENIEAFLRKVRARMIEEGYS 781

Query:   425 PDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFI 484
             P TK  L D EE +K+  L  HSE+LA+  GII +  G  IR+ KNLRVCGDCH   KF+
Sbjct:   782 PLTKYALIDAEEMEKEEALCGHSEKLAMALGIISSGHGKIIRVTKNLRVCGDCHEMAKFM 841

Query:   485 SKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             SK+ +REI++RD++RFH F+DG CSC  +W
Sbjct:   842 SKLTRREIVLRDSNRFHQFKDGHCSCRGFW 871

GO:0009507 "chloroplast" evidence=ISM

GO:0010087 "phloem or xylem histogenesis" evidence=IMP

GO:0010305 "leaf vascular tissue pattern formation" evidence=IMP

GO:0010588 "cotyledon vascular tissue pattern formation" evidence=IMP

GO:0048366 "leaf development" evidence=IMP

TAIR|locus:2078653 AT3G02010 [Arabidopsis thaliana (taxid:3702)]

 Score = 1161 (413.8 bits), Expect = 4.6e-120, Sum P(2) = 4.6e-120
 Identities = 224/515 (43%), Positives = 331/515 (64%)

Query:     1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
             MP  D VS+N VI   ++   YE +L+  R+M  +     +F  +++L I A+   +  G
Sbjct:   311 MPELDFVSYNVVISSYSQADQYEASLHFFREMQCMGFDRRNFPFATMLSIAANLSSLQMG 370

Query:    61 KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
             +++H  A+    D+ + +G+SL++MYAKC   E++  +F  LP +  +SW ++I+G VQ 
Sbjct:   371 RQLHCQALLATADSILHVGNSLVDMYAKCEMFEEAELIFKSLPQRTTVSWTALISGYVQK 430

Query:   121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
             GL   GLK F +M  + ++    +F++++ A A   +L LGKQLH  IIR+G  +N+F  
Sbjct:   431 GLHGAGLKLFTKMRGSNLRADQSTFATVLKASASFASLLLGKQLHAFIIRSGNLENVFSG 490

Query:   181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
             S L+DMYAKCG+I+ A  +F++M   + VSW A+I  +A +G+   AI  F +M + G++
Sbjct:   491 SGLVDMYAKCGSIKDAVQVFEEMPDRNAVSWNALISAHADNGDGEAAIGAFAKMIESGLQ 550

Query:   241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
             P+SV+ + VLTACSH G +++   YF +M+  YGI P  +HYA + DLLGR G+  EA +
Sbjct:   551 PDSVSILGVLTACSHCGFVEQGTEYFQAMSPIYGITPKKKHYACMLDLLGRNGRFAEAEK 610

Query:   301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDP-NNMGAYVILSNTYAAAR 359
              +  M   P E +W ++L+ACR+HKN  LA + AEK+F ++   +  AYV +SN YAAA 
Sbjct:   611 LMDEMPFEPDEIMWSSVLNACRIHKNQSLAERAAEKLFSMEKLRDAAAYVSMSNIYAAAG 670

Query:   360 RWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERME 419
              W+    ++  MR +G+KK PA SW+EV +K + F + D++HP    I   + EL   +E
Sbjct:   671 EWEKVRDVKKAMRERGIKKVPAYSWVEVNHKIHVFSSNDQTHPNGDEIVRKINELTAEIE 730

Query:   420 QEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHT 479
             +EGY PDT  V+ DV+E+ K   L YHSERLA+ F +I TP+G  I ++KNLR C DCH 
Sbjct:   731 REGYKPDTSSVVQDVDEQMKIESLKYHSERLAVAFALISTPEGCPIVVMKNLRACRDCHA 790

Query:   480 AIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             AIK ISKIV+REI VRD SRFHHF +G CSCGDYW
Sbjct:   791 AIKLISKIVKREITVRDTSRFHHFSEGVCSCGDYW 825

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2115130 AT4G37170 "AT4G37170" [Arabidopsis thaliana (taxid:3702)]

 Score = 1177 (419.4 bits), Expect = 1.4e-119, P = 1.4e-119
 Identities = 220/515 (42%), Positives = 334/515 (64%)

Query:     1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNV-NLKPDSFTLSSVLPIFADYVDVIK 59
             M   D  SW  ++ G  +    EEAL +   M  V N +P+ FT+S  +   A    + +
Sbjct:   177 MTEKDSYSWTAMVTGYVKKDQPEEALVLYSLMQRVPNSRPNIFTVSIAVAAAAAVKCIRR 236

Query:    60 GKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQ 119
             GKEIHG+ +R GLD++  + SSL++MY KC  ++++  +F  +  KD +SW S+I    +
Sbjct:   237 GKEIHGHIVRAGLDSDEVLWSSLMDMYGKCGCIDEARNIFDKIVEKDVVSWTSMIDRYFK 296

Query:   120 NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFI 179
             +  + EG   F +++ +  +P   +F+ ++ ACA LTT  LGKQ+HG + R GFD   F 
Sbjct:   297 SSRWREGFSLFSELVGSCERPNEYTFAGVLNACADLTTEELGKQVHGYMTRVGFDPYSFA 356

Query:   180 ASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV 239
             +SSL+DMY KCGNI  A+ + D     D+VSWT++I G A +G   +A+  F+ + K G 
Sbjct:   357 SSSLVDMYTKCGNIESAKHVVDGCPKPDLVSWTSLIGGCAQNGQPDEALKYFDLLLKSGT 416

Query:   240 KPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAY 299
             KP+ V FV VL+AC+HAGL++K   +F S+T+ + ++ + +HY  + DLL R+G+ ++  
Sbjct:   417 KPDHVTFVNVLSACTHAGLVEKGLEFFYSITEKHRLSHTSDHYTCLVDLLARSGRFEQLK 476

Query:   300 EFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR 359
               IS M   P++ +W ++L  C  + N++LA + A+++F I+P N   YV ++N YAAA 
Sbjct:   477 SVISEMPMKPSKFLWASVLGGCSTYGNIDLAEEAAQELFKIEPENPVTYVTMANIYAAAG 536

Query:   360 RWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERME 419
             +W++   +R  M+  G+ K P  SW E+K K + F+A D SHP Y++I E L+EL ++M+
Sbjct:   537 KWEEEGKMRKRMQEIGVTKRPGSSWTEIKRKRHVFIAADTSHPMYNQIVEFLRELRKKMK 596

Query:   420 QEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHT 479
             +EGYVP T  VLHDVE+EQK+  L YHSE+LA+ F I+ T +GT I++ KNLR C DCH 
Sbjct:   597 EEGYVPATSLVLHDVEDEQKEENLVYHSEKLAVAFAILSTEEGTAIKVFKNLRSCVDCHG 656

Query:   480 AIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             AIKFIS I +R+I VRD++RFH FE+G+CSCGDYW
Sbjct:   657 AIKFISNITKRKITVRDSTRFHCFENGQCSCGDYW 691

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2202074 CRR22 "CHLORORESPIRATORY REDUCTION22" [Arabidopsis thaliana (taxid:3702)]

 Score = 1167 (415.9 bits), Expect = 1.6e-118, P = 1.6e-118
 Identities = 221/510 (43%), Positives = 331/510 (64%)

Query:     5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIH 64
             ++VSWN++I    +N   +EA+ I ++M +  +KP   ++   L   AD  D+ +G+ IH
Sbjct:   301 NVVSWNSMIDAYVQNENPKEAMLIFQKMLDEGVKPTDVSVMGALHACADLGDLERGRFIH 360

Query:    65 GYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFD 124
               ++  GLD NV + +SLI+MY KC  V+ +  +F  L  +  +SWN++I G  QNG   
Sbjct:   361 KLSVELGLDRNVSVVNSLISMYCKCKEVDTAASMFGKLQSRTLVSWNAMILGFAQNGRPI 420

Query:   125 EGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL 184
             + L +F QM    +KP   ++ S++ A A L+  H  K +HG ++R+  D N+F+ ++L+
Sbjct:   421 DALNYFSQMRSRTVKPDTFTYVSVITAIAELSITHHAKWIHGVVMRSCLDKNVFVTTALV 480

Query:   185 DMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV 244
             DMYAKCG I +AR IFD M    + +W A+I G   HG    A+ LFE+M+K  +KPN V
Sbjct:   481 DMYAKCGAIMIARLIFDMMSERHVTTWNAMIDGYGTHGFGKAALELFEEMQKGTIKPNGV 540

Query:   245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN 304
              F++V++ACSH+GL++     F  M ++Y I  S +HY A+ DLLGRAG+L EA++FI  
Sbjct:   541 TFLSVISACSHSGLVEAGLKCFYMMKENYSIELSMDHYGAMVDLLGRAGRLNEAWDFIMQ 600

Query:   305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDA 364
             M   P  NV+  +L AC++HKNV  A K AE++F ++P++ G +V+L+N Y AA  W+  
Sbjct:   601 MPVKPAVNVYGAMLGACQIHKNVNFAEKAAERLFELNPDDGGYHVLLANIYRAASMWEKV 660

Query:   365 ASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYV 424
               +RV M  +G++KTP CS +E+KN+ ++F +G  +HP   +I   L++L+  +++ GYV
Sbjct:   661 GQVRVSMLRQGLRKTPGCSMVEIKNEVHSFFSGSTAHPDSKKIYAFLEKLICHIKEAGYV 720

Query:   425 PDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFI 484
             PDT  VL  VE + K+ LL  HSE+LAI FG++ T  GTTI + KNLRVC DCH A K+I
Sbjct:   721 PDTNLVL-GVENDVKEQLLSTHSEKLAISFGLLNTTAGTTIHVRKNLRVCADCHNATKYI 779

Query:   485 SKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             S +  REI+VRD  RFHHF++G CSCGDYW
Sbjct:   780 SLVTGREIVVRDMQRFHHFKNGACSCGDYW 809

GO:0005739 "mitochondrion" evidence=ISM

GO:0004519 "endonuclease activity" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

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

TAIR|locus:2125899 AT4G33170 [Arabidopsis thaliana (taxid:3702)]

 Score = 1164 (414.8 bits), Expect = 3.3e-118, P = 3.3e-118
 Identities = 210/510 (41%), Positives = 329/510 (64%)

Query:     5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIH 64
             DLV+WN ++ G  ++    + L +   M     + D FTL++V         + +GK++H
Sbjct:   481 DLVAWNAMMAGYTQSHDGHKTLKLFALMHKQGERSDDFTLATVFKTCGFLFAINQGKQVH 540

Query:    65 GYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFD 124
              YAI+ G D ++ + S +++MY KC  +  +   F  +PV D ++W ++I+GC++NG  +
Sbjct:   541 AYAIKSGYDLDLWVSSGILDMYVKCGDMSAAQFAFDSIPVPDDVAWTTMISGCIENGEEE 600

Query:   125 EGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL 184
                  F QM +  + P   + +++  A + LT L  G+Q+H   ++    ++ F+ +SL+
Sbjct:   601 RAFHVFSQMRLMGVLPDEFTIATLAKASSCLTALEQGRQIHANALKLNCTNDPFVGTSLV 660

Query:   185 DMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV 244
             DMYAKCG+I  A C+F ++++ +I +W A+++G A HG   + + LF+QM+  G+KP+ V
Sbjct:   661 DMYAKCGSIDDAYCLFKRIEMMNITAWNAMLVGLAQHGEGKETLQLFKQMKSLGIKPDKV 720

Query:   245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN 304
              F+ VL+ACSH+GL+ +A+ +  SM  DYGI P  EHY+ +AD LGRAG +++A   I +
Sbjct:   721 TFIGVLSACSHSGLVSEAYKHMRSMHGDYGIKPEIEHYSCLADALGRAGLVKQAENLIES 780

Query:   305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDA 364
             M    + +++ TLL+ACRV  + E   +VA K+  ++P +  AYV+LSN YAAA +W + 
Sbjct:   781 MSMEASASMYRTLLAACRVQGDTETGKRVATKLLELEPLDSSAYVLLSNMYAAASKWDEM 840

Query:   365 ASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYV 424
                R  M+   +KK P  SWIEVKNK + FV  D+S+     I   +K+++  ++QEGYV
Sbjct:   841 KLARTMMKGHKVKKDPGFSWIEVKNKIHIFVVDDRSNRQTELIYRKVKDMIRDIKQEGYV 900

Query:   425 PDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAIKFI 484
             P+T   L DVEEE+K+  LYYHSE+LA+ FG++ TP  T IR+IKNLRVCGDCH A+K+I
Sbjct:   901 PETDFTLVDVEEEEKERALYYHSEKLAVAFGLLSTPPSTPIRVIKNLRVCGDCHNAMKYI 960

Query:   485 SKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             +K+  REI++RD +RFH F+DG CSCGDYW
Sbjct:   961 AKVYNREIVLRDANRFHRFKDGICSCGDYW 990

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2149664 MEF1 "mitochondrial RNA editing factor 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1158 (412.7 bits), Expect = 1.4e-117, P = 1.4e-117
 Identities = 222/513 (43%), Positives = 328/513 (63%)

Query:     2 PVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGK 61
             P     +W+++I   A+N L   +L  +++M   NL+PD   L S     A       G+
Sbjct:    77 PQKSSTTWSSIISCFAQNELPWMSLEFLKKMMAGNLRPDDHVLPSATKSCAILSRCDIGR 136

Query:    62 EIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNG 121
              +H  +++ G DA+V +GSSL++MYAKC  +  + ++F  +P ++ ++W+ ++ G  Q G
Sbjct:   137 SVHCLSMKTGYDADVFVGSSLVDMYAKCGEIVYARKMFDEMPQRNVVTWSGMMYGYAQMG 196

Query:   122 LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIAS 181
               +E L  F++ L   +     SFSS++  CA+ T L LG+Q+HG  I++ FD + F+ S
Sbjct:   197 ENEEALWLFKEALFENLAVNDYSFSSVISVCANSTLLELGRQIHGLSIKSSFDSSSFVGS 256

Query:   182 SLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP 241
             SL+ +Y+KCG    A  +F+++ + ++  W A++   A H +    I LF++M+  G+KP
Sbjct:   257 SLVSLYSKCGVPEGAYQVFNEVPVKNLGIWNAMLKAYAQHSHTQKVIELFKRMKLSGMKP 316

Query:   242 NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEF 301
             N + F+ VL ACSHAGL+D+   YF+ M K+  I P+ +HYA++ D+LGRAG+LQEA E 
Sbjct:   317 NFITFLNVLNACSHAGLVDEGRYYFDQM-KESRIEPTDKHYASLVDMLGRAGRLQEALEV 375

Query:   302 ISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRW 361
             I+NM   PTE+VW  LL++C VHKN ELA   A+K+F + P + G ++ LSN YAA  R+
Sbjct:   376 ITNMPIDPTESVWGALLTSCTVHKNTELAAFAADKVFELGPVSSGMHISLSNAYAADGRF 435

Query:   362 KDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQE 421
             +DAA  R  +R++G KK    SW+E +NK + F AG++ H     I E L EL E ME+ 
Sbjct:   436 EDAAKARKLLRDRGEKKETGLSWVEERNKVHTFAAGERRHEKSKEIYEKLAELGEEMEKA 495

Query:   422 GYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTAI 481
             GY+ DT  VL +V+ ++K   + YHSERLAI FG+I  P    IR++KNLRVCGDCH AI
Sbjct:   496 GYIADTSYVLREVDGDEKNQTIRYHSERLAIAFGLITFPADRPIRVMKNLRVCGDCHNAI 555

Query:   482 KFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             KF+S   +R IIVRDN+RFH FEDGKCSC DYW
Sbjct:   556 KFMSVCTRRVIIVRDNNRFHRFEDGKCSCNDYW 588

GO:0005739 "mitochondrion" evidence=ISM

GO:0016554 "cytidine to uridine editing" evidence=IMP

TAIR|locus:2148101 AT5G16860 "AT5G16860" [Arabidopsis thaliana (taxid:3702)]

 Score = 1155 (411.6 bits), Expect = 3.0e-117, P = 3.0e-117
 Identities = 229/524 (43%), Positives = 328/524 (62%)

Query:     5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIH 64
             D+V+W+  I G A+ GL  EAL + RQM +  +KP+  TL SVL   A    ++ GKEIH
Sbjct:   329 DVVTWSAAISGYAQRGLGYEALGVCRQMLSSGIKPNEVTLISVLSGCASVGALMHGKEIH 388

Query:    65 GYAIR---------HGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVK--DAISWNSI 113
              YAI+         HG D N+ I + LI+MYAKC +V+ +  +F  L  K  D ++W  +
Sbjct:   389 CYAIKYPIDLRKNGHG-DENMVI-NQLIDMYAKCKKVDTARAMFDSLSPKERDVVTWTVM 446

Query:   114 IAGCVQNGLFDEGLKFFRQMLI--AKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN 171
             I G  Q+G  ++ L+   +M     + +P   + S  + ACA L  L +GKQ+H   +RN
Sbjct:   447 IGGYSQHGDANKALELLSEMFEEDCQTRPNAFTISCALVACASLAALRIGKQIHAYALRN 506

Query:   172 GFDD-NMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISL 230
               +   +F+++ L+DMYAKCG+I  AR +FD M   + V+WT+++ G  +HG   +A+ +
Sbjct:   507 QQNAVPLFVSNCLIDMYAKCGSISDARLVFDNMMAKNEVTWTSLMTGYGMHGYGEEALGI 566

Query:   231 FEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLG 290
             F++M + G K + V  + VL ACSH+G+ID+   YFN M   +G++P  EHYA + DLLG
Sbjct:   567 FDEMRRIGFKLDGVTLLVVLYACSHSGMIDQGMEYFNRMKTVFGVSPGPEHYACLVDLLG 626

Query:   291 RAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVI 350
             RAG+L  A   I  M   P   VW+  LS CR+H  VEL    AEKI  +  N+ G+Y +
Sbjct:   627 RAGRLNAALRLIEEMPMEPPPVVWVAFLSCCRIHGKVELGEYAAEKITELASNHDGSYTL 686

Query:   351 LSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEA 410
             LSN YA A RWKD   +R  MR+KG+KK P CSW+E       F  GDK+HP    I + 
Sbjct:   687 LSNLYANAGRWKDVTRIRSLMRHKGVKKRPGCSWVEGIKGTTTFFVGDKTHPHAKEIYQV 746

Query:   411 LKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKN 470
             L + ++R++  GYVP+T   LHDV++E+K +LL+ HSE+LA+ +GI+ TP G  IRI KN
Sbjct:   747 LLDHMQRIKDIGYVPETGFALHDVDDEEKDDLLFEHSEKLALAYGILTTPQGAAIRITKN 806

Query:   471 LRVCGDCHTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             LRVCGDCHTA  ++S+I+  +II+RD+SRFHHF++G CSC  YW
Sbjct:   807 LRVCGDCHTAFTYMSRIIDHDIILRDSSRFHHFKNGSCSCKGYW 850

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2118964 EMB2758 "embryo defective 2758" [Arabidopsis thaliana (taxid:3702)]

 Score = 1150 (409.9 bits), Expect = 1.0e-116, P = 1.0e-116
 Identities = 220/517 (42%), Positives = 330/517 (63%)

Query:     1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
             M V DL+SWN++I     N     A+++ ++M    ++PD  TL S+  I +   D+   
Sbjct:   308 MYVRDLISWNSIIKAYELNEQPLRAISLFQEMRLSRIQPDCLTLISLASILSQLGDIRAC 367

Query:    61 KEIHGYAIRHG-LDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQ 119
             + + G+ +R G    ++ IG++++ MYAK   V+ +  +F  LP  D ISWN+II+G  Q
Sbjct:   368 RSVQGFTLRKGWFLEDITIGNAVVVMYAKLGLVDSARAVFNWLPNTDVISWNTIISGYAQ 427

Query:   120 NGLFDEGLKFFRQMLI-AKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMF 178
             NG   E ++ +  M    +I     ++ S++PAC+    L  G +LHG +++NG   ++F
Sbjct:   428 NGFASEAIEMYNIMEEEGEIAANQGTWVSVLPACSQAGALRQGMKLHGRLLKNGLYLDVF 487

Query:   179 IASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG 238
             + +SL DMY KCG +  A  +F ++   + V W  +I  +  HG+   A+ LF++M  +G
Sbjct:   488 VVTSLADMYGKCGRLEDALSLFYQIPRVNSVPWNTLIACHGFHGHGEKAVMLFKEMLDEG 547

Query:   239 VKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA 298
             VKP+ + FV +L+ACSH+GL+D+    F  M  DYGI PS +HY  + D+ GRAG+L+ A
Sbjct:   548 VKPDHITFVTLLSACSHSGLVDEGQWCFEMMQTDYGITPSLKHYGCMVDMYGRAGQLETA 607

Query:   299 YEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVA-EKIFMIDPNNMGAYVILSNTYAA 357
              +FI +M   P  ++W  LLSACRVH NV+L GK+A E +F ++P ++G +V+LSN YA+
Sbjct:   608 LKFIKSMSLQPDASIWGALLSACRVHGNVDL-GKIASEHLFEVEPEHVGYHVLLSNMYAS 666

Query:   358 ARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLER 417
             A +W+    +R     KG++KTP  S +EV NK   F  G+++HP Y  +   L  L  +
Sbjct:   667 AGKWEGVDEIRSIAHGKGLRKTPGWSSMEVDNKVEVFYTGNQTHPMYEEMYRELTALQAK 726

Query:   418 MEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDC 477
             ++  GYVPD + VL DVE+++K+++L  HSERLAI F +I TP  TTIRI KNLRVCGDC
Sbjct:   727 LKMIGYVPDHRFVLQDVEDDEKEHILMSHSERLAIAFALIATPAKTTIRIFKNLRVCGDC 786

Query:   478 HTAIKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
             H+  KFISKI +REIIVRD++RFHHF++G CSCGDYW
Sbjct:   787 HSVTKFISKITEREIIVRDSNRFHHFKNGVCSCGDYW 823

GO:0005739 "mitochondrion" evidence=ISM

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

---

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)
Q9LW63	PP251_ARATH	No assigned EC number	0.6731	0.9221	0.6629	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	514
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-162
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-159
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	9e-60
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-54
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	6e-36
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-35
pfam14432	116	pfam14432, DYW_deaminase, DYW family of nucleic ac	6e-30
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-12
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-11
pfam13041	50	pfam13041, PPR_2, PPR repeat family	8e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-07
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-07
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	7e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	9e-05
pfam01535	31	pfam01535, PPR, PPR repeat	2e-04
pfam01535	31	pfam01535, PPR, PPR repeat	3e-04
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	4e-04
COG0457	291	COG0457, NrfG, FOG: TPR repeat [General function p	7e-04
pfam01535	31	pfam01535, PPR, PPR repeat	8e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.001
pfam12854	34	pfam12854, PPR_1, PPR repeat	0.001
pfam12854	34	pfam12854, PPR_1, PPR repeat	0.004

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

 Score =  476 bits (1227), Expect = e-162
 Identities = 202/514 (39%), Positives = 314/514 (61%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  +L SW T+I GL   G Y EA  + R+M       +  T   +L   A       G
Sbjct: 184 MPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAG 243

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           +++H   ++ G+  +  +  +LI+MY+KC  +ED+  +F  +P K  ++WNS++AG   +
Sbjct: 244 QQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALH 303

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G  +E L  + +M  + +     +FS ++   + L  L   KQ H  +IR GF  ++   
Sbjct: 304 GYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVAN 363

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           ++L+D+Y+K G +  AR +FD+M   +++SW A+I G   HG    A+ +FE+M  +GV 
Sbjct: 364 TALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVA 423

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
           PN V F+AVL+AC ++GL ++ W  F SM++++ I P   HYA + +LLGR G L EAY 
Sbjct: 424 PNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYA 483

Query: 301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR 360
            I      PT N+W  LL+ACR+HKN+EL    AEK++ + P  +  YV+L N Y ++ R
Sbjct: 484 MIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGR 543

Query: 361 WKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ 420
             +AA +   ++ KG+   PAC+WIEVK + ++F +GD+ HP    I + L EL++ + +
Sbjct: 544 QAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISE 603

Query: 421 EGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA 480
            GYV +  E+L DV+E+++K    YHSE+LAI FG+I T + T ++I ++ R+C DCH  
Sbjct: 604 YGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKV 663

Query: 481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW 514
           IKFI+ + +REI+VRD SRFHHF+ GKCSCGDYW
Sbjct: 664 IKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697

Length = 697

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

 Score =  473 bits (1220), Expect = e-159
 Identities = 220/513 (42%), Positives = 314/513 (61%), Gaps = 5/513 (0%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           M   D VSW  +I G  +NGL ++AL     M   N+ PD  T++SVL   A   D+  G
Sbjct: 349 METKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVG 408

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAG-CVQ 119
            ++H  A R GL + V + ++LI MY+KC  ++ +  +F  +P KD ISW SIIAG  + 
Sbjct: 409 VKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLN 468

Query: 120 NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFI 179
           N  F E L FFRQM +  +KP  V+  + + ACA +  L  GK++H  ++R G   + F+
Sbjct: 469 NRCF-EALIFFRQM-LLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFL 526

Query: 180 ASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV 239
            ++LLD+Y +CG +  A   F+  +  D+VSW  ++ G   HG    A+ LF +M + GV
Sbjct: 527 PNALLDLYVRCGRMNYAWNQFNSHE-KDVVSWNILLTGYVAHGKGSMAVELFNRMVESGV 585

Query: 240 KPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAY 299
            P+ V F+++L ACS +G++ +   YF+SM + Y I P+ +HYA V DLLGRAGKL EAY
Sbjct: 586 NPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAY 645

Query: 300 EFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR 359
            FI+ M   P   VW  LL+ACR+H++VEL    A+ IF +DPN++G Y++L N YA A 
Sbjct: 646 NFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAG 705

Query: 360 RWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERME 419
           +W + A +R  MR  G+   P CSW+EVK K +AF+  D+SHP    IN  L+   E+M+
Sbjct: 706 KWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMK 765

Query: 420 QEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHT 479
             G        + ++ E  K ++   HSERLAI FG+I T  G  I + KNL +C +CH 
Sbjct: 766 ASGLAGSESSSMDEI-EVSKDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHN 824

Query: 480 AIKFISKIVQREIIVRDNSRFHHFEDGKCSCGD 512
            +KFISKIV+REI VRD  +FHHF+DG+CSCGD
Sbjct: 825 TVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857

Length = 857

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

 Score =  211 bits (538), Expect = 9e-60
 Identities = 100/335 (29%), Positives = 178/335 (53%), Gaps = 15/335 (4%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  DL SWN ++ G A+ G ++EAL +  +M    ++PD +T   VL       D+ +G
Sbjct: 147 MPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARG 206

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           +E+H + +R G + +V + ++LI MY KC  V  +  +F  +P +D ISWN++I+G  +N
Sbjct: 207 REVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFEN 266

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G   EGL+ F  M    + P  ++ +S++ AC  L    LG+++HG +++ GF  ++ + 
Sbjct: 267 GECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVC 326

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           +SL+ MY   G+   A  +F +M+  D VSWTA+I G   +G    A+  +  ME+D V 
Sbjct: 327 NSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVS 386

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVA----DLLGRAGKLQ 296
           P+ +   +VL+AC+  G +D           +         Y  VA    ++  +   + 
Sbjct: 387 PDEITIASVLSACACLGDLDVG-----VKLHELAERKGLISYVVVANALIEMYSKCKCID 441

Query: 297 EAYEFISNMHAGPTENV--WLTLLSACRV-HKNVE 328
           +A E   N+   P ++V  W ++++  R+ ++  E
Sbjct: 442 KALEVFHNI---PEKDVISWTSIIAGLRLNNRCFE 473

Length = 857

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

 Score =  195 bits (497), Expect = 3e-54
 Identities = 112/387 (28%), Positives = 182/387 (47%), Gaps = 54/387 (13%)

Query: 1   MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKG 60
           MP  D +SWN +I G   NG   E L +   M  +++ PD  T++SV+       D   G
Sbjct: 248 MPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLG 307

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           +E+HGY ++ G   +V + +SLI MY       ++ ++F  +  KDA+SW ++I+G  +N
Sbjct: 308 REMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKN 367

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           GL D+ L+ +  M    + P  ++ +S++ ACA L  L +G +LH    R G    + +A
Sbjct: 368 GLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVA 427

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
           ++L++MY+KC  I  A  +F  +   D++SWT++I G  L+    +A+  F QM    +K
Sbjct: 428 NALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLLT-LK 486

Query: 241 PNSVAFVAVLTACSHAG--------------------------LID---------KAWSY 265
           PNSV  +A L+AC+  G                          L+D          AW+ 
Sbjct: 487 PNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQ 546

Query: 266 FNSMTKDYG-----IAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSA 320
           FNS  KD       +     H        G+     E +  +      P E  +++LL A
Sbjct: 547 FNSHEKDVVSWNILLTGYVAH--------GKGSMAVELFNRMVESGVNPDEVTFISLLCA 598

Query: 321 CR----VHKNVELAGKVAEKIFMIDPN 343
           C     V + +E    + EK + I PN
Sbjct: 599 CSRSGMVTQGLEYFHSMEEK-YSITPN 624

Length = 857

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

 Score =  141 bits (357), Expect = 6e-36
 Identities = 83/299 (27%), Positives = 150/299 (50%), Gaps = 14/299 (4%)

Query: 61  KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQN 120
           K ++ +    G + +  + + ++ M+ KC  + D+ RLF  +P ++  SW +II G V  
Sbjct: 143 KAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDA 202

Query: 121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA 180
           G + E    FR+M          +F  ++ A A L +   G+QLH C+++ G   + F++
Sbjct: 203 GNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVS 262

Query: 181 SSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
            +L+DMY+KCG+I  ARC+FD M     V+W +++ G ALHG + +A+ L+ +M   GV 
Sbjct: 263 CALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVS 322

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE 300
            +   F  ++   S   L++ A      + +  G         A+ DL  + G++++A  
Sbjct: 323 IDQFTFSIMIRIFSRLALLEHAKQAHAGLIRT-GFPLDIVANTALVDLYSKWGRMEDARN 381

Query: 301 FISNMHAGPTENV--WLTLLSACRVH----KNVELAGK-VAEKIFMIDPNNMGAYVILS 352
               M   P +N+  W  L++    H    K VE+  + +AE +    PN++    +LS
Sbjct: 382 VFDRM---PRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVA---PNHVTFLAVLS 434

Length = 697

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

 Score =  140 bits (354), Expect = 3e-35
 Identities = 103/443 (23%), Positives = 197/443 (44%), Gaps = 63/443 (14%)

Query: 10  NTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIR 69
           N+ +  L  +G  E+AL ++  M  + +  D     ++  +      V +G  +   A+ 
Sbjct: 55  NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALS 114

Query: 70  HGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKF 129
                 V +G+++++M+ +   +  +  +F  +P +D  SWN ++ G  + G FDE L  
Sbjct: 115 SHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCL 174

Query: 130 FRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK 189
           + +ML A ++P   +F  ++  C  +  L  G+++H  ++R GF+ ++ + ++L+ MY K
Sbjct: 175 YHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVK 234

Query: 190 CGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAV 249
           CG++  AR +FD+M   D +SW A+I G   +G   + + LF  M +  V P+ +   +V
Sbjct: 235 CGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSV 294

Query: 250 LTACS-----------HAGLIDKAW----SYFNSMTKDYGIAPSFEHYAAV------ADL 288
           ++AC            H  ++   +    S  NS+ + Y    S+     V       D 
Sbjct: 295 ISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDA 354

Query: 289 L------------GRAGKLQEAYEFISNMHAGPTENVWLTLLSAC----RVHKNVELAGK 332
           +            G   K  E Y  +   +  P E    ++LSAC     +   V+L  +
Sbjct: 355 VSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLH-E 413

Query: 333 VAEKIFMIDPNNMGAYVILSNT----YAAARRWKDAASLRVFMRNKGMKKTPACSWIEVK 388
           +AE+  +I      +YV+++N     Y+  +    A  L VF     + +    SW  + 
Sbjct: 414 LAERKGLI------SYVVVANALIEMYSKCKCIDKA--LEVF---HNIPEKDVISWTSI- 461

Query: 389 NKAYAFVAGDKSHPFYHRINEAL 411
                 +AG +     +R  EAL
Sbjct: 462 ------IAGLR---LNNRCFEAL 475

Length = 857

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

 Score =  112 bits (283), Expect = 6e-30
 Identities = 56/132 (42%), Positives = 79/132 (59%), Gaps = 23/132 (17%)

Query: 380 PACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQK 439
           P C W E        ++GD SHP       + +EL +R++ EG VP+TKE+ HDV+ E+ 
Sbjct: 1   PGCVWSEG----KKTLSGDGSHP------TSKEELFQRIKVEGVVPETKEIGHDVDAEEF 50

Query: 440 K------NLLYYHSERLAIVFGIICTPDGTTIRIIKNL-RVCGDCHTAIKFISKIVQREI 492
           +       LL  H+E+ A+ +G++      T RIIK L R+CGDCH   ++I+K   REI
Sbjct: 51  RDNGIKGKLLASHAEKQALAYGLL------TTRIIKVLKRMCGDCHEFFRYIAKYTGREI 104

Query: 493 IVRDNSRFHHFE 504
           IVRD SRFHHF+
Sbjct: 105 IVRDPSRFHHFK 116

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

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

 Score = 68.7 bits (168), Expect = 3e-12
 Identities = 37/140 (26%), Positives = 69/140 (49%), Gaps = 1/140 (0%)

Query: 121 GLFDEGLKFFRQMLI-AKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFI 179
           G   E L+ F  +           ++ +++ AC  L ++   K ++  +  +GF+ + ++
Sbjct: 101 GRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYM 160

Query: 180 ASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV 239
            + +L M+ KCG +  AR +FD+M   ++ SW  +I G    GN  +A +LF +M +DG 
Sbjct: 161 MNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGS 220

Query: 240 KPNSVAFVAVLTACSHAGLI 259
                 FV +L A +  G  
Sbjct: 221 DAEPRTFVVMLRASAGLGSA 240

Length = 697

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

 Score = 67.2 bits (164), Expect = 1e-11
 Identities = 74/323 (22%), Positives = 136/323 (42%), Gaps = 60/323 (18%)

Query: 71  GLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVK----DAISWNSIIAGCVQNGLFDEG 126
           G++ANV    +LI+  A+  +V  +   + ++  K    D + +N++I+ C Q+G  D  
Sbjct: 502 GVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRA 561

Query: 127 LKFFRQML--IAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL 184
                +M      I P H++  ++M ACA                               
Sbjct: 562 FDVLAEMKAETHPIDPDHITVGALMKACA------------------------------- 590

Query: 185 DMYAKCGNIRLARCIFDKMDLHDIVS----WTAVIMGNALHGNAHDAISLFEQMEKDGVK 240
                 G +  A+ ++  +  ++I      +T  +   +  G+   A+S+++ M+K GVK
Sbjct: 591 ----NAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVK 646

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA-- 298
           P+ V F A++    HAG +DKA+       K  GI      Y+++      A   ++A  
Sbjct: 647 PDEVFFSALVDVAGHAGDLDKAFEILQDARKQ-GIKLGTVSYSSLMGACSNAKNWKKALE 705

Query: 299 -YEFISNMHAGPTENVWLTLLSA-C---RVHKNVELAGKVAEKIFMIDPNNMGAYVILSN 353
            YE I ++   PT +    L++A C   ++ K +E+  ++  K   + P N   Y IL  
Sbjct: 706 LYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEM--KRLGLCP-NTITYSIL-- 760

Query: 354 TYAAARRWKDA-ASLRVFMRNKG 375
              A+ R  DA   L +  + K 
Sbjct: 761 -LVASERKDDADVGLDLLSQAKE 782

Length = 1060

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

 Score = 48.2 bits (116), Expect = 8e-08
 Identities = 14/50 (28%), Positives = 26/50 (52%)

Query: 105 KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH 154
            D +++N++I G  + G  +E LK F +M    IKP   ++S ++     
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 47.4 bits (114), Expect = 2e-07
 Identities = 14/49 (28%), Positives = 26/49 (53%)

Query: 207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSH 255
           D+V++  +I G    G   +A+ LF +M+K G+KPN   +  ++     
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 47.0 bits (113), Expect = 3e-07
 Identities = 16/44 (36%), Positives = 28/44 (63%)

Query: 5  DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVL 48
          D+V++NT+I G  + G  EEAL +  +M    +KP+ +T S ++
Sbjct: 2  DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILI 45

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

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

 Score = 51.8 bits (124), Expect = 7e-07
 Identities = 53/274 (19%), Positives = 108/274 (39%), Gaps = 21/274 (7%)

Query: 117 CVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDN 176
           C +     E  +F + +    +     +F+ +M  CA    +    ++   +   G   +
Sbjct: 416 CKKQRAVKEAFRFAKLIRNPTLS----TFNMLMSVCASSQDIDGALRVLRLVQEAGLKAD 471

Query: 177 MFIASSLLDMYAKCGNIRLARCIFDKMD-------LHDIVSWTAVIMGNALHGNAHDAIS 229
             + ++L+   AK G +     +F +M        +H   ++ A+I G A  G    A  
Sbjct: 472 CKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVH---TFGALIDGCARAGQVAKAFG 528

Query: 230 LFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKD-YGIAPSFEHYAAVADL 288
            +  M    VKP+ V F A+++AC  +G +D+A+     M  + + I P      A+   
Sbjct: 529 AYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKA 588

Query: 289 LGRAGKLQEAYEFISNMHA---GPTENVWLTLLSACRVHKNVELAGKVAEKIFMID--PN 343
              AG++  A E    +H      T  V+   +++C    + + A  + + +      P+
Sbjct: 589 CANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPD 648

Query: 344 NMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK 377
            +  +  L +    A     A  +    R +G+K
Sbjct: 649 EV-FFSALVDVAGHAGDLDKAFEILQDARKQGIK 681

Length = 1060

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

 Score = 39.4 bits (93), Expect = 9e-05
 Identities = 10/33 (30%), Positives = 21/33 (63%)

Query: 108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKP 140
           +++N++I G  + G  +E L+ F++M    I+P
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEP 33

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

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

 Score = 37.8 bits (89), Expect = 2e-04
 Identities = 9/27 (33%), Positives = 19/27 (70%)

Query: 108 ISWNSIIAGCVQNGLFDEGLKFFRQML 134
           +++NS+I+G  + G  +E L+ F++M 
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMK 27

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

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

 Score = 37.4 bits (88), Expect = 3e-04
 Identities = 10/31 (32%), Positives = 20/31 (64%)

Query: 209 VSWTAVIMGNALHGNAHDAISLFEQMEKDGV 239
           V++ ++I G    G   +A+ LF++M++ GV
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 37.4 bits (88), Expect = 4e-04
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 7  VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDS 41
          V++NT+I GL + G  EEAL + ++M    ++PD 
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPDV 35

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

>gnl|CDD|223533 COG0457, NrfG, FOG: TPR repeat [General function prediction only]

 Score = 41.4 bits (95), Expect = 7e-04
 Identities = 37/212 (17%), Positives = 70/212 (33%), Gaps = 9/212 (4%)

Query: 162 KQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDK-----MDLHDIVSWTAVIM 216
           + L   +      D   +   L     K G +  A  + +K     +  +   +   + +
Sbjct: 44  ELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGL 103

Query: 217 GNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA 276
                G   +A+ L E+       P+    +  L A    G  ++A   +    +     
Sbjct: 104 LLEALGKYEEALELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEKALELDPEL 163

Query: 277 PSF-EHYAAVADLLGRAGKLQEAYEFISNMHAGPTEN---VWLTLLSACRVHKNVELAGK 332
               E   A+  LL   G+ +EA E +        ++     L L          E A +
Sbjct: 164 NELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALE 223

Query: 333 VAEKIFMIDPNNMGAYVILSNTYAAARRWKDA 364
             EK   +DP+N  A   L+       R+++A
Sbjct: 224 YYEKALELDPDNAEALYNLALLLLELGRYEEA 255

Length = 291

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

 Score = 36.7 bits (86), Expect = 8e-04
 Identities = 10/26 (38%), Positives = 18/26 (69%)

Query: 7  VSWNTVIVGLARNGLYEEALNIVRQM 32
          V++N++I G  + G  EEAL + ++M
Sbjct: 1  VTYNSLISGYCKAGKLEEALELFKEM 26

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

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

 Score = 36.2 bits (85), Expect = 0.001
 Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)

Query: 241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS 278
           P+ V +  ++      G +++A   FN M K  GI P+
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEM-KKRGIKPN 37

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

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

 Score = 36.6 bits (86), Expect = 0.001
 Identities = 12/28 (42%), Positives = 21/28 (75%)

Query: 5  DLVSWNTVIVGLARNGLYEEALNIVRQM 32
          D+V++NT+I GL R G  +EA+ ++ +M
Sbjct: 6  DVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 34.6 bits (81), Expect = 0.004
 Identities = 8/28 (28%), Positives = 17/28 (60%)

Query: 106 DAISWNSIIAGCVQNGLFDEGLKFFRQM 133
           D +++N++I G  + G  DE ++   +M
Sbjct: 6   DVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	514
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PF14432	116	DYW_deaminase: DYW family of nucleic acid deaminas	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.94
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.94
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.88
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.87
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.86
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.85
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.84
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.82
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.82
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.82
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.82
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.81
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.77
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.76
PRK14574	822	hmsH outer membrane protein; Provisional	99.71
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.71
PRK14574	822	hmsH outer membrane protein; Provisional	99.7
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.66
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.64
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.6
KOG2076	895	consensus RNA polymerase III transcription factor	99.58
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.58
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.54
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.53
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.51
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.5
KOG2003	840	consensus TPR repeat-containing protein [General f	99.49
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.48
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.47
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.47
KOG1126	638	consensus DNA-binding cell division cycle control	99.46
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.44
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.43
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.43
KOG1126	638	consensus DNA-binding cell division cycle control	99.43
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.42
PF13041	50	PPR_2: PPR repeat family	99.42
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.41
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.4
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.4
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.39
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.39
PF13041	50	PPR_2: PPR repeat family	99.36
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.35
KOG2076	895	consensus RNA polymerase III transcription factor	99.33
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.33
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.32
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.3
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.3
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.28
KOG2003	840	consensus TPR repeat-containing protein [General f	99.28
PRK12370	553	invasion protein regulator; Provisional	99.23
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.22
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.22
PRK12370	553	invasion protein regulator; Provisional	99.21
KOG1129	478	consensus TPR repeat-containing protein [General f	99.19
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.14
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.12
PRK11189	296	lipoprotein NlpI; Provisional	99.07
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.06
PRK11189	296	lipoprotein NlpI; Provisional	99.03
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.95
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.94
KOG1129	478	consensus TPR repeat-containing protein [General f	98.92
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.91
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.87
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.85
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.82
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	98.82
KOG1125	579	consensus TPR repeat-containing protein [General f	98.78
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.76
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.75
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.75
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.75
PRK04841	903	transcriptional regulator MalT; Provisional	98.75
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.75
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.73
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.73
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	98.71
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.69
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.67
PF12854	34	PPR_1: PPR repeat	98.67
PF12854	34	PPR_1: PPR repeat	98.66
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.66
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.66
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	98.62
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.58
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.56
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.54
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.53
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.53
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.52
PRK04841	903	transcriptional regulator MalT; Provisional	98.52
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.51
PRK15359	144	type III secretion system chaperone protein SscB;	98.49
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.48
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.45
PLN02789	320	farnesyltranstransferase	98.45
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.44
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.4
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.39
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.37
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.37
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.34
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.34
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.33
KOG1125	579	consensus TPR repeat-containing protein [General f	98.32
PRK15359	144	type III secretion system chaperone protein SscB;	98.32
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.31
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.3
PLN02789	320	farnesyltranstransferase	98.29
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.28
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.27
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.25
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.24
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.23
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.22
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.18
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.16
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.14
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.13
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.13
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.1
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.09
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.09
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.08
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.08
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.06
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.05
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.04
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.03
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.98
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.89
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.87
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.85
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.85
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.83
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.82
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.81
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.73
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.72
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.69
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.68
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.67
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.62
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	97.6
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.53
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.53
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.51
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.5
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.46
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.46
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.4
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.39
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.39
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.36
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.34
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.34
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.33
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.32
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.31
PRK15331	165	chaperone protein SicA; Provisional	97.31
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.29
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.28
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.28
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.27
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.27
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.26
KOG0553	304	consensus TPR repeat-containing protein [General f	97.25
PF13371	73	TPR_9: Tetratricopeptide repeat	97.22
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.2
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.2
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.2
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.18
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.18
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.15
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.12
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.11
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	97.06
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.05
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.04
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.04
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	96.99
PF13431	34	TPR_17: Tetratricopeptide repeat	96.99
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	96.98
PF12688	120	TPR_5: Tetratrico peptide repeat	96.96
KOG0553	304	consensus TPR repeat-containing protein [General f	96.95
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.93
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.92
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	96.88
PF12688	120	TPR_5: Tetratrico peptide repeat	96.84
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	96.84
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.7
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.66
PRK10803	263	tol-pal system protein YbgF; Provisional	96.59
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.59
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.57
PF13428	44	TPR_14: Tetratricopeptide repeat	96.54
PRK10803	263	tol-pal system protein YbgF; Provisional	96.51
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.49
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.38
KOG3941	406	consensus Intermediate in Toll signal transduction	96.28
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.25
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	96.21
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.2
PF13371	73	TPR_9: Tetratricopeptide repeat	96.19
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.19
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.16
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.1
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.1
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	96.07
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.88
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	95.87
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.8
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.69
COG3898	531	Uncharacterized membrane-bound protein [Function u	95.68
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	95.53
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	95.49
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.48
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.41
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.22
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.21
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	94.98
PF03704	146	BTAD: Bacterial transcriptional activator domain;	94.92
COG3118	304	Thioredoxin domain-containing protein [Posttransla	94.86
KOG1585	308	consensus Protein required for fusion of vesicles	94.82
COG0457	291	NrfG FOG: TPR repeat [General function prediction	94.7
KOG3941	406	consensus Intermediate in Toll signal transduction	94.64
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.64
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	94.59
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.54
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	94.45
KOG1941	518	consensus Acetylcholine receptor-associated protei	94.42
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	94.38
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	94.26
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	94.19
KOG4555	175	consensus TPR repeat-containing protein [Function	94.17
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	94.02
smart00299	140	CLH Clathrin heavy chain repeat homology.	94.02
PRK11906	458	transcriptional regulator; Provisional	93.99
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.89
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	93.8
PF13512	142	TPR_18: Tetratricopeptide repeat	93.79
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	93.68
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	93.64
PRK09687	280	putative lyase; Provisional	93.44
PRK11906	458	transcriptional regulator; Provisional	93.44
COG4105	254	ComL DNA uptake lipoprotein [General function pred	93.29
PRK15331	165	chaperone protein SicA; Provisional	92.99
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.8
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	92.76
KOG1258	577	consensus mRNA processing protein [RNA processing	92.66
KOG2610	491	consensus Uncharacterized conserved protein [Funct	92.26
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	92.19
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	91.98
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	91.91
COG4105	254	ComL DNA uptake lipoprotein [General function pred	91.66
COG3118	304	Thioredoxin domain-containing protein [Posttransla	91.51
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	91.41
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	91.4
PF13512	142	TPR_18: Tetratricopeptide repeat	91.34
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	90.9
COG3629	280	DnrI DNA-binding transcriptional activator of the	90.89
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	90.88
KOG1585	308	consensus Protein required for fusion of vesicles	90.84
KOG4555	175	consensus TPR repeat-containing protein [Function	90.79
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	90.64
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	90.48
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	90.39
COG0457	291	NrfG FOG: TPR repeat [General function prediction	90.31
PRK11619	644	lytic murein transglycosylase; Provisional	90.06
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	89.87
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	89.72
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	89.59
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	89.33
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	89.27
PRK09687	280	putative lyase; Provisional	89.15
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	89.02
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	88.61
PRK12798	421	chemotaxis protein; Reviewed	88.31
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	88.25
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	88.15
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	88.09
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	87.93
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	87.91
PF13428	44	TPR_14: Tetratricopeptide repeat	87.87
PF13431	34	TPR_17: Tetratricopeptide repeat	87.63
KOG4570	418	consensus Uncharacterized conserved protein [Funct	87.4
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	87.27
KOG4234	271	consensus TPR repeat-containing protein [General f	87.15
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	87.1
KOG4279	1226	consensus Serine/threonine protein kinase [Signal	86.93
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	86.85
KOG4570	418	consensus Uncharacterized conserved protein [Funct	86.73
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	86.64
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	86.17
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	85.99
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	85.76
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	85.57
PRK13800	897	putative oxidoreductase/HEAT repeat-containing pro	85.43
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	84.23
COG3947	361	Response regulator containing CheY-like receiver a	83.97
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	83.87
KOG2610	491	consensus Uncharacterized conserved protein [Funct	83.54
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	83.45
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	83.43
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	82.35
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	82.34
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	82.12
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	81.78
PF09477	116	Type_III_YscG: Bacterial type II secretion system	81.56
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	81.36
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	81.29
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	81.23
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	81.06
PHA02875	413	ankyrin repeat protein; Provisional	80.81
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	80.67
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	80.14

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

Probab=100.00  E-value=1.3e-118  Score=950.46  Aligned_cols=514  Identities=39%  Similarity=0.739  Sum_probs=510.0

Q ss_pred             CCCCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHH
Q 040365            1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGS   80 (514)
Q Consensus         1 m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (514)
                      |+.||+++||++|.+|++.|++++|+++|++|.+.|+.||..||+.++.+|+..|..+.+.++|..+.+.|+.+|..++|
T Consensus       184 m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n  263 (697)
T PLN03081        184 MPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSC  263 (697)
T ss_pred             CCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHH
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH
Q 040365           81 SLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHL  160 (514)
Q Consensus        81 ~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~  160 (514)
                      +||++|+++|++++|.++|++|+++|+++||+||.+|++.|++++|+++|++|.+.|+.||..||++++.+|++.|++++
T Consensus       264 ~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~  343 (697)
T PLN03081        264 ALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEH  343 (697)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCC
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK  240 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  240 (514)
                      |.++|..|.+.|++||..++|+|+++|+|+|++++|.++|++|.++|+++||+||.+|+++|+.++|+++|++|.+.|+.
T Consensus       344 a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~  423 (697)
T PLN03081        344 AKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVA  423 (697)
T ss_pred             HHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 040365          241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSA  320 (514)
Q Consensus       241 p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~  320 (514)
                      ||.+||+.++.+|++.|++++|.++|+.|.+++|+.|+..+|++|+++|++.|++++|.+++++|+.+|+..+|++|+.+
T Consensus       424 Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a  503 (697)
T PLN03081        424 PNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTA  503 (697)
T ss_pred             CCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHH
Confidence            99999999999999999999999999999888899999999999999999999999999999999999999999999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccEEEECCEEEEEEeCCCC
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKS  400 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~  400 (514)
                      |+.+|+++.|..+++++.+++|++..+|+.|+++|++.|+|++|.++++.|+++|+++.||+||+++++.+|.|++||.+
T Consensus       504 ~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~~k~~g~s~i~~~~~~~~f~~~d~~  583 (697)
T PLN03081        504 CRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRL  583 (697)
T ss_pred             HHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCCccCCCeeEEEECCeEEEEccCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChHHHHHHHHHHHHHHHhCCcccCCcccccccchHhHhhhHhhhHHHHHHHHccccCCCCCeEEEEecccccccchhh
Q 040365          401 HPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA  480 (514)
Q Consensus       401 ~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~~~~~h~e~la~~~~~~~~~~~~~~~i~~nl~~c~d~h~~  480 (514)
                      ||+.+++++.++++..+|++.||+||+..+++++++++|+..+.+||||||++|||+++|+|+||||+||||+|+|||+|
T Consensus       584 h~~~~~i~~~l~~l~~~~~~~gy~~~~~~~~~~~~~~~~~~~~~~hsekla~a~~l~~~~~~~~i~i~knlr~c~dch~~  663 (697)
T PLN03081        584 HPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKV  663 (697)
T ss_pred             CccHHHHHHHHHHHHHHHHHcCCCCCcchhhccccHHHHHHHHHhccHHHHHHhhCccCCCCCeEEEecCCEECCCchhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHhhhcceeEEEecCCcccccCCcccCCCCCC
Q 040365          481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGDYW  514 (514)
Q Consensus       481 ~~~~s~~~~~~i~~rd~~~~h~f~~g~csc~~~w  514 (514)
                      +|+||++++|+|||||.+|||||+||+|||+|||
T Consensus       664 ~k~~s~~~~r~i~~rd~~rfh~f~~g~csc~d~w  697 (697)
T PLN03081        664 IKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW  697 (697)
T ss_pred             HHHHhhhcceEEEEecCCccccCCCCcccccccC
Confidence            9999999999999999999999999999999999

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=5.2e-113  Score=928.32  Aligned_cols=509  Identities=43%  Similarity=0.797  Sum_probs=501.9

Q ss_pred             CCCCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHH
Q 040365            1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGS   80 (514)
Q Consensus         1 m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (514)
                      |+.||+++||+||.+|++.|++++|+++|++|.+.|+.||..||++++.+|++.|+++.|.++|+.+.+.|+.|+..++|
T Consensus       349 m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n  428 (857)
T PLN03077        349 METKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVAN  428 (857)
T ss_pred             CCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHH
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH
Q 040365           81 SLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHL  160 (514)
Q Consensus        81 ~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~  160 (514)
                      +||++|+++|++++|.++|++|.++|+++||+||.+|+++|+.++|+++|++|.. +++||..||++++.+|++.|+++.
T Consensus       429 ~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~  507 (857)
T PLN03077        429 ALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMC  507 (857)
T ss_pred             HHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHH
Confidence            9999999999999999999999999999999999999999999999999999986 599999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCC
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK  240 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  240 (514)
                      ++++|..+++.|+.+|..++|+||++|+|+|++++|.++|+.+ .+|+++||+||.+|+++|+.++|+++|++|.+.|+.
T Consensus       508 ~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~  586 (857)
T PLN03077        508 GKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVN  586 (857)
T ss_pred             hHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhc-CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC
Confidence            9999999999999999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 040365          241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSA  320 (514)
Q Consensus       241 p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~  320 (514)
                      ||.+||+.+|.+|++.|++++|.++|+.|.+++|+.|+..+|++|+++|++.|++++|.+++++|+.+||..+|++|+.+
T Consensus       587 Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~~~pd~~~~~aLl~a  666 (857)
T PLN03077        587 PDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNA  666 (857)
T ss_pred             CCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCCCCCCHHHHHHHHHH
Confidence            99999999999999999999999999999878899999999999999999999999999999999999999999999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccEEEECCEEEEEEeCCCC
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKS  400 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~  400 (514)
                      |..+|+.+.|+.+.+++++++|+++..|..|+++|+..|+|++|.++++.|+++|++|+||+|||++++.+|.|++||.+
T Consensus       667 c~~~~~~e~~e~~a~~l~~l~p~~~~~y~ll~n~ya~~g~~~~a~~vr~~M~~~g~~k~~g~s~ie~~~~~~~f~~~d~~  746 (857)
T PLN03077        667 CRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDES  746 (857)
T ss_pred             HHHcCChHHHHHHHHHHHhhCCCCcchHHHHHHHHHHCCChHHHHHHHHHHHHcCCCCCCCccEEEECCEEEEEecCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCChHHHHHHHHHHHHHHHhCCcccCCcccccccchHhHhhhHhhhHHHHHHHHccccCCCCCeEEEEecccccccchhh
Q 040365          401 HPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA  480 (514)
Q Consensus       401 ~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~~~~~h~e~la~~~~~~~~~~~~~~~i~~nl~~c~d~h~~  480 (514)
                      ||+.++||..|++|..+|++.||+||+..++ ++++++|+..+++||||||++|||++||+|+||||+||||||+|||++
T Consensus       747 h~~~~~i~~~l~~l~~~~~~~g~~~~~~~~~-~~~~~~k~~~~~~hse~la~a~~l~~~~~~~~i~i~knlr~c~dch~~  825 (857)
T PLN03077        747 HPQIKEINTVLEGFYEKMKASGLAGSESSSM-DEIEVSKDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNT  825 (857)
T ss_pred             CcchHHHHHHHHHHHHHHHhCCcCCCcchhc-cccHHHHHHHHHhccHHHHHHHhhhcCCCCCeEEEeCCCEeCccHHHH
Confidence            9999999999999999999999999999888 557889999999999999999999999999999999999999999999


Q ss_pred             hHHHhhhcceeEEEecCCcccccCCcccCCCC
Q 040365          481 IKFISKIVQREIIVRDNSRFHHFEDGKCSCGD  512 (514)
Q Consensus       481 ~~~~s~~~~~~i~~rd~~~~h~f~~g~csc~~  512 (514)
                      +||||++++|||||||.+|||||+||+|||+|
T Consensus       826 ~k~~s~~~~r~i~~rd~~rfh~f~~g~csc~d  857 (857)
T PLN03077        826 VKFISKIVRREISVRDTEQFHHFKDGECSCGD  857 (857)
T ss_pred             HHHHHHHhCeEEEEecCCcceeCCCCcccCCC
Confidence            99999999999999999999999999999998

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.2e-67  Score=573.43  Aligned_cols=481  Identities=24%  Similarity=0.410  Sum_probs=432.3

Q ss_pred             CCCCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHH
Q 040365            1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGS   80 (514)
Q Consensus         1 m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (514)
                      |++||+++||+||.+|++.|++++|+++|++|...|+.||.+||++++++|+..+++..+.++|..+++.|+.||..++|
T Consensus       147 m~~~d~~~~n~li~~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n  226 (857)
T PLN03077        147 MPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVN  226 (857)
T ss_pred             CCCCCeeEHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHh
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH
Q 040365           81 SLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHL  160 (514)
Q Consensus        81 ~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~  160 (514)
                      +||++|+++|++++|.++|++|++||+++||+||.+|++.|++++|+++|++|...|+.||..||++++.+|++.|+++.
T Consensus       227 ~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~  306 (857)
T PLN03077        227 ALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERL  306 (857)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCC
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK  240 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  240 (514)
                      |.++|..+.+.|+.||..+||+|+++|+++|++++|.++|++|..||+++||+||.+|++.|++++|+++|++|.+.|+.
T Consensus       307 a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~  386 (857)
T PLN03077        307 GREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVS  386 (857)
T ss_pred             HHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 040365          241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSA  320 (514)
Q Consensus       241 p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~  320 (514)
                      ||..||+.++.+|++.|++++|.++++.|.+ .|+.|+..+|++|+++|+++|++++|.++|++|+ +||..+|++++.+
T Consensus       387 Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~-~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~-~~d~vs~~~mi~~  464 (857)
T PLN03077        387 PDEITIASVLSACACLGDLDVGVKLHELAER-KGLISYVVVANALIEMYSKCKCIDKALEVFHNIP-EKDVISWTSIIAG  464 (857)
T ss_pred             CCceeHHHHHHHHhccchHHHHHHHHHHHHH-hCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCC-CCCeeeHHHHHHH
Confidence            9999999999999999999999999999965 4999999999999999999999999999999998 6799999999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccEEEECCE----------
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNK----------  390 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~----------  390 (514)
                      |.+.|+.++|..+|++|.+.-++|..+|..++.+|++.|..+.+.+++..|.+.|+.++.......++..          
T Consensus       465 ~~~~g~~~eA~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~  544 (857)
T PLN03077        465 LRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAW  544 (857)
T ss_pred             HHHCCCHHHHHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHH
Confidence            9999999999999999987656677888888877777777777777777777777665442221111000          


Q ss_pred             ------------EEEEEeCCCCCCChHHHHHHHHHHHHHHHhCCcccCCcccccccchHhHhhhH---hhhHHHHHHHHc
Q 040365          391 ------------AYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLL---YYHSERLAIVFG  455 (514)
Q Consensus       391 ------------~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~~~---~~h~e~la~~~~  455 (514)
                                  ...++.|+..|++.+++.    +++++|++.|+.||..++...+..+.+.+.+   ....+.+.-.+|
T Consensus       545 ~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~----~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~g  620 (857)
T PLN03077        545 NQFNSHEKDVVSWNILLTGYVAHGKGSMAV----ELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYS  620 (857)
T ss_pred             HHHHhcCCChhhHHHHHHHHHHcCCHHHHH----HHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhC
Confidence                        013456666778777766    8999999999999998887777666665554   223444544677


Q ss_pred             cccCCCCCeEEEEecccccccchhhhHHHhhhc
Q 040365          456 IICTPDGTTIRIIKNLRVCGDCHTAIKFISKIV  488 (514)
Q Consensus       456 ~~~~~~~~~~~i~~nl~~c~d~h~~~~~~s~~~  488 (514)
                      +.+...+.. ++++-+..+|+..+|.++|.+|+
T Consensus       621 i~P~~~~y~-~lv~~l~r~G~~~eA~~~~~~m~  652 (857)
T PLN03077        621 ITPNLKHYA-CVVDLLGRAGKLTEAYNFINKMP  652 (857)
T ss_pred             CCCchHHHH-HHHHHHHhCCCHHHHHHHHHHCC
Confidence            766654444 78999999999999999999986

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

Probab=100.00  E-value=3.7e-64  Score=533.98  Aligned_cols=489  Identities=19%  Similarity=0.306  Sum_probs=428.9

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCC-CCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVN-LKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSL   82 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (514)
                      ++.++|+++|.+|.+.|++++|+++|+.|...+ +.||..||+.++.+|++.++++.|.++|..|.+.|+.||..++|+|
T Consensus        85 ~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~L  164 (697)
T PLN03081         85 KSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRV  164 (697)
T ss_pred             CCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHH
Confidence            467799999999999999999999999998764 7899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHH
Q 040365           83 INMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGK  162 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~  162 (514)
                      +++|+++|++++|.++|++|++||+++||+||.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|..+.+.
T Consensus       165 i~~y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~  244 (697)
T PLN03081        165 LLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQ  244 (697)
T ss_pred             HHHHhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC
Q 040365          163 QLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN  242 (514)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~  242 (514)
                      ++|..+.+.|+.+|..++|+|+++|+++|++++|.++|++|.++|+++||+||.+|++.|+.++|+++|++|.+.|+.||
T Consensus       245 ~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd  324 (697)
T PLN03081        245 QLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSID  324 (697)
T ss_pred             HHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 040365          243 SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACR  322 (514)
Q Consensus       243 ~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~  322 (514)
                      ..||+.++.+|++.|++++|.+++..|.+. |+.|+..+|++|+++|+++|++++|.++|++|. +||..+|++|+.+|.
T Consensus       325 ~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~-g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~-~~d~~t~n~lI~~y~  402 (697)
T PLN03081        325 QFTFSIMIRIFSRLALLEHAKQAHAGLIRT-GFPLDIVANTALVDLYSKWGRMEDARNVFDRMP-RKNLISWNALIAGYG  402 (697)
T ss_pred             HHHHHHHHHHHHhccchHHHHHHHHHHHHh-CCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC-CCCeeeHHHHHHHHH
Confidence            999999999999999999999999999665 999999999999999999999999999999997 689999999999999


Q ss_pred             hcCCHHHHHHHHHHHHhcC-CCCcchHHHHHHHHHHccChhHHHHHHHHHHh-CCCccCCcccEEEECCEEEEEEeCCCC
Q 040365          323 VHKNVELAGKVAEKIFMID-PNNMGAYVILSNTYAAARRWKDAASLRVFMRN-KGMKKTPACSWIEVKNKAYAFVAGDKS  400 (514)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~g~~~~~~~s~~~~~~~~~~~~~~~~~  400 (514)
                      ++|+.++|.++|++|.+.+ .+|..+|+.++.+|++.|++++|.++|+.|.+ .|+.|+...+...        +.+...
T Consensus       403 ~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~l--------i~~l~r  474 (697)
T PLN03081        403 NHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACM--------IELLGR  474 (697)
T ss_pred             HcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhH--------HHHHHh
Confidence            9999999999999999876 55789999999999999999999999999986 5998877554432        334445


Q ss_pred             CCChHHHHHHHHHHHHHHHhCCcccCCcccccccchHhHhhhHhhhHHHHHHHHccccCCCCCeEEEEecccccccchhh
Q 040365          401 HPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICTPDGTTIRIIKNLRVCGDCHTA  480 (514)
Q Consensus       401 ~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~~~~~h~e~la~~~~~~~~~~~~~~~i~~nl~~c~d~h~~  480 (514)
                      .+..++++    +++   ++.++.||...+...+..+.+.+.+..-.+.....+++.+...+..+.+++-+..+|+..+|
T Consensus       475 ~G~~~eA~----~~~---~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A  547 (697)
T PLN03081        475 EGLLDEAY----AMI---RRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEA  547 (697)
T ss_pred             cCCHHHHH----HHH---HHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHH
Confidence            56666665    333   45688898765444444443333321111111122455444445555667778899999999


Q ss_pred             hHHHhhhcceeEEE-------ecCCcccccCCcccC
Q 040365          481 IKFISKIVQREIIV-------RDNSRFHHFEDGKCS  509 (514)
Q Consensus       481 ~~~~s~~~~~~i~~-------rd~~~~h~f~~g~cs  509 (514)
                      .+++..|..+.+-.       .-.+..|.|-.|..+
T Consensus       548 ~~v~~~m~~~g~~k~~g~s~i~~~~~~~~f~~~d~~  583 (697)
T PLN03081        548 AKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRL  583 (697)
T ss_pred             HHHHHHHHHcCCccCCCeeEEEECCeEEEEccCCCC
Confidence            99999999886532       223456777666443

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.2e-60  Score=510.65  Aligned_cols=475  Identities=17%  Similarity=0.249  Sum_probs=399.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHH
Q 040365            8 SWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYA   87 (514)
Q Consensus         8 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~   87 (514)
                      .++.++.+|.+.|..++|+.+|+.|..    ||..||+.++.+|++.|+++.|.++|+.|.+.|+.||..+|++||++|+
T Consensus       408 ~~~~li~~~~~~g~~~eAl~lf~~M~~----pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~  483 (1060)
T PLN03218        408 YHAKFFKACKKQRAVKEAFRFAKLIRN----PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCA  483 (1060)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHcCC----CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            344555556666777777777666653    8999999999999999999999999999999999999999999999999


Q ss_pred             HCCCHHHHHHHHccCC----CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHH
Q 040365           88 KCARVEDSHRLFCLLP----VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQ  163 (514)
Q Consensus        88 ~~g~~~~A~~~f~~~~----~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~  163 (514)
                      ++|++++|.++|++|.    .||.++||+||.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|++++|.+
T Consensus       484 k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~  563 (1060)
T PLN03218        484 KSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFD  563 (1060)
T ss_pred             hCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            9999999999999998    589999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH--cCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          164 LHGCIIR--NGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD----LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       164 ~~~~~~~--~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~----~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      +|++|.+  .|+.||..+|++||++|+++|++++|.++|+.|.    .|+..+||++|.+|++.|++++|+++|++|.+.
T Consensus       564 lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~  643 (1060)
T PLN03218        564 VLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKK  643 (1060)
T ss_pred             HHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc
Confidence            9999986  6789999999999999999999999999999997    557799999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC---CCCCHHHH
Q 040365          238 GVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH---AGPTENVW  314 (514)
Q Consensus       238 g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~p~~~~~  314 (514)
                      |+.||..||+.++.+|++.|++++|.++|+.|.+ .|+.|+..+|++||++|+++|++++|.++|++|.   ..||..+|
T Consensus       644 Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k-~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~Pdvvty  722 (1060)
T PLN03218        644 GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARK-QGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTM  722 (1060)
T ss_pred             CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHH
Confidence            9999999999999999999999999999999965 4999999999999999999999999999999984   57999999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcC-CCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccEEEEC-----
Q 040365          315 LTLLSACRVHKNVELAGKVAEKIFMID-PNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVK-----  388 (514)
Q Consensus       315 ~~ll~~~~~~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~-----  388 (514)
                      ++|+.+|++.|++++|.++|++|.+.+ .+|..+|..|+.+|++.|++++|.++++.|.+.|+.|+..++...++     
T Consensus       723 N~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~  802 (1060)
T PLN03218        723 NALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRR  802 (1060)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999998876 56789999999999999999999999999999999998755443221     


Q ss_pred             --------CEEEEEEeCCCCCCChH-HHHHHHHHHHHHHHhCCcccCCcccccccchHhHhhhHhhhHHHHHHHHccccC
Q 040365          389 --------NKAYAFVAGDKSHPFYH-RINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNLLYYHSERLAIVFGIICT  459 (514)
Q Consensus       389 --------~~~~~~~~~~~~~~~~~-~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~~~~~h~e~la~~~~~~~~  459 (514)
                              ..+..|-.+   ++... .-....-.++++|.+.|+.||..++...+....+.+.. ...+.+--.+++.+.
T Consensus       803 y~ka~~l~~~v~~f~~g---~~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~~vL~cl~~~~~~-~~~~~m~~~m~~~~~  878 (1060)
T PLN03218        803 FEKACALGEPVVSFDSG---RPQIENKWTSWALMVYRETISAGTLPTMEVLSQVLGCLQLPHDA-TLRNRLIENLGISAD  878 (1060)
T ss_pred             HHHHhhhhhhhhhhhcc---ccccccchHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhcccccH-HHHHHHHHHhccCCC
Confidence                    011112111   11110 11123348999999999999987665544322222221 122344445666666


Q ss_pred             CCCCeE--EEEecccccccchhhhHHHhhhcceeEE
Q 040365          460 PDGTTI--RIIKNLRVCGDCHTAIKFISKIVQREII  493 (514)
Q Consensus       460 ~~~~~~--~i~~nl~~c~d~h~~~~~~s~~~~~~i~  493 (514)
                      +++...  .+++.+  |..-..|..++..|..+.|+
T Consensus       879 ~~~~~~y~~Li~g~--~~~~~~A~~l~~em~~~Gi~  912 (1060)
T PLN03218        879 SQKQSNLSTLVDGF--GEYDPRAFSLLEEAASLGVV  912 (1060)
T ss_pred             CcchhhhHHHHHhh--ccChHHHHHHHHHHHHcCCC
Confidence            655432  245543  11125799999888877554

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.6e-58  Score=494.46  Aligned_cols=418  Identities=18%  Similarity=0.238  Sum_probs=377.4

Q ss_pred             CCCCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHH
Q 040365            1 MPVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGS   80 (514)
Q Consensus         1 m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (514)
                      |+.||+.+||.+|.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|+++.|.++|++|.+.|+.||..+|+
T Consensus       432 M~~pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTyn  511 (1060)
T PLN03218        432 IRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFG  511 (1060)
T ss_pred             cCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            57799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHCCCHHHHHHHHccCC----CCChhHHHHHHHHHHHCCChhHHHHHHHHHHH--CCCCCCHHHHHHHHHHHhc
Q 040365           81 SLINMYAKCARVEDSHRLFCLLP----VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLI--AKIKPRHVSFSSIMPACAH  154 (514)
Q Consensus        81 ~li~~~~~~g~~~~A~~~f~~~~----~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~--~g~~p~~~t~~~ll~~~~~  154 (514)
                      +||++|++.|++++|.++|+.|.    .||.++||+||.+|++.|++++|.++|.+|..  .|+.||..||++++.+|++
T Consensus       512 aLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k  591 (1060)
T PLN03218        512 ALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACAN  591 (1060)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHH
Confidence            99999999999999999999996    58999999999999999999999999999986  6799999999999999999


Q ss_pred             cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCChHHHHHH
Q 040365          155 LTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD----LHDIVSWTAVIMGNALHGNAHDAISL  230 (514)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~----~~d~~~~~~li~~~~~~g~~~~A~~l  230 (514)
                      .|++++|.++|+.|.+.|+.|+..+||++|.+|++.|++++|.++|++|.    .||..+|+++|.+|++.|+.++|.++
T Consensus       592 ~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l  671 (1060)
T PLN03218        592 AGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEI  671 (1060)
T ss_pred             CCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999997    67999999999999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC---C
Q 040365          231 FEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH---A  307 (514)
Q Consensus       231 ~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~  307 (514)
                      |++|.+.|+.||..+|+.++.+|++.|++++|.++|+.|.+ .|+.|+..+|++||.+|++.|++++|.++|++|.   .
T Consensus       672 ~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~-~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi  750 (1060)
T PLN03218        672 LQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKS-IKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGL  750 (1060)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            99999999999999999999999999999999999999955 5999999999999999999999999999999985   5


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC-CCCcchHHHHHHHHH----Hcc-------------------ChhH
Q 040365          308 GPTENVWLTLLSACRVHKNVELAGKVAEKIFMID-PNNMGAYVILSNTYA----AAR-------------------RWKD  363 (514)
Q Consensus       308 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~----~~g-------------------~~~~  363 (514)
                      .||..+|++|+.+|.+.|+++.|.+++++|.+.+ .+|..+|+.|+.+|.    +++                   ..++
T Consensus       751 ~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~  830 (1060)
T PLN03218        751 CPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSW  830 (1060)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHH
Confidence            6999999999999999999999999999999877 557789999887643    222                   2367


Q ss_pred             HHHHHHHHHhCCCccCCcccEEEECCEEEEEEeCCCCCCChHHHHHHHHHHHHHHHhCCcccCCcccc
Q 040365          364 AASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVL  431 (514)
Q Consensus       364 a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~  431 (514)
                      |..+|++|.+.|+.|+..+....+...            ...+.......+++.|...|..|+..+..
T Consensus       831 Al~lf~eM~~~Gi~Pd~~T~~~vL~cl------------~~~~~~~~~~~m~~~m~~~~~~~~~~~y~  886 (1060)
T PLN03218        831 ALMVYRETISAGTLPTMEVLSQVLGCL------------QLPHDATLRNRLIENLGISADSQKQSNLS  886 (1060)
T ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHh------------cccccHHHHHHHHHHhccCCCCcchhhhH
Confidence            999999999999999876544333111            00111223345666666666666654433

>PF14432 DYW_deaminase: DYW family of nucleic acid deaminases

Probab=100.00  E-value=9.1e-35  Score=230.06  Aligned_cols=106  Identities=70%  Similarity=1.204  Sum_probs=98.2

Q ss_pred             cccEEEECCEEEEEEeCCCCCCChHHHHHHHHHHHHHHHhCCcccCCcccccccchHhH--------hhhHhhhHHHHHH
Q 040365          381 ACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQK--------KNLLYYHSERLAI  452 (514)
Q Consensus       381 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~--------~~~~~~h~e~la~  452 (514)
                      |+||+++    |.|++||.+||+.        ++..+|...||.|++..+.++++++++        +..+.+||||||+
T Consensus         2 ~~~w~~~----h~F~sgd~shp~~--------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~d~~~~~~~~~~HSEKlAi   69 (116)
T PF14432_consen    2 GCSWIEV----HSFVSGDRSHPQS--------ELINKMKEEGYVPDTKEVGHDVDEEEKHDYDEEEKEESLCYHSEKLAI   69 (116)
T ss_pred             CCCccce----EEEEeCCCcCccH--------HHHHHHHHcCCcchhhhhCCCchhhhhhhcccccchhhhhccHHHHHH
Confidence            6899987    9999999999988        566788889999999999998887665        6689999999999


Q ss_pred             HHccccCCCCCeEEEEecc-cccccchhhhHHHhhhcceeEEEecCCcccccC
Q 040365          453 VFGIICTPDGTTIRIIKNL-RVCGDCHTAIKFISKIVQREIIVRDNSRFHHFE  504 (514)
Q Consensus       453 ~~~~~~~~~~~~~~i~~nl-~~c~d~h~~~~~~s~~~~~~i~~rd~~~~h~f~  504 (514)
                      ||||+++      +|+||+ |||+|||+|+|+||++++|+|+|||++|||||+
T Consensus        70 afgli~~------~vvkn~~RvC~DCH~~~K~iS~~~~ReIiVRD~~rfHhFk  116 (116)
T PF14432_consen   70 AFGLINT------RVVKNLKRVCGDCHSFIKFISKITGREIIVRDSNRFHHFK  116 (116)
T ss_pred             Hhcccce------eEEecCCccchHHHHHHHHHHHHHCeEEEEeCCCeeeeCC
Confidence            9999998      999999 999999999999999999999999999999997

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

Probab=99.94  E-value=4.5e-23  Score=227.73  Aligned_cols=364  Identities=12%  Similarity=0.035  Sum_probs=283.6

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLI   83 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (514)
                      .+...+..+...+...|++++|...|+.+...+ +.+..++..+...+...|+.++|...+..+.+.+ +.+...+..++
T Consensus       497 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~  574 (899)
T TIGR02917       497 DFFPAAANLARIDIQEGNPDDAIQRFEKVLTID-PKNLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALA  574 (899)
T ss_pred             CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHH
Confidence            355677788888888899999999988887754 4456677888888888888888888888887765 56667778888


Q ss_pred             HHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH
Q 040365           84 NMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHL  160 (514)
Q Consensus        84 ~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~  160 (514)
                      ..|.+.|++++|..+++.+.   ..+..+|..+...|.+.|++++|+..|+++.+.. +.+...+..+..++...|++++
T Consensus       575 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  653 (899)
T TIGR02917       575 QYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAK  653 (899)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHH
Confidence            88888888888888888775   3466788888888888888888888888887653 3456667778888888888888


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      |..++..+.+.. +.+...+..++..+.+.|++++|.++++.+.   ..+...|..+...+...|++++|++.|+++...
T Consensus       654 A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  732 (899)
T TIGR02917       654 AITSLKRALELK-PDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKR  732 (899)
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh
Confidence            888888887764 5567788888888888888888888888875   335567777888888888888888888888775


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHH
Q 040365          238 GVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWL  315 (514)
Q Consensus       238 g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~  315 (514)
                        .|+..++..+..++.+.|++++|.+.++.+.+.  .+.+...+..+...|.+.|++++|.+.|+++.  .+++..+++
T Consensus       733 --~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~  808 (899)
T TIGR02917       733 --APSSQNAIKLHRALLASGNTAEAVKTLEAWLKT--HPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLN  808 (899)
T ss_pred             --CCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHH
Confidence              355566777788888888888888888877653  23367777888888888888888888888763  234667777


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCC
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  376 (514)
                      .+...+...|+ ++|+..++++.+..|+++..+..++.+|...|++++|.+.++++.+.+.
T Consensus       809 ~l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~  868 (899)
T TIGR02917       809 NLAWLYLELKD-PRALEYAEKALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAP  868 (899)
T ss_pred             HHHHHHHhcCc-HHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            88888888887 6788888888887787777777788888888888888888888776653

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=99.94  E-value=6.8e-23  Score=226.28  Aligned_cols=362  Identities=11%  Similarity=-0.001  Sum_probs=321.0

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLI   83 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (514)
                      ++..+|+.+...|...|++++|...|+++.+.. +.+...+..+...+...|++++|.+.++.+++.+ +.+..++..+.
T Consensus       463 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~  540 (899)
T TIGR02917       463 DNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGNPDDAIQRFEKVLTID-PKNLRAILALA  540 (899)
T ss_pred             CCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHH
Confidence            467789999999999999999999999998754 3455677788888999999999999999999876 66788999999


Q ss_pred             HHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH
Q 040365           84 NMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHL  160 (514)
Q Consensus        84 ~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~  160 (514)
                      ..|.+.|+.++|...|+++.   ..+...+..++..|.+.|++++|+.+++++... .+.+..+|..+..++...|++++
T Consensus       541 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~  619 (899)
T TIGR02917       541 GLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADA-APDSPEAWLMLGRAQLAAGDLNK  619 (899)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHH
Confidence            99999999999999999874   345677889999999999999999999999875 35677889999999999999999


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      |...+..+.+.. +.+...+..+...|.+.|++++|...|+++.   +.+..+|..++..+...|++++|..+++.+...
T Consensus       620 A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  698 (899)
T TIGR02917       620 AVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQ  698 (899)
T ss_pred             HHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            999999998875 5567788899999999999999999999875   446789999999999999999999999999887


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHH
Q 040365          238 GVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWL  315 (514)
Q Consensus       238 g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~  315 (514)
                      + +++...+..+...+...|++++|...|+.+...   .|+...+..+..++.+.|++++|.+.++++.  .+.+..++.
T Consensus       699 ~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~  774 (899)
T TIGR02917       699 H-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKR---APSSQNAIKLHRALLASGNTAEAVKTLEAWLKTHPNDAVLRT  774 (899)
T ss_pred             C-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh---CCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence            4 456677888889999999999999999998653   5666788889999999999999999998873  335678899


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .+...|...|+.++|...++++.+..|+++.++..++.+|...|+ .+|...+++..+.
T Consensus       775 ~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~  832 (899)
T TIGR02917       775 ALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKALKL  832 (899)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhh
Confidence            999999999999999999999999999999999999999999999 8899999988765

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=99.88  E-value=9.9e-20  Score=181.49  Aligned_cols=290  Identities=13%  Similarity=0.121  Sum_probs=191.7

Q ss_pred             HHHCCCHHHHHHHHccCCC--C-ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC---HHHHHHHHHHHhccCChH
Q 040365           86 YAKCARVEDSHRLFCLLPV--K-DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR---HVSFSSIMPACAHLTTLH  159 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~--~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~---~~t~~~ll~~~~~~~~~~  159 (514)
                      +...|++++|...|.++.+  | +..+|..+...+.+.|++++|+.+++.+...+..++   ..++..+...+.+.|+++
T Consensus        45 ~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~  124 (389)
T PRK11788         45 FLLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLD  124 (389)
T ss_pred             HHhcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHH
Confidence            3445555555555555542  1 233455555555566666666666655554321111   123445555555666666


Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCC--------hhHHHHHHHHHHhCCChHHHHHHH
Q 040365          160 LGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHD--------IVSWTAVIMGNALHGNAHDAISLF  231 (514)
Q Consensus       160 ~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d--------~~~~~~li~~~~~~g~~~~A~~l~  231 (514)
                      .|..++..+.+.. +.+..+++.++..|.+.|++++|.+.|+.+...+        ...|..+...+.+.|++++|...|
T Consensus       125 ~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~  203 (389)
T PRK11788        125 RAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALL  203 (389)
T ss_pred             HHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            6666666655442 3445556666666666666666666666654211        113455666677788888888888


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC--HhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC
Q 040365          232 EQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS--FEHYAAVADLLGRAGKLQEAYEFISNMH-AG  308 (514)
Q Consensus       232 ~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~  308 (514)
                      +++.+.. +.+...+..+...+.+.|++++|.++|+.+.+.   .|+  ...+..++.+|.+.|++++|.+.++++. ..
T Consensus       204 ~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~---~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~  279 (389)
T PRK11788        204 KKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQ---DPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEY  279 (389)
T ss_pred             HHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH---ChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            8877642 223456667777888888888888888887643   333  4567778888888888888888888764 35


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH---ccChhHHHHHHHHHHhCCCccCCc
Q 040365          309 PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA---ARRWKDAASLRVFMRNKGMKKTPA  381 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~---~g~~~~a~~~~~~m~~~g~~~~~~  381 (514)
                      |+...+..+...+...|++++|..+++++++..|++. .+..++..+..   .|+.+++..++++|.+++++++|.
T Consensus       280 p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~-~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        280 PGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLR-GFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             CCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHH-HHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCC
Confidence            7766778888889999999999999999998888765 56666666554   558999999999999999999985

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

Probab=99.87  E-value=5e-18  Score=178.46  Aligned_cols=357  Identities=14%  Similarity=0.025  Sum_probs=283.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHH
Q 040365            9 WNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAK   88 (514)
Q Consensus         9 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~   88 (514)
                      +......|.+.|++++|+..|++.+..  .|+...|..+..++...|++++|...+..+++.. +.+..++..+..+|..
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~a~a~~~  206 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-PDYSKALNRRANAYDG  206 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence            445667788899999999999998864  6888889999999999999999999999999875 5567788889999999


Q ss_pred             CCCHHHHHHHHccCC---------------------------------CCChhHHHHHHHH-------------------
Q 040365           89 CARVEDSHRLFCLLP---------------------------------VKDAISWNSIIAG-------------------  116 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~---------------------------------~~d~~~~~~li~~-------------------  116 (514)
                      .|++++|..-|....                                 .++..++..+...                   
T Consensus       207 lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  286 (615)
T TIGR00990       207 LGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNEL  286 (615)
T ss_pred             cCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhccccc
Confidence            999999976553221                                 0011111111000                   


Q ss_pred             -------H----------HHCCChhHHHHHHHHHHHCC-CCC-CHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcH
Q 040365          117 -------C----------VQNGLFDEGLKFFRQMLIAK-IKP-RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNM  177 (514)
Q Consensus       117 -------~----------~~~g~~~~A~~l~~~m~~~g-~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~  177 (514)
                             +          ...+++++|++.|++..+.+ ..| +...+..+...+...|++++|...++..++.. +.+.
T Consensus       287 ~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~-P~~~  365 (615)
T TIGR00990       287 DEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD-PRVT  365 (615)
T ss_pred             ccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcH
Confidence                   0          11257889999999988764 234 34566777777888999999999999998864 4446


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHH
Q 040365          178 FIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAVLTAC  253 (514)
Q Consensus       178 ~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~  253 (514)
                      ..+..+...|...|++++|...|++..   ..+...|..+...+...|++++|+..|++....  .|+ ...+..+...+
T Consensus       366 ~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P~~~~~~~~la~~~  443 (615)
T TIGR00990       366 QSYIKRASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DPDFIFSHIQLGVTQ  443 (615)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CccCHHHHHHHHHHH
Confidence            678888999999999999999999874   346788999999999999999999999999885  454 56677788889


Q ss_pred             HccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCH--------HHHHHHHHHHHh
Q 040365          254 SHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPTE--------NVWLTLLSACRV  323 (514)
Q Consensus       254 ~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~--------~~~~~ll~~~~~  323 (514)
                      .+.|++++|...|+...+.   .| +...|..+...+...|++++|.+.|++.. ..|+.        ..++..+..+..
T Consensus       444 ~~~g~~~eA~~~~~~al~~---~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~  520 (615)
T TIGR00990       444 YKEGSIASSMATFRRCKKN---FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQW  520 (615)
T ss_pred             HHCCCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHH
Confidence            9999999999999998653   45 57888999999999999999999998853 22321        112222333445


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .|++++|..+++++++++|++...+..++.+|...|++++|.+.+++..+.
T Consensus       521 ~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       521 KQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             hhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            799999999999999999999989999999999999999999999988654

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.86  E-value=9.5e-19  Score=174.41  Aligned_cols=286  Identities=13%  Similarity=0.113  Sum_probs=225.6

Q ss_pred             HHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCC-C------hhHHHHHHHHHHHCCC
Q 040365           50 IFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVK-D------AISWNSIIAGCVQNGL  122 (514)
Q Consensus        50 ~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~-d------~~~~~~li~~~~~~g~  122 (514)
                      .+...|++++|...+..+++.+ +.+..++..+...|.+.|++++|..+++.+... +      ...++.+...|.+.|+
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~  122 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGL  122 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence            3456678888888888888764 455667788888888888888888888776532 1      2457778888888888


Q ss_pred             hhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCc----HHHHHHHHHHHHhcCCHHHHHH
Q 040365          123 FDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDN----MFIASSLLDMYAKCGNIRLARC  198 (514)
Q Consensus       123 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~li~~y~k~g~~~~A~~  198 (514)
                      +++|+.+|.++.+.. +++..++..++..+...|++++|.+.+..+.+.+..+.    ...+..+...|.+.|++++|.+
T Consensus       123 ~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  201 (389)
T PRK11788        123 LDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARA  201 (389)
T ss_pred             HHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHH
Confidence            888888888887652 45667788888888888888888888888877653222    2245667788899999999999


Q ss_pred             HHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCC
Q 040365          199 IFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGI  275 (514)
Q Consensus       199 ~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~  275 (514)
                      .|+++.   ..+...+..+...|.+.|++++|.++|+++...+..+...++..+..++...|++++|...++.+.+.   
T Consensus       202 ~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~---  278 (389)
T PRK11788        202 LLKKALAADPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE---  278 (389)
T ss_pred             HHHHHHhHCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---
Confidence            999875   23456788888999999999999999999987532222466788999999999999999999998654   


Q ss_pred             CCCHhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHh---cCCHHHHHHHHHHHHhc
Q 040365          276 APSFEHYAAVADLLGRAGKLQEAYEFISNM-HAGPTENVWLTLLSACRV---HKNVELAGKVAEKIFMI  340 (514)
Q Consensus       276 ~p~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~~  340 (514)
                      .|+...+..++..+.+.|++++|.++++++ ...|+...++.++..+..   +|+.+++..+++++++.
T Consensus       279 ~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~  347 (389)
T PRK11788        279 YPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGE  347 (389)
T ss_pred             CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHH
Confidence            577677788999999999999999999876 445999999988887764   56888999988888763

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.85  E-value=2.9e-17  Score=172.40  Aligned_cols=326  Identities=10%  Similarity=-0.048  Sum_probs=257.6

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCC
Q 040365           11 TVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA   90 (514)
Q Consensus        11 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g   90 (514)
                      -++..+.+.|++++|+.+++........ +...+..++.+....|+++.|.+.++.+++.. |.+...+..+...+.+.|
T Consensus        47 ~~~~~~~~~g~~~~A~~l~~~~l~~~p~-~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g  124 (656)
T PRK15174         47 LFAIACLRKDETDVGLTLLSDRVLTAKN-GRDLLRRWVISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKSK  124 (656)
T ss_pred             HHHHHHHhcCCcchhHHHhHHHHHhCCC-chhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcC
Confidence            4566788899999999999998876422 33455555666777999999999999999875 666778888999999999


Q ss_pred             CHHHHHHHHccCCC---CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHH
Q 040365           91 RVEDSHRLFCLLPV---KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGC  167 (514)
Q Consensus        91 ~~~~A~~~f~~~~~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  167 (514)
                      ++++|...|++...   .+...|..+...+.+.|++++|...++++....  |+.......+..+...|++++|...+..
T Consensus       125 ~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~--P~~~~a~~~~~~l~~~g~~~eA~~~~~~  202 (656)
T PRK15174        125 QYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEV--PPRGDMIATCLSFLNKSRLPEDHDLARA  202 (656)
T ss_pred             CHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            99999999988753   356788889999999999999999999887653  3332222223447788999999999999


Q ss_pred             HHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHH----HHHHHHHHHHcCCC
Q 040365          168 IIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHD----AISLFEQMEKDGVK  240 (514)
Q Consensus       168 ~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~----A~~l~~~m~~~g~~  240 (514)
                      +++....++......+...+.+.|++++|...|++..   ..+...+..+...|.+.|++++    |+..|++..+.  .
T Consensus       203 ~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l--~  280 (656)
T PRK15174        203 LLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF--N  280 (656)
T ss_pred             HHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh--C
Confidence            8876533444555566788899999999999998875   3466788889999999999886    79999998874  4


Q ss_pred             CC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCHHH-HHH
Q 040365          241 PN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPTENV-WLT  316 (514)
Q Consensus       241 p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~~~-~~~  316 (514)
                      |+ ...+..+...+...|++++|...++...+.   .| +...+..+...|.+.|++++|.+.++++. ..|+... +..
T Consensus       281 P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l---~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~  357 (656)
T PRK15174        281 SDNVRIVTLYADALIRTGQNEKAIPLLQQSLAT---HPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKWNRY  357 (656)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHH
Confidence            54 567888888999999999999999988653   55 46677778899999999999999998874 4465444 344


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          317 LLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       317 ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      +..++...|+.++|...++++++..|++.
T Consensus       358 ~a~al~~~G~~deA~~~l~~al~~~P~~~  386 (656)
T PRK15174        358 AAAALLQAGKTSEAESVFEHYIQARASHL  386 (656)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhChhhc
Confidence            56778899999999999999999988753

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

Probab=99.84  E-value=1.9e-18  Score=166.06  Aligned_cols=356  Identities=13%  Similarity=0.128  Sum_probs=294.4

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCC-hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhH-HHHHHH
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPD-SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCI-GSSLIN   84 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~-~~~li~   84 (514)
                      .+|+.+...+-..|++++|+.+++.|.+.  +|+ ...|..+..++...|+.+.|.+.+...++.  .|+... .+.+-.
T Consensus       117 e~ysn~aN~~kerg~~~~al~~y~~aiel--~p~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lgn  192 (966)
T KOG4626|consen  117 EAYSNLANILKERGQLQDALALYRAAIEL--KPKFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLGN  192 (966)
T ss_pred             HHHHHHHHHHHHhchHHHHHHHHHHHHhc--CchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--CcchhhhhcchhH
Confidence            46888889999999999999999999985  454 568999999999999999999999999886  455443 344455


Q ss_pred             HHHHCCCHHHHHHHHccCC--CCC-hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHhccCChHH
Q 040365           85 MYAKCARVEDSHRLFCLLP--VKD-AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR-HVSFSSIMPACAHLTTLHL  160 (514)
Q Consensus        85 ~~~~~g~~~~A~~~f~~~~--~~d-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~  160 (514)
                      ..-..|++.+|...+.+..  +|. .++|+-|...+-.+|+..+|++.|++....  .|+ ...|..+-..|...+.++.
T Consensus       193 Llka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl--dP~f~dAYiNLGnV~ke~~~~d~  270 (966)
T KOG4626|consen  193 LLKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL--DPNFLDAYINLGNVYKEARIFDR  270 (966)
T ss_pred             HHHhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcC--CCcchHHHhhHHHHHHHHhcchH
Confidence            5566799999988887654  333 467999999999999999999999998763  454 3567788888888889999


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--CC-hhHHHHHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--HD-IVSWTAVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      |...+.+..... +....++..|...|-..|.++-|+..+++..+  |+ ...||.|..++-..|+..+|.+.|.+....
T Consensus       271 Avs~Y~rAl~lr-pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l  349 (966)
T KOG4626|consen  271 AVSCYLRALNLR-PNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRL  349 (966)
T ss_pred             HHHHHHHHHhcC-CcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHh
Confidence            988888877654 44566777788889999999999999998763  33 468999999999999999999999998874


Q ss_pred             CCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHH
Q 040365          238 GVKPNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRAGKLQEAYEFISNM-HAGPT-ENV  313 (514)
Q Consensus       238 g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~  313 (514)
                        .|+. ...+.|...+...|.+++|..+|....   .+.|. ....+.|...|-..|++++|..-+++. .++|+ ...
T Consensus       350 --~p~hadam~NLgni~~E~~~~e~A~~ly~~al---~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda  424 (966)
T KOG4626|consen  350 --CPNHADAMNNLGNIYREQGKIEEATRLYLKAL---EVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADA  424 (966)
T ss_pred             --CCccHHHHHHHHHHHHHhccchHHHHHHHHHH---hhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHH
Confidence              5553 578889999999999999999998765   55664 567888999999999999999999875 46676 467


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          314 WLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       314 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++.+...|...|+.+.|.+.+.+++..+|.-+.++..|..+|-.+|+..+|..-++...+-
T Consensus       425 ~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLkl  485 (966)
T KOG4626|consen  425 LSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKL  485 (966)
T ss_pred             HHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHcc
Confidence            8999999999999999999999999999988889999999999999999999998887653

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

Probab=99.82  E-value=1.4e-17  Score=160.19  Aligned_cols=351  Identities=14%  Similarity=0.114  Sum_probs=298.3

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHH-HHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVL-PIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSL   82 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll-~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (514)
                      ..+..|..+..++...|+.+.|.+.|.+.++.  .|+.+...+-+ ......|++++|...+.++++.. +.-..+|+.|
T Consensus       148 ~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lgnLlka~Grl~ea~~cYlkAi~~q-p~fAiawsnL  224 (966)
T KOG4626|consen  148 KFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLGNLLKAEGRLEEAKACYLKAIETQ-PCFAIAWSNL  224 (966)
T ss_pred             hhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--CcchhhhhcchhHHHHhhcccchhHHHHHHHHhhC-Cceeeeehhc
Confidence            36778999999999999999999999998874  57665443333 33345689999999999998874 3445678999


Q ss_pred             HHHHHHCCCHHHHHHHHccCCCCC---hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHhccCCh
Q 040365           83 INMYAKCARVEDSHRLFCLLPVKD---AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR-HVSFSSIMPACAHLTTL  158 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~~~d---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~  158 (514)
                      ...+-..|++..|...|++...-|   ..+|-.|...|...+.+++|+..|.+....  .|+ ...+..+...|-..|.+
T Consensus       225 g~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~l--rpn~A~a~gNla~iYyeqG~l  302 (966)
T KOG4626|consen  225 GCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGNVYKEARIFDRAVSCYLRALNL--RPNHAVAHGNLACIYYEQGLL  302 (966)
T ss_pred             chHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhc--CCcchhhccceEEEEeccccH
Confidence            999999999999999999987543   457888999999999999999999888764  454 56677788888999999


Q ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          159 HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      +.|...+++.++.. +.-...|+.|..++-..|++.+|.+.+.+..   ..-..+.+.|...|...|.+++|..+|....
T Consensus       303 dlAI~~Ykral~~~-P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al  381 (966)
T KOG4626|consen  303 DLAIDTYKRALELQ-PNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKAL  381 (966)
T ss_pred             HHHHHHHHHHHhcC-CCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHH
Confidence            99999999999874 4446789999999999999999999999876   3345788999999999999999999999988


Q ss_pred             HcCCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-H
Q 040365          236 KDGVKPNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRAGKLQEAYEFISNM-HAGPT-E  311 (514)
Q Consensus       236 ~~g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~  311 (514)
                      +  +.|.- ..++.|...|-+.|++++|+..+++..   .+.|+ ...|+.+...|...|+.+.|.+.+.+. ...|. .
T Consensus       382 ~--v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykeal---rI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~A  456 (966)
T KOG4626|consen  382 E--VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEAL---RIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFA  456 (966)
T ss_pred             h--hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHH---hcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHH
Confidence            7  56664 578899999999999999999999885   67896 688999999999999999999999876 45564 4


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHH
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAA  365 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~  365 (514)
                      ...+.|.+.+...|+..+|+..++..+.+.|+-+.+|..++.+..-..+|.+-.
T Consensus       457 eAhsNLasi~kDsGni~~AI~sY~~aLklkPDfpdA~cNllh~lq~vcdw~D~d  510 (966)
T KOG4626|consen  457 EAHSNLASIYKDSGNIPEAIQSYRTALKLKPDFPDAYCNLLHCLQIVCDWTDYD  510 (966)
T ss_pred             HHHhhHHHHhhccCCcHHHHHHHHHHHccCCCCchhhhHHHHHHHHHhcccchH
Confidence            678999999999999999999999999999999999999998887777776633

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.82  E-value=1.3e-16  Score=167.57  Aligned_cols=326  Identities=9%  Similarity=-0.052  Sum_probs=266.0

Q ss_pred             hhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC---CChhHHHHHHHHHH
Q 040365           42 FTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPV---KDAISWNSIIAGCV  118 (514)
Q Consensus        42 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~---~d~~~~~~li~~~~  118 (514)
                      .....++..+.+.|++++|..++...+... +.+......++......|++++|...|+.+..   .+...|..+...+.
T Consensus        43 ~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~  121 (656)
T PRK15174         43 QNIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLL  121 (656)
T ss_pred             cCHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            345667788889999999999999998875 44555666666777889999999999999863   35678888999999


Q ss_pred             HCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHH
Q 040365          119 QNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARC  198 (514)
Q Consensus       119 ~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~  198 (514)
                      +.|++++|+..|++..+.. +.+...+..+..++...|++++|...+..+..... .+...+..+. .+...|++++|..
T Consensus       122 ~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P-~~~~a~~~~~-~l~~~g~~~eA~~  198 (656)
T PRK15174        122 KSKQYATVADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQAQEVP-PRGDMIATCL-SFLNKSRLPEDHD  198 (656)
T ss_pred             HcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCC-CCHHHHHHHH-HHHHcCCHHHHHH
Confidence            9999999999999998752 33456777888899999999999999998877652 3333443333 4788999999999


Q ss_pred             HHHhCCCC----ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHH----HHHHHHHhH
Q 040365          199 IFDKMDLH----DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDK----AWSYFNSMT  270 (514)
Q Consensus       199 ~~~~m~~~----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~----a~~~~~~m~  270 (514)
                      .++.+...    +...+..+...+...|++++|+..|++..... +.+...+..+..++...|++++    |...|+...
T Consensus       199 ~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al  277 (656)
T PRK15174        199 LARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHAL  277 (656)
T ss_pred             HHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHH
Confidence            99987532    33445556678889999999999999999853 2245677788889999999986    899999886


Q ss_pred             HhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcch
Q 040365          271 KDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGA  347 (514)
Q Consensus       271 ~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~  347 (514)
                      +   +.| +...+..+...+.+.|++++|...+++.. ..| +...+..+..++...|++++|...++++.+.+|+++..
T Consensus       278 ~---l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~  354 (656)
T PRK15174        278 Q---FNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKW  354 (656)
T ss_pred             h---hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHH
Confidence            4   456 57888999999999999999999998863 334 46678888999999999999999999999999988777


Q ss_pred             HHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          348 YVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       348 ~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      +..++.++...|++++|.+.++...+..
T Consensus       355 ~~~~a~al~~~G~~deA~~~l~~al~~~  382 (656)
T PRK15174        355 NRYAAAALLQAGKTSEAESVFEHYIQAR  382 (656)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            7777889999999999999999886653

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.82  E-value=2.4e-16  Score=176.53  Aligned_cols=354  Identities=11%  Similarity=0.051  Sum_probs=228.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCC-chhHH------------
Q 040365           13 IVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDA-NVCIG------------   79 (514)
Q Consensus        13 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~-~~~~~------------   79 (514)
                      ...+...|++++|+..|++..+.. +.+...+..+..++.+.|++++|...++++++..... ....+            
T Consensus       276 G~~~~~~g~~~~A~~~l~~aL~~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~  354 (1157)
T PRK11447        276 GLAAVDSGQGGKAIPELQQAVRAN-PKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLL  354 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHH
Confidence            345667888889999998888753 3356677788888888899999998888888764221 11111            


Q ss_pred             HHHHHHHHHCCCHHHHHHHHccCCC---CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH----
Q 040365           80 SSLINMYAKCARVEDSHRLFCLLPV---KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPAC----  152 (514)
Q Consensus        80 ~~li~~~~~~g~~~~A~~~f~~~~~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~----  152 (514)
                      ..+...+.+.|++++|...|++...   .+...+..+...+...|++++|++.|++..+.. +.+...+..+...+    
T Consensus       355 ~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~~~~  433 (1157)
T PRK11447        355 IQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYRQQS  433 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcC
Confidence            1224456788888888888887652   355677778888888889999988888887642 22233333333333    


Q ss_pred             --------------------------------------hccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHH
Q 040365          153 --------------------------------------AHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIR  194 (514)
Q Consensus       153 --------------------------------------~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~  194 (514)
                                                            ...|++++|.+.+++.++.. +.+..++..+...|.+.|+++
T Consensus       434 ~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~~~  512 (1157)
T PRK11447        434 PEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQRS  512 (1157)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHH
Confidence                                                  23455555555555555443 223444444555555555555


Q ss_pred             HHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH---------HHHHHHHHHHccCCHHHH
Q 040365          195 LARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV---------AFVAVLTACSHAGLIDKA  262 (514)
Q Consensus       195 ~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~---------t~~~ll~a~~~~g~~~~a  262 (514)
                      +|...|+++.   ..+...+..+...+...|+.++|+..++++......++..         .+..+...+...|+.++|
T Consensus       513 ~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA  592 (1157)
T PRK11447        513 QADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEA  592 (1157)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHH
Confidence            5555555442   1133333333333444555555555554432211111111         112334455566666777


Q ss_pred             HHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040365          263 WSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRVHKNVELAGKVAEKIFMI  340 (514)
Q Consensus       263 ~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  340 (514)
                      ..+++.      .+++...+..+.+.+.+.|++++|++.|++.. .. .+...+..+...+...|++++|+..++++.+.
T Consensus       593 ~~~l~~------~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~  666 (1157)
T PRK11447        593 EALLRQ------QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPAT  666 (1157)
T ss_pred             HHHHHh------CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence            666551      12355666778888888899999998888763 23 35778888888898999999999999988888


Q ss_pred             CCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          341 DPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       341 ~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      .|+++..+..+..++...|++++|.++++.+....
T Consensus       667 ~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~  701 (1157)
T PRK11447        667 ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQA  701 (1157)
T ss_pred             CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhC
Confidence            88888888888888889999999999998887653

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.82  E-value=6.8e-16  Score=172.90  Aligned_cols=361  Identities=9%  Similarity=0.000  Sum_probs=278.0

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChh---hHH------------HHHHHHhCCCChHHHHHHHHHHHH
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSF---TLS------------SVLPIFADYVDVIKGKEIHGYAIR   69 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~---t~~------------~ll~~~~~~~~~~~a~~~~~~~~~   69 (514)
                      |...|..|...|.+.|++++|+..|++..+..  |+..   .+.            .....+...|++++|...++++++
T Consensus       302 ~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~--p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~  379 (1157)
T PRK11447        302 DSEALGALGQAYSQQGDRARAVAQFEKALALD--PHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQ  379 (1157)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            66788888899999999999999999988753  3221   111            123456678899999999999988


Q ss_pred             hCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC--C-ChhHHHH----------------------------------
Q 040365           70 HGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPV--K-DAISWNS----------------------------------  112 (514)
Q Consensus        70 ~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~--~-d~~~~~~----------------------------------  112 (514)
                      .. +.+...+..|...|...|++++|.+.|++...  | +...+..                                  
T Consensus       380 ~~-P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~~~~a~~~L~~l~~~~~~~~A~~~l~~l~~~~~~~~~~~~~~  458 (1157)
T PRK11447        380 VD-NTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPGNTNAVRGLANLYRQQSPEKALAFIASLSASQRRSIDDIERS  458 (1157)
T ss_pred             hC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            75 55667777888899999999999998887652  2 2222222                                  


Q ss_pred             --------HHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHH
Q 040365          113 --------IIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL  184 (514)
Q Consensus       113 --------li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  184 (514)
                              +...+...|++++|++.|++..+.. +-+...+..+...+.+.|++++|...++.+++.. +.+...+..+.
T Consensus       459 l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~-P~~~~~~~a~a  536 (1157)
T PRK11447        459 LQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQK-PNDPEQVYAYG  536 (1157)
T ss_pred             hhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHH
Confidence                    2344556899999999999988753 2345566778889999999999999999998764 44555555566


Q ss_pred             HHHHhcCCHHHHHHHHHhCCCC----Chh---------HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040365          185 DMYAKCGNIRLARCIFDKMDLH----DIV---------SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLT  251 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~~~----d~~---------~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  251 (514)
                      ..+.+.|+.++|...++.++..    +..         .+..+...+...|+.++|+.+++.     .+++...+..+..
T Consensus       537 l~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~-----~p~~~~~~~~La~  611 (1157)
T PRK11447        537 LYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQ-----QPPSTRIDLTLAD  611 (1157)
T ss_pred             HHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHh-----CCCCchHHHHHHH
Confidence            6778899999999999998632    111         123456678889999999999882     2345566777888


Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCCC-CC-CHHHHHHHHHHHHhcCCHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMHA-GP-TENVWLTLLSACRVHKNVE  328 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p-~~~~~~~ll~~~~~~~~~~  328 (514)
                      .+.+.|+.++|+..|+...+.   .| +...+..++..|...|++++|.+.++.... .| +..++..+..++...|+++
T Consensus       612 ~~~~~g~~~~A~~~y~~al~~---~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~  688 (1157)
T PRK11447        612 WAQQRGDYAAARAAYQRVLTR---EPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDTA  688 (1157)
T ss_pred             HHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHH
Confidence            999999999999999998753   55 678899999999999999999999998752 33 5667788888999999999


Q ss_pred             HHHHHHHHHHhcCCCCc------chHHHHHHHHHHccChhHHHHHHHHHHh-CCCcc
Q 040365          329 LAGKVAEKIFMIDPNNM------GAYVILSNTYAAARRWKDAASLRVFMRN-KGMKK  378 (514)
Q Consensus       329 ~a~~~~~~~~~~~p~~~------~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~g~~~  378 (514)
                      +|..++++++...|+++      ..+..++..+...|++++|...++.... .|+.|
T Consensus       689 eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~~~~~~~  745 (1157)
T PRK11447        689 AAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMVASGITP  745 (1157)
T ss_pred             HHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcCCCC
Confidence            99999999998775543      3566678999999999999999988753 35543

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.81  E-value=7.6e-16  Score=165.07  Aligned_cols=360  Identities=9%  Similarity=0.025  Sum_probs=223.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHH
Q 040365            9 WNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAK   88 (514)
Q Consensus         9 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~   88 (514)
                      +..+...+.+.|++++|+.+|++..... +.+...+..+...+...|+.++|...++.+++.. +.+.. +..+..++..
T Consensus        52 ~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~  128 (765)
T PRK10049         52 YAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLILTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKR  128 (765)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHH
Confidence            4455555555555555555555544431 2223333444444455555555555555555442 33333 4445555555


Q ss_pred             CCCHHHHHHHHccCCC--C-ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHH------HHHHHHHHHh-----c
Q 040365           89 CARVEDSHRLFCLLPV--K-DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHV------SFSSIMPACA-----H  154 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~~--~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~------t~~~ll~~~~-----~  154 (514)
                      .|+.++|...++++.+  | +...+..+...+...+..++|++.+++...   .|+..      ....++....     .
T Consensus       129 ~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~  205 (765)
T PRK10049        129 AGRHWDELRAMTQALPRAPQTQQYPTEYVQALRNNRLSAPALGAIDDANL---TPAEKRDLEADAAAELVRLSFMPTRSE  205 (765)
T ss_pred             CCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCChHHHHHHHHhCCC---CHHHHHHHHHHHHHHHHHhhcccccCh
Confidence            5555555555554431  1 333344444444455555555555443322   12110      0011111111     1


Q ss_pred             cCCh---HHHHHHHHHHHHc-CCCCcHH--HHHH---HHHHHHhcCCHHHHHHHHHhCCCCC--hh--HHHHHHHHHHhC
Q 040365          155 LTTL---HLGKQLHGCIIRN-GFDDNMF--IASS---LLDMYAKCGNIRLARCIFDKMDLHD--IV--SWTAVIMGNALH  221 (514)
Q Consensus       155 ~~~~---~~a~~~~~~~~~~-~~~~~~~--~~~~---li~~y~k~g~~~~A~~~~~~m~~~d--~~--~~~~li~~~~~~  221 (514)
                      .+++   +.|.+.++.+++. ...|+..  ....   .+.++...|++++|+..|+.+...+  ..  .-..+...|...
T Consensus       206 ~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~  285 (765)
T PRK10049        206 KERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPWAQRWVASAYLKL  285 (765)
T ss_pred             hHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHhc
Confidence            1122   4566666666643 1222211  1111   1234457799999999999987432  11  122256789999


Q ss_pred             CChHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC----------CCCC---HhHHHHH
Q 040365          222 GNAHDAISLFEQMEKDGVKP---NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG----------IAPS---FEHYAAV  285 (514)
Q Consensus       222 g~~~~A~~l~~~m~~~g~~p---~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~----------~~p~---~~~~~~l  285 (514)
                      |++++|+..|+++.......   .......+..++...|++++|..+++.+.....          -.|+   ...+..+
T Consensus       286 g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~  365 (765)
T PRK10049        286 HQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLL  365 (765)
T ss_pred             CCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHH
Confidence            99999999999987643111   124566677788999999999999999865321          1122   2345677


Q ss_pred             HHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhH
Q 040365          286 ADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKD  363 (514)
Q Consensus       286 i~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  363 (514)
                      ...+...|++++|++.++++.  .+.+...+..+...+...|++++|+..++++++++|++...+..++..+...|+|++
T Consensus       366 a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~  445 (765)
T PRK10049        366 SQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQ  445 (765)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHH
Confidence            888999999999999999874  234678899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhC
Q 040365          364 AASLRVFMRNK  374 (514)
Q Consensus       364 a~~~~~~m~~~  374 (514)
                      |..+++.+.+.
T Consensus       446 A~~~~~~ll~~  456 (765)
T PRK10049        446 MDVLTDDVVAR  456 (765)
T ss_pred             HHHHHHHHHHh
Confidence            99999999764

>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=99.77  E-value=8.3e-15  Score=154.20  Aligned_cols=354  Identities=13%  Similarity=0.033  Sum_probs=265.5

Q ss_pred             CCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCC----------
Q 040365            3 VSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGL----------   72 (514)
Q Consensus         3 ~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~----------   72 (514)
                      .|+...|..+..+|.+.|++++|+..+...++.. +.+...|..+..++...|++++|..-+..+...+-          
T Consensus       157 ~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~a~a~~~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~  235 (615)
T TIGR00990       157 KPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-PDYSKALNRRANAYDGLGKYADALLDLTASCIIDGFRNEQSAQAV  235 (615)
T ss_pred             CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccHHHHHHH
Confidence            4677789999999999999999999999998753 33455788889999999999999765544322110          


Q ss_pred             -------------------CCchhHHHHH------------------------------HHHH------HHCCCHHHHHH
Q 040365           73 -------------------DANVCIGSSL------------------------------INMY------AKCARVEDSHR   97 (514)
Q Consensus        73 -------------------~~~~~~~~~l------------------------------i~~~------~~~g~~~~A~~   97 (514)
                                         +++...+..+                              +..+      ...+++++|.+
T Consensus       236 ~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~  315 (615)
T TIGR00990       236 ERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELDEETGNGQLQLGLKSPESKADESYEEAAR  315 (615)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccccccccccchHHHHHHHHHhhhhhhHHHHHH
Confidence                               1110011100                              1111      11257888999


Q ss_pred             HHccCCC------CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040365           98 LFCLLPV------KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR-HVSFSSIMPACAHLTTLHLGKQLHGCIIR  170 (514)
Q Consensus        98 ~f~~~~~------~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~  170 (514)
                      .|+....      .+...|+.+...+...|++++|+..|++..+.  .|+ ...|..+...+...|++++|...++.+++
T Consensus       316 ~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~  393 (615)
T TIGR00990       316 AFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL--DPRVTQSYIKRASMNLELGDPDKAEEDFDKALK  393 (615)
T ss_pred             HHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            8887653      24557888889999999999999999998875  454 55788888889999999999999999988


Q ss_pred             cCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHH
Q 040365          171 NGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAF  246 (514)
Q Consensus       171 ~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~  246 (514)
                      .. +.+..++..+...|...|++++|...|++..   ..+...|..+...+.+.|++++|+..|++....  .|+ ...+
T Consensus       394 ~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~  470 (615)
T TIGR00990       394 LN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKN--FPEAPDVY  470 (615)
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHH
Confidence            75 5667889999999999999999999999875   335677888889999999999999999998874  444 5778


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCH--------hHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHH
Q 040365          247 VAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSF--------EHYAAVADLLGRAGKLQEAYEFISNM-HAGP-TENVWLT  316 (514)
Q Consensus       247 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~--------~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~  316 (514)
                      ..+..++...|++++|+..|+....   +.|+.        ..++.....+...|++++|.+++++. ...| +...+..
T Consensus       471 ~~lg~~~~~~g~~~~A~~~~~~Al~---l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~  547 (615)
T TIGR00990       471 NYYGELLLDQNKFDEAIEKFDTAIE---LEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVAT  547 (615)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHh---cCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHH
Confidence            8889999999999999999998764   33321        11222233344579999999999885 3344 4567889


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          317 LLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       317 ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      +...+...|++++|...++++.++.+.....        .....+.+|.++.....+
T Consensus       548 la~~~~~~g~~~eAi~~~e~A~~l~~~~~e~--------~~a~~~~~a~~~~~~~~~  596 (615)
T TIGR00990       548 MAQLLLQQGDVDEALKLFERAAELARTEGEL--------VQAISYAEATRTQIQVQE  596 (615)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHhccHHHH--------HHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999887653321        122344555555544443

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.76  E-value=3.4e-15  Score=160.14  Aligned_cols=357  Identities=12%  Similarity=-0.001  Sum_probs=268.0

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCC
Q 040365           11 TVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA   90 (514)
Q Consensus        11 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g   90 (514)
                      -.+......|+.++|++++....... +.+...+..+..++...|++++|.++++.+++.. +.+...+..+...+.+.|
T Consensus        20 d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~l~~~g   97 (765)
T PRK10049         20 DWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLILTLADAG   97 (765)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCC
Confidence            34566777899999999999997632 3445568889999999999999999999998874 556777889999999999


Q ss_pred             CHHHHHHHHccCCC--C-ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHH
Q 040365           91 RVEDSHRLFCLLPV--K-DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGC  167 (514)
Q Consensus        91 ~~~~A~~~f~~~~~--~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  167 (514)
                      +.++|...+++...  | +.. |..+...+...|+.++|+..++++.+.. +-+...+..+..++...+..+.|.+.++.
T Consensus        98 ~~~eA~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~-P~~~~~~~~la~~l~~~~~~e~Al~~l~~  175 (765)
T PRK10049         98 QYDEALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPRA-PQTQQYPTEYVQALRNNRLSAPALGAIDD  175 (765)
T ss_pred             CHHHHHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCChHHHHHHHHh
Confidence            99999999998752  3 455 8889999999999999999999998863 22444455667777788888989888876


Q ss_pred             HHHcCCCCcH------HHHHHHHHHHH-----hcCCH---HHHHHHHHhCCC-----CChh-HH----HHHHHHHHhCCC
Q 040365          168 IIRNGFDDNM------FIASSLLDMYA-----KCGNI---RLARCIFDKMDL-----HDIV-SW----TAVIMGNALHGN  223 (514)
Q Consensus       168 ~~~~~~~~~~------~~~~~li~~y~-----k~g~~---~~A~~~~~~m~~-----~d~~-~~----~~li~~~~~~g~  223 (514)
                      +.+   .|+.      .....++..+.     ..+++   ++|.+.++.+..     |+.. .+    ...+..+...|+
T Consensus       176 ~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~  252 (765)
T PRK10049        176 ANL---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDR  252 (765)
T ss_pred             CCC---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhh
Confidence            553   2221      11222233222     22334   678887777651     2211 11    111345567799


Q ss_pred             hHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC--CHhHHHHHHHHHHhcCCHHHHHH
Q 040365          224 AHDAISLFEQMEKDGVK-PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP--SFEHYAAVADLLGRAGKLQEAYE  300 (514)
Q Consensus       224 ~~~A~~l~~~m~~~g~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p--~~~~~~~li~~~~~~g~~~~A~~  300 (514)
                      +++|+..|+++.+.+.. |+.. -..+..++...|++++|..+|+.+.+.....+  .......+..++.+.|++++|.+
T Consensus       253 ~~eA~~~~~~ll~~~~~~P~~a-~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~  331 (765)
T PRK10049        253 YKDVISEYQRLKAEGQIIPPWA-QRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALT  331 (765)
T ss_pred             HHHHHHHHHHhhccCCCCCHHH-HHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHH
Confidence            99999999999987532 4432 22256789999999999999999865321111  13456667778899999999999


Q ss_pred             HHHhCCCC-C-------------C---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhH
Q 040365          301 FISNMHAG-P-------------T---ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKD  363 (514)
Q Consensus       301 ~~~~m~~~-p-------------~---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  363 (514)
                      +++.+... |             +   ...+..+...+...|+.++|+..++++....|.++..+..++.++...|++++
T Consensus       332 ~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~  411 (765)
T PRK10049        332 VTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRA  411 (765)
T ss_pred             HHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHH
Confidence            99887422 2             3   23456677788999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCC
Q 040365          364 AASLRVFMRNKG  375 (514)
Q Consensus       364 a~~~~~~m~~~g  375 (514)
                      |.+.+++..+..
T Consensus       412 A~~~l~~al~l~  423 (765)
T PRK10049        412 AENELKKAEVLE  423 (765)
T ss_pred             HHHHHHHHHhhC
Confidence            999999887654

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.71  E-value=7.8e-13  Score=139.75  Aligned_cols=361  Identities=10%  Similarity=0.042  Sum_probs=257.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCC
Q 040365           11 TVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA   90 (514)
Q Consensus        11 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g   90 (514)
                      .++..+...|+.++|+..+++.... -..+...+..+...+...|++++|.++++.+++.. +.++.++..|+..|...+
T Consensus        73 dll~l~~~~G~~~~A~~~~eka~~p-~n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~  150 (822)
T PRK14574         73 DWLQIAGWAGRDQEVIDVYERYQSS-MNISSRGLASAARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAG  150 (822)
T ss_pred             HHHHHHHHcCCcHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcC
Confidence            7778888888888998888888721 11112223333456778899999999999998876 556777778888899999


Q ss_pred             CHHHHHHHHccCCCCChhHHHHHHHHHHH--CCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHH----
Q 040365           91 RVEDSHRLFCLLPVKDAISWNSIIAGCVQ--NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQL----  164 (514)
Q Consensus        91 ~~~~A~~~f~~~~~~d~~~~~~li~~~~~--~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~----  164 (514)
                      +.++|++.++.+...+......+..+|..  .++..+|++.++++.+.. +-+...+..+..+..+.|....|.++    
T Consensus       151 q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~  229 (822)
T PRK14574        151 RGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEAVRLA-PTSEEVLKNHLEILQRNRIVEPALRLAKEN  229 (822)
T ss_pred             CHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhC
Confidence            99999999988875443332224444444  556656999999988763 22344444455555544433333222    


Q ss_pred             --------------------------------------------HHHHHHc-C-CCCcHHH-HHH---HHHHHHhcCCHH
Q 040365          165 --------------------------------------------HGCIIRN-G-FDDNMFI-ASS---LLDMYAKCGNIR  194 (514)
Q Consensus       165 --------------------------------------------~~~~~~~-~-~~~~~~~-~~~---li~~y~k~g~~~  194 (514)
                                                                  ++.+... + .++.... ..+   .+-++.+.|+..
T Consensus       230 p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~  309 (822)
T PRK14574        230 PNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTA  309 (822)
T ss_pred             ccccCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHH
Confidence                                                        2222221 1 1222111 222   344667889999


Q ss_pred             HHHHHHHhCCCC----ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC-----CCCCHHHHHHHHHHHHccCCHHHHHHH
Q 040365          195 LARCIFDKMDLH----DIVSWTAVIMGNALHGNAHDAISLFEQMEKDG-----VKPNSVAFVAVLTACSHAGLIDKAWSY  265 (514)
Q Consensus       195 ~A~~~~~~m~~~----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-----~~p~~~t~~~ll~a~~~~g~~~~a~~~  265 (514)
                      ++++.|+.+...    ...+--++.++|...+++++|+.+|+++....     ..++......|..++...+++++|..+
T Consensus       310 ~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~  389 (822)
T PRK14574        310 DLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQF  389 (822)
T ss_pred             HHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHH
Confidence            999999999833    23455678889999999999999999987643     122334457889999999999999999


Q ss_pred             HHHhHHhcC----------CCCC---HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHH
Q 040365          266 FNSMTKDYG----------IAPS---FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELA  330 (514)
Q Consensus       266 ~~~m~~~~~----------~~p~---~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a  330 (514)
                      ++.+.+...          -.|+   ...+..++..+...|++.+|++.++++.  .+-|...+..+...+...|.+..|
T Consensus       390 l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A  469 (822)
T PRK14574        390 AVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKA  469 (822)
T ss_pred             HHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHH
Confidence            999965211          0122   2344556777899999999999999874  335788899999999999999999


Q ss_pred             HHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          331 GKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       331 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +..++.+..++|++..+...++.++...|+|.+|.++.+.+.+.
T Consensus       470 ~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~~  513 (822)
T PRK14574        470 EQELKAVESLAPRSLILERAQAETAMALQEWHQMELLTDDVISR  513 (822)
T ss_pred             HHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999998877654

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.71  E-value=5e-13  Score=144.07  Aligned_cols=353  Identities=11%  Similarity=0.026  Sum_probs=242.6

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhC-CCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHH
Q 040365           10 NTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFAD-YVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAK   88 (514)
Q Consensus        10 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~-~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~   88 (514)
                      -.+...|.+.|++++|+.++.++.+.+. .+..-...+-.++.. .++ +.+..++..    .+..++.+..++++.|.+
T Consensus       186 L~~~rlY~~l~dw~~Ai~lL~~L~k~~p-l~~~~~~~L~~ay~q~l~~-~~a~al~~~----~lk~d~~l~~ala~~yi~  259 (987)
T PRK09782        186 TDLLQRAIYLKQWSQADTLYNEARQQNT-LSAAERRQWFDVLLAGQLD-DRLLALQSQ----GIFTDPQSRITYATALAY  259 (987)
T ss_pred             HHHHHHHHHHhCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHhhCH-HHHHHHhch----hcccCHHHHHHHHHHHHH
Confidence            3348899999999999999999999863 334445556667776 466 667777442    334688899999999999


Q ss_pred             CCCHHHHHHHHccCCC-----CChhHHHH---------------------------H---HH------------------
Q 040365           89 CARVEDSHRLFCLLPV-----KDAISWNS---------------------------I---IA------------------  115 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~~-----~d~~~~~~---------------------------l---i~------------------  115 (514)
                      .|+.++|.+++.+++.     |+..+|--                           +   +.                  
T Consensus       260 ~G~~~~A~~~L~~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (987)
T PRK09782        260 RGEKARLQHYLIENKPLFTTDAQEKSWLYLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQKLLATL  339 (987)
T ss_pred             CCCHHHHHHHHHhCcccccCCCccHHHHHHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            9999999999988751     11111100                           0   01                  


Q ss_pred             ---------------------------------------------HHHHCCChhHHHHHHHHHHHC-C-CCCCHHHHHHH
Q 040365          116 ---------------------------------------------GCVQNGLFDEGLKFFRQMLIA-K-IKPRHVSFSSI  148 (514)
Q Consensus       116 ---------------------------------------------~~~~~g~~~~A~~l~~~m~~~-g-~~p~~~t~~~l  148 (514)
                                                                   ...+.|+.++|.++|+..... + -.++.....-+
T Consensus       340 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l  419 (987)
T PRK09782        340 PANEMLEERYAVSVATRNKAEALRLARLLYQQEPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARL  419 (987)
T ss_pred             CcchHHHHHHhhccccCchhHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHH
Confidence                                                         113455666666666655331 0 01111111122


Q ss_pred             HHHHhcc---------------------------------------------------------------CChHHHHHHH
Q 040365          149 MPACAHL---------------------------------------------------------------TTLHLGKQLH  165 (514)
Q Consensus       149 l~~~~~~---------------------------------------------------------------~~~~~a~~~~  165 (514)
                      +..+.+.                                                               ++.++|...+
T Consensus       420 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~~~~~eAi~a~  499 (987)
T PRK09782        420 ASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRDTLPGVALYAW  499 (987)
T ss_pred             HHHHHhCCcccchHHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHhCCcHHHHHHH
Confidence            2222222                                                               3444455544


Q ss_pred             HHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCH
Q 040365          166 GCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD--LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNS  243 (514)
Q Consensus       166 ~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~  243 (514)
                      .......  |+......+...+...|++++|...|+++.  .++...+..+...+.+.|+.++|...|++..+..  |+.
T Consensus       500 ~~Al~~~--Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~--P~~  575 (987)
T PRK09782        500 LQAEQRQ--PDAWQHRAVAYQAYQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRG--LGD  575 (987)
T ss_pred             HHHHHhC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--Ccc
Confidence            4444432  343333334444567888888888888765  2344556667777888888888888888887753  443


Q ss_pred             -HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHH
Q 040365          244 -VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSA  320 (514)
Q Consensus       244 -~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~  320 (514)
                       ..+..+.......|++++|...++...+   +.|+...|..+..++.+.|+.++|...+++.. ..| +...+..+..+
T Consensus       576 ~~l~~~La~~l~~~Gr~~eAl~~~~~AL~---l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~a  652 (987)
T PRK09782        576 NALYWWLHAQRYIPGQPELALNDLTRSLN---IAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYA  652 (987)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHH---hCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence             2333344445566999999999988863   46778888899999999999999999998863 334 56778888889


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      +...|+.++|+..++++++.+|+++..+..+..+|...|++++|...+++..+..
T Consensus       653 L~~~G~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~  707 (987)
T PRK09782        653 LWDSGDIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDI  707 (987)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999999999887544

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.70  E-value=5e-13  Score=141.23  Aligned_cols=359  Identities=14%  Similarity=0.067  Sum_probs=274.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChh-hHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHH
Q 040365            9 WNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSF-TLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYA   87 (514)
Q Consensus         9 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~   87 (514)
                      |...| ...+.|+++.|+..|++..+.  .|+.. ....++..+...|+.++|...++..+.. -+.......++...|.
T Consensus        38 y~~ai-i~~r~Gd~~~Al~~L~qaL~~--~P~~~~av~dll~l~~~~G~~~~A~~~~eka~~p-~n~~~~~llalA~ly~  113 (822)
T PRK14574         38 YDSLI-IRARAGDTAPVLDYLQEESKA--GPLQSGQVDDWLQIAGWAGRDQEVIDVYERYQSS-MNISSRGLASAARAYR  113 (822)
T ss_pred             HHHHH-HHHhCCCHHHHHHHHHHHHhh--CccchhhHHHHHHHHHHcCCcHHHHHHHHHhccC-CCCCHHHHHHHHHHHH
Confidence            44444 467889999999999999875  35542 2227788888889999999999998821 1222333344466899


Q ss_pred             HCCCHHHHHHHHccCCC--C-ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHH
Q 040365           88 KCARVEDSHRLFCLLPV--K-DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQL  164 (514)
Q Consensus        88 ~~g~~~~A~~~f~~~~~--~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~  164 (514)
                      ..|++++|.++|+++.+  | |...+..++..|.+.++.++|++.++++...  .|+...+..++..+...++..+|.+.
T Consensus       114 ~~gdyd~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~  191 (822)
T PRK14574        114 NEKRWDQALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQA  191 (822)
T ss_pred             HcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHH
Confidence            99999999999999873  2 5566778889999999999999999999775  57766665555555556667669999


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC----------------------------------------
Q 040365          165 HGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD----------------------------------------  204 (514)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~----------------------------------------  204 (514)
                      ++++++.. +.+...+..++....+.|-...|.++..+-+                                        
T Consensus       192 ~ekll~~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~a  270 (822)
T PRK14574        192 SSEAVRLA-PTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKA  270 (822)
T ss_pred             HHHHHHhC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHH
Confidence            99999885 5667777777888887777766655554332                                        


Q ss_pred             --------C-----CCh-hHHH----HHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040365          205 --------L-----HDI-VSWT----AVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYF  266 (514)
Q Consensus       205 --------~-----~d~-~~~~----~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  266 (514)
                              .     |.. ..|.    =.+-++...|++.++++.|+.|...|.+.-..+-..+..+|...+.+++|..++
T Consensus       271 la~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~  350 (822)
T PRK14574        271 LADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPIL  350 (822)
T ss_pred             HHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHH
Confidence                    0     100 0111    134466778999999999999999886644457889999999999999999999


Q ss_pred             HHhHHhcC----CCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCC-CC---------------CH-HHHHHHHHHHHhcC
Q 040365          267 NSMTKDYG----IAPSFEHYAAVADLLGRAGKLQEAYEFISNMHA-GP---------------TE-NVWLTLLSACRVHK  325 (514)
Q Consensus       267 ~~m~~~~~----~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p---------------~~-~~~~~ll~~~~~~~  325 (514)
                      +.+....+    ..++......|.-+|...+++++|..+++++.. .|               |- .....++..+.-.|
T Consensus       351 ~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~g  430 (822)
T PRK14574        351 SSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALN  430 (822)
T ss_pred             HHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcC
Confidence            99866432    223455567889999999999999999998742 12               21 23344567788999


Q ss_pred             CHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          326 NVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++.+|++.++++....|.|......++.++...|...+|.+.++.....
T Consensus       431 dl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l  479 (822)
T PRK14574        431 DLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVESL  479 (822)
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh
Confidence            9999999999999999999999999999999999999999999776554

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.66  E-value=9.3e-13  Score=142.02  Aligned_cols=347  Identities=12%  Similarity=0.029  Sum_probs=258.7

Q ss_pred             CChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHh-C-CCCchhHHHHHHHHHHHCCCHH---H
Q 040365           20 GLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRH-G-LDANVCIGSSLINMYAKCARVE---D   94 (514)
Q Consensus        20 g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-g-~~~~~~~~~~li~~~~~~g~~~---~   94 (514)
                      +...++...++.|.+.. +-+....--+--...+.|+.++|.+++...... + -..+....+-|+..|.+.+.+.   .
T Consensus       356 ~~~~~~~~~~~~~y~~~-~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~  434 (987)
T PRK09782        356 RNKAEALRLARLLYQQE-PANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAK  434 (987)
T ss_pred             CchhHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHH
Confidence            44455555555565541 113333333333445778889999998888762 1 1234556668888888887733   3


Q ss_pred             HHHHHc-------------------------cCC---CC--ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHH
Q 040365           95 SHRLFC-------------------------LLP---VK--DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVS  144 (514)
Q Consensus        95 A~~~f~-------------------------~~~---~~--d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  144 (514)
                      |..+-.                         ...   .+  +...|..+...+.. +++++|+..|.+....  .|+...
T Consensus       435 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~  511 (987)
T PRK09782        435 VAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQ  511 (987)
T ss_pred             HHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHH
Confidence            322211                         111   12  56677888877776 8999999988887764  477665


Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHH---HHHHHHHhC
Q 040365          145 FSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWT---AVIMGNALH  221 (514)
Q Consensus       145 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~---~li~~~~~~  221 (514)
                      ...+..++...|++++|...+..+...  +|+...+..+...+.+.|+.++|...|++....+...++   .+.......
T Consensus       512 ~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~  589 (987)
T PRK09782        512 HRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIP  589 (987)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhC
Confidence            555566667899999999999987654  344445667788899999999999999887644332233   333344456


Q ss_pred             CChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHH
Q 040365          222 GNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYE  300 (514)
Q Consensus       222 g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~  300 (514)
                      |++++|+..|++..+.  .|+...+..+..++.+.|+.++|...++....   ..| +...+..+...+...|++++|.+
T Consensus       590 Gr~~eAl~~~~~AL~l--~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~---l~Pd~~~a~~nLG~aL~~~G~~eeAi~  664 (987)
T PRK09782        590 GQPELALNDLTRSLNI--APSANAYVARATIYRQRHNVPAAVSDLRAALE---LEPNNSNYQAALGYALWDSGDIAQSRE  664 (987)
T ss_pred             CCHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            9999999999999874  67888899999999999999999999999864   466 57788888899999999999999


Q ss_pred             HHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCc
Q 040365          301 FISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       301 ~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  377 (514)
                      .+++.. ..| +...+..+..++...|++++|+..++++++++|+++.+.........+..+++.|.+-+++--.-.+.
T Consensus       665 ~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P~~a~i~~~~g~~~~~~~~~~~a~~~~~r~~~~~~~  743 (987)
T PRK09782        665 MLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDIDNQALITPLTPEQNQQRFNFRRLHEEVGRRWTFSFD  743 (987)
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHhhcCcc
Confidence            999863 334 67889999999999999999999999999999999999989999999999999999988776554443

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.64  E-value=4.4e-12  Score=117.84  Aligned_cols=332  Identities=16%  Similarity=0.168  Sum_probs=244.7

Q ss_pred             CCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHH
Q 040365            3 VSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSL   82 (514)
Q Consensus         3 ~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (514)
                      .++..++..||.|+++-...+.|.+++++-.....+.+..+||.+|.+-.-    ..++.+..+|+...+.||..|+|++
T Consensus       204 PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~----~~~K~Lv~EMisqkm~Pnl~TfNal  279 (625)
T KOG4422|consen  204 PKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSY----SVGKKLVAEMISQKMTPNLFTFNAL  279 (625)
T ss_pred             CCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHh----hccHHHHHHHHHhhcCCchHhHHHH
Confidence            456789999999999999999999999999988889999999999987653    3348899999999999999999999


Q ss_pred             HHHHHHCCCHHHHHHHH----ccCC----CCChhHHHHHHHHHHHCCChhH-HHHHHHHHHHC----CCC---C-CHHHH
Q 040365           83 INMYAKCARVEDSHRLF----CLLP----VKDAISWNSIIAGCVQNGLFDE-GLKFFRQMLIA----KIK---P-RHVSF  145 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f----~~~~----~~d~~~~~~li~~~~~~g~~~~-A~~l~~~m~~~----g~~---p-~~~t~  145 (514)
                      +.+.++.|+++.|++.+    .+|+    +|...+|..+|..+.+.+++.+ |..++.+....    .++   | |..-|
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            99999999988766544    4454    7899999999999999888754 44455554431    222   2 45667


Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHcC----CCCc---HHHHHHHHHHHHhcCCHHHHHHHHHhCC----CCChhHHHHH
Q 040365          146 SSIMPACAHLTTLHLGKQLHGCIIRNG----FDDN---MFIASSLLDMYAKCGNIRLARCIFDKMD----LHDIVSWTAV  214 (514)
Q Consensus       146 ~~ll~~~~~~~~~~~a~~~~~~~~~~~----~~~~---~~~~~~li~~y~k~g~~~~A~~~~~~m~----~~d~~~~~~l  214 (514)
                      .+.+..|.+..+.+.|.+++..+....    +.|+   .+.|..+....+....++.-...|+.|.    -|+..+...+
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            899999999999999999998765431    2333   3456678888889999999999999986    3466677778


Q ss_pred             HHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccC---------CHHH-----HHHHH-------HHhHHhc
Q 040365          215 IMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAG---------LIDK-----AWSYF-------NSMTKDY  273 (514)
Q Consensus       215 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g---------~~~~-----a~~~~-------~~m~~~~  273 (514)
                      +.+....|+++-.-+++.++...|..-+...-.-++...++..         ++..     |..++       .++.   
T Consensus       440 lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r---  516 (625)
T KOG4422|consen  440 LRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQR---  516 (625)
T ss_pred             HHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHH---
Confidence            8888888988888888888887764433333333333333322         0000     11111       1121   


Q ss_pred             CCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC-------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040365          274 GIAPSFEHYAAVADLLGRAGKLQEAYEFISNM-------HAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMID  341 (514)
Q Consensus       274 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m-------~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  341 (514)
                      .........++..-.+.|.|+.++|.+++.-+       +..|......-|+.+..+.++...|..+++-+...+
T Consensus       517 ~~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a~~~n  591 (625)
T KOG4422|consen  517 AQDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLASAFN  591 (625)
T ss_pred             hccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Confidence            23345567788888899999999999988755       223555455566777788888888888888876655

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

Probab=99.60  E-value=5.6e-15  Score=139.89  Aligned_cols=255  Identities=17%  Similarity=0.132  Sum_probs=110.6

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHH-HHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSI-MPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG  191 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l-l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g  191 (514)
                      +...+.+.|++++|++++++......+|+...|..+ ...+-..++.+.|.+.++.+.+.+ +.+...+..++.. ...+
T Consensus        14 ~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~-~~~~~~~~~l~~l-~~~~   91 (280)
T PF13429_consen   14 LARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD-KANPQDYERLIQL-LQDG   91 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccc-cccc
Confidence            355566777777777777554443223444444433 334455677777777777777665 2355566666666 6788


Q ss_pred             CHHHHHHHHHhCC--CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040365          192 NIRLARCIFDKMD--LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG-VKPNSVAFVAVLTACSHAGLIDKAWSYFNS  268 (514)
Q Consensus       192 ~~~~A~~~~~~m~--~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~  268 (514)
                      ++++|.++++..-  .++...+..++..+.+.|+++++.++++++.... .+++...|..+...+.+.|+.++|...++.
T Consensus        92 ~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~  171 (280)
T PF13429_consen   92 DPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRK  171 (280)
T ss_dssp             --------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred             cccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            8888888877663  3456677788888889999999999999977533 345667778888888999999999999998


Q ss_pred             hHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          269 MTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       269 m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      ..+.   .| +......++..+...|+.+++.++++...  .+.|...|..+..++...|+.+.|...++++...+|+|+
T Consensus       172 al~~---~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~  248 (280)
T PF13429_consen  172 ALEL---DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDP  248 (280)
T ss_dssp             HHHH----TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-H
T ss_pred             HHHc---CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence            8754   66 57788889999999999999877776653  134566789999999999999999999999999999999


Q ss_pred             chHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          346 GAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       346 ~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      .....++.++...|+.++|.+++.+.-
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            999999999999999999999987654

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

Probab=99.58  E-value=1e-11  Score=125.59  Aligned_cols=331  Identities=14%  Similarity=0.150  Sum_probs=243.0

Q ss_pred             HhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHcc---CCCCChhHHHHHHHHHHHCCChhHHH
Q 040365           51 FADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCL---LPVKDAISWNSIIAGCVQNGLFDEGL  127 (514)
Q Consensus        51 ~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~---~~~~d~~~~~~li~~~~~~g~~~~A~  127 (514)
                      ....|++++|..++.++++.. +.....|-+|...|-..|+++++...+-.   +...|..-|-.+.....+.|.+++|.
T Consensus       149 lfarg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~qA~  227 (895)
T KOG2076|consen  149 LFARGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQAR  227 (895)
T ss_pred             HHHhCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHHHH
Confidence            333488999999999888876 66778888899999999998888776643   33557788888888888889999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHH----HHHHHHhcCCHHHHHHHHHhC
Q 040365          128 KFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASS----LLDMYAKCGNIRLARCIFDKM  203 (514)
Q Consensus       128 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----li~~y~k~g~~~~A~~~~~~m  203 (514)
                      -.|.+..+.. +++...+---...|-+.|+...|..-+.++....-+.|..-...    .+..|...++-+.|.+.++..
T Consensus       228 ~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~  306 (895)
T KOG2076|consen  228 YCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGA  306 (895)
T ss_pred             HHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            9998888763 44544455556678888888888888888887653333333333    345566677778888888776


Q ss_pred             CC--C---ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHH--------------------------HHHHHH
Q 040365          204 DL--H---DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAF--------------------------VAVLTA  252 (514)
Q Consensus       204 ~~--~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~--------------------------~~ll~a  252 (514)
                      ..  .   +...++.++..|.+...++.|......+......||..-+                          .-+.-+
T Consensus       307 ~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~ic  386 (895)
T KOG2076|consen  307 LSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMIC  386 (895)
T ss_pred             HhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhh
Confidence            53  2   3456788888888888888888888887762222222111                          112223


Q ss_pred             HHccCCHHHHHHHHHHhHHhcCCCC--CHhHHHHHHHHHHhcCCHHHHHHHHHhCCCC---CCHHHHHHHHHHHHhcCCH
Q 040365          253 CSHAGLIDKAWSYFNSMTKDYGIAP--SFEHYAAVADLLGRAGKLQEAYEFISNMHAG---PTENVWLTLLSACRVHKNV  327 (514)
Q Consensus       253 ~~~~g~~~~a~~~~~~m~~~~~~~p--~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---p~~~~~~~ll~~~~~~~~~  327 (514)
                      +.+....+....+..-..+ ..+.|  ++..|.-+.++|...|++.+|+++|..+...   .+...|..+..++...|.+
T Consensus       387 L~~L~~~e~~e~ll~~l~~-~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~  465 (895)
T KOG2076|consen  387 LVHLKERELLEALLHFLVE-DNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEY  465 (895)
T ss_pred             hhcccccchHHHHHHHHHH-hcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhH
Confidence            3344433333333333323 35444  6788999999999999999999999988533   3577999999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccE
Q 040365          328 ELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSW  384 (514)
Q Consensus       328 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~  384 (514)
                      +.|.+.+++++.+.|++..+-..|+..|.+.|+.++|.++++.|..-+-..-+++.|
T Consensus       466 e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~  522 (895)
T KOG2076|consen  466 EEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAW  522 (895)
T ss_pred             HHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccc
Confidence            999999999999999999999999999999999999999999887433223345555

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.58  E-value=9.9e-12  Score=115.54  Aligned_cols=317  Identities=17%  Similarity=0.207  Sum_probs=195.1

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHH--hCCCChHHH-HHHHHHHHHhCCCCchhHHHHH
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIF--ADYVDVIKG-KEIHGYAIRHGLDANVCIGSSL   82 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~--~~~~~~~~a-~~~~~~~~~~g~~~~~~~~~~l   82 (514)
                      +++=|.|+. ....|..+++.-+|+.|...|+..+...-..++...  -...++.-+ .+-|-.|.+.| +.+..+|   
T Consensus       116 V~~E~nL~k-mIS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~-E~S~~sW---  190 (625)
T KOG4422|consen  116 VETENNLLK-MISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFG-EDSTSSW---  190 (625)
T ss_pred             hcchhHHHH-HHhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccc-ccccccc---
Confidence            445566554 445688889999999999888776665544444432  222333222 23344455544 2222332   


Q ss_pred             HHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHH
Q 040365           83 INMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGK  162 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~  162 (514)
                           |.|++.+   ++-+...+...++.+||.|.++-...+.|.++|++-.....+.+..+|+.+|.+-+    +..++
T Consensus       191 -----K~G~vAd---L~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S----~~~~K  258 (625)
T KOG4422|consen  191 -----KSGAVAD---LLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASS----YSVGK  258 (625)
T ss_pred             -----ccccHHH---HHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHH----hhccH
Confidence                 3455544   44445556778999999999999999999999999999888999999999998765    34458


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHH----hCC----CCChhHHHHHHHHHHhCCChHH-HHHHHHH
Q 040365          163 QLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFD----KMD----LHDIVSWTAVIMGNALHGNAHD-AISLFEQ  233 (514)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~----~m~----~~d~~~~~~li~~~~~~g~~~~-A~~l~~~  233 (514)
                      ++..+|+...+.||..++|+++.+.++.|+++.|++.+-    +|.    +|...+|..+|..+.+.++..+ |..++.+
T Consensus       259 ~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~d  338 (625)
T KOG4422|consen  259 KLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWIND  338 (625)
T ss_pred             HHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHH
Confidence            899999999999999999999999999999988765433    232    5566666666666666555433 3333333


Q ss_pred             HHH----cCCCC----CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC---CCCC---HhHHHHHHHHHHhcCCHHHHH
Q 040365          234 MEK----DGVKP----NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG---IAPS---FEHYAAVADLLGRAGKLQEAY  299 (514)
Q Consensus       234 m~~----~g~~p----~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~---~~p~---~~~~~~li~~~~~~g~~~~A~  299 (514)
                      +..    ..++|    |..-|...+..|.+..+.+.|.++...+....+   +.|+   ..-|..+.++.+....++.-+
T Consensus       339 I~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~  418 (625)
T KOG4422|consen  339 IQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTL  418 (625)
T ss_pred             HHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            332    11222    234455666666666666666665554422111   1122   122344455555555555555


Q ss_pred             HHHHhCCC---CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040365          300 EFISNMHA---GPTENVWLTLLSACRVHKNVELAGKVAEKIFM  339 (514)
Q Consensus       300 ~~~~~m~~---~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  339 (514)
                      ..++.|.-   -|+..+-..++.+....+.++..-+++..+..
T Consensus       419 ~~Y~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~  461 (625)
T KOG4422|consen  419 KWYEDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKE  461 (625)
T ss_pred             HHHHHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHH
Confidence            55555531   14444445555555555555555555544433

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.54  E-value=1.4e-11  Score=122.31  Aligned_cols=278  Identities=9%  Similarity=-0.031  Sum_probs=200.5

Q ss_pred             CCChHHHHHHHHHHHHhCCCCchhHHHHH-HHHHHHCCCHHHHHHHHccCCC--CChhHHH--HHHHHHHHCCChhHHHH
Q 040365           54 YVDVIKGKEIHGYAIRHGLDANVCIGSSL-INMYAKCARVEDSHRLFCLLPV--KDAISWN--SIIAGCVQNGLFDEGLK  128 (514)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~l-i~~~~~~g~~~~A~~~f~~~~~--~d~~~~~--~li~~~~~~g~~~~A~~  128 (514)
                      .|+++.|++......+..  +++.++-.+ .....+.|+.+.|.+.|.++.+  |+....-  .....+...|++++|+.
T Consensus        97 eGd~~~A~k~l~~~~~~~--~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~  174 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHA--EQPVVNYLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARH  174 (398)
T ss_pred             CCCHHHHHHHHHHHHhcc--cchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHH
Confidence            578888887766654432  223333333 3344677888888888877764  2322111  23566777888888888


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcH-------HHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          129 FFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNM-------FIASSLLDMYAKCGNIRLARCIFD  201 (514)
Q Consensus       129 l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~li~~y~k~g~~~~A~~~~~  201 (514)
                      .++++.+.. +-+...+..+...+.+.|+++.+.+++..+.+.+..++.       ..+..++....+..+.+...++++
T Consensus       175 ~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~  253 (398)
T PRK10747        175 GVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWK  253 (398)
T ss_pred             HHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            888887754 334556667777888888888888888888877643322       233445555555666777788888


Q ss_pred             hCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-
Q 040365          202 KMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-  277 (514)
Q Consensus       202 ~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-  277 (514)
                      .++   ..++.....+..++...|+.++|.+++++..+.  .||...  .++.+....++.+++.+..+...+.   .| 
T Consensus       254 ~lp~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk~---~P~  326 (398)
T PRK10747        254 NQSRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERL--VLLIPRLKTNNPEQLEKVLRQQIKQ---HGD  326 (398)
T ss_pred             hCCHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHH--HHHHhhccCCChHHHHHHHHHHHhh---CCC
Confidence            876   347778888999999999999999999988874  445421  2333444568999999999988765   45 


Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMID  341 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  341 (514)
                      |+..+.++...+.+.|++++|.+.|+... ..|+...+..|...+...|+.++|.+++++.+.+-
T Consensus       327 ~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~  391 (398)
T PRK10747        327 TPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEAAAMRRDGLMLT  391 (398)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence            66778899999999999999999999864 56999998999999999999999999999987653

>TIGR00540 hemY_coli hemY protein

Probab=99.53  E-value=6.7e-11  Score=118.00  Aligned_cols=282  Identities=11%  Similarity=-0.020  Sum_probs=158.8

Q ss_pred             CCCChHHHHHHHHHHHHhCCCCch-hHHHHHHHHHHHCCCHHHHHHHHccCCC--CCh--hHHHHHHHHHHHCCChhHHH
Q 040365           53 DYVDVIKGKEIHGYAIRHGLDANV-CIGSSLINMYAKCARVEDSHRLFCLLPV--KDA--ISWNSIIAGCVQNGLFDEGL  127 (514)
Q Consensus        53 ~~~~~~~a~~~~~~~~~~g~~~~~-~~~~~li~~~~~~g~~~~A~~~f~~~~~--~d~--~~~~~li~~~~~~g~~~~A~  127 (514)
                      ..|+++.|.+.+....+..  |+. ..+-.....+.+.|+.+.|.+.|.+..+  |+.  ...-+....+.+.|+++.|+
T Consensus        96 ~~g~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al  173 (409)
T TIGR00540        96 AEGDYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAAR  173 (409)
T ss_pred             hCCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHH
Confidence            4577777777776665543  332 2233334556667777777777766421  222  22333456666777777777


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHH-------HHHHHHHHhcCCHHHHHHHH
Q 040365          128 KFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIA-------SSLLDMYAKCGNIRLARCIF  200 (514)
Q Consensus       128 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-------~~li~~y~k~g~~~~A~~~~  200 (514)
                      +.++++.+.. +-+...+..+...+.+.|+++.+.+.+..+.+.+..+.....       ..+++.-......+...+.+
T Consensus       174 ~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~  252 (409)
T TIGR00540       174 HGVDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWW  252 (409)
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            7777777653 234445666677777777777777777777776543322221       11111111222233444444


Q ss_pred             HhCCC---CChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHH---HHHHHHHHccCCHHHHHHHHHHhHHhcC
Q 040365          201 DKMDL---HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAF---VAVLTACSHAGLIDKAWSYFNSMTKDYG  274 (514)
Q Consensus       201 ~~m~~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~---~~ll~a~~~~g~~~~a~~~~~~m~~~~~  274 (514)
                      +..+.   .+...+..+...+...|+.++|.+++++..+.  .||....   ..........++.+.+.+.++...+...
T Consensus       253 ~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p  330 (409)
T TIGR00540       253 KNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVD  330 (409)
T ss_pred             HHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCC
Confidence            44442   36666777777777777777777777777664  3443311   1111122234566666666666554322


Q ss_pred             CCCCHhHHHHHHHHHHhcCCHHHHHHHHHh--C-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040365          275 IAPSFEHYAAVADLLGRAGKLQEAYEFISN--M-HAGPTENVWLTLLSACRVHKNVELAGKVAEKIFM  339 (514)
Q Consensus       275 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~--m-~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  339 (514)
                      -.|+.....++...+.+.|++++|.+.|+.  . ...||...+..+...+.+.|+.++|.+++++.+.
T Consensus       331 ~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       331 DKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             CChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            222214455666666677777777777662  2 3356666666666666677777777666666543

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

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

Probab=99.51  E-value=1.4e-13  Score=130.36  Aligned_cols=254  Identities=16%  Similarity=0.086  Sum_probs=80.8

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCChhhH-HHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCC
Q 040365           12 VIVGLARNGLYEEALNIVRQMGNVNLKPDSFTL-SSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA   90 (514)
Q Consensus        12 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g   90 (514)
                      +...+.+.|++++|+++++.-.....+|+...| ..+.......++.+.|.+.++.+...+ +.++..+..++.. ...+
T Consensus        14 ~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~-~~~~~~~~~l~~l-~~~~   91 (280)
T PF13429_consen   14 LARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD-KANPQDYERLIQL-LQDG   91 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccc-cccc
Confidence            345566677777777777544333223433333 333334445677777777777777665 2345556666666 5667


Q ss_pred             CHHHHHHHHccCC--CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCC-CCCCHHHHHHHHHHHhccCChHHHHHHHHH
Q 040365           91 RVEDSHRLFCLLP--VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAK-IKPRHVSFSSIMPACAHLTTLHLGKQLHGC  167 (514)
Q Consensus        91 ~~~~A~~~f~~~~--~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  167 (514)
                      +.++|.+++...-  .++...+..++..+.+.++++++.+++++..... .+++...|..+...+.+.|+.++|...+++
T Consensus        92 ~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~  171 (280)
T PF13429_consen   92 DPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYRK  171 (280)
T ss_dssp             --------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred             cccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            7777776665542  2345556666677777777777777777765432 234555566666666677777777777777


Q ss_pred             HHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH
Q 040365          168 IIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV  244 (514)
Q Consensus       168 ~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~  244 (514)
                      .++.. |.|..+.+.++..+...|+.+++.+++....   ..|...|..+..+|...|+.++|+..|++..... +.|..
T Consensus       172 al~~~-P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~-p~d~~  249 (280)
T PF13429_consen  172 ALELD-PDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN-PDDPL  249 (280)
T ss_dssp             HHHH--TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS-TT-HH
T ss_pred             HHHcC-CCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccccccc-ccccc
Confidence            76654 3346666666767776776666555554443   3355566666666666666666666666666531 22455


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      +...+..++...|+.++|.++..+.
T Consensus       250 ~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  250 WLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             HHHHHHHHHT---------------
T ss_pred             ccccccccccccccccccccccccc
Confidence            5566666666666666666665554

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.50  E-value=5.2e-11  Score=118.16  Aligned_cols=275  Identities=9%  Similarity=0.009  Sum_probs=210.9

Q ss_pred             CCCHHHHHHHHccCCCC--C-hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHH--HHHHHHhccCChHHHHH
Q 040365           89 CARVEDSHRLFCLLPVK--D-AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFS--SIMPACAHLTTLHLGKQ  163 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~~~--d-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~--~ll~~~~~~~~~~~a~~  163 (514)
                      .|+++.|++.+...++.  + ...|-.......+.|++++|.+.|.++.+.  .|+...+.  .....+...|+++.|.+
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~  174 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARH  174 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHH
Confidence            69999999999876643  2 333433345558899999999999999874  56654443  33567888999999999


Q ss_pred             HHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCCh-----------hHHHHHHHHHHhCCChHHHHHHHH
Q 040365          164 LHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDI-----------VSWTAVIMGNALHGNAHDAISLFE  232 (514)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~-----------~~~~~li~~~~~~g~~~~A~~l~~  232 (514)
                      .++.+.+.. +.+..+...+...|.+.|++++|.+++..+.+...           .+|..++.......+.+...++++
T Consensus       175 ~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~  253 (398)
T PRK10747        175 GVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWK  253 (398)
T ss_pred             HHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            999999886 66788899999999999999999999998874321           134444444444555666677777


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-C
Q 040365          233 QMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-T  310 (514)
Q Consensus       233 ~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~  310 (514)
                      .+... .+.+......+..++...|+.++|..+++...+.   .|+....  ++.+....++.+++.+.++... ..| |
T Consensus       254 ~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~---~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~~P~~  327 (398)
T PRK10747        254 NQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR---QYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQHGDT  327 (398)
T ss_pred             hCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CCCHHHH--HHHhhccCCChHHHHHHHHHHHhhCCCC
Confidence            66443 3446677888999999999999999999988653   4555322  2233335599999999998764 335 5


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ......+...|...+++++|...|+++.+..|++ ..+..|..++.+.|+.++|.+++++-..
T Consensus       328 ~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~-~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        328 PLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDA-YDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            5668889999999999999999999999999875 5688999999999999999999986543

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

Probab=99.49  E-value=1.2e-10  Score=109.01  Aligned_cols=340  Identities=14%  Similarity=0.137  Sum_probs=216.0

Q ss_pred             HHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCC------------chhHHHH
Q 040365           14 VGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDA------------NVCIGSS   81 (514)
Q Consensus        14 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~------------~~~~~~~   81 (514)
                      --+.+.|++++|+..|+...+.  .||-.+-..++-.+...|+.++.++.|..|+.....+            +....|.
T Consensus       284 vtfiq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll~e  361 (840)
T KOG2003|consen  284 VTFIQAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNE  361 (840)
T ss_pred             eeEEecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHHHH
Confidence            3467789999999999988775  4776654444444555688899999999887653222            2222222


Q ss_pred             HH-----HHHHHCCC--HH----HHHHHHccCCCCChhH---HHH------------------HHHHHHHCCChhHHHHH
Q 040365           82 LI-----NMYAKCAR--VE----DSHRLFCLLPVKDAIS---WNS------------------IIAGCVQNGLFDEGLKF  129 (514)
Q Consensus        82 li-----~~~~~~g~--~~----~A~~~f~~~~~~d~~~---~~~------------------li~~~~~~g~~~~A~~l  129 (514)
                      -|     .-.-+...  .+    .|.++..-...||-..   |..                  -..-|.++|+++.|+++
T Consensus       362 ai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~aiei  441 (840)
T KOG2003|consen  362 AIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEGAIEI  441 (840)
T ss_pred             HHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHHHH
Confidence            22     11111111  11    1222222222332110   110                  12347889999999998


Q ss_pred             HHHHHHCCCCCCHHHHH--HHHHHH----------------------------------hccCChHHHHHHHHHHHHcCC
Q 040365          130 FRQMLIAKIKPRHVSFS--SIMPAC----------------------------------AHLTTLHLGKQLHGCIIRNGF  173 (514)
Q Consensus       130 ~~~m~~~g~~p~~~t~~--~ll~~~----------------------------------~~~~~~~~a~~~~~~~~~~~~  173 (514)
                      ++-..+..-+.-...-+  +++...                                  ...|++++|.+.+.+.+...-
T Consensus       442 lkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~ngd~dka~~~ykeal~nda  521 (840)
T KOG2003|consen  442 LKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFANGDLDKAAEFYKEALNNDA  521 (840)
T ss_pred             HHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeeecCcHHHHHHHHHHHHcCch
Confidence            88776543221111111  111111                                  123566666666666655432


Q ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040365          174 DDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVL  250 (514)
Q Consensus       174 ~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  250 (514)
                      .-....|| +.-.|-+.|++++|.+.|-++.   ..++...-.+.+.|-...++..|++++-+.... ++.|...+.-|.
T Consensus       522 sc~ealfn-iglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~sl-ip~dp~ilskl~  599 (840)
T KOG2003|consen  522 SCTEALFN-IGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLA  599 (840)
T ss_pred             HHHHHHHH-hcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHHHHHHH
Confidence            22222222 2334566777777777776653   345555556666777777777777777665542 344556777788


Q ss_pred             HHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCHHHHHHHHHHH-HhcCCH
Q 040365          251 TACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPTENVWLTLLSAC-RVHKNV  327 (514)
Q Consensus       251 ~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~~~~~~ll~~~-~~~~~~  327 (514)
                      ..|-+.|+-.+|.+.+-.   .+..-| +.++..-|..-|....-+++|..+|++.. ..|+..-|..++..| ++.|++
T Consensus       600 dlydqegdksqafq~~yd---syryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgny  676 (840)
T KOG2003|consen  600 DLYDQEGDKSQAFQCHYD---SYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGNY  676 (840)
T ss_pred             HHhhcccchhhhhhhhhh---cccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhcccH
Confidence            888888888888877653   234444 78888888888888888899999998864 679999999988765 678999


Q ss_pred             HHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          328 ELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       328 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      +.|..+++......|.|......|...+...|.
T Consensus       677 qka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  677 QKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence            999999999999999999999999998887774

>TIGR00540 hemY_coli hemY protein

Probab=99.48  E-value=7.2e-11  Score=117.78  Aligned_cols=291  Identities=12%  Similarity=0.027  Sum_probs=209.9

Q ss_pred             HHHHHHHHH--hcCChhHHHHHHHHHhhCCCCCChh-hHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            9 WNTVIVGLA--RNGLYEEALNIVRQMGNVNLKPDSF-TLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         9 ~~~li~~~~--~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      ...+..|..  ..|+++.|.+.+....+.  .|++. .+-....+..+.|+.+.+.+.+..+.+..-.+...+.-.....
T Consensus        85 ~~~~~~glla~~~g~~~~A~~~l~~~~~~--~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l  162 (409)
T TIGR00540        85 QKQTEEALLKLAEGDYAKAEKLIAKNADH--AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRI  162 (409)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHH
Confidence            344444443  369999999999887765  45543 3444566777889999999999998876422223455556888


Q ss_pred             HHHCCCHHHHHHHHccCCC---CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHH-HHHHHH---hccCCh
Q 040365           86 YAKCARVEDSHRLFCLLPV---KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFS-SIMPAC---AHLTTL  158 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~-~ll~~~---~~~~~~  158 (514)
                      +...|+.+.|...++.+.+   .+...+..+...+.+.|++++|.+++..+.+.++. +...+. .-..+.   ...+..
T Consensus       163 ~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~~  241 (409)
T TIGR00540       163 LLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAMA  241 (409)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998863   36678889999999999999999999999998754 333331 111221   122222


Q ss_pred             HHHHHHHHHHHHcC---CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--CChhH---HHHHHHHHHhCCChHHHHHH
Q 040365          159 HLGKQLHGCIIRNG---FDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--HDIVS---WTAVIMGNALHGNAHDAISL  230 (514)
Q Consensus       159 ~~a~~~~~~~~~~~---~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d~~~---~~~li~~~~~~g~~~~A~~l  230 (514)
                      +.+.+.+..+.+..   .+.+...+..+...+...|+.++|.+++++..+  ||...   +..........++.+.+++.
T Consensus       242 ~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~  321 (409)
T TIGR00540       242 DEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKL  321 (409)
T ss_pred             hcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHH
Confidence            33333444444432   124788899999999999999999999999863  43331   12222233446788899999


Q ss_pred             HHHHHHcCCCCCHH---HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          231 FEQMEKDGVKPNSV---AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       231 ~~~m~~~g~~p~~~---t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      +++..+.  .|+..   ...++...|.+.|++++|.++|+... .....|+...+..+...+.+.|+.++|.+++++.
T Consensus       322 ~e~~lk~--~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~-a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       322 IEKQAKN--VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVA-ACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHHh--CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhH-HhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9887764  55554   45578888999999999999999532 2356899988999999999999999999999863

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

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

Probab=99.47  E-value=3e-10  Score=115.92  Aligned_cols=367  Identities=13%  Similarity=0.036  Sum_probs=263.6

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCC--CChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLK--PDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSS   81 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~   81 (514)
                      .|++..|-|..-|.-.|+++.++.+...+......  --..+|-.+.+++-..|++++|...|.+..+..-..-+..+--
T Consensus       268 ~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~G  347 (1018)
T KOG2002|consen  268 ENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVG  347 (1018)
T ss_pred             CCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccc
Confidence            47788889999999999999999999988764311  1123577788999999999999999988887642222444566


Q ss_pred             HHHHHHHCCCHHHHHHHHccCCC--C-ChhHHHHHHHHHHHCC----ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhc
Q 040365           82 LINMYAKCARVEDSHRLFCLLPV--K-DAISWNSIIAGCVQNG----LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH  154 (514)
Q Consensus        82 li~~~~~~g~~~~A~~~f~~~~~--~-d~~~~~~li~~~~~~g----~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~  154 (514)
                      |..+|.+.|+++.|...|+.+..  | +..+.-.|...|+..+    ..+.|..++.+..+. .+.|...|..+...+-.
T Consensus       348 lgQm~i~~~dle~s~~~fEkv~k~~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~-~~~d~~a~l~laql~e~  426 (1018)
T KOG2002|consen  348 LGQMYIKRGDLEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQ-TPVDSEAWLELAQLLEQ  426 (1018)
T ss_pred             hhHHHHHhchHHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhc-ccccHHHHHHHHHHHHh
Confidence            88999999999999999998763  3 4566667777777765    456677777666554 24566677666665544


Q ss_pred             cCChHHHHHHHHH----HHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC-------CCh------hHHHHHHHH
Q 040365          155 LTTLHLGKQLHGC----IIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL-------HDI------VSWTAVIMG  217 (514)
Q Consensus       155 ~~~~~~a~~~~~~----~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~-------~d~------~~~~~li~~  217 (514)
                      . +...+..++..    +...+-++.+.+.|.+...+...|++++|...|.....       +|.      .+-..+...
T Consensus       427 ~-d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl  505 (1018)
T KOG2002|consen  427 T-DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARL  505 (1018)
T ss_pred             c-ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHH
Confidence            3 33333554443    34456567888999999999999999999999987642       222      122234455


Q ss_pred             HHhCCChHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHH
Q 040365          218 NALHGNAHDAISLFEQMEKDGVKPNSV-AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       218 ~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  296 (514)
                      +-..++.+.|.+.|......  .|+-+ .|..++......+...+|...++....  ....++..++.+...+.+...+.
T Consensus       506 ~E~l~~~~~A~e~Yk~Ilke--hp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~--~d~~np~arsl~G~~~l~k~~~~  581 (1018)
T KOG2002|consen  506 LEELHDTEVAEEMYKSILKE--HPGYIDAYLRLGCMARDKNNLYEASLLLKDALN--IDSSNPNARSLLGNLHLKKSEWK  581 (1018)
T ss_pred             HHhhhhhhHHHHHHHHHHHH--CchhHHHHHHhhHHHHhccCcHHHHHHHHHHHh--cccCCcHHHHHHHHHHHhhhhhc
Confidence            55678899999999999885  56654 344444333345778888888888765  33445566666777887777777


Q ss_pred             HHHHHHHhC----CCCCCHHHHHHHHHHHH------------hcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          297 EAYEFISNM----HAGPTENVWLTLLSACR------------VHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       297 ~A~~~~~~m----~~~p~~~~~~~ll~~~~------------~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      -|.+-|+.+    ...+|+.+.-+|.+.|.            ..+..+.|+++|.+++..+|.|..+-+.++-+++..|+
T Consensus       582 ~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg~  661 (1018)
T KOG2002|consen  582 PAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKGR  661 (1018)
T ss_pred             ccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchhhhhhhccC
Confidence            777744443    33467777667766553            23456788889999999999998888888889999999


Q ss_pred             hhHHHHHHHHHHhCCC
Q 040365          361 WKDAASLRVFMRNKGM  376 (514)
Q Consensus       361 ~~~a~~~~~~m~~~g~  376 (514)
                      +.+|..+|.+.++...
T Consensus       662 ~~~A~dIFsqVrEa~~  677 (1018)
T KOG2002|consen  662 FSEARDIFSQVREATS  677 (1018)
T ss_pred             chHHHHHHHHHHHHHh
Confidence            9999999999988765

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

Probab=99.47  E-value=2.4e-09  Score=104.88  Aligned_cols=370  Identities=12%  Similarity=0.046  Sum_probs=286.6

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHH
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMY   86 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~   86 (514)
                      .+|+.-...|.+.+.++-|..+|...++- .+-+...|......--..|..+.-..+++.++..- +.....|--...-+
T Consensus       517 ~tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~~ek~hgt~Esl~Allqkav~~~-pkae~lwlM~ake~  594 (913)
T KOG0495|consen  517 STWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQC-PKAEILWLMYAKEK  594 (913)
T ss_pred             hHHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CcchhHHHHHHHHH
Confidence            46777777888888888888888887764 23345566666665566788888888888888763 45556666667777


Q ss_pred             HHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHH
Q 040365           87 AKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQ  163 (514)
Q Consensus        87 ~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~  163 (514)
                      -..|++..|+.+++..-   ..+...|-+-+.....+.++++|..+|.+....  .|+...|.--+..---++..++|.+
T Consensus       595 w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~~--sgTeRv~mKs~~~er~ld~~eeA~r  672 (913)
T KOG0495|consen  595 WKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARSI--SGTERVWMKSANLERYLDNVEEALR  672 (913)
T ss_pred             HhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--CCcchhhHHHhHHHHHhhhHHHHHH
Confidence            77899999988877654   235667888888888899999999999888764  5666666555555556788899999


Q ss_pred             HHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCC
Q 040365          164 LHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--H-DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK  240 (514)
Q Consensus       164 ~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  240 (514)
                      +++..++. ++.-.-.|-.+...|-+.++++.|++.|..-.+  | .+..|-.+...=-+.|..-.|..+|++....+ +
T Consensus       673 llEe~lk~-fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk~~~~~rAR~ildrarlkN-P  750 (913)
T KOG0495|consen  673 LLEEALKS-FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEKDGQLVRARSILDRARLKN-P  750 (913)
T ss_pred             HHHHHHHh-CCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHHhcchhhHHHHHHHHHhcC-C
Confidence            99888876 455566777888888888999999988877652  2 45678777777778888999999999888764 3


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 040365          241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSA  320 (514)
Q Consensus       241 p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~  320 (514)
                      -|..-|...+..-.+.|..++|..+..+..++  ++.+...|..-|-+..+.++-..+.+-+++-.  .|..+.-++...
T Consensus       751 k~~~lwle~Ir~ElR~gn~~~a~~lmakALQe--cp~sg~LWaEaI~le~~~~rkTks~DALkkce--~dphVllaia~l  826 (913)
T KOG0495|consen  751 KNALLWLESIRMELRAGNKEQAELLMAKALQE--CPSSGLLWAEAIWLEPRPQRKTKSIDALKKCE--HDPHVLLAIAKL  826 (913)
T ss_pred             CcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccchhHHHHHHhccCcccchHHHHHHHhcc--CCchhHHHHHHH
Confidence            36678888888889999999999988887664  44467788888888888888777766666654  456666777778


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccEEEEC
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVK  388 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~  388 (514)
                      +....+++.|...|++....+|++..+|..+...+...|.-++-.+++.+....  .|..|..|..+.
T Consensus       827 fw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev~~~c~~~--EP~hG~~W~avS  892 (913)
T KOG0495|consen  827 FWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEVLKKCETA--EPTHGELWQAVS  892 (913)
T ss_pred             HHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHHHHHHhcc--CCCCCcHHHHHh
Confidence            888899999999999999999999999999999999999999999999887654  366677886553

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

Probab=99.46  E-value=1.6e-11  Score=120.59  Aligned_cols=275  Identities=11%  Similarity=0.017  Sum_probs=211.1

Q ss_pred             CHHHHHHHHccCCC--CCh-hHHHHHHHHHHHCCChhHHHHHHHHHHHCC--CCCCHHHHHHHHHHHhccCChHHHHHHH
Q 040365           91 RVEDSHRLFCLLPV--KDA-ISWNSIIAGCVQNGLFDEGLKFFRQMLIAK--IKPRHVSFSSIMPACAHLTTLHLGKQLH  165 (514)
Q Consensus        91 ~~~~A~~~f~~~~~--~d~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--~~p~~~t~~~ll~~~~~~~~~~~a~~~~  165 (514)
                      +..+|...|..+++  +|. ....-+..+|...+++++|.++|+..++..  ..-+...|++++--+-+.    .+...+
T Consensus       334 ~~~~A~~~~~klp~h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~----v~Ls~L  409 (638)
T KOG1126|consen  334 NCREALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDE----VALSYL  409 (638)
T ss_pred             HHHHHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhh----HHHHHH
Confidence            46788888888663  233 334456788888999999999999887642  112556777777554321    122222


Q ss_pred             H-HHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC---ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC
Q 040365          166 G-CIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH---DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP  241 (514)
Q Consensus       166 ~-~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  241 (514)
                      . .+++. -+..+.+|-++.++|.-.++.+.|++.|++...-   ...+|+.+..-+.....+|.|...|+..+.  +.|
T Consensus       410 aq~Li~~-~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~--~~~  486 (638)
T KOG1126|consen  410 AQDLIDT-DPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALG--VDP  486 (638)
T ss_pred             HHHHHhh-CCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhc--CCc
Confidence            2 22222 2556789999999999999999999999988633   567888887788888999999999998765  344


Q ss_pred             CH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHH
Q 040365          242 NS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTL  317 (514)
Q Consensus       242 ~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~l  317 (514)
                      .. -.|-.+...|.+.++++.|.-.|+...   .+.| +.....++...+-+.|+.++|+++++++-  .+.|+..--.-
T Consensus       487 rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~---~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~  563 (638)
T KOG1126|consen  487 RHYNAWYGLGTVYLKQEKLEFAEFHFQKAV---EINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHR  563 (638)
T ss_pred             hhhHHHHhhhhheeccchhhHHHHHHHhhh---cCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHH
Confidence            43 456678888999999999999999775   6788 67777888888999999999999999863  23355554555


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          318 LSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       318 l~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ...+...+++++|.+.++++.++-|++...|..++..|-+.|+.+.|..-|.-+.+..
T Consensus       564 ~~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ld  621 (638)
T KOG1126|consen  564 ASILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLD  621 (638)
T ss_pred             HHHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCC
Confidence            6667788999999999999999999999999999999999999999999998776543

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

Probab=99.44  E-value=1.6e-09  Score=102.11  Aligned_cols=314  Identities=12%  Similarity=0.079  Sum_probs=221.8

Q ss_pred             HHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHH-HHHHHHHHHCCChhHHHH
Q 040365           50 IFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISW-NSIIAGCVQNGLFDEGLK  128 (514)
Q Consensus        50 ~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~-~~li~~~~~~g~~~~A~~  128 (514)
                      .+.+.|....|...+...+..    -+..|.+-+....-.-+++.+..+....+..+...- --+..++....+.+++++
T Consensus       173 v~k~~~~~s~A~~sfv~~v~~----~P~~W~AWleL~~lit~~e~~~~l~~~l~~~~h~M~~~F~~~a~~el~q~~e~~~  248 (559)
T KOG1155|consen  173 VLKELGLLSLAIDSFVEVVNR----YPWFWSAWLELSELITDIEILSILVVGLPSDMHWMKKFFLKKAYQELHQHEEALQ  248 (559)
T ss_pred             HHHhhchHHHHHHHHHHHHhc----CCcchHHHHHHHHhhchHHHHHHHHhcCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            334455555555555554432    123333333333334445555544444443211111 123455666667788888


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCC--CCcHHHHHHHHHHHHhcCCHHH-HHHHHHhCCC
Q 040365          129 FFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGF--DDNMFIASSLLDMYAKCGNIRL-ARCIFDKMDL  205 (514)
Q Consensus       129 l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~li~~y~k~g~~~~-A~~~~~~m~~  205 (514)
                      -.......|++-+...-+....+.-...++++|+.+|+.+.+...  -.|..+|+.++-.--.+..+.- |..++ .+.+
T Consensus       249 k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~-~idK  327 (559)
T KOG1155|consen  249 KKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVS-NIDK  327 (559)
T ss_pred             HHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHH-Hhcc
Confidence            888888887765555555555556677889999999999988741  1255666666533222222222 22222 2233


Q ss_pred             CChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHH
Q 040365          206 HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYA  283 (514)
Q Consensus       206 ~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~  283 (514)
                      --+.|...+.+-|+-.++.++|...|++..+.  .|. ...|+.+..-|....+...|++-++..+   .+.| |-..|-
T Consensus       328 yR~ETCCiIaNYYSlr~eHEKAv~YFkRALkL--Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAv---di~p~DyRAWY  402 (559)
T KOG1155|consen  328 YRPETCCIIANYYSLRSEHEKAVMYFKRALKL--NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAV---DINPRDYRAWY  402 (559)
T ss_pred             CCccceeeehhHHHHHHhHHHHHHHHHHHHhc--CcchhHHHHHhhHHHHHhcccHHHHHHHHHHH---hcCchhHHHHh
Confidence            34456667777888899999999999999885  454 4668888889999999999999999886   5566 788999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccCh
Q 040365          284 AVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRW  361 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  361 (514)
                      .|.++|.-.+...=|+-+|++.. .+| |...|.+|..+|.+.++.++|+..|.++...+..+...|+.|++.|-+.++.
T Consensus       403 GLGQaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~  482 (559)
T KOG1155|consen  403 GLGQAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDL  482 (559)
T ss_pred             hhhHHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhH
Confidence            99999999999999999999874 444 7899999999999999999999999999999877888999999999999999


Q ss_pred             hHHHHHHHHHHh
Q 040365          362 KDAASLRVFMRN  373 (514)
Q Consensus       362 ~~a~~~~~~m~~  373 (514)
                      ++|.+.+++-.+
T Consensus       483 ~eAa~~yek~v~  494 (559)
T KOG1155|consen  483 NEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHHHHHHHH
Confidence            999999987765

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

Probab=99.43  E-value=2.7e-10  Score=102.61  Aligned_cols=267  Identities=10%  Similarity=0.119  Sum_probs=137.9

Q ss_pred             cCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhC-CC--CchhHHHHHHHHHHHCCCHHHH
Q 040365           19 NGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHG-LD--ANVCIGSSLINMYAKCARVEDS   95 (514)
Q Consensus        19 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g-~~--~~~~~~~~li~~~~~~g~~~~A   95 (514)
                      ++++++|.++|-+|.+.. +.+..+--++-+.+.+.|.++.|..+|+.+.++. +.  .-..+...|..-|.+.|-+|.|
T Consensus        48 s~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRA  126 (389)
T COG2956          48 SNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRA  126 (389)
T ss_pred             hcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHH
Confidence            356777777777777632 2222344556666777777777777777776642 11  1112344566667777777777


Q ss_pred             HHHHccCCCCC---hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHH----HHHHHHHHhccCChHHHHHHHHHH
Q 040365           96 HRLFCLLPVKD---AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVS----FSSIMPACAHLTTLHLGKQLHGCI  168 (514)
Q Consensus        96 ~~~f~~~~~~d---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t----~~~ll~~~~~~~~~~~a~~~~~~~  168 (514)
                      +.+|..+.+.+   ..+.-.|+..|-+..+|++|++.-+++...+-.+..+-    |.-+...+....+++.|...+.+.
T Consensus       127 E~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kA  206 (389)
T COG2956         127 EDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKA  206 (389)
T ss_pred             HHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            77777765432   23445567777777777777777776666543333221    222222333334445555555544


Q ss_pred             HHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHH
Q 040365          169 IRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVA  248 (514)
Q Consensus       169 ~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~  248 (514)
                      .+.+ +..+..--.+.+.                               +...|+++.|.+.++...+.+..--..+...
T Consensus       207 lqa~-~~cvRAsi~lG~v-------------------------------~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~  254 (389)
T COG2956         207 LQAD-KKCVRASIILGRV-------------------------------ELAKGDYQKAVEALERVLEQNPEYLSEVLEM  254 (389)
T ss_pred             HhhC-ccceehhhhhhHH-------------------------------HHhccchHHHHHHHHHHHHhChHHHHHHHHH
Confidence            4432 2222222233344                               4445555555555555554432222234445


Q ss_pred             HHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHH-HhCCCCCCHHHHHHHHHHH
Q 040365          249 VLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFI-SNMHAGPTENVWLTLLSAC  321 (514)
Q Consensus       249 ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~-~~m~~~p~~~~~~~ll~~~  321 (514)
                      |..+|.+.|+.+++..++..+.+.   .+....-..+.+.-....-.+.|..++ +.+..+|+...+..|+..-
T Consensus       255 L~~~Y~~lg~~~~~~~fL~~~~~~---~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~Pt~~gf~rl~~~~  325 (389)
T COG2956         255 LYECYAQLGKPAEGLNFLRRAMET---NTGADAELMLADLIELQEGIDAAQAYLTRQLRRKPTMRGFHRLMDYH  325 (389)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHc---cCCccHHHHHHHHHHHhhChHHHHHHHHHHHhhCCcHHHHHHHHHhh
Confidence            555555556665555555555432   233333333333333333344444433 3344556666666666544

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

Probab=99.43  E-value=4e-10  Score=106.82  Aligned_cols=352  Identities=14%  Similarity=0.061  Sum_probs=238.1

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCC-hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCC
Q 040365           12 VIVGLARNGLYEEALNIVRQMGNVNLKPD-SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA   90 (514)
Q Consensus        12 li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g   90 (514)
                      .-.-|-++|.+++|++.|.+.+..  .|| +..|.....+|...|++++..+--...++.. +.-+-++..-.+++-..|
T Consensus       121 ~GN~~f~~kkY~eAIkyY~~AI~l--~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~-P~Y~KAl~RRA~A~E~lg  197 (606)
T KOG0547|consen  121 KGNKFFRNKKYDEAIKYYTQAIEL--CPDEPIFYSNRAACYESLGDWEKVIEDCTKALELN-PDYVKALLRRASAHEQLG  197 (606)
T ss_pred             hhhhhhhcccHHHHHHHHHHHHhc--CCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcC-cHHHHHHHHHHHHHHhhc
Confidence            344577899999999999999874  688 6677778888889999998887777776653 222334455556666667


Q ss_pred             CHHHHHH----------------------HHcc---------CC---CC---ChhHHHHHHHHHH---------------
Q 040365           91 RVEDSHR----------------------LFCL---------LP---VK---DAISWNSIIAGCV---------------  118 (514)
Q Consensus        91 ~~~~A~~----------------------~f~~---------~~---~~---d~~~~~~li~~~~---------------  118 (514)
                      ++++|+.                      ++..         +.   +|   +....++....|.               
T Consensus       198 ~~~eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~~~~~~ksD  277 (606)
T KOG0547|consen  198 KFDEALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLFDNKSDKSD  277 (606)
T ss_pred             cHHHHHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccccCCCccch
Confidence            6666542                      1111         11   11   1111111111110               


Q ss_pred             ----------HCC---ChhHHHHHHHHHHHC-CCCCCHH---------HHHHHHH--HHhccCChHHHHHHHHHHHHcCC
Q 040365          119 ----------QNG---LFDEGLKFFRQMLIA-KIKPRHV---------SFSSIMP--ACAHLTTLHLGKQLHGCIIRNGF  173 (514)
Q Consensus       119 ----------~~g---~~~~A~~l~~~m~~~-g~~p~~~---------t~~~ll~--~~~~~~~~~~a~~~~~~~~~~~~  173 (514)
                                ..+   .+.+|.+.+.+-... -..++..         .-..++.  ...-.|+.-.+.+-++..++...
T Consensus       278 a~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~~~~I~l~~  357 (606)
T KOG0547|consen  278 AALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDFDAAIKLDP  357 (606)
T ss_pred             hhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhHHHHHhcCc
Confidence                      001   112222222111000 0011111         0111111  12234677788888888888753


Q ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHH
Q 040365          174 DDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAV  249 (514)
Q Consensus       174 ~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~l  249 (514)
                      . +...|--+..+|....+-++-.+.|+...   ..|..+|..-...+.-.+++++|..=|++.+.  +.|+ ...|..+
T Consensus       358 ~-~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~--L~pe~~~~~iQl  434 (606)
T KOG0547|consen  358 A-FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAIS--LDPENAYAYIQL  434 (606)
T ss_pred             c-cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhh--cChhhhHHHHHH
Confidence            3 33346667778999999999999998875   44666777777777778899999999999887  4554 4678888


Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC---------HHHHHHHHH
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT---------ENVWLTLLS  319 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~---------~~~~~~ll~  319 (514)
                      -.+..+.+.++++...|+...++  ++-.++.|+.....+...++++.|.+.|+... .+|+         +.+-.+++-
T Consensus       435 ~~a~Yr~~k~~~~m~~Fee~kkk--FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~plV~Ka~l~  512 (606)
T KOG0547|consen  435 CCALYRQHKIAESMKTFEEAKKK--FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAPLVHKALLV  512 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHh--CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchhhhhhhHhh
Confidence            88888999999999999999764  44568899999999999999999999998753 3333         222222332


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          320 ACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      . .-.+++..|..+++++++++|....+|..|...-.+.|+.++|.++|++-.
T Consensus       513 ~-qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  513 L-QWKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             h-chhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            2 244899999999999999999999999999999999999999999999654

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

Probab=99.43  E-value=1.8e-11  Score=120.19  Aligned_cols=244  Identities=18%  Similarity=0.125  Sum_probs=196.5

Q ss_pred             ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcC--CCCcHHHHHHHHHHHHhcCCHHH-HHH
Q 040365          122 LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNG--FDDNMFIASSLLDMYAKCGNIRL-ARC  198 (514)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~li~~y~k~g~~~~-A~~  198 (514)
                      +..+|+.+|.+.... +.-+......+..+|..++++++++.+|+.+.+..  ...+..+|.+.+--+-+.=.+.. |..
T Consensus       334 ~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~  412 (638)
T KOG1126|consen  334 NCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQD  412 (638)
T ss_pred             HHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHH
Confidence            568899999985543 44455677788899999999999999999998763  23466778777755443222222 222


Q ss_pred             HHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC
Q 040365          199 IFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP  277 (514)
Q Consensus       199 ~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p  277 (514)
                      +.+ +.+-...+|-++..+|.-+++.+.|++.|++..+  +.| ...+|+.+..-+.....+|.|...|+...     ..
T Consensus       413 Li~-~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al-----~~  484 (638)
T KOG1126|consen  413 LID-TDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRKAL-----GV  484 (638)
T ss_pred             HHh-hCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHhhh-----cC
Confidence            222 2244678999999999999999999999999988  567 56888888888888999999999999764     45


Q ss_pred             CHhHHHH---HHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          278 SFEHYAA---VADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       278 ~~~~~~~---li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      ++.+|++   |...|.+.++++.|+-.|+++. ..| +.++...+...+.+.|+.++|+++++++..++|.|+-.-...+
T Consensus       485 ~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~  564 (638)
T KOG1126|consen  485 DPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRA  564 (638)
T ss_pred             CchhhHHHHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHH
Confidence            6666665   4666999999999999999874 455 5677788888899999999999999999999999999999999


Q ss_pred             HHHHHccChhHHHHHHHHHHhC
Q 040365          353 NTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       353 ~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ..+...+++++|++.++++++-
T Consensus       565 ~il~~~~~~~eal~~LEeLk~~  586 (638)
T KOG1126|consen  565 SILFSLGRYVEALQELEELKEL  586 (638)
T ss_pred             HHHHhhcchHHHHHHHHHHHHh
Confidence            9999999999999999999864

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

Probab=99.42  E-value=7.2e-12  Score=126.02  Aligned_cols=265  Identities=14%  Similarity=0.152  Sum_probs=196.5

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCC
Q 040365          128 KFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHD  207 (514)
Q Consensus       128 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d  207 (514)
                      .++-.+...|+.|+.+||.+++.-|+..|+.+.|- +|..|.-...+.+..+++.++......++.+.+.       +|-
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-------ep~   82 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-------EPL   82 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-------CCc
Confidence            45677888999999999999999999999999999 9999998888999999999999999999987776       778


Q ss_pred             hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHH
Q 040365          208 IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       208 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  287 (514)
                      ..+|+.+..+|.++|+...    |+...+        -...+...++..|--..-..++..+.-..+.-|+..   ..+.
T Consensus        83 aDtyt~Ll~ayr~hGDli~----fe~veq--------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~---n~il  147 (1088)
T KOG4318|consen   83 ADTYTNLLKAYRIHGDLIL----FEVVEQ--------DLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAE---NAIL  147 (1088)
T ss_pred             hhHHHHHHHHHHhccchHH----HHHHHH--------HHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHH---HHHH
Confidence            8899999999999999765    333222        223345556666666666666665433334445543   3555


Q ss_pred             HHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCC-HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHH
Q 040365          288 LLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKN-VELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~-~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~  366 (514)
                      .+.-.|.++.+.+++..+|...........+.-+..... +++-....+.+.+  ..++.+|..+...-..+|+.+.|..
T Consensus       148 llv~eglwaqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e--~~~s~~l~a~l~~alaag~~d~Ak~  225 (1088)
T KOG4318|consen  148 LLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVE--APTSETLHAVLKRALAAGDVDGAKN  225 (1088)
T ss_pred             HHHHHHHHHHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhc--CCChHHHHHHHHHHHhcCchhhHHH
Confidence            667778899999999888743111111113555544433 3333333333333  3467899999999999999999999


Q ss_pred             HHHHHHhCCCccCCcccEEEECCEEEEEEeCCCCCCChHHHHHHHHHHHHHHHhCCcccCCccccc
Q 040365          367 LRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLH  432 (514)
Q Consensus       367 ~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~  432 (514)
                      ++..|+++|+.-.+...|..+.|               .+....++.+++.|++.|+.|+..+...
T Consensus       226 ll~emke~gfpir~HyFwpLl~g---------------~~~~q~~e~vlrgmqe~gv~p~seT~ad  276 (1088)
T KOG4318|consen  226 LLYEMKEKGFPIRAHYFWPLLLG---------------INAAQVFEFVLRGMQEKGVQPGSETQAD  276 (1088)
T ss_pred             HHHHHHHcCCCcccccchhhhhc---------------CccchHHHHHHHHHHHhcCCCCcchhHH
Confidence            99999999999999999976643               1223455688999999999999866543

>PF13041 PPR_2: PPR repeat family

Probab=99.42  E-value=4.1e-13  Score=90.15  Aligned_cols=50  Identities=34%  Similarity=0.664  Sum_probs=48.5

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhC
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFAD   53 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~   53 (514)
                      ||+++||++|++|++.|++++|+++|++|.+.|++||..||+.+|++|++
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            89999999999999999999999999999999999999999999999975

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

Probab=99.41  E-value=3.2e-09  Score=100.36  Aligned_cols=174  Identities=14%  Similarity=0.178  Sum_probs=132.2

Q ss_pred             ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH-------HHHHHHHHH---HccCCHHHHHHHHHHhHHhcCCC
Q 040365          207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV-------AFVAVLTAC---SHAGLIDKAWSYFNSMTKDYGIA  276 (514)
Q Consensus       207 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-------t~~~ll~a~---~~~g~~~~a~~~~~~m~~~~~~~  276 (514)
                      |-.+|--.+..-...|+.+...++|++.... ++|-..       .|.-+=-+|   ....+++.+.++|+...+   +-
T Consensus       321 nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~---lI  396 (677)
T KOG1915|consen  321 NYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLD---LI  396 (677)
T ss_pred             CchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh---hc
Confidence            4456777777777789999999999998875 566321       122221222   346788999999988764   45


Q ss_pred             C-CHhHHHHHHHHH----HhcCCHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHH
Q 040365          277 P-SFEHYAAVADLL----GRAGKLQEAYEFISNMH-AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVI  350 (514)
Q Consensus       277 p-~~~~~~~li~~~----~~~g~~~~A~~~~~~m~-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~  350 (514)
                      | ...++.-+--+|    .|+.++..|.+++.... .-|-..++...|..-.+.++++....++++.++.+|.|..+|.-
T Consensus       397 PHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~Pe~c~~W~k  476 (677)
T KOG1915|consen  397 PHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFSPENCYAWSK  476 (677)
T ss_pred             CcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcChHhhHHHHH
Confidence            5 455555554444    47889999999998764 45888899999998899999999999999999999999999999


Q ss_pred             HHHHHHHccChhHHHHHHHHHHhCCCccCCcccE
Q 040365          351 LSNTYAAARRWKDAASLRVFMRNKGMKKTPACSW  384 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~  384 (514)
                      .+..-...|+++.|..+|+...+....-.|..-|
T Consensus       477 yaElE~~LgdtdRaRaifelAi~qp~ldmpellw  510 (677)
T KOG1915|consen  477 YAELETSLGDTDRARAIFELAISQPALDMPELLW  510 (677)
T ss_pred             HHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHH
Confidence            9999999999999999999988776554555444

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

Probab=99.40  E-value=2.9e-09  Score=98.92  Aligned_cols=287  Identities=11%  Similarity=0.043  Sum_probs=169.9

Q ss_pred             cCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHH
Q 040365           19 NGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRL   98 (514)
Q Consensus        19 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~   98 (514)
                      .|++.+|..+..+-.+++-.| ...|.....+--+.|+.+.+-+.+.++.+..-.++..+.-+........|+.+.|+.-
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 EGDFQQAEKLLRRNAEHGEQP-VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcch-HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            456666666666555544222 2234444445555566666666666655553344555555555555556666655554


Q ss_pred             HccC---CCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCC
Q 040365           99 FCLL---PVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDD  175 (514)
Q Consensus        99 f~~~---~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  175 (514)
                      .++.   ..++..........|.+.|++.+...++.+|.+.|+--|+..-                            ..
T Consensus       176 v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~----------------------------~l  227 (400)
T COG3071         176 VDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAA----------------------------RL  227 (400)
T ss_pred             HHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHH----------------------------HH
Confidence            4432   2345555555666666666666666666666555543222100                            00


Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040365          176 NMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTA  252 (514)
Q Consensus       176 ~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a  252 (514)
                      ...+++.+++-....+..+.-...++..+   +.++..-.+++.-+.+.|+.++|.++..+..+.+..|+..    .+-.
T Consensus       228 e~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~~~  303 (400)
T COG3071         228 EQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RLIP  303 (400)
T ss_pred             HHHHHHHHHHHHhccccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HHHh
Confidence            12234444444444444444444555554   3345556666777777888888888888877776666622    2234


Q ss_pred             HHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHH
Q 040365          253 CSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM-HAGPTENVWLTLLSACRVHKNVELAG  331 (514)
Q Consensus       253 ~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~ll~~~~~~~~~~~a~  331 (514)
                      +.+.++.+.-++..+.-.+.++-.|  ..+.+|...|.+.+.+.+|.+.|+.. +..|+..+|+-+..++.+.|+.+.|.
T Consensus       304 ~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~  381 (400)
T COG3071         304 RLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAE  381 (400)
T ss_pred             hcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHH
Confidence            5566777766666666666555544  56677777888888888888888764 45678888888888888888888888


Q ss_pred             HHHHHHHhc
Q 040365          332 KVAEKIFMI  340 (514)
Q Consensus       332 ~~~~~~~~~  340 (514)
                      +..++.+.+
T Consensus       382 ~~r~e~L~~  390 (400)
T COG3071         382 QVRREALLL  390 (400)
T ss_pred             HHHHHHHHH
Confidence            877776643

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

Probab=99.40  E-value=8.2e-10  Score=112.87  Aligned_cols=360  Identities=14%  Similarity=0.132  Sum_probs=229.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhh--HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            8 SWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFT--LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         8 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t--~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      +|--+.++|-..|++++|...|.+....  .||.++  +..+.+.+...|+++.+...|+.+.+.- +.+..+.-.|...
T Consensus       309 s~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~--~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iLG~L  385 (1018)
T KOG2002|consen  309 SFYQLGRSYHAQGDFEKAFKYYMESLKA--DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKILGCL  385 (1018)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHcc--CCCCccccccchhHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHHHhH
Confidence            3555677888889999999988777664  355443  4456777888888999988888888774 5566677777777


Q ss_pred             HHHCC----CHHHHHHHHccCCCC---ChhHHHHHHHHHHHCCChhHHHHHHHHHH----HCCCCCCHHHHHHHHHHHhc
Q 040365           86 YAKCA----RVEDSHRLFCLLPVK---DAISWNSIIAGCVQNGLFDEGLKFFRQML----IAKIKPRHVSFSSIMPACAH  154 (514)
Q Consensus        86 ~~~~g----~~~~A~~~f~~~~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~----~~g~~p~~~t~~~ll~~~~~  154 (514)
                      |+..+    ..+.|..+.....++   |..+|-.+...+-+. ++..++.+|....    ..+-.+.....+.+......
T Consensus       386 ya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e~~-d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~  464 (1018)
T KOG2002|consen  386 YAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWLELAQLLEQT-DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFR  464 (1018)
T ss_pred             HHhhhhhhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHhc-ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHH
Confidence            77664    345555555544332   333443333333322 2222233333321    22223334444444444444


Q ss_pred             cCChH--------------------------------------------HHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc
Q 040365          155 LTTLH--------------------------------------------LGKQLHGCIIRNGFDDNMFIASSLLDMYAKC  190 (514)
Q Consensus       155 ~~~~~--------------------------------------------~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~  190 (514)
                      .|+++                                            .|.+++..+++.. +.-+..|--|..+.-..
T Consensus       465 ~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkeh-p~YId~ylRl~~ma~~k  543 (1018)
T KOG2002|consen  465 LGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEH-PGYIDAYLRLGCMARDK  543 (1018)
T ss_pred             hcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC-chhHHHHHHhhHHHHhc
Confidence            44444                                            4444444444431 11111122222222222


Q ss_pred             CCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHc-----------
Q 040365          191 GNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKD-GVKPNSVAFVAVLTACSH-----------  255 (514)
Q Consensus       191 g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~t~~~ll~a~~~-----------  255 (514)
                      +.+.+|...+....   ..++..|+.+...|.....+..|.+-|...... ...+|..+..+|.+.|..           
T Consensus       544 ~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek  623 (1018)
T KOG2002|consen  544 NNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEK  623 (1018)
T ss_pred             cCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHH
Confidence            44556666665554   345566776776777777777777766666542 233677777777776643           


Q ss_pred             -cCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHHHHH
Q 040365          256 -AGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMHAG--PTENVWLTLLSACRVHKNVELAG  331 (514)
Q Consensus       256 -~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~ll~~~~~~~~~~~a~  331 (514)
                       .+..+.|+++|....+   ..| |...-+.+.-.++..|++.+|.++|......  .+..+|-.|..+|...|++-.|+
T Consensus       624 ~kk~~~KAlq~y~kvL~---~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AI  700 (1018)
T KOG2002|consen  624 EKKHQEKALQLYGKVLR---NDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAI  700 (1018)
T ss_pred             HHHHHHHHHHHHHHHHh---cCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHH
Confidence             2346778888887764   345 7777788888899999999999999887522  34567999999999999999999


Q ss_pred             HHHHHHHhcC--CCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          332 KVAEKIFMID--PNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       332 ~~~~~~~~~~--p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      +.|+..+...  .+++.....|..++.+.|+|.+|.+.........
T Consensus       701 qmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~  746 (1018)
T KOG2002|consen  701 QMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLA  746 (1018)
T ss_pred             HHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC
Confidence            9999988753  4567788899999999999999999887776544

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

Probab=99.39  E-value=8.8e-09  Score=101.07  Aligned_cols=361  Identities=12%  Similarity=0.089  Sum_probs=245.9

Q ss_pred             HHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHH----HhCCCCchhHHHHHHHHHHHCCC
Q 040365           16 LARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAI----RHGLDANVCIGSSLINMYAKCAR   91 (514)
Q Consensus        16 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~----~~g~~~~~~~~~~li~~~~~~g~   91 (514)
                      |++..-++.|..+++..++. ++-+...|.+....=-..|+.+....+....+    ..|+..+..-|-.=...+-+.|.
T Consensus       416 larLetYenAkkvLNkaRe~-iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~ags  494 (913)
T KOG0495|consen  416 LARLETYENAKKVLNKAREI-IPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGS  494 (913)
T ss_pred             HHHHHHHHHHHHHHHHHHhh-CCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCC
Confidence            33333444444444444332 33334444333333333444444433333221    22334444444333344444444


Q ss_pred             HHHHHHHHccCC-----C-CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHH
Q 040365           92 VEDSHRLFCLLP-----V-KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLH  165 (514)
Q Consensus        92 ~~~A~~~f~~~~-----~-~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~  165 (514)
                      +-.+..+.....     + .--.+|+.-...|.+.+.++-|..+|....+. .+-+...|..+...--..|..+....++
T Consensus       495 v~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~~ek~hgt~Esl~All  573 (913)
T KOG0495|consen  495 VITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAMFEKSHGTRESLEALL  573 (913)
T ss_pred             hhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHhcCcHHHHHHHH
Confidence            444433333321     1 11235666667777778888888888887764 3445556666655556678888888888


Q ss_pred             HHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC
Q 040365          166 GCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN  242 (514)
Q Consensus       166 ~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~  242 (514)
                      ++++..- +.....|-....-+.+.|++..|+.++...-   ..+...|-+-+..-..+.++++|..+|.+...  ..|+
T Consensus       574 qkav~~~-pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~--~sgT  650 (913)
T KOG0495|consen  574 QKAVEQC-PKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARS--ISGT  650 (913)
T ss_pred             HHHHHhC-CcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhc--cCCc
Confidence            8888763 4455566666777788899999999988774   33567898888999999999999999999887  4567


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHH
Q 040365          243 SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM-HAGP-TENVWLTLLSA  320 (514)
Q Consensus       243 ~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~ll~~  320 (514)
                      ...|.--+..---.+++++|++++++..+.|  +.-...|-.+.+.+-+.++++.|.+.|..- ..-| ....|-.|...
T Consensus       651 eRv~mKs~~~er~ld~~eeA~rllEe~lk~f--p~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakl  728 (913)
T KOG0495|consen  651 ERVWMKSANLERYLDNVEEALRLLEEALKSF--PDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKL  728 (913)
T ss_pred             chhhHHHhHHHHHhhhHHHHHHHHHHHHHhC--CchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHH
Confidence            7777666666667899999999999887653  223567888889999999999999887654 3335 46788888888


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccEE
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWI  385 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~  385 (514)
                      --+.|++-.|..++++..-.+|.++..|...+.+-.+.|+.+.|..+..+..+.-  |..|.-|.
T Consensus       729 eEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQec--p~sg~LWa  791 (913)
T KOG0495|consen  729 EEKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQEC--PSSGLLWA  791 (913)
T ss_pred             HHHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CccchhHH
Confidence            8999999999999999999999999999999999999999999999887776542  44455564

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.39  E-value=1.8e-10  Score=105.51  Aligned_cols=199  Identities=14%  Similarity=0.058  Sum_probs=162.3

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLT  251 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  251 (514)
                      .....+..+...|.+.|++++|.+.|++..   +.+...+..+...|...|++++|.+.+++..+.. +.+...+..+..
T Consensus        29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~  107 (234)
T TIGR02521        29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGT  107 (234)
T ss_pred             cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHH
Confidence            345667778888999999999999998764   3356778888888999999999999999988753 334566777888


Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~~~~~~  329 (514)
                      .+...|++++|...++..............+..+...+...|++++|.+.+++.. .. .+...|..+...+...|++++
T Consensus       108 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~  187 (234)
T TIGR02521       108 FLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKD  187 (234)
T ss_pred             HHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHH
Confidence            8899999999999999886532222245667778888999999999999998763 22 346778889999999999999


Q ss_pred             HHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          330 AGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      |...+++..+..|+++..+..++..+...|++++|..+.+.+...
T Consensus       188 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       188 ARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            999999999988888888889999999999999999998877643

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.

>PF13041 PPR_2: PPR repeat family

Probab=99.36  E-value=2.2e-12  Score=86.57  Aligned_cols=50  Identities=28%  Similarity=0.628  Sum_probs=47.8

Q ss_pred             CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhc
Q 040365          105 KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH  154 (514)
Q Consensus       105 ~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~  154 (514)
                      ||+++||++|.+|++.|++++|+++|++|.+.|++||..||++++++|++
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            78999999999999999999999999999999999999999999999874

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.35  E-value=4e-10  Score=111.74  Aligned_cols=232  Identities=18%  Similarity=0.131  Sum_probs=179.6

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHHc-----C-CCCcHH-HHHHHHHHHHhcCCHHHHHHHHHhCC---------
Q 040365          141 RHVSFSSIMPACAHLTTLHLGKQLHGCIIRN-----G-FDDNMF-IASSLLDMYAKCGNIRLARCIFDKMD---------  204 (514)
Q Consensus       141 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~~~-~~~~li~~y~k~g~~~~A~~~~~~m~---------  204 (514)
                      -..|...+...|...|+++.|.+++...++.     | ..|.+. ..+.+...|...+++++|..+|+++.         
T Consensus       198 ~~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~  277 (508)
T KOG1840|consen  198 RLRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGE  277 (508)
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCC
Confidence            3456667888999999999999999988765     2 123332 33457789999999999999998874         


Q ss_pred             -CC-ChhHHHHHHHHHHhCCChHHHHHHHHHHHH-----cCCC-CCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcC-
Q 040365          205 -LH-DIVSWTAVIMGNALHGNAHDAISLFEQMEK-----DGVK-PNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYG-  274 (514)
Q Consensus       205 -~~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~-----~g~~-p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~-  274 (514)
                       .| -..+++.|..+|.+.|++++|..++++..+     .|.. |.. .-++.+...|...+.+++|..+++...+.+. 
T Consensus       278 ~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~  357 (508)
T KOG1840|consen  278 DHPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLD  357 (508)
T ss_pred             CCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHh
Confidence             11 235788888899999999999988887654     1222 233 2366777889999999999999988766544 


Q ss_pred             -CCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-------CC--C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040365          275 -IAP----SFEHYAAVADLLGRAGKLQEAYEFISNMH-------AG--P-TENVWLTLLSACRVHKNVELAGKVAEKIFM  339 (514)
Q Consensus       275 -~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~-------~~--p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  339 (514)
                       ..+    -..+++.|...|...|++++|+++++++.       .+  + ....++.|..+|.+.+++++|.++|.+...
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             222    24789999999999999999999998863       11  2 235678889999999999999999988765


Q ss_pred             c----C---CCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          340 I----D---PNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       340 ~----~---p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      .    +   |+...+|..|+.+|...|++++|.++.+...
T Consensus       438 i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  438 IMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            3    3   4455788899999999999999999998875

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

Probab=99.33  E-value=9.3e-09  Score=104.63  Aligned_cols=355  Identities=12%  Similarity=0.066  Sum_probs=258.6

Q ss_pred             HHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHH
Q 040365           16 LARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDS   95 (514)
Q Consensus        16 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A   95 (514)
                      +++ |+.++|..++.+.++.. +.+...|.++...+-+.|+.+++...+-.+--.. +.|...|-.+.+...+.|.++.|
T Consensus       150 far-g~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~~~i~qA  226 (895)
T KOG2076|consen  150 FAR-GDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQLGNINQA  226 (895)
T ss_pred             HHh-CCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhcccHHHH
Confidence            444 99999999999999875 5566789999999999999999987765554433 66788999999999999999999


Q ss_pred             HHHHccCCCCChh---HHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHH----HHHHHHHhccCChHHHHHHHHHH
Q 040365           96 HRLFCLLPVKDAI---SWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSF----SSIMPACAHLTTLHLGKQLHGCI  168 (514)
Q Consensus        96 ~~~f~~~~~~d~~---~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~----~~ll~~~~~~~~~~~a~~~~~~~  168 (514)
                      .-.|.+..+.++.   .+---+..|-+.|+...|++-|.++.+...+.|..-+    -.++..+...++-+.|.+.+...
T Consensus       227 ~~cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~  306 (895)
T KOG2076|consen  227 RYCYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGA  306 (895)
T ss_pred             HHHHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            9999987644333   3333457788999999999999999886432222222    23455566667778888888777


Q ss_pred             HHc-CCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC----CCh----------------------hHHH----HHHHH
Q 040365          169 IRN-GFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL----HDI----------------------VSWT----AVIMG  217 (514)
Q Consensus       169 ~~~-~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~----~d~----------------------~~~~----~li~~  217 (514)
                      ... +-..+...++.++.+|.+...++.|......+..    +|.                      .+|+    -+.-+
T Consensus       307 ~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~ic  386 (895)
T KOG2076|consen  307 LSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMIC  386 (895)
T ss_pred             HhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhh
Confidence            663 2344566778899999999999998777665532    111                      1121    12233


Q ss_pred             HHhCCChHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCH
Q 040365          218 NALHGNAHDAISLFEQMEKDGVKP--NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKL  295 (514)
Q Consensus       218 ~~~~g~~~~A~~l~~~m~~~g~~p--~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  295 (514)
                      +......+....+..-..+..+.|  +..-|.-+..++...|.+.+|+.+|..+... ...-+...|-.+..+|-..|..
T Consensus       387 L~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~-~~~~~~~vw~~~a~c~~~l~e~  465 (895)
T KOG2076|consen  387 LVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNR-EGYQNAFVWYKLARCYMELGEY  465 (895)
T ss_pred             hhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcC-ccccchhhhHHHHHHHHHHhhH
Confidence            444444444445555555555444  3456888999999999999999999999654 2222577899999999999999


Q ss_pred             HHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC---------CCcchHHHHHHHHHHccChhHH
Q 040365          296 QEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDP---------NNMGAYVILSNTYAAARRWKDA  364 (514)
Q Consensus       296 ~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p---------~~~~~~~~l~~~~~~~g~~~~a  364 (514)
                      ++|.+.++... ..| +...--+|-..+.+.|+.++|.+.++.+..-++         ++..........|.+.|+.++-
T Consensus       466 e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l~~~gk~E~f  545 (895)
T KOG2076|consen  466 EEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDILFQVGKREEF  545 (895)
T ss_pred             HHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHHHHhhhHHHH
Confidence            99999999863 334 445566788889999999999999998764332         2233445677888999999887


Q ss_pred             HHHHHHHHhC
Q 040365          365 ASLRVFMRNK  374 (514)
Q Consensus       365 ~~~~~~m~~~  374 (514)
                      ..+-..|...
T Consensus       546 i~t~~~Lv~~  555 (895)
T KOG2076|consen  546 INTASTLVDD  555 (895)
T ss_pred             HHHHHHHHHH
Confidence            7777776554

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

Probab=99.33  E-value=4e-09  Score=102.00  Aligned_cols=260  Identities=14%  Similarity=0.036  Sum_probs=207.8

Q ss_pred             hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 040365          107 AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDM  186 (514)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  186 (514)
                      +...-....-+...+++.+.++++....+. .++....+..-|..+...|+..+-..+-..+++. .|....+|-++.--
T Consensus       244 ~dll~~~ad~~y~~c~f~~c~kit~~lle~-dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~aVg~Y  321 (611)
T KOG1173|consen  244 LDLLAEKADRLYYGCRFKECLKITEELLEK-DPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFAVGCY  321 (611)
T ss_pred             HHHHHHHHHHHHHcChHHHHHHHhHHHHhh-CCCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhhHHHH
Confidence            333444456677889999999999998875 3556566666666788888887777777777776 46677889899888


Q ss_pred             HHhcCCHHHHHHHHHhCCCCC---hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040365          187 YAKCGNIRLARCIFDKMDLHD---IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAW  263 (514)
Q Consensus       187 y~k~g~~~~A~~~~~~m~~~d---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  263 (514)
                      |.-.|...+|++.|.+...-|   ...|-.+...|+-.|..+.|+..+...-+. ++-...-+.-+..-|.+.++.+.|.
T Consensus       322 Yl~i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~kLAe  400 (611)
T KOG1173|consen  322 YLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKLAE  400 (611)
T ss_pred             HHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHHHH
Confidence            989999999999999876333   468999999999999999999999887663 2222233444555688899999999


Q ss_pred             HHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--------CCC-CHHHHHHHHHHHHhcCCHHHHHHH
Q 040365          264 SYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--------AGP-TENVWLTLLSACRVHKNVELAGKV  333 (514)
Q Consensus       264 ~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--------~~p-~~~~~~~ll~~~~~~~~~~~a~~~  333 (514)
                      ++|.+..   ++.| |+...+-+.-..-..+.+.+|..+|+...        .++ -..+|+.|..+|++.+.+++|+..
T Consensus       401 ~Ff~~A~---ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~  477 (611)
T KOG1173|consen  401 KFFKQAL---AIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDY  477 (611)
T ss_pred             HHHHHHH---hcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHH
Confidence            9999774   7777 66777777666677889999999988653        112 345788999999999999999999


Q ss_pred             HHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          334 AEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       334 ~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      +++.+.+.|.++.+|.+++-.|...|+.+.|...|.+..
T Consensus       478 ~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL  516 (611)
T KOG1173|consen  478 YQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKAL  516 (611)
T ss_pred             HHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHH
Confidence            999999999999999999999999999999999998764

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

Probab=99.32  E-value=5.6e-09  Score=98.58  Aligned_cols=284  Identities=12%  Similarity=0.083  Sum_probs=168.0

Q ss_pred             HHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCC------ChhHHHHHHHHHHHCC
Q 040365           48 LPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVK------DAISWNSIIAGCVQNG  121 (514)
Q Consensus        48 l~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~------d~~~~~~li~~~~~~g  121 (514)
                      ..++-.....+++.+-.......|++.+...-+....+.-...++|.|+.+|+++...      |..+|+-++  |+++.
T Consensus       234 ~~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~L--Yv~~~  311 (559)
T KOG1155|consen  234 KKAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVL--YVKND  311 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHH--HHHhh
Confidence            3445555566677777777777777666666665566666667777777777777643      445555444  23332


Q ss_pred             ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          122 LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFD  201 (514)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~  201 (514)
                      +..  +.++.+-...--+--+.|...+.+-|+-.++.++|...|+..++.+ +....+|+.+..-|....+...|.+.++
T Consensus       312 ~sk--Ls~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYR  388 (559)
T KOG1155|consen  312 KSK--LSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYR  388 (559)
T ss_pred             hHH--HHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHH
Confidence            221  1222111111012223455666666666777777777777777765 4455666767777777777777777776


Q ss_pred             hCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC
Q 040365          202 KMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP  277 (514)
Q Consensus       202 ~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p  277 (514)
                      ...   ++|-..|-.+.++|...+.+.=|+-.|++...  .+| |...|.+|..+|.+.++.++|+..|.....-  -..
T Consensus       389 rAvdi~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~--~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~--~dt  464 (559)
T KOG1155|consen  389 RAVDINPRDYRAWYGLGQAYEIMKMHFYALYYFQKALE--LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILL--GDT  464 (559)
T ss_pred             HHHhcCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHh--cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhc--ccc
Confidence            543   45666777777777777777777777777666  344 3456777777777777777777777766432  122


Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--------CCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--------AGPTE-NVWLTLLSACRVHKNVELAGKVAEKIFMI  340 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--------~~p~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  340 (514)
                      +...+..|.++|-+.++.++|...|++-.        ..|.. .+---|..-+.+.+++++|.........-
T Consensus       465 e~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~~  536 (559)
T KOG1155|consen  465 EGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARLFLAEYFKKMKDFDEASYYATLVLKG  536 (559)
T ss_pred             chHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHhhcchHHHHHHHHHHhcC
Confidence            44666677777777777777766665431        11211 11111444456666666666655554443

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

Probab=99.30  E-value=6.2e-09  Score=96.78  Aligned_cols=276  Identities=11%  Similarity=0.052  Sum_probs=206.5

Q ss_pred             CCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHH
Q 040365           89 CARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLH  165 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~  165 (514)
                      .|++..|+++..+-.   +..+..|..-..+--+.|+.+.+-.++.+..+..-.++...+.+........|+.+.|..-.
T Consensus        97 eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v  176 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENV  176 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHH
Confidence            589999999887654   33455566666777888999999999988877533455555666677788889999999888


Q ss_pred             HHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCC-----------hhHHHHHHHHHHhCCChHHHHHHHHHH
Q 040365          166 GCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHD-----------IVSWTAVIMGNALHGNAHDAISLFEQM  234 (514)
Q Consensus       166 ~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d-----------~~~~~~li~~~~~~g~~~~A~~l~~~m  234 (514)
                      +.+.+.+ +.+..+.......|.+.|++.....++..+.+..           ..+|+.++.-....+..+.-...|++.
T Consensus       177 ~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~  255 (400)
T COG3071         177 DQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQ  255 (400)
T ss_pred             HHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhc
Confidence            8888876 6677888888999999999999999999887442           246777777766666666655666665


Q ss_pred             HHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHH----HhCCCCCC
Q 040365          235 EKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFI----SNMHAGPT  310 (514)
Q Consensus       235 ~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~----~~m~~~p~  310 (514)
                      ..+ .+-+...-.+++.-+...|+.++|.++.....+. +..|+..   .++ ...+-++.+.-.+..    ...+..  
T Consensus       256 pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~-~~D~~L~---~~~-~~l~~~d~~~l~k~~e~~l~~h~~~--  327 (400)
T COG3071         256 PRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKR-QWDPRLC---RLI-PRLRPGDPEPLIKAAEKWLKQHPED--  327 (400)
T ss_pred             cHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHh-ccChhHH---HHH-hhcCCCCchHHHHHHHHHHHhCCCC--
Confidence            443 4445555667777888999999999998888765 5555521   112 223444444433333    334443  


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +..+.+|...|.+++.+.+|...|+..+...|. ...|..++.+|.+.|+.++|.+++++-.-.
T Consensus       328 p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s-~~~~~~la~~~~~~g~~~~A~~~r~e~L~~  390 (400)
T COG3071         328 PLLLSTLGRLALKNKLWGKASEALEAALKLRPS-ASDYAELADALDQLGEPEEAEQVRREALLL  390 (400)
T ss_pred             hhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCC-hhhHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            478899999999999999999999999888875 679999999999999999999999877643

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

Probab=99.30  E-value=7.5e-09  Score=93.48  Aligned_cols=285  Identities=13%  Similarity=0.131  Sum_probs=171.6

Q ss_pred             CCHHHHHHHHccCCCCChhHH---HHHHHHHHHCCChhHHHHHHHHHHHCCCCCCH------HHHHHHHHHHhccCChHH
Q 040365           90 ARVEDSHRLFCLLPVKDAISW---NSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRH------VSFSSIMPACAHLTTLHL  160 (514)
Q Consensus        90 g~~~~A~~~f~~~~~~d~~~~---~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~------~t~~~ll~~~~~~~~~~~  160 (514)
                      .+.++|.++|-+|.+-|..|+   -+|.+.|.+.|..+.|+++-..+.++   ||.      ...-.+..-|...|-++.
T Consensus        49 ~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~qr~lAl~qL~~Dym~aGl~DR  125 (389)
T COG2956          49 NQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQRLLALQQLGRDYMAAGLLDR  125 (389)
T ss_pred             cCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHHHHHHHHHHHHHHHHhhhhhH
Confidence            344444444444443333322   23444444445555555444444332   111      111123333444555555


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChh--------HHHHHHHHHHhCCChHHHHHHHH
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIV--------SWTAVIMGNALHGNAHDAISLFE  232 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~--------~~~~li~~~~~~g~~~~A~~l~~  232 (514)
                      |+.+|..+.+.+ ..-......|+..|-+..+|++|+++-+++.+-+..        -|--+...+....+.+.|..++.
T Consensus       126 AE~~f~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~  204 (389)
T COG2956         126 AEDIFNQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLK  204 (389)
T ss_pred             HHHHHHHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            555555554433 112223344555666666666666655544322221        23334455556778899999999


Q ss_pred             HHHHcCCCCCHH-HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC
Q 040365          233 QMEKDGVKPNSV-AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT  310 (514)
Q Consensus       233 ~m~~~g~~p~~~-t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~  310 (514)
                      +..+.  .|+.+ .-..+.......|+++.|.+.++.+.+. +..--..+...|..+|...|+.++...++.++. ..+.
T Consensus       205 kAlqa--~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQ-n~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g  281 (389)
T COG2956         205 KALQA--DKKCVRASIILGRVELAKGDYQKAVEALERVLEQ-NPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTG  281 (389)
T ss_pred             HHHhh--CccceehhhhhhHHHHhccchHHHHHHHHHHHHh-ChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCC
Confidence            98885  34332 3344566788899999999999999765 333346788899999999999999999998763 4455


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH-H--HccChhHHHHHHHHHHhCCCccCCcc
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY-A--AARRWKDAASLRVFMRNKGMKKTPAC  382 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~-~--~~g~~~~a~~~~~~m~~~g~~~~~~~  382 (514)
                      ...-..+-..-....-.+.|...+.+-+...|.-- .+..|+... .  .-|++.+...++..|....++..|.+
T Consensus       282 ~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~Pt~~-gf~rl~~~~l~daeeg~~k~sL~~lr~mvge~l~~~~~Y  355 (389)
T COG2956         282 ADAELMLADLIELQEGIDAAQAYLTRQLRRKPTMR-GFHRLMDYHLADAEEGRAKESLDLLRDMVGEQLRRKPRY  355 (389)
T ss_pred             ccHHHHHHHHHHHhhChHHHHHHHHHHHhhCCcHH-HHHHHHHhhhccccccchhhhHHHHHHHHHHHHhhcCCc
Confidence            55556666655666667788888877777778644 444455443 2  44679999999999988877766643

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

Probab=99.28  E-value=8.7e-10  Score=111.40  Aligned_cols=256  Identities=13%  Similarity=0.071  Sum_probs=166.4

Q ss_pred             HHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCC
Q 040365           27 NIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKD  106 (514)
Q Consensus        27 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d  106 (514)
                      .++-.|...|+.||.+||.+++.-|+..|+.+.|- +|..|.-..++....+++.++......++.+.+.       +|.
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-------ep~   82 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-------EPL   82 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-------CCc
Confidence            46677888999999999999999999999999888 9999988888889999999999999999888776       778


Q ss_pred             hhHHHHHHHHHHHCCChhH---HHHHHHHHH----HCCCCCCHHHHHHHHHHHhccC-C------hHHHHHHHHHHHHcC
Q 040365          107 AISWNSIIAGCVQNGLFDE---GLKFFRQML----IAKIKPRHVSFSSIMPACAHLT-T------LHLGKQLHGCIIRNG  172 (514)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~---A~~l~~~m~----~~g~~p~~~t~~~ll~~~~~~~-~------~~~a~~~~~~~~~~~  172 (514)
                      ..+|+.|..+|.+.|+..-   ..+.+....    ..|+..-..-+...+.+|-+.- +      ..--+.+++..++.+
T Consensus        83 aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll  162 (1088)
T KOG4318|consen   83 ADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLL  162 (1088)
T ss_pred             hhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999999998654   222122211    1232222222222222221110 0      111122233333332


Q ss_pred             C-CCcHHHHHH-H--HHHHHh-cCCHHHHHHHHHhCC-CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHH
Q 040365          173 F-DDNMFIASS-L--LDMYAK-CGNIRLARCIFDKMD-LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAF  246 (514)
Q Consensus       173 ~-~~~~~~~~~-l--i~~y~k-~g~~~~A~~~~~~m~-~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~  246 (514)
                      . .|....++. .  +.-... ...+++-...-.... .++..++.+.+..-.-.|+.+.|..++.+|.+.|+..+..-|
T Consensus       163 ~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyF  242 (1088)
T KOG4318|consen  163 AKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYF  242 (1088)
T ss_pred             hhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccc
Confidence            1 111110000 0  111111 111222222222222 478888999998888899999999999999999988888777


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCC
Q 040365          247 VAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGK  294 (514)
Q Consensus       247 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~  294 (514)
                      -.|+-+   .++..-+..+++.|.. .|+.|+.+|+.-.+-.+...|.
T Consensus       243 wpLl~g---~~~~q~~e~vlrgmqe-~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  243 WPLLLG---INAAQVFEFVLRGMQE-KGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             hhhhhc---CccchHHHHHHHHHHH-hcCCCCcchhHHHHHhhhcchh
Confidence            777755   7777788888888844 5999998888776666555444

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

Probab=99.28  E-value=4.4e-09  Score=98.74  Aligned_cols=180  Identities=16%  Similarity=0.151  Sum_probs=124.4

Q ss_pred             cCCHHHHHHHHHhCCCCChhHHHHHH---HHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040365          190 CGNIRLARCIFDKMDLHDIVSWTAVI---MGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYF  266 (514)
Q Consensus       190 ~g~~~~A~~~~~~m~~~d~~~~~~li---~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  266 (514)
                      .|++++|.+.+.+....|...-.+|.   -.+-..|+.++|++.|-++..- +.-+...+..+.+.|-...+..+|++++
T Consensus       503 ngd~dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~  581 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELL  581 (840)
T ss_pred             cCcHHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHH
Confidence            35566666666666555544333332   2345567777777777666542 2335566666777777777888888877


Q ss_pred             HHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHh-CC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          267 NSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISN-MH-AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       267 ~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~-m~-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      .+..   .+.| |+....-|.+.|-+.|+-..|.+..-+ .. ++-+..+..-|..-|....-.+.++..|+++.-+.|+
T Consensus       582 ~q~~---slip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~  658 (840)
T KOG2003|consen  582 MQAN---SLIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPN  658 (840)
T ss_pred             HHhc---ccCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCcc
Confidence            6653   4455 788899999999999999999886543 33 3346666666667777777889999999998877775


Q ss_pred             CcchHHHHH-HHHHHccChhHHHHHHHHHHhC
Q 040365          344 NMGAYVILS-NTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       344 ~~~~~~~l~-~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                       ..-|..++ .++-+.|++..|..+++....+
T Consensus       659 -~~kwqlmiasc~rrsgnyqka~d~yk~~hrk  689 (840)
T KOG2003|consen  659 -QSKWQLMIASCFRRSGNYQKAFDLYKDIHRK  689 (840)
T ss_pred             -HHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence             45666554 5567889999999999988654

>PRK12370 invasion protein regulator; Provisional

Probab=99.23  E-value=1.1e-08  Score=106.16  Aligned_cols=258  Identities=13%  Similarity=0.022  Sum_probs=185.2

Q ss_pred             CChhHHHHHHHHHHH-----CCChhHHHHHHHHHHHCCCCCCH-HHHHHHHHHHh---------ccCChHHHHHHHHHHH
Q 040365          105 KDAISWNSIIAGCVQ-----NGLFDEGLKFFRQMLIAKIKPRH-VSFSSIMPACA---------HLTTLHLGKQLHGCII  169 (514)
Q Consensus       105 ~d~~~~~~li~~~~~-----~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~~~~---------~~~~~~~a~~~~~~~~  169 (514)
                      .+..+|...+.+-..     .+..++|+.+|++..+.  .|+. ..|..+..++.         ..+++++|...+++++
T Consensus       254 ~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~l--dP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al  331 (553)
T PRK12370        254 NSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNM--SPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKAT  331 (553)
T ss_pred             CChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHH
Confidence            355566666666422     13467899999998875  4554 34444443332         2345789999999998


Q ss_pred             HcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CC-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH-H
Q 040365          170 RNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD--LH-DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV-A  245 (514)
Q Consensus       170 ~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t  245 (514)
                      +.. +.+...+..+...+...|++++|...|++..  .| +...|..+...+...|++++|+..+++..+.  .|+.. .
T Consensus       332 ~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l--~P~~~~~  408 (553)
T PRK12370        332 ELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINECLKL--DPTRAAA  408 (553)
T ss_pred             hcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCChhh
Confidence            876 5677888888899999999999999999875  33 5667888899999999999999999999885  45432 3


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCH-HHHHHHHHHHH
Q 040365          246 FVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPTE-NVWLTLLSACR  322 (514)
Q Consensus       246 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~-~~~~~ll~~~~  322 (514)
                      +..++..+...|++++|...++++.+.  ..| ++..+..+...|...|++++|.+.++++. ..|+. ..++.|...+.
T Consensus       409 ~~~~~~~~~~~g~~eeA~~~~~~~l~~--~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~  486 (553)
T PRK12370        409 GITKLWITYYHTGIDDAIRLGDELRSQ--HLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYC  486 (553)
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHh--ccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHh
Confidence            333444566689999999999988653  134 45567778888999999999999998864 33543 34555666667


Q ss_pred             hcCCHHHHHHHHHHHHhcC---CCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          323 VHKNVELAGKVAEKIFMID---PNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~---p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ..|  +.+...++++.+..   |.++.   .+...|+-.|+-+.+... +++.+.|
T Consensus       487 ~~g--~~a~~~l~~ll~~~~~~~~~~~---~~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        487 QNS--ERALPTIREFLESEQRIDNNPG---LLPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             ccH--HHHHHHHHHHHHHhhHhhcCch---HHHHHHHHHhhhHHHHHH-HHhhccc
Confidence            777  47888777777643   43333   366677778888777777 7777654

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.22  E-value=4e-09  Score=96.53  Aligned_cols=194  Identities=14%  Similarity=0.076  Sum_probs=140.8

Q ss_pred             hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHH
Q 040365           41 SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGC  117 (514)
Q Consensus        41 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~  117 (514)
                      ...+..+...+...|++++|.+.+..+++.. +.+...+..+...|...|++++|.+.|++..   ..+...+..+...+
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  109 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLNPNNGDVLNNYGTFL  109 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHH
Confidence            4556667777777888888888888777664 4456677777788888888888888877654   23456677777788


Q ss_pred             HHCCChhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHH
Q 040365          118 VQNGLFDEGLKFFRQMLIAKIKP-RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLA  196 (514)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A  196 (514)
                      ...|++++|.+.|++.......| ....+..+..++...|++++|.+.+....+.. +.+...+..+...|.+.|++++|
T Consensus       110 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  188 (234)
T TIGR02521       110 CQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDA  188 (234)
T ss_pred             HHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHH
Confidence            88888888888888877643222 33455566677778888888888888887764 34556677788888888888888


Q ss_pred             HHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          197 RCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       197 ~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      ...+++..   ..+...+..+...+...|+.++|..+.+.+..
T Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       189 RAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            88887754   33556666777777788888888888777654

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.

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

Probab=99.22  E-value=4.7e-07  Score=86.07  Aligned_cols=365  Identities=8%  Similarity=0.054  Sum_probs=251.9

Q ss_pred             CCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHH
Q 040365            3 VSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSL   82 (514)
Q Consensus         3 ~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (514)
                      .+|+..|--.+..=.++..+..|..+++.....=.+.|.. |---+-.=-..|++..|+++|+.-.+  ..|+...|++.
T Consensus       104 ~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdql-WyKY~ymEE~LgNi~gaRqiferW~~--w~P~eqaW~sf  180 (677)
T KOG1915|consen  104 YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQL-WYKYIYMEEMLGNIAGARQIFERWME--WEPDEQAWLSF  180 (677)
T ss_pred             cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHH-HHHHHHHHHHhcccHHHHHHHHHHHc--CCCcHHHHHHH
Confidence            4677778888888888888889999998887642222332 22233333456889999999987765  47999999999


Q ss_pred             HHHHHHCCCHHHHHHHHccCC--CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHC-CC-CCCHHHHHHHHHHHhccCCh
Q 040365           83 INMYAKCARVEDSHRLFCLLP--VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIA-KI-KPRHVSFSSIMPACAHLTTL  158 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~--~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~-~p~~~t~~~ll~~~~~~~~~  158 (514)
                      |+.=.+...++.|+.++++..  .|++.+|--...--.++|+..-|.++|....+. |- ..+...|++...--.+...+
T Consensus       181 I~fElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~  260 (677)
T KOG1915|consen  181 IKFELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEY  260 (677)
T ss_pred             HHHHHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999998854  688888877777777788888887777776542 10 01111222222111122222


Q ss_pred             HHHHHHHH--------------------------------------------HHHHcCCCCcHHHHHHHHHHHHhcCCHH
Q 040365          159 HLGKQLHG--------------------------------------------CIIRNGFDDNMFIASSLLDMYAKCGNIR  194 (514)
Q Consensus       159 ~~a~~~~~--------------------------------------------~~~~~~~~~~~~~~~~li~~y~k~g~~~  194 (514)
                      +.|.-++.                                            .+++.+ +.|-.+|--.++.-...|+.+
T Consensus       261 ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~n-p~nYDsWfdylrL~e~~g~~~  339 (677)
T KOG1915|consen  261 ERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKN-PYNYDSWFDYLRLEESVGDKD  339 (677)
T ss_pred             HHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhC-CCCchHHHHHHHHHHhcCCHH
Confidence            33322222                                            222222 445666777777778889999


Q ss_pred             HHHHHHHhCC--CCCh---hHHHHHHH--------HHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH----ccC
Q 040365          195 LARCIFDKMD--LHDI---VSWTAVIM--------GNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACS----HAG  257 (514)
Q Consensus       195 ~A~~~~~~m~--~~d~---~~~~~li~--------~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~----~~g  257 (514)
                      ..+++|++..  .|..   .-|...|-        .=....+.+.+.++|+..++. ++-..+||.-+--.|+    ++.
T Consensus       340 ~Ire~yErAIanvpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~l-IPHkkFtFaKiWlmyA~feIRq~  418 (677)
T KOG1915|consen  340 RIRETYERAIANVPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLDL-IPHKKFTFAKIWLMYAQFEIRQL  418 (677)
T ss_pred             HHHHHHHHHHccCCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhh-cCcccchHHHHHHHHHHHHHHHc
Confidence            9999999875  2211   22332221        112467888999999988873 3444577765544443    567


Q ss_pred             CHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          258 LIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAE  335 (514)
Q Consensus       258 ~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~  335 (514)
                      ++..|.+++....   |.-|...++...|+.=.+.+.++....++++.. ..| |-.+|......-...|+.+.|..+|+
T Consensus       419 ~l~~ARkiLG~AI---G~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaife  495 (677)
T KOG1915|consen  419 NLTGARKILGNAI---GKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIFE  495 (677)
T ss_pred             ccHHHHHHHHHHh---ccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            8899999998775   888999999999999999999999999998863 334 66788888888888999999999999


Q ss_pred             HHHhcCCCC--cchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          336 KIFMIDPNN--MGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       336 ~~~~~~p~~--~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      -+++....+  ...|-..+..-...|.++.|..+++.+.++.
T Consensus       496 lAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt  537 (677)
T KOG1915|consen  496 LAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRT  537 (677)
T ss_pred             HHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhc
Confidence            887654211  1344555666678899999999999887764

>PRK12370 invasion protein regulator; Provisional

Probab=99.21  E-value=9.6e-09  Score=106.54  Aligned_cols=242  Identities=9%  Similarity=-0.019  Sum_probs=149.7

Q ss_pred             CChHHHHHHHHHHHHhCCCCchhHHHHHHHHHH---------HCCCHHHHHHHHccCCC---CChhHHHHHHHHHHHCCC
Q 040365           55 VDVIKGKEIHGYAIRHGLDANVCIGSSLINMYA---------KCARVEDSHRLFCLLPV---KDAISWNSIIAGCVQNGL  122 (514)
Q Consensus        55 ~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~---------~~g~~~~A~~~f~~~~~---~d~~~~~~li~~~~~~g~  122 (514)
                      +++++|.+.++++++.. +.+...+..+..+|.         ..+++++|...+++..+   .+..+|..+...+...|+
T Consensus       275 ~~~~~A~~~~~~Al~ld-P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~  353 (553)
T PRK12370        275 YSLQQALKLLTQCVNMS-PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINTIHSE  353 (553)
T ss_pred             HHHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccC
Confidence            34567778888777664 334455555554443         22347778877776552   356677777777778888


Q ss_pred             hhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          123 FDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDK  202 (514)
Q Consensus       123 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~  202 (514)
                      +++|...|++..+.+ +.+...+..+..++...|++++|...++..++.. +.+...+..++..+...|++++|...+++
T Consensus       354 ~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~-P~~~~~~~~~~~~~~~~g~~eeA~~~~~~  431 (553)
T PRK12370        354 YIVGSLLFKQANLLS-PISADIKYYYGWNLFMAGQLEEALQTINECLKLD-PTRAAAGITKLWITYYHTGIDDAIRLGDE  431 (553)
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCChhhHHHHHHHHHhccCHHHHHHHHHH
Confidence            888888888877753 3344556667777778888888888888887764 22233333344456667888888888877


Q ss_pred             CC---CC-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHH-HHHHHHHccCCHHHHHHHHHHhHHhcCCCC
Q 040365          203 MD---LH-DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFV-AVLTACSHAGLIDKAWSYFNSMTKDYGIAP  277 (514)
Q Consensus       203 m~---~~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~-~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p  277 (514)
                      ..   .| +...+..+...|...|+.++|...+.++...  .|+..+.. .+...+...|  +.+...++.+.+...-.|
T Consensus       432 ~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~~~~~~  507 (553)
T PRK12370        432 LRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ--EITGLIAVNLLYAEYCQNS--ERALPTIREFLESEQRID  507 (553)
T ss_pred             HHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc--cchhHHHHHHHHHHHhccH--HHHHHHHHHHHHHhhHhh
Confidence            63   23 3445666777777888888888888776553  45544433 3333445555  467776666655444444


Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH  306 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~  306 (514)
                      .......  ..|.-.|+-+.+..+ +++.
T Consensus       508 ~~~~~~~--~~~~~~g~~~~~~~~-~~~~  533 (553)
T PRK12370        508 NNPGLLP--LVLVAHGEAIAEKMW-NKFK  533 (553)
T ss_pred             cCchHHH--HHHHHHhhhHHHHHH-HHhh
Confidence            3223323  334445555555555 5554

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

Probab=99.19  E-value=1.7e-09  Score=97.63  Aligned_cols=225  Identities=13%  Similarity=0.036  Sum_probs=147.0

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C-ChhHHHHHHHHHHhCC
Q 040365          146 SSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--H-DIVSWTAVIMGNALHG  222 (514)
Q Consensus       146 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~-d~~~~~~li~~~~~~g  222 (514)
                      +.+.++|.++|.+.+|+..++..++..  |-+.+|-.|-..|.+..+...|..+|.+-.+  | |+....-+...+-..+
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q~--~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~  304 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQF--PHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAME  304 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhcC--CchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHH
Confidence            445555566666666666665555543  2333444455556666666666666655431  2 3333333444455556


Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFI  302 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~  302 (514)
                      +.++|.++|+...+.. ..|.....++...|.-.++.+.|..+++++.. .|+ -+++.|+.+.-+|...+++|-++.-|
T Consensus       305 ~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLq-mG~-~speLf~NigLCC~yaqQ~D~~L~sf  381 (478)
T KOG1129|consen  305 QQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQ-MGA-QSPELFCNIGLCCLYAQQIDLVLPSF  381 (478)
T ss_pred             hHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHH-hcC-CChHHHhhHHHHHHhhcchhhhHHHH
Confidence            6666666666665531 22344455555566666667777777666643 243 24556666666666666676666666


Q ss_pred             HhCC---CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          303 SNMH---AGPT--ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       303 ~~m~---~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ++..   ..|+  ..+|..|.......||+..|.+.|+-.+..+|++..+++.|.-.-.+.|++++|..+++......
T Consensus       382 ~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~~  459 (478)
T KOG1129|consen  382 QRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKSVM  459 (478)
T ss_pred             HHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhhhC
Confidence            5542   1233  46788888888999999999999999999999999999999999999999999999999887643

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.14  E-value=8.6e-08  Score=89.43  Aligned_cols=302  Identities=10%  Similarity=-0.012  Sum_probs=213.8

Q ss_pred             CChhhHHHHHHHHhC--CCChHHHHHHHHHHHHh-CCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHH--
Q 040365           39 PDSFTLSSVLPIFAD--YVDVIKGKEIHGYAIRH-GLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSI--  113 (514)
Q Consensus        39 p~~~t~~~ll~~~~~--~~~~~~a~~~~~~~~~~-g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~l--  113 (514)
                      |+..+...-+.++++  .++...+.+.+..+... -++.++....++.+.|...|+.++|...|+....-|+.+...|  
T Consensus       192 ~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~  271 (564)
T KOG1174|consen  192 DHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDL  271 (564)
T ss_pred             CCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHH
Confidence            444444444554433  34445555555544433 3677888999999999999999999999998765544433332  


Q ss_pred             -HHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCC
Q 040365          114 -IAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGN  192 (514)
Q Consensus       114 -i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~  192 (514)
                       .-.+.+.|+.+....+...+.... +-+...|-.-+...-..++++.|..+-++.++.. +.++..+-.-...+...|+
T Consensus       272 Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~-~r~~~alilKG~lL~~~~R  349 (564)
T KOG1174|consen  272 YAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSE-PRNHEALILKGRLLIALER  349 (564)
T ss_pred             HHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccC-cccchHHHhccHHHHhccc
Confidence             233467888888888877776532 2233333333333445677888888887777764 3444444444566778899


Q ss_pred             HHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHH-HHHH-ccCCHHHHHHHHH
Q 040365          193 IRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVL-TACS-HAGLIDKAWSYFN  267 (514)
Q Consensus       193 ~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll-~a~~-~~g~~~~a~~~~~  267 (514)
                      .++|.-.|+...   .-+..+|.-++..|...|++.+|.-+-+..... +.-+..+...+. ..|. ....-++|..+++
T Consensus       350 ~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~e  428 (564)
T KOG1174|consen  350 HTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAE  428 (564)
T ss_pred             hHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHH
Confidence            999999998764   358899999999999999999999877765543 233445554442 2222 2334578888888


Q ss_pred             HhHHhcCCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          268 SMTKDYGIAPS-FEHYAAVADLLGRAGKLQEAYEFISNM-HAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       268 ~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      .-.   .+.|+ ....+.+...+.+.|..+++..++++. ...||...-+.|...+...+.+++|...|..++.++|++.
T Consensus       429 k~L---~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~~~  505 (564)
T KOG1174|consen  429 KSL---KINPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQDPKSK  505 (564)
T ss_pred             hhh---ccCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCccch
Confidence            654   56775 456677888899999999999999986 4569999999999999999999999999999999999875


Q ss_pred             c
Q 040365          346 G  346 (514)
Q Consensus       346 ~  346 (514)
                      .
T Consensus       506 ~  506 (564)
T KOG1174|consen  506 R  506 (564)
T ss_pred             H
Confidence            3

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

Probab=99.12  E-value=5.2e-08  Score=94.43  Aligned_cols=252  Identities=11%  Similarity=0.021  Sum_probs=140.8

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCC
Q 040365           12 VIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCAR   91 (514)
Q Consensus        12 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~   91 (514)
                      -..-+-..+++++.++++....+.. ++....+..-|..+...|+..+-..+=..+++. .|....+|-++.--|.--|.
T Consensus       250 ~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~aVg~YYl~i~k  327 (611)
T KOG1173|consen  250 KADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFAVGCYYLMIGK  327 (611)
T ss_pred             HHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhhHHHHHHHhcC
Confidence            3344555667777777777766543 455555555555666666665555454455554 35556667777666666677


Q ss_pred             HHHHHHHHccCCCCC---hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 040365           92 VEDSHRLFCLLPVKD---AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCI  168 (514)
Q Consensus        92 ~~~A~~~f~~~~~~d---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  168 (514)
                      .++|++.|.....-|   ...|-.....|+-.|..+.|+..|...-+. ++-....+.-+.--|.+.++++.|.++|.+.
T Consensus       328 ~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~A  406 (611)
T KOG1173|consen  328 YSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKLAEKFFKQA  406 (611)
T ss_pred             cHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHHHHHHHHHH
Confidence            777777776654322   346777777777777777777776665442 1112222222333466677777777777776


Q ss_pred             HHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC----------ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC
Q 040365          169 IRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH----------DIVSWTAVIMGNALHGNAHDAISLFEQMEKDG  238 (514)
Q Consensus       169 ~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~----------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  238 (514)
                      .... |.|+.+.+-+.-++.+.+.+.+|...|+....+          -..+|+.+..+|.+.+.+++|+..|++.... 
T Consensus       407 ~ai~-P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l-  484 (611)
T KOG1173|consen  407 LAIA-PSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLL-  484 (611)
T ss_pred             HhcC-CCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHc-
Confidence            6653 556666666666666667777777666654310          1122444444444444444444444444432 


Q ss_pred             CCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040365          239 VKPNSVAFVAVLTACSHAGLIDKAWSYFNS  268 (514)
Q Consensus       239 ~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~  268 (514)
                      .+-|..|+.++.-.+...|+++.|.+.|..
T Consensus       485 ~~k~~~~~asig~iy~llgnld~Aid~fhK  514 (611)
T KOG1173|consen  485 SPKDASTHASIGYIYHLLGNLDKAIDHFHK  514 (611)
T ss_pred             CCCchhHHHHHHHHHHHhcChHHHHHHHHH
Confidence            122334444444444444444444444443

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.07  E-value=5.2e-08  Score=92.68  Aligned_cols=213  Identities=15%  Similarity=0.058  Sum_probs=136.7

Q ss_pred             ChHHHHHHHHHHHHcC-CCCc--HHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHH
Q 040365          157 TLHLGKQLHGCIIRNG-FDDN--MFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISL  230 (514)
Q Consensus       157 ~~~~a~~~~~~~~~~~-~~~~--~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l  230 (514)
                      ..+.+..-+.+++... ..|+  ...+..+...|.+.|+.++|...|++..   ..+...|+.+...+...|++++|+..
T Consensus        41 ~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~  120 (296)
T PRK11189         41 QQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEA  120 (296)
T ss_pred             HHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            4455556666666432 2222  3456677778888888888888887764   34567888888888888888888888


Q ss_pred             HHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCC
Q 040365          231 FEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGP  309 (514)
Q Consensus       231 ~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p  309 (514)
                      |++..+.  .|+ ..++..+..++...|++++|.+.|+...+.   .|+..........+...++.++|.+.+++....-
T Consensus       121 ~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~---~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~  195 (296)
T PRK11189        121 FDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD---DPNDPYRALWLYLAESKLDPKQAKENLKQRYEKL  195 (296)
T ss_pred             HHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC
Confidence            8888773  554 456777777788888888888888877643   4532211222223445677888888886532111


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHH-------hcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCC
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIF-------MIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~-------~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  376 (514)
                      +...|.. .......|+...+ ..++.+.       ++.|..+.+|..++..|.+.|++++|...|++..+.+.
T Consensus       196 ~~~~~~~-~~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~  267 (296)
T PRK11189        196 DKEQWGW-NIVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNV  267 (296)
T ss_pred             CccccHH-HHHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            1122321 1222334544433 2334433       33455667888888888889999999988888876553

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.06  E-value=4.8e-08  Score=97.17  Aligned_cols=231  Identities=13%  Similarity=0.095  Sum_probs=173.9

Q ss_pred             HHHHHHHHHHHCCChhHHHHHHHHHHHC-----C-CCCCHHHH-HHHHHHHhccCChHHHHHHHHHHHHc-----C--CC
Q 040365          109 SWNSIIAGCVQNGLFDEGLKFFRQMLIA-----K-IKPRHVSF-SSIMPACAHLTTLHLGKQLHGCIIRN-----G--FD  174 (514)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g-~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~-----~--~~  174 (514)
                      +..-+...|...|++++|..+++...+.     | ..|...+. ..+...|...+++++|..+|+.++..     |  .+
T Consensus       201 ~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~  280 (508)
T KOG1840|consen  201 TLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHP  280 (508)
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            3444888999999999999999887654     2 13444333 33666788899999999999988753     2  12


Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCC----------CCCh-hHHHHHHHHHHhCCChHHHHHHHHHHHHc---CCC
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMD----------LHDI-VSWTAVIMGNALHGNAHDAISLFEQMEKD---GVK  240 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~----------~~d~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~---g~~  240 (514)
                      .-..+++.|..+|.+.|++++|...+++..          .+++ ...+.+...+...+++++|..+++...+.   -+.
T Consensus       281 ~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g  360 (508)
T KOG1840|consen  281 AVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPG  360 (508)
T ss_pred             HHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhcc
Confidence            224566777888999999999888777653          2233 24667777888999999999999876541   133


Q ss_pred             CCH----HHHHHHHHHHHccCCHHHHHHHHHHhHHhc-----CCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC----
Q 040365          241 PNS----VAFVAVLTACSHAGLIDKAWSYFNSMTKDY-----GIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH----  306 (514)
Q Consensus       241 p~~----~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~-----~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~----  306 (514)
                      ++.    .++..+...+.+.|++++|.++|++.....     +..+ ....++.|...|.+.++.++|.++|.+..    
T Consensus       361 ~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~  440 (508)
T KOG1840|consen  361 EDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMK  440 (508)
T ss_pred             ccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHH
Confidence            333    578899999999999999999999886643     1123 24677888899999999999999988752    


Q ss_pred             ----CCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040365          307 ----AGPTE-NVWLTLLSACRVHKNVELAGKVAEKIFM  339 (514)
Q Consensus       307 ----~~p~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~  339 (514)
                          ..|++ .+|..|...|...|+++.|+++.+.+..
T Consensus       441 ~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  441 LCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence                23554 5799999999999999999999998874

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.03  E-value=2.7e-07  Score=87.79  Aligned_cols=218  Identities=12%  Similarity=-0.025  Sum_probs=145.9

Q ss_pred             CChhHHHHHHHHHHHCC-CCCC--HHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHH
Q 040365          121 GLFDEGLKFFRQMLIAK-IKPR--HVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLAR  197 (514)
Q Consensus       121 g~~~~A~~l~~~m~~~g-~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~  197 (514)
                      +..+.++.-+.++.... ..|+  ...|......+...|+.++|...+.+.++.. +.+...++.+...|...|++++|.
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~  118 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAY  118 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            45566666666666432 2222  2345556666777888888888888887765 556778888888889999999998


Q ss_pred             HHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC
Q 040365          198 CIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG  274 (514)
Q Consensus       198 ~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~  274 (514)
                      ..|++..   ..+..+|..+...+...|++++|++.|++..+.  .|+..........+...++.++|...|.....  .
T Consensus       119 ~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~--~  194 (296)
T PRK11189        119 EAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRYE--K  194 (296)
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHh--h
Confidence            8888874   235677888888888899999999999998874  45543222222234456789999999976543  2


Q ss_pred             CCCCHhHHHHHHHHHHhcCCHHHH--HHHHHh-CCCC-----CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc
Q 040365          275 IAPSFEHYAAVADLLGRAGKLQEA--YEFISN-MHAG-----PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG  346 (514)
Q Consensus       275 ~~p~~~~~~~li~~~~~~g~~~~A--~~~~~~-m~~~-----p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~  346 (514)
                      ..|+... ..++..  ..|++.++  .+.+.+ ....     .....|..|...+...|++++|+..|+++++.+|++..
T Consensus       195 ~~~~~~~-~~~~~~--~lg~~~~~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~~~~~  271 (296)
T PRK11189        195 LDKEQWG-WNIVEF--YLGKISEETLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNVYNFV  271 (296)
T ss_pred             CCccccH-HHHHHH--HccCCCHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCchHH
Confidence            2333222 223333  34444333  322222 1111     13457999999999999999999999999999976543

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

Probab=98.95  E-value=4.8e-06  Score=79.74  Aligned_cols=218  Identities=12%  Similarity=0.003  Sum_probs=171.2

Q ss_pred             HHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHH
Q 040365          117 CVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLA  196 (514)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A  196 (514)
                      +.-.|+...|...|+..+.....++. .|.-+..+|....+.++..+.|+...+.+ +.|..+|..-..++.-.+++++|
T Consensus       336 ~fL~g~~~~a~~d~~~~I~l~~~~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~ld-p~n~dvYyHRgQm~flL~q~e~A  413 (606)
T KOG0547|consen  336 HFLKGDSLGAQEDFDAAIKLDPAFNS-LYIKRAAAYADENQSEKMWKDFNKAEDLD-PENPDVYYHRGQMRFLLQQYEEA  413 (606)
T ss_pred             hhhcCCchhhhhhHHHHHhcCcccch-HHHHHHHHHhhhhccHHHHHHHHHHHhcC-CCCCchhHhHHHHHHHHHHHHHH
Confidence            34578889999999998886433332 27777888999999999999999999886 56677888888888899999999


Q ss_pred             HHHHHhCCC---CChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhc
Q 040365          197 RCIFDKMDL---HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDY  273 (514)
Q Consensus       197 ~~~~~~m~~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~  273 (514)
                      ..-|++...   .++.+|-.+--+.-+.++++++...|++..+. ++--...|+.....+...++++.|.+.|+....  
T Consensus       414 ~aDF~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~--  490 (606)
T KOG0547|consen  414 IADFQKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIE--  490 (606)
T ss_pred             HHHHHHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHh--
Confidence            999998763   35667777777777889999999999999886 444567888899999999999999999998753  


Q ss_pred             CCCCC---------HhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040365          274 GIAPS---------FEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMID  341 (514)
Q Consensus       274 ~~~p~---------~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  341 (514)
                       +.|+         +.+.-.++-.- -.+++..|.+++++.. ..| ....+-+|...-.+.|+.++|+++|++...+-
T Consensus       491 -LE~~~~~~~v~~~plV~Ka~l~~q-wk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~lA  567 (606)
T KOG0547|consen  491 -LEPREHLIIVNAAPLVHKALLVLQ-WKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSAQLA  567 (606)
T ss_pred             -hccccccccccchhhhhhhHhhhc-hhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence             3443         22222222222 3389999999999874 333 45678999999999999999999999987763

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

Probab=98.94  E-value=1.2e-07  Score=82.00  Aligned_cols=162  Identities=16%  Similarity=0.145  Sum_probs=135.4

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHH
Q 040365          210 SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVAD  287 (514)
Q Consensus       210 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~  287 (514)
                      +...+.-+|.+.|+...|..-+++.++.  .|+ .-++..+...|.+.|..+.|.+.|+...   .+.| +..+.|....
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~--DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAl---sl~p~~GdVLNNYG~  111 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEH--DPSYYLAHLVRAHYYQKLGENDLADESYRKAL---SLAPNNGDVLNNYGA  111 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChhhHHHHHHHHH---hcCCCccchhhhhhH
Confidence            3445667788888888888888888875  454 4678888888889999999999988775   4566 5677788888


Q ss_pred             HHHhcCCHHHHHHHHHhCCCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhH
Q 040365          288 LLGRAGKLQEAYEFISNMHAGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKD  363 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  363 (514)
                      -+|..|++++|...|++....|+    ..+|..+.-+..+.|+.+.|...+++.++.+|+.+.+...+.....+.|++-.
T Consensus       112 FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~  191 (250)
T COG3063         112 FLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAP  191 (250)
T ss_pred             HHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchH
Confidence            88999999999999988754443    46788888888999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCC
Q 040365          364 AASLRVFMRNKGM  376 (514)
Q Consensus       364 a~~~~~~m~~~g~  376 (514)
                      |...++....++.
T Consensus       192 Ar~~~~~~~~~~~  204 (250)
T COG3063         192 ARLYLERYQQRGG  204 (250)
T ss_pred             HHHHHHHHHhccc
Confidence            9999998887765

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

Probab=98.92  E-value=5.1e-08  Score=88.20  Aligned_cols=220  Identities=10%  Similarity=-0.018  Sum_probs=114.1

Q ss_pred             HHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC--C-ChhHHHHHHHHHHHCC
Q 040365           45 SSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPV--K-DAISWNSIIAGCVQNG  121 (514)
Q Consensus        45 ~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~--~-d~~~~~~li~~~~~~g  121 (514)
                      ..+.+.|.+.|-+.+|..-++..++.  .|-+.+|-.|-..|.+-.+...|+.+|.+-.+  | |+.-..-+.+.+-..+
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~  304 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAME  304 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHH
Confidence            33444555555555555555555444  34444455555555555555555555554432  2 2222233444455555


Q ss_pred             ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          122 LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFD  201 (514)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~  201 (514)
                      +.++|+++|+...+.. +.+......+...|.-.++++.|..++.++++.| ..+...|+.+.-++.-.+++|-+...|+
T Consensus       305 ~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG-~~speLf~NigLCC~yaqQ~D~~L~sf~  382 (478)
T KOG1129|consen  305 QQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQMG-AQSPELFCNIGLCCLYAQQIDLVLPSFQ  382 (478)
T ss_pred             hHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHHhc-CCChHHHhhHHHHHHhhcchhhhHHHHH
Confidence            5556666655554431 2233344444444455555566666666666555 2344455555555555555555555555


Q ss_pred             hCC----CCCh--hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          202 KMD----LHDI--VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       202 ~m~----~~d~--~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      +..    .++.  ..|..+-......|++.-|.+.|+-....+ .-+...++.|.-.-.+.|++++|..+++..
T Consensus       383 RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d-~~h~ealnNLavL~~r~G~i~~Arsll~~A  455 (478)
T KOG1129|consen  383 RALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD-AQHGEALNNLAVLAARSGDILGARSLLNAA  455 (478)
T ss_pred             HHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC-cchHHHHHhHHHHHhhcCchHHHHHHHHHh
Confidence            432    2322  345555555555666666666666555432 113355666665566667777777776655

>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=98.91  E-value=4.8e-06  Score=84.04  Aligned_cols=149  Identities=17%  Similarity=0.101  Sum_probs=84.4

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCChh-hHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCC-
Q 040365           13 IVGLARNGLYEEALNIVRQMGNVNLKPDSF-TLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA-   90 (514)
Q Consensus        13 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g-   90 (514)
                      ...+...|++++|++.+..-...  -+|.. .+......+.+.|+.++|..++..+++.+ |.+..-|..|..+..-.. 
T Consensus        11 ~~il~e~g~~~~AL~~L~~~~~~--I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN-Pdn~~Yy~~L~~~~g~~~~   87 (517)
T PF12569_consen   11 NSILEEAGDYEEALEHLEKNEKQ--ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN-PDNYDYYRGLEEALGLQLQ   87 (517)
T ss_pred             HHHHHHCCCHHHHHHHHHhhhhh--CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHhhhcc
Confidence            34567789999999999775443  35544 45666777889999999999999999886 556666666666653332 


Q ss_pred             ----CHHHHHHHHccCCCC--ChhHHHHHHHHHHHCCCh-hHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHH
Q 040365           91 ----RVEDSHRLFCLLPVK--DAISWNSIIAGCVQNGLF-DEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQ  163 (514)
Q Consensus        91 ----~~~~A~~~f~~~~~~--d~~~~~~li~~~~~~g~~-~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~  163 (514)
                          +.+....+++++...  ...+.-.+.-.+.....+ ..+...+..+...|+++   +|+.+-..|......+-..+
T Consensus        88 ~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~K~~~i~~  164 (517)
T PF12569_consen   88 LSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDPEKAAIIES  164 (517)
T ss_pred             cccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcChhHHHHHHH
Confidence                456666666665422  111111111111111122 23444556666677644   34444444544443333333


Q ss_pred             HHHH
Q 040365          164 LHGC  167 (514)
Q Consensus       164 ~~~~  167 (514)
                      +...
T Consensus       165 l~~~  168 (517)
T PF12569_consen  165 LVEE  168 (517)
T ss_pred             HHHH
Confidence            3333

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 [], [].

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

Probab=98.87  E-value=9e-06  Score=79.93  Aligned_cols=197  Identities=11%  Similarity=-0.025  Sum_probs=103.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCC-CCCH--HHHHHHHHH
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV-KPNS--VAFVAVLTA  252 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~~--~t~~~ll~a  252 (514)
                      ....+...+...|++++|.+.+++..   +.+...+..+...|...|++++|..++++...... .|+.  ..|..+...
T Consensus       116 ~~~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~  195 (355)
T cd05804         116 LLGMLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALF  195 (355)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHH
Confidence            33344555666666666666666653   23345556666666666666666666666555321 1222  223345556


Q ss_pred             HHccCCHHHHHHHHHHhHHhcCCCCCHhHH-H--HHHHHHHhcCCHHHHHHH---HHh---C-CCCCCHHHHHHHHHHHH
Q 040365          253 CSHAGLIDKAWSYFNSMTKDYGIAPSFEHY-A--AVADLLGRAGKLQEAYEF---ISN---M-HAGPTENVWLTLLSACR  322 (514)
Q Consensus       253 ~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~-~--~li~~~~~~g~~~~A~~~---~~~---m-~~~p~~~~~~~ll~~~~  322 (514)
                      +...|++++|..+++.........+..... +  .++..+...|..+.+.+.   ...   . +.............++.
T Consensus       196 ~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~  275 (355)
T cd05804         196 YLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALA  275 (355)
T ss_pred             HHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHh
Confidence            666677777777766653221111111111 1  222222333322222221   111   1 11111122234556677


Q ss_pred             hcCCHHHHHHHHHHHHhcC-C--------CCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          323 VHKNVELAGKVAEKIFMID-P--------NNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~-p--------~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ..|+.+.|..+++.+.... .        ...........++...|++++|.+.+......+
T Consensus       276 ~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~a  337 (355)
T cd05804         276 GAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDDL  337 (355)
T ss_pred             cCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            7788888888887775532 1        123444566777889999999999998877654

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.

>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=98.85  E-value=2.2e-06  Score=86.50  Aligned_cols=148  Identities=13%  Similarity=0.102  Sum_probs=100.9

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhc-------------CCCCCH--hHHHHHHHHHH
Q 040365          226 DAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDY-------------GIAPSF--EHYAAVADLLG  290 (514)
Q Consensus       226 ~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~-------------~~~p~~--~~~~~li~~~~  290 (514)
                      .+..++..+...|+++   +|+.|-..|......+-..+++.......             .-.|+.  .++.-+...|-
T Consensus       129 ~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~K~~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd  205 (517)
T PF12569_consen  129 RLDEYLRPQLRKGVPS---LFSNLKPLYKDPEKAAIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYD  205 (517)
T ss_pred             HHHHHHHHHHhcCCch---HHHHHHHHHcChhHHHHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHH
Confidence            3444556666677553   45555555555544444444444443211             012333  24455677788


Q ss_pred             hcCCHHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHH
Q 040365          291 RAGKLQEAYEFISNMH-AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLR  368 (514)
Q Consensus       291 ~~g~~~~A~~~~~~m~-~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~  368 (514)
                      +.|++++|++++++.. ..|+ +..|..-...+...|++++|...++.+.++++.|-..-+-.+..+.++|+.++|.++.
T Consensus       206 ~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~  285 (517)
T PF12569_consen  206 YLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTA  285 (517)
T ss_pred             HhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            8899999999988753 3455 5667777888889999999999999999998887766667778888999999999999


Q ss_pred             HHHHhCCC
Q 040365          369 VFMRNKGM  376 (514)
Q Consensus       369 ~~m~~~g~  376 (514)
                      ......+.
T Consensus       286 ~~Ftr~~~  293 (517)
T PF12569_consen  286 SLFTREDV  293 (517)
T ss_pred             HhhcCCCC
Confidence            88877765

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 [], [].

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

Probab=98.82  E-value=2.1e-05  Score=77.30  Aligned_cols=198  Identities=10%  Similarity=-0.043  Sum_probs=120.0

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCC-CCChhh-HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHH--
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNL-KPDSFT-LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGS--   80 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~--   80 (514)
                      ....|..+...+...|+.+.+...+........ .++... .......+...|++++|.++++.+++.. |.+..+++  
T Consensus         5 ~~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~~   83 (355)
T cd05804           5 FALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALKLH   83 (355)
T ss_pred             cHHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHh
Confidence            345677777777777888887766666554321 122211 1112233456788999999988888764 44544444  


Q ss_pred             -HHHHHHHHCCCHHHHHHHHccCCCC---ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccC
Q 040365           81 -SLINMYAKCARVEDSHRLFCLLPVK---DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLT  156 (514)
Q Consensus        81 -~li~~~~~~g~~~~A~~~f~~~~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~  156 (514)
                       .+.......+..+.+.+.++.....   +...+..+...+...|++++|...+++..+.. +.+...+..+..++...|
T Consensus        84 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g  162 (355)
T cd05804          84 LGAFGLGDFSGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQG  162 (355)
T ss_pred             HHHHHhcccccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcC
Confidence             2222223345566666666543222   22233445567778888888888888887753 334556666777777788


Q ss_pred             ChHHHHHHHHHHHHcCC-CCcH--HHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          157 TLHLGKQLHGCIIRNGF-DDNM--FIASSLLDMYAKCGNIRLARCIFDKMD  204 (514)
Q Consensus       157 ~~~~a~~~~~~~~~~~~-~~~~--~~~~~li~~y~k~g~~~~A~~~~~~m~  204 (514)
                      ++++|.+.+....+... .++.  ..+..+...|...|++++|..+|++..
T Consensus       163 ~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~  213 (355)
T cd05804         163 RFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHI  213 (355)
T ss_pred             CHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            88888888777766431 1222  234456667777777777777777754

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.

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

Probab=98.82  E-value=4.9e-05  Score=75.50  Aligned_cols=364  Identities=13%  Similarity=0.083  Sum_probs=204.3

Q ss_pred             hcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHH
Q 040365           18 RNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHR   97 (514)
Q Consensus        18 ~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~   97 (514)
                      .-|+-++|....+.-.+.. .-+.+.|..+.-......++++|...+..+++.+ +.|..++.-|.-.-++.|+++....
T Consensus        53 ~lg~~~ea~~~vr~glr~d-~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~  130 (700)
T KOG1156|consen   53 CLGKKEEAYELVRLGLRND-LKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLE  130 (700)
T ss_pred             cccchHHHHHHHHHHhccC-cccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHH
Confidence            3466677776666555432 2344556665555566677777777777777765 5566666655555555566555444


Q ss_pred             HHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCC-CCCCHHHHHHHH------HHHhccCChHHHHHHHHH
Q 040365           98 LFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAK-IKPRHVSFSSIM------PACAHLTTLHLGKQLHGC  167 (514)
Q Consensus        98 ~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll------~~~~~~~~~~~a~~~~~~  167 (514)
                      .-....   ......|..+..++.-.|+...|..++++..+.. -.|+...|.-..      ......|.++.|.+.+..
T Consensus       131 tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~  210 (700)
T KOG1156|consen  131 TRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLD  210 (700)
T ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHh
Confidence            333322   2344567777777777777777777777766543 234544443222      123445556666555544


Q ss_pred             HHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--CChhHHHHH-HHHHHhCCC---------------------
Q 040365          168 IIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--HDIVSWTAV-IMGNALHGN---------------------  223 (514)
Q Consensus       168 ~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d~~~~~~l-i~~~~~~g~---------------------  223 (514)
                      .... +......-..-.+.+.+.|++++|..++..+..  ||-..|+-. ..++.+--+                     
T Consensus       211 ~e~~-i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~  289 (700)
T KOG1156|consen  211 NEKQ-IVDKLAFEETKADLLMKLGQLEEAVKVYRRLLERNPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHEC  289 (700)
T ss_pred             hhhH-HHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhCchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCccccc
Confidence            3322 122233333445566677777777777766653  333333222 222211111                     


Q ss_pred             --------------hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHH----HHHHHHHHhHHh--------cCC-C
Q 040365          224 --------------AHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLID----KAWSYFNSMTKD--------YGI-A  276 (514)
Q Consensus       224 --------------~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~----~a~~~~~~m~~~--------~~~-~  276 (514)
                                    .+..-+++..+.+.|++|-   |..+.+.+-.-...+    -+..+...+...        ... +
T Consensus       290 p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~v---f~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~  366 (700)
T KOG1156|consen  290 PRRLPLSVLNGEELKEIVDKYLRPLLSKGVPSV---FKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEP  366 (700)
T ss_pred             chhccHHHhCcchhHHHHHHHHHHHhhcCCCch---hhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCC
Confidence                          1122233444555555432   222222222211111    122222222110        001 3


Q ss_pred             CCHh--HHHHHHHHHHhcCCHHHHHHHHHhCCC-CCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          277 PSFE--HYAAVADLLGRAGKLQEAYEFISNMHA-GPTEN-VWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       277 p~~~--~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      |+..  ++-.++..+-+.|+++.|..+++.... .|+.+ .|..=...+...|++++|...++++.+++..|...-.--+
T Consensus       367 PttllWt~y~laqh~D~~g~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~aDR~INsKcA  446 (700)
T KOG1156|consen  367 PTTLLWTLYFLAQHYDKLGDYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDTADRAINSKCA  446 (700)
T ss_pred             chHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccchhHHHHHHHH
Confidence            4443  445677889999999999999998753 35543 3444557788899999999999999999966543333456


Q ss_pred             HHHHHccChhHHHHHHHHHHhCCCc-----cCCcccEEEE
Q 040365          353 NTYAAARRWKDAASLRVFMRNKGMK-----KTPACSWIEV  387 (514)
Q Consensus       353 ~~~~~~g~~~~a~~~~~~m~~~g~~-----~~~~~s~~~~  387 (514)
                      +-..++.+.++|.++.....+.|..     .+..|.|..+
T Consensus       447 KYmLrAn~i~eA~~~~skFTr~~~~~~~~L~~mqcmWf~~  486 (700)
T KOG1156|consen  447 KYMLRANEIEEAEEVLSKFTREGFGAVNNLAEMQCMWFQL  486 (700)
T ss_pred             HHHHHccccHHHHHHHHHhhhcccchhhhHHHhhhHHHhH
Confidence            6677899999999999999877641     1235677654

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.78  E-value=6.2e-07  Score=87.49  Aligned_cols=219  Identities=11%  Similarity=0.055  Sum_probs=171.7

Q ss_pred             HhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHH
Q 040365          152 CAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAI  228 (514)
Q Consensus       152 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~  228 (514)
                      +.+.|++.+|.-.|+..++.. +.+...|--|.-.....++-..|+..+++..   ..|....-+|.-.|...|.-.+|+
T Consensus       295 lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~Al  373 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQAL  373 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHHH
Confidence            356778888888888888775 6678888888888888888888888887765   345667777778888889889999


Q ss_pred             HHHHHHHHcCCC--------CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHH
Q 040365          229 SLFEQMEKDGVK--------PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE  300 (514)
Q Consensus       229 ~l~~~m~~~g~~--------p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~  300 (514)
                      ..++.-.....+        ++..+-..  ........+....++|-.+....+..+|++++.+|.-.|--.|.+++|.+
T Consensus       374 ~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiD  451 (579)
T KOG1125|consen  374 KMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVD  451 (579)
T ss_pred             HHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHH
Confidence            988887653211        01000000  12223334556667777777766766888899999999999999999999


Q ss_pred             HHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          301 FISNM-HAGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       301 ~~~~m-~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      -|+.. ..+| |..+||-|...+....+.++|+..|.+++++.|.=.++...|+-.|...|.+++|.+.|-....
T Consensus       452 cf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~  526 (579)
T KOG1125|consen  452 CFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALS  526 (579)
T ss_pred             HHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHH
Confidence            99986 4556 6788999999999999999999999999999999999999999999999999999998876654

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.76  E-value=2.7e-05  Score=71.45  Aligned_cols=192  Identities=10%  Similarity=0.070  Sum_probs=116.2

Q ss_pred             HHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhC---CCCChhHHHHHHHHHHhCCCh
Q 040365          148 IMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKM---DLHDIVSWTAVIMGNALHGNA  224 (514)
Q Consensus       148 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m---~~~d~~~~~~li~~~~~~g~~  224 (514)
                      .+..+...|+...+......+++.. +.|...+..-..+|...|++..|+.-+...   ...+..+..-+-..+..-|+.
T Consensus       161 ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~  239 (504)
T KOG0624|consen  161 QLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDA  239 (504)
T ss_pred             HHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhH
Confidence            3445566788888888888888765 678888888888888888888887665544   355666666777777788888


Q ss_pred             HHHHHHHHHHHHcCCCCCHHH-H---HHH---H------HHHHccCCHHHHHHHHHHhHHhcCCCCC-----HhHHHHHH
Q 040365          225 HDAISLFEQMEKDGVKPNSVA-F---VAV---L------TACSHAGLIDKAWSYFNSMTKDYGIAPS-----FEHYAAVA  286 (514)
Q Consensus       225 ~~A~~l~~~m~~~g~~p~~~t-~---~~l---l------~a~~~~g~~~~a~~~~~~m~~~~~~~p~-----~~~~~~li  286 (514)
                      +.++...++-++  +.||... |   ..|   .      ......+.+.++..-.+...+.   .|.     ...+..+-
T Consensus       240 ~~sL~~iRECLK--ldpdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~---ep~~~~ir~~~~r~~c  314 (504)
T KOG0624|consen  240 ENSLKEIRECLK--LDPDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKN---EPEETMIRYNGFRVLC  314 (504)
T ss_pred             HHHHHHHHHHHc--cCcchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhc---CCcccceeeeeeheee
Confidence            888888887776  4676532 1   111   0      1112234444444444444322   222     22333444


Q ss_pred             HHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          287 DLLGRAGKLQEAYEFISNM-HAGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       287 ~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      .++...|++.+|++.-.+. ...|| +.++.--..+|.....++.|+.-|+++.+.+++|.
T Consensus       315 ~C~~~d~~~~eAiqqC~evL~~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~n~sn~  375 (504)
T KOG0624|consen  315 TCYREDEQFGEAIQQCKEVLDIDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKALELNESNT  375 (504)
T ss_pred             ecccccCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcccH
Confidence            4555556666666555543 22333 55555555666666666666666666666666554

>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=98.75  E-value=2e-07  Score=87.55  Aligned_cols=80  Identities=16%  Similarity=0.114  Sum_probs=41.2

Q ss_pred             CHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccCh-hHHHHHHHH
Q 040365          294 KLQEAYEFISNMHAG--PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRW-KDAASLRVF  370 (514)
Q Consensus       294 ~~~~A~~~~~~m~~~--p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~-~~a~~~~~~  370 (514)
                      .+.+|..+|+++..+  +++.+.+.+..++...|++++|+.++++.++.+|.++.+...++.+....|+. +.+.+.+.+
T Consensus       182 ~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l~q  261 (290)
T PF04733_consen  182 KYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYLSQ  261 (290)
T ss_dssp             CCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHHHH
Confidence            345555555554322  44455555555555556666666666655555566655555565555555555 444555555


Q ss_pred             HHh
Q 040365          371 MRN  373 (514)
Q Consensus       371 m~~  373 (514)
                      ++.
T Consensus       262 L~~  264 (290)
T PF04733_consen  262 LKQ  264 (290)
T ss_dssp             CHH
T ss_pred             HHH
Confidence            443

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.

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

Probab=98.75  E-value=0.00011  Score=73.03  Aligned_cols=351  Identities=13%  Similarity=0.133  Sum_probs=182.8

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhC-CCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNV-NLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      ..|-..+..+.+.|+.......|+..+.. .+......|...+.-....+-++.+..+++.-++.    ++..-+--|.-
T Consensus       103 RIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie~  178 (835)
T KOG2047|consen  103 RIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIEY  178 (835)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHHH
Confidence            35666666666666666666666665442 12222334555566555666666666666665543    22224555556


Q ss_pred             HHHCCCHHHHHHHHccCCCC----------ChhHHHHHHHHHHHCCChhH---HHHHHHHHHHCCCCCCH--HHHHHHHH
Q 040365           86 YAKCARVEDSHRLFCLLPVK----------DAISWNSIIAGCVQNGLFDE---GLKFFRQMLIAKIKPRH--VSFSSIMP  150 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~~----------d~~~~~~li~~~~~~g~~~~---A~~l~~~m~~~g~~p~~--~t~~~ll~  150 (514)
                      +++.+++++|.+.+..+...          +-..|+-+-...+++-+.-.   ...+++.+..  .-||.  ..|.+|..
T Consensus       179 L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~--rftDq~g~Lw~SLAd  256 (835)
T KOG2047|consen  179 LAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIR--RFTDQLGFLWCSLAD  256 (835)
T ss_pred             HHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcc--cCcHHHHHHHHHHHH
Confidence            66666666666655554321          22234444333333322111   1122222221  12222  23445555


Q ss_pred             HHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc----------------C------CHHHHHHHHHhCC----
Q 040365          151 ACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKC----------------G------NIRLARCIFDKMD----  204 (514)
Q Consensus       151 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~----------------g------~~~~A~~~~~~m~----  204 (514)
                      -|.+.|.++.|..++.+.+..-  .++.-++.+.+.|+.-                |      +++-...-|+.+.    
T Consensus       257 YYIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~  334 (835)
T KOG2047|consen  257 YYIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRP  334 (835)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccc
Confidence            5555555555555555444331  1111122222222211                1      1122222232221    


Q ss_pred             -----------CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC------HHHHHHHHHHHHccCCHHHHHHHHH
Q 040365          205 -----------LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN------SVAFVAVLTACSHAGLIDKAWSYFN  267 (514)
Q Consensus       205 -----------~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~------~~t~~~ll~a~~~~g~~~~a~~~~~  267 (514)
                                 ..++..|..-+..  ..|+..+-...|.+..+. +.|-      ...|..+...|-..|+++.|..+|+
T Consensus       335 ~~lNsVlLRQn~~nV~eW~kRV~l--~e~~~~~~i~tyteAv~~-vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvife  411 (835)
T KOG2047|consen  335 LLLNSVLLRQNPHNVEEWHKRVKL--YEGNAAEQINTYTEAVKT-VDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFE  411 (835)
T ss_pred             hHHHHHHHhcCCccHHHHHhhhhh--hcCChHHHHHHHHHHHHc-cCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHH
Confidence                       2244455544443  356777777788877764 4442      2346677777888888888888888


Q ss_pred             HhHHhcCCCC---CHhHHHHHHHHHHhcCCHHHHHHHHHhCC---CC-----------------CCHHHHHHHHHHHHhc
Q 040365          268 SMTKDYGIAP---SFEHYAAVADLLGRAGKLQEAYEFISNMH---AG-----------------PTENVWLTLLSACRVH  324 (514)
Q Consensus       268 ~m~~~~~~~p---~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~-----------------p~~~~~~~ll~~~~~~  324 (514)
                      ...+. ..+-   -..+|..-.++=.+..+++.|+++++...   .+                 .+..+|...++---..
T Consensus       412 ka~~V-~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~  490 (835)
T KOG2047|consen  412 KATKV-PYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESL  490 (835)
T ss_pred             HhhcC-CccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHh
Confidence            77542 2111   13456666666677788888888887652   11                 1234566666666677


Q ss_pred             CCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHH
Q 040365          325 KNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRV  369 (514)
Q Consensus       325 ~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~  369 (514)
                      |-++....++++++++.--.|..-...+..+-...-++++.++++
T Consensus       491 gtfestk~vYdriidLriaTPqii~NyAmfLEeh~yfeesFk~YE  535 (835)
T KOG2047|consen  491 GTFESTKAVYDRIIDLRIATPQIIINYAMFLEEHKYFEESFKAYE  535 (835)
T ss_pred             ccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            778888888888887764344343444444445555677777775

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

Probab=98.75  E-value=1.2e-06  Score=93.25  Aligned_cols=201  Identities=13%  Similarity=0.101  Sum_probs=170.2

Q ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC--------ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHH
Q 040365          174 DDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH--------DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVA  245 (514)
Q Consensus       174 ~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~--------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  245 (514)
                      |.....|-..|......+++++|++++++....        -.-.|.++++.-...|.-+...++|++..+.-  -....
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~~V 1532 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAYTV 1532 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chHHH
Confidence            455677888888899999999999999987521        34579999988888898899999999998741  12356


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC---CHHHHHHHHHHH
Q 040365          246 FVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP---TENVWLTLLSAC  321 (514)
Q Consensus       246 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p---~~~~~~~ll~~~  321 (514)
                      |..|...|.+.+.+++|.++++.|.++++  -....|...++.+.+..+-++|..++.+.- .-|   ......-.+..-
T Consensus      1533 ~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLE 1610 (1710)
T KOG1070|consen 1533 HLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLE 1610 (1710)
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHH
Confidence            88999999999999999999999999877  567889999999999999999999998752 223   344555566667


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCcc
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKK  378 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~  378 (514)
                      .++|+.+++..+|+.++...|.....|+.++++-.+.|..+.++.+|++....++.+
T Consensus      1611 Fk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1611 FKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             hhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            899999999999999999999999999999999999999999999999999988763

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.75  E-value=2.6e-05  Score=86.81  Aligned_cols=324  Identities=10%  Similarity=-0.028  Sum_probs=205.0

Q ss_pred             hCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC----CC----C--hh--HHHHHHHHHHH
Q 040365           52 ADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP----VK----D--AI--SWNSIIAGCVQ  119 (514)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~----~~----d--~~--~~~~li~~~~~  119 (514)
                      ...|+...+...+..+.......+..........+...|++++|...++...    ..    +  ..  ....+...+..
T Consensus       385 ~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  464 (903)
T PRK04841        385 FNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAIN  464 (903)
T ss_pred             HhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHh
Confidence            3456666665555544211112223333445556677899999888776542    11    1  11  11223345568


Q ss_pred             CCChhHHHHHHHHHHHCCCCCCH----HHHHHHHHHHhccCChHHHHHHHHHHHHcCC---CC--cHHHHHHHHHHHHhc
Q 040365          120 NGLFDEGLKFFRQMLIAKIKPRH----VSFSSIMPACAHLTTLHLGKQLHGCIIRNGF---DD--NMFIASSLLDMYAKC  190 (514)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~---~~--~~~~~~~li~~y~k~  190 (514)
                      .|++++|...+++....-...+.    ...+.+...+...|+++.|...+.......-   .+  .......+...+...
T Consensus       465 ~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~  544 (903)
T PRK04841        465 DGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQ  544 (903)
T ss_pred             CCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHC
Confidence            89999999999987663111221    2334455566788999999999888765311   11  223455667788899


Q ss_pred             CCHHHHHHHHHhCCC-------C----ChhHHHHHHHHHHhCCChHHHHHHHHHHHHc--CCCCC--HHHHHHHHHHHHc
Q 040365          191 GNIRLARCIFDKMDL-------H----DIVSWTAVIMGNALHGNAHDAISLFEQMEKD--GVKPN--SVAFVAVLTACSH  255 (514)
Q Consensus       191 g~~~~A~~~~~~m~~-------~----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g~~p~--~~t~~~ll~a~~~  255 (514)
                      |+++.|...+++...       +    ....+..+...+...|++++|...+.+....  ...|.  ...+..+......
T Consensus       545 G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~  624 (903)
T PRK04841        545 GFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLA  624 (903)
T ss_pred             CCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHH
Confidence            999999998876531       1    1223445555677789999999999887652  11222  2334445567778


Q ss_pred             cCCHHHHHHHHHHhHHhcCCCCCHhHH-----HHHHHHHHhcCCHHHHHHHHHhCCCC--CCH----HHHHHHHHHHHhc
Q 040365          256 AGLIDKAWSYFNSMTKDYGIAPSFEHY-----AAVADLLGRAGKLQEAYEFISNMHAG--PTE----NVWLTLLSACRVH  324 (514)
Q Consensus       256 ~g~~~~a~~~~~~m~~~~~~~p~~~~~-----~~li~~~~~~g~~~~A~~~~~~m~~~--p~~----~~~~~ll~~~~~~  324 (514)
                      .|+.++|...+........-......+     ...+..+...|+.+.|.+++......  ...    ..+..+..++...
T Consensus       625 ~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~  704 (903)
T PRK04841        625 RGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILL  704 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHc
Confidence            999999999988874321111111111     11224456689999999998775421  111    1245567778899


Q ss_pred             CCHHHHHHHHHHHHhcC------CCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          325 KNVELAGKVAEKIFMID------PNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       325 ~~~~~a~~~~~~~~~~~------p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      |+.++|...++++....      +....++..+..+|...|+.++|...+.+..+..
T Consensus       705 g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        705 GQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             CCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            99999999999987752      1223467788899999999999999999887654

>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=98.75  E-value=1.4e-06  Score=81.81  Aligned_cols=161  Identities=11%  Similarity=0.072  Sum_probs=111.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc--
Q 040365          178 FIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSH--  255 (514)
Q Consensus       178 ~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~--  255 (514)
                      .+......+|...|++++|.+++...  .+.......+..|.+.++++.|.+.++.|.+.  . +..+...+..++..  
T Consensus       103 ~~~~~~A~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~-eD~~l~qLa~awv~l~  177 (290)
T PF04733_consen  103 IVQLLAATILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQI--D-EDSILTQLAEAWVNLA  177 (290)
T ss_dssp             HHHHHHHHHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC--S-CCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc--C-CcHHHHHHHHHHHHHH
Confidence            33333445567778888888877765  45566667778888888888888888888764  3 33444445544432  


Q ss_pred             --cCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCH-HHH
Q 040365          256 --AGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRVHKNV-ELA  330 (514)
Q Consensus       256 --~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~~~~-~~a  330 (514)
                        .+.+.+|..+|+++..  ...+++.+.+.+.-+....|++++|.+++++.- .. .|..+...++......|+. +.+
T Consensus       178 ~g~e~~~~A~y~f~El~~--~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~  255 (290)
T PF04733_consen  178 TGGEKYQDAFYIFEELSD--KFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAA  255 (290)
T ss_dssp             HTTTCCCHHHHHHHHHHC--CS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHH
T ss_pred             hCchhHHHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHH
Confidence              3468889999998854  345677888888888888999999998888753 22 3556777778777777877 677


Q ss_pred             HHHHHHHHhcCCCCc
Q 040365          331 GKVAEKIFMIDPNNM  345 (514)
Q Consensus       331 ~~~~~~~~~~~p~~~  345 (514)
                      .+.+.++....|+.+
T Consensus       256 ~~~l~qL~~~~p~h~  270 (290)
T PF04733_consen  256 ERYLSQLKQSNPNHP  270 (290)
T ss_dssp             HHHHHHCHHHTTTSH
T ss_pred             HHHHHHHHHhCCCCh
Confidence            888888888888754

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.

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

Probab=98.73  E-value=6.1e-06  Score=71.69  Aligned_cols=188  Identities=15%  Similarity=0.103  Sum_probs=81.0

Q ss_pred             HhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHH
Q 040365          152 CAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAI  228 (514)
Q Consensus       152 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~  228 (514)
                      |.+.|+...|+.-+++.++.. +.+..++..+...|-+.|+.+.|.+-|++..   ..+-...|....-+|..|++++|.
T Consensus        45 YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~~eA~  123 (250)
T COG3063          45 YLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRPEEAM  123 (250)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCChHHHH
Confidence            333333333333333333332 2223333334444444444444444444322   222333344444444445555555


Q ss_pred             HHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          229 SLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH  306 (514)
Q Consensus       229 ~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~  306 (514)
                      ..|++......-|. ..||..+.-+..+.|+.+.|..+|++..+   ..| .......+.+...+.|++..|..+++...
T Consensus       124 q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~---~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~  200 (250)
T COG3063         124 QQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALE---LDPQFPPALLELARLHYKAGDYAPARLYLERYQ  200 (250)
T ss_pred             HHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHH---hCcCCChHHHHHHHHHHhcccchHHHHHHHHHH
Confidence            55555444221111 23444444444455555555555554432   123 23334444455555555555555555432


Q ss_pred             --CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          307 --AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       307 --~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                        ..++..+.--.+..-...||.+.+.+.=.++....|.
T Consensus       201 ~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~  239 (250)
T COG3063         201 QRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPY  239 (250)
T ss_pred             hcccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence              1244444444444445555555555544444444444

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.73  E-value=9.6e-06  Score=74.60  Aligned_cols=114  Identities=17%  Similarity=0.151  Sum_probs=61.9

Q ss_pred             CCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCC--CCHHHHHHHH-HHHHhcCCHHHHHHH
Q 040365          257 GLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAG--PTENVWLTLL-SACRVHKNVELAGKV  333 (514)
Q Consensus       257 g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~ll-~~~~~~~~~~~a~~~  333 (514)
                      .++++.+.+++++ +.+=...|...+ .+..+++..|.+.+|+++|-.+..+  .|..+|.+++ .+|...++++.|-. 
T Consensus       373 ~qFddVl~YlnSi-~sYF~NdD~Fn~-N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~-  449 (557)
T KOG3785|consen  373 FQFDDVLTYLNSI-ESYFTNDDDFNL-NLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWD-  449 (557)
T ss_pred             HHHHHHHHHHHHH-HHHhcCcchhhh-HHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHH-
Confidence            3455555555555 222222233332 3556666777777777777665421  3555665544 34556666666543 


Q ss_pred             HHHHHhcC-CCCc-chHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          334 AEKIFMID-PNNM-GAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       334 ~~~~~~~~-p~~~-~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                        .++..+ |.+. .....+++-|.+++.+--|.+.|..+...+
T Consensus       450 --~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lD  491 (557)
T KOG3785|consen  450 --MMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILD  491 (557)
T ss_pred             --HHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccC
Confidence              334443 2222 223345566777777777777777776544

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.71  E-value=8.4e-05  Score=69.99  Aligned_cols=56  Identities=18%  Similarity=0.096  Sum_probs=28.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          315 LTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       315 ~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                      +.+...|...|..+.++.++++.+...|++ ...+.|...+...+.+.+|...|...
T Consensus       442 ~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~-~LH~~Lgd~~~A~Ne~Q~am~~y~~A  497 (564)
T KOG1174|consen  442 NLIAELCQVEGPTKDIIKLLEKHLIIFPDV-NLHNHLGDIMRAQNEPQKAMEYYYKA  497 (564)
T ss_pred             HHHHHHHHhhCccchHHHHHHHHHhhcccc-HHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            344444555555555555555555544432 34555555555555555555555443

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.69  E-value=5.6e-06  Score=82.76  Aligned_cols=102  Identities=16%  Similarity=0.176  Sum_probs=43.2

Q ss_pred             CCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHH
Q 040365          120 NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCI  199 (514)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~  199 (514)
                      ..++.+|+.+++.++...  .-..-|..+..-|+..|+++.|+++|.+.   +      .++--|+||.+.|++++|.++
T Consensus       745 akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~---~------~~~dai~my~k~~kw~da~kl  813 (1636)
T KOG3616|consen  745 AKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEA---D------LFKDAIDMYGKAGKWEDAFKL  813 (1636)
T ss_pred             hhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhc---c------hhHHHHHHHhccccHHHHHHH
Confidence            334444444444443322  11222334444455555555555444321   1      223344555555555555555


Q ss_pred             HHhCCCC--ChhHHHHHHHHHHhCCChHHHHHHHH
Q 040365          200 FDKMDLH--DIVSWTAVIMGNALHGNAHDAISLFE  232 (514)
Q Consensus       200 ~~~m~~~--d~~~~~~li~~~~~~g~~~~A~~l~~  232 (514)
                      -.+...|  .+++|-+-..-+-.+|++.+|.++|-
T Consensus       814 a~e~~~~e~t~~~yiakaedldehgkf~eaeqlyi  848 (1636)
T KOG3616|consen  814 AEECHGPEATISLYIAKAEDLDEHGKFAEAEQLYI  848 (1636)
T ss_pred             HHHhcCchhHHHHHHHhHHhHHhhcchhhhhheeE
Confidence            4444322  22333333333444555555544443

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

Probab=98.67  E-value=0.00019  Score=70.73  Aligned_cols=142  Identities=18%  Similarity=0.138  Sum_probs=99.1

Q ss_pred             ChHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHccCCHHHHHHHHH--------HhHHhcCCCCCHhHHHHHHHHHHhc
Q 040365          223 NAHDAISLFEQMEKDGVKPNS--VAFVAVLTACSHAGLIDKAWSYFN--------SMTKDYGIAPSFEHYAAVADLLGRA  292 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~--~t~~~ll~a~~~~g~~~~a~~~~~--------~m~~~~~~~p~~~~~~~li~~~~~~  292 (514)
                      .+.+|.+++...-+.  .|+.  +.....+......|+++.|.+++.        .+.+ .+.  .+.+...++.++.+.
T Consensus       356 ~~~ka~e~L~~~~~~--~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~-~~~--~P~~V~aiv~l~~~~  430 (652)
T KOG2376|consen  356 KHKKAIELLLQFADG--HPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILE-AKH--LPGTVGAIVALYYKI  430 (652)
T ss_pred             HHhhhHHHHHHHhcc--CCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhh-hcc--ChhHHHHHHHHHHhc
Confidence            466777777766553  3433  445566667788999999999998        4422 233  345566788888888


Q ss_pred             CCHHHHHHHHHhC--------CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhH
Q 040365          293 GKLQEAYEFISNM--------HAGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKD  363 (514)
Q Consensus       293 g~~~~A~~~~~~m--------~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  363 (514)
                      ++-+.|.+++.+.        ..++. ..+|.-+...-.++|+-++|...++++.+.+|++..+...++.+|+.. +.+.
T Consensus       431 ~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~ea~s~leel~k~n~~d~~~l~~lV~a~~~~-d~ek  509 (652)
T KOG2376|consen  431 KDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEEEASSLLEELVKFNPNDTDLLVQLVTAYARL-DPEK  509 (652)
T ss_pred             cCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchHHHHHHHHHHHHhCCchHHHHHHHHHHHHhc-CHHH
Confidence            8876666666544        22222 233444555557789999999999999999999999999999999876 5666


Q ss_pred             HHHHHHH
Q 040365          364 AASLRVF  370 (514)
Q Consensus       364 a~~~~~~  370 (514)
                      |..+-+.
T Consensus       510 a~~l~k~  516 (652)
T KOG2376|consen  510 AESLSKK  516 (652)
T ss_pred             HHHHhhc
Confidence            6665443

>PF12854 PPR_1: PPR repeat

Probab=98.67  E-value=3.8e-08  Score=59.33  Aligned_cols=34  Identities=29%  Similarity=0.542  Sum_probs=27.8

Q ss_pred             cCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          171 NGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD  204 (514)
Q Consensus       171 ~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~  204 (514)
                      .|+.||..+||+||++|++.|++++|.++|++|+
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            3678888888888888888888888888888874

>PF12854 PPR_1: PPR repeat

Probab=98.66  E-value=3.5e-08  Score=59.48  Aligned_cols=33  Identities=30%  Similarity=0.534  Sum_probs=25.4

Q ss_pred             CCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC
Q 040365           71 GLDANVCIGSSLINMYAKCARVEDSHRLFCLLP  103 (514)
Q Consensus        71 g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~  103 (514)
                      |+.||..+||+||++|++.|++++|.++|++|+
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            667777777777777777777777777777774

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

Probab=98.66  E-value=8.4e-05  Score=75.34  Aligned_cols=365  Identities=16%  Similarity=0.091  Sum_probs=219.3

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCC-CCchhHHHHHH
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGL-DANVCIGSSLI   83 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-~~~~~~~~~li   83 (514)
                      |...|..+.-++.+.|+++.+.+.|++....- --....|..+-..+...|.-..|..+++......- ++|+.++-..-
T Consensus       322 d~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~-~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmas  400 (799)
T KOG4162|consen  322 DAAIFDHLTFALSRCGQFEVLAEQFEQALPFS-FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMAS  400 (799)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh-hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHH
Confidence            45567777777788888888888887765432 22334566666666666776777777766544321 22333333222


Q ss_pred             HHHHH-CCCHHH----HHHHHccCC----CCChhHHHHHHHHHHHC-----------CChhHHHHHHHHHHHCC-CCCCH
Q 040365           84 NMYAK-CARVED----SHRLFCLLP----VKDAISWNSIIAGCVQN-----------GLFDEGLKFFRQMLIAK-IKPRH  142 (514)
Q Consensus        84 ~~~~~-~g~~~~----A~~~f~~~~----~~d~~~~~~li~~~~~~-----------g~~~~A~~l~~~m~~~g-~~p~~  142 (514)
                      ..|.+ .+.+++    |.++.+...    ......|-.+.-+|...           ....++++.+++..+.+ -.|+.
T Consensus       401 klc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp~~  480 (799)
T KOG4162|consen  401 KLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDPLV  480 (799)
T ss_pred             HHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCchH
Confidence            33322 233333    333333211    12333444444444321           12345666666665533 34444


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC--C-------------
Q 040365          143 VSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH--D-------------  207 (514)
Q Consensus       143 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~--d-------------  207 (514)
                      .-|.++  -++..++++.|.+...+..+.+-..+...|..|.-.+...+++.+|+.+.+.....  +             
T Consensus       481 if~lal--q~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~  558 (799)
T KOG4162|consen  481 IFYLAL--QYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIEL  558 (799)
T ss_pred             HHHHHH--HHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhhh
Confidence            444443  34556677777777777777655666667776666677777777777766554210  0             


Q ss_pred             --------hhHHHHHHHHHH-----------------------hCCChHHHHHHHHHHH--------HcC---------C
Q 040365          208 --------IVSWTAVIMGNA-----------------------LHGNAHDAISLFEQME--------KDG---------V  239 (514)
Q Consensus       208 --------~~~~~~li~~~~-----------------------~~g~~~~A~~l~~~m~--------~~g---------~  239 (514)
                              +.|...++...-                       -.++..+|.+..+++.        ..|         +
T Consensus       559 ~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~  638 (799)
T KOG4162|consen  559 TFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSSTV  638 (799)
T ss_pred             hcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCcccc
Confidence                    111111111110                       0111222222211110        001         1


Q ss_pred             C--CCH------HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC
Q 040365          240 K--PNS------VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP  309 (514)
Q Consensus       240 ~--p~~------~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p  309 (514)
                      .  |+.      ..+......+...+..++|...+.+..   ++.| ....|......+...|.+++|.+.|.... ..|
T Consensus       639 ~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~---~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP  715 (799)
T KOG4162|consen  639 LPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEAS---KIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDP  715 (799)
T ss_pred             cCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHH---hcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCC
Confidence            1  221      123344556677788888887777663   4445 56777777788899999999999887653 445


Q ss_pred             -CHHHHHHHHHHHHhcCCHHHHHH--HHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          310 -TENVWLTLLSACRVHKNVELAGK--VAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       310 -~~~~~~~ll~~~~~~~~~~~a~~--~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                       ++.+..++...+.+.|+...|..  ++..+.+.+|.++..|..|...+-+.|+.++|...|....+-.
T Consensus       716 ~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qLe  784 (799)
T KOG4162|consen  716 DHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQLE  784 (799)
T ss_pred             CCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHhhc
Confidence             46788999999999999998888  9999999999999999999999999999999999999876543

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

Probab=98.66  E-value=0.00036  Score=69.47  Aligned_cols=152  Identities=13%  Similarity=0.116  Sum_probs=93.6

Q ss_pred             CCChHHHHHHHHHHHHcCCCCCHH-HHHHHHHHH---HccCCHHHHHHHHHHhHHhcCCCCCH--hHHHHHHHHHHhcCC
Q 040365          221 HGNAHDAISLFEQMEKDGVKPNSV-AFVAVLTAC---SHAGLIDKAWSYFNSMTKDYGIAPSF--EHYAAVADLLGRAGK  294 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~a~---~~~g~~~~a~~~~~~m~~~~~~~p~~--~~~~~li~~~~~~g~  294 (514)
                      +.-++++.++|++-...--.|+.. .|+..|.-+   ...-.++.|..+|++..+  |.+|.-  ..|-.....=-+-|.
T Consensus       524 h~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdLFEqaL~--~Cpp~~aKtiyLlYA~lEEe~GL  601 (835)
T KOG2047|consen  524 HKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDLFEQALD--GCPPEHAKTIYLLYAKLEEEHGL  601 (835)
T ss_pred             hHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHhhH
Confidence            444566666665543332235542 233333322   234578999999999876  666532  223223333345688


Q ss_pred             HHHHHHHHHhCCCC--CC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc--hHHHHHHHHHHccChhHHHHHH
Q 040365          295 LQEAYEFISNMHAG--PT--ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG--AYVILSNTYAAARRWKDAASLR  368 (514)
Q Consensus       295 ~~~A~~~~~~m~~~--p~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~--~~~~l~~~~~~~g~~~~a~~~~  368 (514)
                      ...|++++++....  +.  ...|+..|.--...=-+.....+++++++.-|++-.  ...-.+..-.+.|..+.|+.++
T Consensus       602 ar~amsiyerat~~v~~a~~l~myni~I~kaae~yGv~~TR~iYekaIe~Lp~~~~r~mclrFAdlEtklGEidRARaIy  681 (835)
T KOG2047|consen  602 ARHAMSIYERATSAVKEAQRLDMYNIYIKKAAEIYGVPRTREIYEKAIESLPDSKAREMCLRFADLETKLGEIDRARAIY  681 (835)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHhCCcccHHHHHHHHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence            89999999987533  22  356888776554444456677888998887666432  2234566678899999999999


Q ss_pred             HHHHhC
Q 040365          369 VFMRNK  374 (514)
Q Consensus       369 ~~m~~~  374 (514)
                      .--.+-
T Consensus       682 a~~sq~  687 (835)
T KOG2047|consen  682 AHGSQI  687 (835)
T ss_pred             Hhhhhc
Confidence            765443

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

Probab=98.62  E-value=0.00021  Score=71.11  Aligned_cols=362  Identities=10%  Similarity=0.085  Sum_probs=246.5

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      ...|-.++..| ..+++...+.+.+..++ +.+-...|.....-.+...|+.++|....+..++.. ..+.+.|..+.-.
T Consensus         8 ~~lF~~~lk~y-E~kQYkkgLK~~~~iL~-k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d-~~S~vCwHv~gl~   84 (700)
T KOG1156|consen    8 NALFRRALKCY-ETKQYKKGLKLIKQILK-KFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRND-LKSHVCWHVLGLL   84 (700)
T ss_pred             HHHHHHHHHHH-HHHHHHhHHHHHHHHHH-hCCccchhHHhccchhhcccchHHHHHHHHHHhccC-cccchhHHHHHHH
Confidence            34455566555 45788889999888877 333344566555555677899999999888877755 4456778888777


Q ss_pred             HHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHH
Q 040365           86 YAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGK  162 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~  162 (514)
                      +-...++++|.+.|....   ..|...|--+--.-++.++++.....-.+..+. .+-....|.....+..-.|+...|.
T Consensus        85 ~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql-~~~~ra~w~~~Avs~~L~g~y~~A~  163 (700)
T KOG1156|consen   85 QRSDKKYDEAIKCYRNALKIEKDNLQILRDLSLLQIQMRDYEGYLETRNQLLQL-RPSQRASWIGFAVAQHLLGEYKMAL  163 (700)
T ss_pred             HhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh-hhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            777889999999998754   346667776666667888888888887777764 2334556777788888899999999


Q ss_pred             HHHHHHHHcC-CCCcHHHHHHHH------HHHHhcCCHHHHHHHHHhCCCC--Chh-HHHHHHHHHHhCCChHHHHHHHH
Q 040365          163 QLHGCIIRNG-FDDNMFIASSLL------DMYAKCGNIRLARCIFDKMDLH--DIV-SWTAVIMGNALHGNAHDAISLFE  232 (514)
Q Consensus       163 ~~~~~~~~~~-~~~~~~~~~~li------~~y~k~g~~~~A~~~~~~m~~~--d~~-~~~~li~~~~~~g~~~~A~~l~~  232 (514)
                      .+.+...+.. -.|+...+.-..      ....+.|.+++|.+-+......  |-. .--+....+.+.++.++|..++.
T Consensus       164 ~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~e~ka~l~~kl~~lEeA~~~y~  243 (700)
T KOG1156|consen  164 EILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVDKLAFEETKADLLMKLGQLEEAVKVYR  243 (700)
T ss_pred             HHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHHHHhhhHHHHHHHHhhHHhHHHHHH
Confidence            9999988765 245555544322      2346789999999888776533  222 33345566788999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHH--ccCCHHHHHHHHHHhHHhc---------------------------------CCCC
Q 040365          233 QMEKDGVKPNSVAFVAVLTACS--HAGLIDKAWSYFNSMTKDY---------------------------------GIAP  277 (514)
Q Consensus       233 ~m~~~g~~p~~~t~~~ll~a~~--~~g~~~~a~~~~~~m~~~~---------------------------------~~~p  277 (514)
                      .++..  .||..-|.-.+..+.  -.+..+....+|....+.+                                 |+++
T Consensus       244 ~Ll~r--nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~  321 (700)
T KOG1156|consen  244 RLLER--NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPS  321 (700)
T ss_pred             HHHhh--CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCc
Confidence            99985  577766655444333  2233332224444442221                                 2221


Q ss_pred             CHhHHHHHHHHHHhcCCHHH----HHHHHHhCC-------------CCCCHHHHHH--HHHHHHhcCCHHHHHHHHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQE----AYEFISNMH-------------AGPTENVWLT--LLSACRVHKNVELAGKVAEKIF  338 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~----A~~~~~~m~-------------~~p~~~~~~~--ll~~~~~~~~~~~a~~~~~~~~  338 (514)
                         ++..+...|-.-...+-    +..+...+.             .+|....|..  +...+-..|+++.|+...+.++
T Consensus       322 ---vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AI  398 (700)
T KOG1156|consen  322 ---VFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAI  398 (700)
T ss_pred             ---hhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHh
Confidence               12222222221111111    111222121             2467777765  5667889999999999999999


Q ss_pred             hcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCC
Q 040365          339 MIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       339 ~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  376 (514)
                      ..-|.-+..|..-+.++..+|..++|...+++..+.+.
T Consensus       399 dHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~  436 (700)
T KOG1156|consen  399 DHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDT  436 (700)
T ss_pred             ccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccc
Confidence            99898888898999999999999999999999887654

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.58  E-value=0.0002  Score=66.20  Aligned_cols=88  Identities=14%  Similarity=0.098  Sum_probs=42.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHH-HHHHHHHHccC
Q 040365          284 AVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYV-ILSNTYAAARR  360 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~-~l~~~~~~~g~  360 (514)
                      ++...+.-..++++.+-+++.+.  ...|...--.+..+.+..|++.+|+++|-++...+-.|..+|. .|+.+|.+.|+
T Consensus       364 smAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkk  443 (557)
T KOG3785|consen  364 SMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLNLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKK  443 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCC
Confidence            34444444445555555555443  1222222233555555566666666665555444433333443 44555556665


Q ss_pred             hhHHHHHHHHH
Q 040365          361 WKDAASLRVFM  371 (514)
Q Consensus       361 ~~~a~~~~~~m  371 (514)
                      .+-|..++-++
T Consensus       444 P~lAW~~~lk~  454 (557)
T KOG3785|consen  444 PQLAWDMMLKT  454 (557)
T ss_pred             chHHHHHHHhc
Confidence            55555554443

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.56  E-value=6.8e-05  Score=72.99  Aligned_cols=212  Identities=14%  Similarity=0.079  Sum_probs=122.9

Q ss_pred             HHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCCh----------hHHHHHHHHHH
Q 040365          150 PACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDI----------VSWTAVIMGNA  219 (514)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~----------~~~~~li~~~~  219 (514)
                      ++.-+..+++.+.+-+.......  .+..-++....+|...|.+......-+...+...          .+...+..+|.
T Consensus       232 naaykkk~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  232 NAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGNAYT  309 (539)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhhhhh
Confidence            33334444555555555444433  3444445555555555555544443333221110          01112223444


Q ss_pred             hCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCH-hHHHHHHHHHHhcCCHHHH
Q 040365          220 LHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSF-EHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       220 ~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A  298 (514)
                      +.++++.|+..|.+....-..||..         .+....+++........   -+.|.. .-...=...+.+.|++.+|
T Consensus       310 k~~~~~~ai~~~~kaLte~Rt~~~l---------s~lk~~Ek~~k~~e~~a---~~~pe~A~e~r~kGne~Fk~gdy~~A  377 (539)
T KOG0548|consen  310 KREDYEGAIKYYQKALTEHRTPDLL---------SKLKEAEKALKEAERKA---YINPEKAEEEREKGNEAFKKGDYPEA  377 (539)
T ss_pred             hHHhHHHHHHHHHHHhhhhcCHHHH---------HHHHHHHHHHHHHHHHH---hhChhHHHHHHHHHHHHHhccCHHHH
Confidence            4555666666666554433333321         11222233333322221   223322 1111124456788999999


Q ss_pred             HHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          299 YEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       299 ~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ...+.++. ..| |...|....-+|.+.|++..|+.-.+..++++|+....|..=+.++....+|+.|.+.|.+-.+..
T Consensus       378 v~~YteAIkr~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale~d  456 (539)
T KOG0548|consen  378 VKHYTEAIKRDPEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALELD  456 (539)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99998864 234 677888899999999999999999999999999988888888888888899999999998776544

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.54  E-value=1.2e-05  Score=73.93  Aligned_cols=180  Identities=12%  Similarity=0.002  Sum_probs=120.5

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--CC-h---hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCH----H
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMDL--HD-I---VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNS----V  244 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d-~---~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~  244 (514)
                      .....+..+...|.+.|++++|...|+++..  |+ .   .+|..+..+|.+.|++++|+..|+++.+.  .|+.    .
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~  108 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL--HPNHPDADY  108 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCchHH
Confidence            3455666677778888888888888887642  22 1   35677777888888888888888888764  2322    1


Q ss_pred             HHHHHHHHHHcc--------CCHHHHHHHHHHhHHhcCCCCCH-hHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHH
Q 040365          245 AFVAVLTACSHA--------GLIDKAWSYFNSMTKDYGIAPSF-EHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWL  315 (514)
Q Consensus       245 t~~~ll~a~~~~--------g~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~  315 (514)
                      ++..+..++...        |+.++|.+.|+.+.+.   .|+. ..+..+...    +......           .....
T Consensus       109 a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~a~~~~----~~~~~~~-----------~~~~~  170 (235)
T TIGR03302       109 AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR---YPNSEYAPDAKKRM----DYLRNRL-----------AGKEL  170 (235)
T ss_pred             HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH---CCCChhHHHHHHHH----HHHHHHH-----------HHHHH
Confidence            344444455543        6777888888877654   3432 222221111    0011100           01122


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCC---cchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNN---MGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~---~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .+...+...|+++.|...++++++..|++   +..+..++.+|.+.|++++|...++.+..+
T Consensus       171 ~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       171 YVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            45667889999999999999999987654   468889999999999999999999988765

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).

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

Probab=98.53  E-value=3.3e-05  Score=82.78  Aligned_cols=220  Identities=14%  Similarity=0.135  Sum_probs=175.4

Q ss_pred             CC-hhhHHHHHHHHhCCCChHHHHHHHHHHHHhC-C---CCchhHHHHHHHHHHHCCCHHHHHHHHccCCCC-C-hhHHH
Q 040365           39 PD-SFTLSSVLPIFADYVDVIKGKEIHGYAIRHG-L---DANVCIGSSLINMYAKCARVEDSHRLFCLLPVK-D-AISWN  111 (514)
Q Consensus        39 p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g-~---~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~-d-~~~~~  111 (514)
                      || ...|..-|.-..+.+++++|+++.+++++.= +   .--..+|.+++++-...|.-+...++|++..+- | ...|.
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd~~~V~~ 1534 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCDAYTVHL 1534 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcchHHHHH
Confidence            44 4578888888899999999999999998751 1   123468899999888889889999999998753 3 34688


Q ss_pred             HHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCC-CCcHHHHHHHHHHHHhc
Q 040365          112 SIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGF-DDNMFIASSLLDMYAKC  190 (514)
Q Consensus       112 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~y~k~  190 (514)
                      .|...|.+.+.+++|-++|+.|.+. +.-....|...+..+.+..+-+.|..++.++++.=. ...+.+..-.+.+-.++
T Consensus      1535 ~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 1535 KLLGIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKY 1613 (1710)
T ss_pred             HHHHHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhc
Confidence            9999999999999999999999875 445677888889999999999999999999887521 12455666677888999


Q ss_pred             CCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHccCCH
Q 040365          191 GNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNS--VAFVAVLTACSHAGLI  259 (514)
Q Consensus       191 g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~--~t~~~ll~a~~~~g~~  259 (514)
                      |+.+.++.+|+...   .+-...|+..|..=.++|+.+.+..+|++....++.|-.  ..|.-.|..-.+.|+-
T Consensus      1614 GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde 1687 (1710)
T KOG1070|consen 1614 GDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDE 1687 (1710)
T ss_pred             CCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCch
Confidence            99999999999986   335678999999999999999999999999998887754  3444555444444443

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.53  E-value=9.5e-05  Score=66.68  Aligned_cols=290  Identities=12%  Similarity=0.097  Sum_probs=165.3

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHH-HHHHHH
Q 040365            9 WNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSS-LINMYA   87 (514)
Q Consensus         9 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~-li~~~~   87 (514)
                      +++.|.-+.+..++++|++++..-.+.. +.+...++.+...|....++..|-..++++-..  .|...-|.. -...+-
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSLY   89 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSLY   89 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHHH
Confidence            5667777777788888888887766653 225555666666666667777777777766543  222221111 011222


Q ss_pred             HCCCHHHHH----------------------------------HHHccCC-CCChhHHHHHHHHHHHCCChhHHHHHHHH
Q 040365           88 KCARVEDSH----------------------------------RLFCLLP-VKDAISWNSIIAGCVQNGLFDEGLKFFRQ  132 (514)
Q Consensus        88 ~~g~~~~A~----------------------------------~~f~~~~-~~d~~~~~~li~~~~~~g~~~~A~~l~~~  132 (514)
                      +.+.+.+|+                                  .+.++.+ +.+..+.+-..-...+.|++++|++-|+.
T Consensus        90 ~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqa  169 (459)
T KOG4340|consen   90 KACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQA  169 (459)
T ss_pred             HhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHH
Confidence            333444444                                  4444444 23334444444445678889999999988


Q ss_pred             HHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCC-------------cH--------HHHHHHH-------
Q 040365          133 MLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDD-------------NM--------FIASSLL-------  184 (514)
Q Consensus       133 m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-------------~~--------~~~~~li-------  184 (514)
                      ..+-+---....|+..+. .-+.++.+.|.+...+++++|+..             |+        ...++|+       
T Consensus       170 AlqvsGyqpllAYniALa-Hy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKa  248 (459)
T KOG4340|consen  170 ALQVSGYQPLLAYNLALA-HYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKA  248 (459)
T ss_pred             HHhhcCCCchhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhhhh
Confidence            776443334566765554 446688888988888888876421             11        1122333       


Q ss_pred             HHHHhcCCHHHHHHHHHhCCCC-----ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCH
Q 040365          185 DMYAKCGNIRLARCIFDKMDLH-----DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLI  259 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~~~-----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~  259 (514)
                      ..+.+.|+++.|.+.+-.|+.+     |++|...+.-.- ..+++.+..+-+.-+.+.+. -...||..++-.|++..-+
T Consensus       249 AIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~nP-fP~ETFANlLllyCKNeyf  326 (459)
T KOG4340|consen  249 AIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQNP-FPPETFANLLLLYCKNEYF  326 (459)
T ss_pred             hhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcCC-CChHHHHHHHHHHhhhHHH
Confidence            3456788888899988888744     566655443221 23445555554554444322 2347888888888888888


Q ss_pred             HHHHHHHHHhHHhcCCC-CCHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          260 DKAWSYFNSMTKDYGIA-PSFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       260 ~~a~~~~~~m~~~~~~~-p~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      +.|-.++.+-.. .... .+...|+.|=....-.-..++|++-++.+
T Consensus       327 ~lAADvLAEn~~-lTyk~L~~Yly~LLdaLIt~qT~pEea~KKL~~L  372 (459)
T KOG4340|consen  327 DLAADVLAENAH-LTYKFLTPYLYDLLDALITCQTAPEEAFKKLDGL  372 (459)
T ss_pred             hHHHHHHhhCcc-hhHHHhhHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            888877754311 0111 12333433322223334556665555443

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

Probab=98.52  E-value=0.0018  Score=65.99  Aligned_cols=197  Identities=12%  Similarity=0.053  Sum_probs=113.7

Q ss_pred             CCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC--C--CChhHH
Q 040365           35 VNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP--V--KDAISW  110 (514)
Q Consensus        35 ~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~--~--~d~~~~  110 (514)
                      ..+..|...|-.+.-+....|+++.+-+.|++....- ......|+.+-..|..+|.-..|..+.+.-.  +  |+..+-
T Consensus       317 ~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~-~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~  395 (799)
T KOG4162|consen  317 KKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFS-FGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISV  395 (799)
T ss_pred             hhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhh-hhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchH
Confidence            3455666777777777777777777777777766543 3345667777777777787777777776543  2  222222


Q ss_pred             HHHH-HHHH-HCCChhHHHHHHHHHHHC------CCCCCHHHHHHHHHHHhcc----C-------ChHHHHHHHHHHHHc
Q 040365          111 NSII-AGCV-QNGLFDEGLKFFRQMLIA------KIKPRHVSFSSIMPACAHL----T-------TLHLGKQLHGCIIRN  171 (514)
Q Consensus       111 ~~li-~~~~-~~g~~~~A~~l~~~m~~~------g~~p~~~t~~~ll~~~~~~----~-------~~~~a~~~~~~~~~~  171 (514)
                      -.|+ ..|. +.+..++++++-.+....      .++|-  .|..+.-+|...    .       ...++.+.++..++.
T Consensus       396 ~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~--~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~  473 (799)
T KOG4162|consen  396 LLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPR--GYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQF  473 (799)
T ss_pred             HHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhh--HHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhc
Confidence            2222 2222 234556666555554441      12222  222222222211    1       123455556666554


Q ss_pred             C-CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          172 G-FDDNMFIASSLLDMYAKCGNIRLARCIFDKMD----LHDIVSWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       172 ~-~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~----~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      + -.|++..|-  .--|+-.++++.|.+...+..    ..+...|..+.-.+...+++.+|+.+.+....
T Consensus       474 d~~dp~~if~l--alq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~  541 (799)
T KOG4162|consen  474 DPTDPLVIFYL--ALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALE  541 (799)
T ss_pred             CCCCchHHHHH--HHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHH
Confidence            4 344444443  334677788888877766543    45778888888888888888888888776654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.52  E-value=0.00031  Score=78.24  Aligned_cols=326  Identities=10%  Similarity=-0.031  Sum_probs=203.9

Q ss_pred             HhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCC------CCc--hhHHHHHHHHHHH
Q 040365           17 ARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGL------DAN--VCIGSSLINMYAK   88 (514)
Q Consensus        17 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~------~~~--~~~~~~li~~~~~   88 (514)
                      ...|++..+..++..+.......+..........+...|+++++...+..+.+.--      .+.  ......+...+..
T Consensus       385 ~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  464 (903)
T PRK04841        385 FNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAIN  464 (903)
T ss_pred             HhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHh
Confidence            34456665555555542211111222223334445677899999988887765311      111  1122333455678


Q ss_pred             CCCHHHHHHHHccCC----CCCh----hHHHHHHHHHHHCCChhHHHHHHHHHHHCCC---CC--CHHHHHHHHHHHhcc
Q 040365           89 CARVEDSHRLFCLLP----VKDA----ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKI---KP--RHVSFSSIMPACAHL  155 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~----~~d~----~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~---~p--~~~t~~~ll~~~~~~  155 (514)
                      .|++++|...+++..    ..+.    .+++.+...+...|++++|...+.+.....-   .+  ...++..+...+...
T Consensus       465 ~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~  544 (903)
T PRK04841        465 DGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQ  544 (903)
T ss_pred             CCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHC
Confidence            899999998887643    2222    3456667778889999999999988764211   11  123445566677889


Q ss_pred             CChHHHHHHHHHHHHc----CCC--C-cHHHHHHHHHHHHhcCCHHHHHHHHHhCCC------C--ChhHHHHHHHHHHh
Q 040365          156 TTLHLGKQLHGCIIRN----GFD--D-NMFIASSLLDMYAKCGNIRLARCIFDKMDL------H--DIVSWTAVIMGNAL  220 (514)
Q Consensus       156 ~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~li~~y~k~g~~~~A~~~~~~m~~------~--d~~~~~~li~~~~~  220 (514)
                      |+++.|...+.+....    +..  + ....+..+...+...|++++|...+++...      +  ....+..+...+..
T Consensus       545 G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~  624 (903)
T PRK04841        545 GFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLA  624 (903)
T ss_pred             CCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHH
Confidence            9999999998877653    211  1 233455666777888999999998887631      1  12344456667788


Q ss_pred             CCChHHHHHHHHHHHHcCCC-CCHHHH-----HHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC---HhHHHHHHHHHHh
Q 040365          221 HGNAHDAISLFEQMEKDGVK-PNSVAF-----VAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS---FEHYAAVADLLGR  291 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~~-p~~~t~-----~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~---~~~~~~li~~~~~  291 (514)
                      .|++++|.+.+.+....... .....+     ...+..+...|+.+.|...+...... .....   ...+..+..++..
T Consensus       625 ~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~-~~~~~~~~~~~~~~~a~~~~~  703 (903)
T PRK04841        625 RGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKP-EFANNHFLQGQWRNIARAQIL  703 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCC-CCccchhHHHHHHHHHHHHHH
Confidence            99999999999888552111 111111     11223445588999999998765321 11111   1113456777889


Q ss_pred             cCCHHHHHHHHHhCCC-------CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          292 AGKLQEAYEFISNMHA-------GP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       292 ~g~~~~A~~~~~~m~~-------~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      .|+.++|...+++...       .+ ...+...+..++...|+.++|...+.+++++...
T Consensus       704 ~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la~~  763 (903)
T PRK04841        704 LGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLANR  763 (903)
T ss_pred             cCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCc
Confidence            9999999998887531       11 1235566677889999999999999999987643

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

Probab=98.51  E-value=0.00071  Score=66.84  Aligned_cols=336  Identities=12%  Similarity=0.102  Sum_probs=196.6

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHH--HHHH--HH
Q 040365           13 IVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSL--INMY--AK   88 (514)
Q Consensus        13 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l--i~~~--~~   88 (514)
                      +.-+.++|++++|+....+....+ +-|...+..-+-+..+.+.+++|..+..   ..+   -..+++..  =.+|  -+
T Consensus        19 ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ik---k~~---~~~~~~~~~fEKAYc~Yr   91 (652)
T KOG2376|consen   19 LNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIK---KNG---ALLVINSFFFEKAYCEYR   91 (652)
T ss_pred             HHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHH---hcc---hhhhcchhhHHHHHHHHH
Confidence            456777899999999999998765 4455678888888899999999885443   222   11122222  3444  56


Q ss_pred             CCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHhccCChHHHHHHHHH
Q 040365           89 CARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR-HVSFSSIMPACAHLTTLHLGKQLHGC  167 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~  167 (514)
                      .+..|+|.+.++.....|..+...-...+-+.|++++|+.+|+.+.+.+.+-- ...-..++.+-+.    -.+.    .
T Consensus        92 lnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~----l~~~----~  163 (652)
T KOG2376|consen   92 LNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAA----LQVQ----L  163 (652)
T ss_pred             cccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHh----hhHH----H
Confidence            79999999999966555555666666778899999999999999987753221 1111222222111    1111    1


Q ss_pred             HHHcCCCCc---HHHHHHHHHHHHhcCCHHHHHHHHHhC--------CCCC-----hh-----HHHHHHHHHHhCCChHH
Q 040365          168 IIRNGFDDN---MFIASSLLDMYAKCGNIRLARCIFDKM--------DLHD-----IV-----SWTAVIMGNALHGNAHD  226 (514)
Q Consensus       168 ~~~~~~~~~---~~~~~~li~~y~k~g~~~~A~~~~~~m--------~~~d-----~~-----~~~~li~~~~~~g~~~~  226 (514)
                      +......|+   ...|| ....+...|++.+|+++++..        ...|     +.     .---|.-.+...|+-++
T Consensus       164 ~q~v~~v~e~syel~yN-~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~e  242 (652)
T KOG2376|consen  164 LQSVPEVPEDSYELLYN-TACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAE  242 (652)
T ss_pred             HHhccCCCcchHHHHHH-HHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHH
Confidence            222222221   12333 344677899999999999887        2111     11     12223345667899999


Q ss_pred             HHHHHHHHHHcCCCCCHHH----HHHHHHHHHccCCHHH--HHHHHHHhHHhc----------CCCCCHhHHHHHHHHHH
Q 040365          227 AISLFEQMEKDGVKPNSVA----FVAVLTACSHAGLIDK--AWSYFNSMTKDY----------GIAPSFEHYAAVADLLG  290 (514)
Q Consensus       227 A~~l~~~m~~~g~~p~~~t----~~~ll~a~~~~g~~~~--a~~~~~~m~~~~----------~~~p~~~~~~~li~~~~  290 (514)
                      |..++...+... .+|...    -|.|+ +...-.++-.  ++..++......          .-.-...--++++.+| 
T Consensus       243 a~~iy~~~i~~~-~~D~~~~Av~~NNLv-a~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~-  319 (652)
T KOG2376|consen  243 ASSIYVDIIKRN-PADEPSLAVAVNNLV-ALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALF-  319 (652)
T ss_pred             HHHHHHHHHHhc-CCCchHHHHHhcchh-hhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence            999999998864 344422    12222 2222111111  122222111000          0000111123344443 


Q ss_pred             hcCCHHHHHHHHHhCCCC-CCHHHHHHHHHHH-HhcC-CHHHHHHHHHHHHhcCCCC-cchHHHHHHHHHHccChhHHHH
Q 040365          291 RAGKLQEAYEFISNMHAG-PTENVWLTLLSAC-RVHK-NVELAGKVAEKIFMIDPNN-MGAYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       291 ~~g~~~~A~~~~~~m~~~-p~~~~~~~ll~~~-~~~~-~~~~a~~~~~~~~~~~p~~-~~~~~~l~~~~~~~g~~~~a~~  366 (514)
                       .+.-+.+.++-...+.. |.. .+.+|+..+ .... ....+..++....+..|.+ ......++......|+|+.|.+
T Consensus       320 -tnk~~q~r~~~a~lp~~~p~~-~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A~~  397 (652)
T KOG2376|consen  320 -TNKMDQVRELSASLPGMSPES-LFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVALE  397 (652)
T ss_pred             -hhhHHHHHHHHHhCCccCchH-HHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHHHH
Confidence             45566777777777644 444 344444443 2222 4667777777777777876 3345566777889999999999


Q ss_pred             HHH
Q 040365          367 LRV  369 (514)
Q Consensus       367 ~~~  369 (514)
                      ++.
T Consensus       398 il~  400 (652)
T KOG2376|consen  398 ILS  400 (652)
T ss_pred             HHH
Confidence            999

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.49  E-value=5.2e-06  Score=69.64  Aligned_cols=121  Identities=15%  Similarity=0.082  Sum_probs=87.9

Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-
Q 040365          229 SLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-  306 (514)
Q Consensus       229 ~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-  306 (514)
                      .+|++..+  +.|+.  +.....++...|++++|...|+...   .+.| +...|..+..++.+.|++++|...|+... 
T Consensus        14 ~~~~~al~--~~p~~--~~~~g~~~~~~g~~~~A~~~~~~al---~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~   86 (144)
T PRK15359         14 DILKQLLS--VDPET--VYASGYASWQEGDYSRAVIDFSWLV---MAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALM   86 (144)
T ss_pred             HHHHHHHH--cCHHH--HHHHHHHHHHcCCHHHHHHHHHHHH---HcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            34555544  34553  4455667778888888888888775   3355 67777788888888888888888888763 


Q ss_pred             -CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          307 -AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       307 -~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                       .+.+...|..+..++...|+.++|+..+++++++.|+++..+.....+..
T Consensus        87 l~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~~~~~~~~~~~~~  137 (144)
T PRK15359         87 LDASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYADASWSEIRQNAQI  137 (144)
T ss_pred             cCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence             23467778888888888888888888888888888888877766655543

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.48  E-value=4.8e-05  Score=68.55  Aligned_cols=286  Identities=12%  Similarity=0.073  Sum_probs=149.6

Q ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC--CChhHHHH-HHHHHHHC
Q 040365           44 LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPV--KDAISWNS-IIAGCVQN  120 (514)
Q Consensus        44 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~--~d~~~~~~-li~~~~~~  120 (514)
                      +.+++.-+.+..++..+.+++..-.+.. +.+....+.|..+|-...++..|-..++++..  |...-|.. -...+-+.
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY~A   91 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLYKA   91 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHh
Confidence            4445555555555555555555544442 22444445555555555555555555555442  22111111 12333445


Q ss_pred             CChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHH
Q 040365          121 GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIF  200 (514)
Q Consensus       121 g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~  200 (514)
                      +.+.+|+++...|...   |+...-..-+.+.                                 .....+++..++.+.
T Consensus        92 ~i~ADALrV~~~~~D~---~~L~~~~lqLqaA---------------------------------IkYse~Dl~g~rsLv  135 (459)
T KOG4340|consen   92 CIYADALRVAFLLLDN---PALHSRVLQLQAA---------------------------------IKYSEGDLPGSRSLV  135 (459)
T ss_pred             cccHHHHHHHHHhcCC---HHHHHHHHHHHHH---------------------------------HhcccccCcchHHHH
Confidence            5555555555554331   1111111111110                                 011234555555555


Q ss_pred             HhCC-CCChhHHHHHHHHHHhCCChHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCC--
Q 040365          201 DKMD-LHDIVSWTAVIMGNALHGNAHDAISLFEQMEK-DGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA--  276 (514)
Q Consensus       201 ~~m~-~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~-~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~--  276 (514)
                      ++.+ +.+..+.+.......+.|++++|.+-|+...+ .|..| ...|+..+. ..+.++.+.|+++..++.++ |++  
T Consensus       136 eQlp~en~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqp-llAYniALa-Hy~~~qyasALk~iSEIieR-G~r~H  212 (459)
T KOG4340|consen  136 EQLPSENEADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQP-LLAYNLALA-HYSSRQYASALKHISEIIER-GIRQH  212 (459)
T ss_pred             HhccCCCccchhccchheeeccccHHHHHHHHHHHHhhcCCCc-hhHHHHHHH-HHhhhhHHHHHHHHHHHHHh-hhhcC
Confidence            5554 23333433333334455555555555555554 23332 234443332 23345555555555554432 221  


Q ss_pred             -------------------CCHhHHHHHHH-------HHHhcCCHHHHHHHHHhCCCC----CCHHHHHHHHHHHHhcCC
Q 040365          277 -------------------PSFEHYAAVAD-------LLGRAGKLQEAYEFISNMHAG----PTENVWLTLLSACRVHKN  326 (514)
Q Consensus       277 -------------------p~~~~~~~li~-------~~~~~g~~~~A~~~~~~m~~~----p~~~~~~~ll~~~~~~~~  326 (514)
                                         |-..+-+.++.       .+.+.|+++.|.+-+..||.+    .|++|...+.-. -..++
T Consensus       213 PElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~-n~~~~  291 (459)
T KOG4340|consen  213 PELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALM-NMDAR  291 (459)
T ss_pred             CccCccceeccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHh-cccCC
Confidence                               11122233333       345789999999999999732    567776554321 23456


Q ss_pred             HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHH
Q 040365          327 VELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVF  370 (514)
Q Consensus       327 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~  370 (514)
                      +..+.+-+.-+++++|-...+|..++-.|++..-++-|..++.+
T Consensus       292 p~~g~~KLqFLL~~nPfP~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  292 PTEGFEKLQFLLQQNPFPPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             ccccHHHHHHHHhcCCCChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            67777777888888887788999999999999999998888753

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

Probab=98.45  E-value=8.6e-06  Score=81.77  Aligned_cols=191  Identities=19%  Similarity=0.238  Sum_probs=158.1

Q ss_pred             CCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040365          172 GFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLT  251 (514)
Q Consensus       172 ~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  251 (514)
                      +++|-......+...+.++|-...|..+|++.     ..|.-.|.+|...|+..+|..+..+-.+  -+||..-|..+.+
T Consensus       393 ~lpp~Wq~q~~laell~slGitksAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGD  465 (777)
T KOG1128|consen  393 HLPPIWQLQRLLAELLLSLGITKSALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGD  465 (777)
T ss_pred             CCCCcchHHHHHHHHHHHcchHHHHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhh
Confidence            34666777788899999999999999999986     4788899999999999999999998877  4789999999999


Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHh-CCCCC-CHHHHHHHHHHHHhcCCHHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN-MHAGP-TENVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~-m~~~p-~~~~~~~ll~~~~~~~~~~~  329 (514)
                      ..-...-+++|+++++....+        .-..+.....+.++++++.+.++. +...| ...+|-.+..+..+.++.+.
T Consensus       466 v~~d~s~yEkawElsn~~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~  537 (777)
T KOG1128|consen  466 VLHDPSLYEKAWELSNYISAR--------AQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQA  537 (777)
T ss_pred             hccChHHHHHHHHHhhhhhHH--------HHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHH
Confidence            888888899999999876432        111122223347889999998875 33343 56789999999999999999


Q ss_pred             HHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCc
Q 040365          330 AGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  377 (514)
                      |...|.+...++|++...|+.+..+|.+.|+-.+|...+++..+-+..
T Consensus       538 av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~  585 (777)
T KOG1128|consen  538 AVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQ  585 (777)
T ss_pred             HHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCC
Confidence            999999999999999999999999999999999999999988877743

>PLN02789 farnesyltranstransferase

Probab=98.45  E-value=8.3e-05  Score=70.90  Aligned_cols=228  Identities=11%  Similarity=0.061  Sum_probs=116.9

Q ss_pred             HHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHH-HHHHHHHHhccC-ChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 040365          109 SWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVS-FSSIMPACAHLT-TLHLGKQLHGCIIRNGFDDNMFIASSLLDM  186 (514)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t-~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  186 (514)
                      +++.+-..+...++.++|+.++.++.+.  .|+..| |..--.++...+ .++++...++.+++.. +.+..+|+.....
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~l--nP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~  115 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRL--NPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWL  115 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHH
Confidence            3444555555666677777777666653  343332 222222333333 3455555555555443 2333334433333


Q ss_pred             HHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040365          187 YAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYF  266 (514)
Q Consensus       187 y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  266 (514)
                      +.+.|..                             ..++++.+++++.+... -|..+|.....++.+.|+++++++.+
T Consensus       116 l~~l~~~-----------------------------~~~~el~~~~kal~~dp-kNy~AW~~R~w~l~~l~~~~eeL~~~  165 (320)
T PLN02789        116 AEKLGPD-----------------------------AANKELEFTRKILSLDA-KNYHAWSHRQWVLRTLGGWEDELEYC  165 (320)
T ss_pred             HHHcCch-----------------------------hhHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            3333331                             01344444444444221 13344444444444445555555555


Q ss_pred             HHhHHhcCCCC-CHhHHHHHHHHHHhc---CC----HHHHHHHHHh-CCCC-CCHHHHHHHHHHHHhc----CCHHHHHH
Q 040365          267 NSMTKDYGIAP-SFEHYAAVADLLGRA---GK----LQEAYEFISN-MHAG-PTENVWLTLLSACRVH----KNVELAGK  332 (514)
Q Consensus       267 ~~m~~~~~~~p-~~~~~~~li~~~~~~---g~----~~~A~~~~~~-m~~~-p~~~~~~~ll~~~~~~----~~~~~a~~  332 (514)
                      +.+.+.   .| +...|+.....+.+.   |.    .+++.++..+ +... -|...|+.+...+...    ++..+|..
T Consensus       166 ~~~I~~---d~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~  242 (320)
T PLN02789        166 HQLLEE---DVRNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSS  242 (320)
T ss_pred             HHHHHH---CCCchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHH
Confidence            555432   12 223333322222222   11    2345555533 3333 3567788887777763    34466888


Q ss_pred             HHHHHHhcCCCCcchHHHHHHHHHHcc------------------ChhHHHHHHHHHH
Q 040365          333 VAEKIFMIDPNNMGAYVILSNTYAAAR------------------RWKDAASLRVFMR  372 (514)
Q Consensus       333 ~~~~~~~~~p~~~~~~~~l~~~~~~~g------------------~~~~a~~~~~~m~  372 (514)
                      .+.++...+|.++.+...|+..|+...                  ..++|.++++.+.
T Consensus       243 ~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~  300 (320)
T PLN02789        243 VCLEVLSKDSNHVFALSDLLDLLCEGLQPTAEFRDTVDTLAEELSDSTLAQAVCSELE  300 (320)
T ss_pred             HHHHhhcccCCcHHHHHHHHHHHHhhhccchhhhhhhhccccccccHHHHHHHHHHHH
Confidence            888888888888888888999887642                  2367888888883

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.44  E-value=2.3e-05  Score=69.51  Aligned_cols=117  Identities=10%  Similarity=0.118  Sum_probs=83.2

Q ss_pred             cCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHH-HhcCC--HHH
Q 040365          256 AGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSAC-RVHKN--VEL  329 (514)
Q Consensus       256 ~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~-~~~~~--~~~  329 (514)
                      .++.+++...++...+.   .| +...|..+...|...|++++|...+++.. .. .+...+..+..++ ...|+  .++
T Consensus        52 ~~~~~~~i~~l~~~L~~---~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~  128 (198)
T PRK10370         52 QQTPEAQLQALQDKIRA---NPQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQ  128 (198)
T ss_pred             chhHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHH
Confidence            45556666666655432   34 67777777777778888888887777653 22 3566677766653 56566  478


Q ss_pred             HHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          330 AGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      |..+++++++.+|+++.++..++..+...|++++|...++++.+..
T Consensus       129 A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~l~  174 (198)
T PRK10370        129 TREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQKVLDLN  174 (198)
T ss_pred             HHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            8888888888888888888888888888888888888888876653

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.40  E-value=4.6e-07  Score=55.36  Aligned_cols=35  Identities=40%  Similarity=0.679  Sum_probs=32.8

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCh
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDS   41 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~   41 (514)
                      ++||++|.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            48999999999999999999999999999999984

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.

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.39  E-value=5.6e-05  Score=67.03  Aligned_cols=154  Identities=13%  Similarity=0.116  Sum_probs=115.7

Q ss_pred             HHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040365          184 LDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAW  263 (514)
Q Consensus       184 i~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  263 (514)
                      +-.|.+.|+++......+.+..+.        ..|...++.++++..+++..+.. +.|...|..+...+...|++++|.
T Consensus        23 ~~~Y~~~g~~~~v~~~~~~~~~~~--------~~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~   93 (198)
T PRK10370         23 VGSYLLSPKWQAVRAEYQRLADPL--------HQFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNAL   93 (198)
T ss_pred             HHHHHHcchHHHHHHHHHHHhCcc--------ccccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            456888888877655544332221        01223566788888888877752 446678888889999999999999


Q ss_pred             HHHHHhHHhcCCCC-CHhHHHHHHHH-HHhcCC--HHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040365          264 SYFNSMTKDYGIAP-SFEHYAAVADL-LGRAGK--LQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKI  337 (514)
Q Consensus       264 ~~~~~m~~~~~~~p-~~~~~~~li~~-~~~~g~--~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~  337 (514)
                      ..|+...+   +.| +...+..+..+ +.+.|+  .++|.+++++.. ..| +...+..|...+...|++++|+..++++
T Consensus        94 ~a~~~Al~---l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~a  170 (198)
T PRK10370         94 LAYRQALQ---LRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQKV  170 (198)
T ss_pred             HHHHHHHH---hCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            99998864   456 67888888886 467777  599999999874 334 6788889999999999999999999999


Q ss_pred             HhcCCCCcchHH
Q 040365          338 FMIDPNNMGAYV  349 (514)
Q Consensus       338 ~~~~p~~~~~~~  349 (514)
                      +++.|++..-+.
T Consensus       171 L~l~~~~~~r~~  182 (198)
T PRK10370        171 LDLNSPRVNRTQ  182 (198)
T ss_pred             HhhCCCCccHHH
Confidence            999987765443

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

Probab=98.37  E-value=0.001  Score=69.45  Aligned_cols=254  Identities=9%  Similarity=0.097  Sum_probs=162.9

Q ss_pred             CCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040365           90 ARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCII  169 (514)
Q Consensus        90 g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~  169 (514)
                      ++++.|.+.-++..+  +..|..+..+-.+.|...+|++-|-+.      -|+..|.-++.++.+.|.+++-.+++....
T Consensus      1089 ~~ldRA~efAe~~n~--p~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL~MaR 1160 (1666)
T KOG0985|consen 1089 GSLDRAYEFAERCNE--PAVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMAR 1160 (1666)
T ss_pred             hhHHHHHHHHHhhCC--hHHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            444444444444433  456999999999999999999887542      367789999999999999999999998888


Q ss_pred             HcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC-----------------------CChhHHHHHHHHHHhCCChHH
Q 040365          170 RNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL-----------------------HDIVSWTAVIMGNALHGNAHD  226 (514)
Q Consensus       170 ~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~-----------------------~d~~~~~~li~~~~~~g~~~~  226 (514)
                      +..-+|.+  -+.||-+|+|.+++.+-+++...-..                       .++.-|..+...+...|+++.
T Consensus      1161 kk~~E~~i--d~eLi~AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~ 1238 (1666)
T KOG0985|consen 1161 KKVREPYI--DSELIFAYAKTNRLTELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQG 1238 (1666)
T ss_pred             HhhcCccc--hHHHHHHHHHhchHHHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence            87666654  45789999999998887665532210                       133445556666666666666


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCC--CCHhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          227 AISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA--PSFEHYAAVADLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       227 A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~--p~~~~~~~li~~~~~~g~~~~A~~~~~~  304 (514)
                      |.+.-++.      .+..||..+-.+|...+.+..|.     |   .|+.  ...+-..-|+..|-..|.++|...+++.
T Consensus      1239 AVD~aRKA------ns~ktWK~VcfaCvd~~EFrlAQ-----i---CGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea 1304 (1666)
T KOG0985|consen 1239 AVDAARKA------NSTKTWKEVCFACVDKEEFRLAQ-----I---CGLNIIVHADELEELIEYYQDRGYFEELISLLEA 1304 (1666)
T ss_pred             HHHHhhhc------cchhHHHHHHHHHhchhhhhHHH-----h---cCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHh
Confidence            66554432      24567777777777666554432     2   2433  2445556678888888888888888876


Q ss_pred             CC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          305 MH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       305 m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..  .+.....|+-|.-.|.+.+ ++...+.++-....     ...--+++++-++.-|.+..-++..-.+
T Consensus      1305 ~LGLERAHMgmfTELaiLYskyk-p~km~EHl~LFwsR-----vNipKviRA~eqahlW~ElvfLY~~y~e 1369 (1666)
T KOG0985|consen 1305 GLGLERAHMGMFTELAILYSKYK-PEKMMEHLKLFWSR-----VNIPKVIRAAEQAHLWSELVFLYDKYEE 1369 (1666)
T ss_pred             hhchhHHHHHHHHHHHHHHHhcC-HHHHHHHHHHHHHh-----cchHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            42  2344555666666665543 33333333322111     0112367777777778887777665443

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

Probab=98.37  E-value=0.00027  Score=73.58  Aligned_cols=189  Identities=16%  Similarity=0.205  Sum_probs=140.7

Q ss_pred             HhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHH
Q 040365          152 CAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLF  231 (514)
Q Consensus       152 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~  231 (514)
                      +...+-+++|..+|...     ..+....+.||+   .-++++.|.+.-++..+|  ..|..+..+-.+.|...+|++-|
T Consensus      1058 ai~~~LyEEAF~ifkkf-----~~n~~A~~VLie---~i~~ldRA~efAe~~n~p--~vWsqlakAQL~~~~v~dAieSy 1127 (1666)
T KOG0985|consen 1058 AIENQLYEEAFAIFKKF-----DMNVSAIQVLIE---NIGSLDRAYEFAERCNEP--AVWSQLAKAQLQGGLVKDAIESY 1127 (1666)
T ss_pred             HhhhhHHHHHHHHHHHh-----cccHHHHHHHHH---HhhhHHHHHHHHHhhCCh--HHHHHHHHHHHhcCchHHHHHHH
Confidence            34444556666666543     334444444443   346677777777776655  46889999999999999999877


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCH
Q 040365          232 EQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTE  311 (514)
Q Consensus       232 ~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~  311 (514)
                      -+.      -|...|.-++..+++.|.+++-..++....++ .-+|.++  +.||-+|++.+++.+.++++.    -||.
T Consensus      1128 ika------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk-~~E~~id--~eLi~AyAkt~rl~elE~fi~----gpN~ 1194 (1666)
T KOG0985|consen 1128 IKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKK-VREPYID--SELIFAYAKTNRLTELEEFIA----GPNV 1194 (1666)
T ss_pred             Hhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-hcCccch--HHHHHHHHHhchHHHHHHHhc----CCCc
Confidence            652      36678999999999999999999999876544 5566655  478999999999999888773    4777


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                      .-.....+-|...|.++.|.-++..        .+.|..|+..+...|.+..|...-++.
T Consensus      1195 A~i~~vGdrcf~~~~y~aAkl~y~~--------vSN~a~La~TLV~LgeyQ~AVD~aRKA 1246 (1666)
T KOG0985|consen 1195 ANIQQVGDRCFEEKMYEAAKLLYSN--------VSNFAKLASTLVYLGEYQGAVDAARKA 1246 (1666)
T ss_pred             hhHHHHhHHHhhhhhhHHHHHHHHH--------hhhHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            7778888889999999999888775        467777888888888887776655443

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.34  E-value=1.9e-05  Score=65.43  Aligned_cols=119  Identities=12%  Similarity=0.039  Sum_probs=97.3

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY  355 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  355 (514)
                      +....-.+.-.+...|++++|..+|+-.-  .+-+..-|..|..+|...|++++|+..+.++..++|+++.++..+..+|
T Consensus        34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~  113 (157)
T PRK15363         34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECY  113 (157)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHH
Confidence            34445556666788999999999998763  3346778999999999999999999999999999999999999999999


Q ss_pred             HHccChhHHHHHHHHHHhCCCccCCcccEEEECCEEEEEEeCCCCCCChHHHHHHHHHHHHHHH
Q 040365          356 AAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERME  419 (514)
Q Consensus       356 ~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~  419 (514)
                      ...|+.+.|.+.|+......                       ..+|+..++.+..+..++.|.
T Consensus       114 L~lG~~~~A~~aF~~Ai~~~-----------------------~~~~~~~~l~~~A~~~L~~l~  154 (157)
T PRK15363        114 LACDNVCYAIKALKAVVRIC-----------------------GEVSEHQILRQRAEKMLQQLS  154 (157)
T ss_pred             HHcCCHHHHHHHHHHHHHHh-----------------------ccChhHHHHHHHHHHHHHHhh
Confidence            99999999999999776532                       125666777766666666554

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

Probab=98.34  E-value=0.00083  Score=68.70  Aligned_cols=326  Identities=11%  Similarity=0.064  Sum_probs=184.0

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhC-C-------C-CCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCc
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNV-N-------L-KPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDAN   75 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g-------~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~   75 (514)
                      +-+.|..|.+.+.+..+.+-|.-.+-.|... |       . .|+ .+=..+.-...+.|-+++|+.++.+..+.+    
T Consensus       756 S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~D----  830 (1416)
T KOG3617|consen  756 SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKRYD----  830 (1416)
T ss_pred             hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHHHH----
Confidence            3456888888888888887777776666431 1       1 122 222222223346677888888888777653    


Q ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHccCCCCC-hhHHHHHHHHHHHCCChhHHHHHHHHH----------HHCC-------
Q 040365           76 VCIGSSLINMYAKCARVEDSHRLFCLLPVKD-AISWNSIIAGCVQNGLFDEGLKFFRQM----------LIAK-------  137 (514)
Q Consensus        76 ~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d-~~~~~~li~~~~~~g~~~~A~~l~~~m----------~~~g-------  137 (514)
                           .|=..|-..|.+++|.++-+.-..-. -.||..-..-+-..++.+.|++.|++.          ....       
T Consensus       831 -----LlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Y  905 (1416)
T KOG3617|consen  831 -----LLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQY  905 (1416)
T ss_pred             -----HHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHH
Confidence                 34455667788888887765322111 123444444444566777777777653          1111       


Q ss_pred             --CCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHH
Q 040365          138 --IKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVI  215 (514)
Q Consensus       138 --~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li  215 (514)
                        -..|...|.--....-..|+++.|..++....+         |-+++...+-.|+.++|-++-++  ..|......+.
T Consensus       906 v~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~iA~e--sgd~AAcYhla  974 (1416)
T KOG3617|consen  906 VRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIKCIQGKTDKAARIAEE--SGDKAACYHLA  974 (1416)
T ss_pred             HHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeEeeccCchHHHHHHHh--cccHHHHHHHH
Confidence              011222222222223344555555555544432         23445555556777777666554  34667777888


Q ss_pred             HHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcc---------------CCHHHHHHHHHHhHHhcCCCCCHh
Q 040365          216 MGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHA---------------GLIDKAWSYFNSMTKDYGIAPSFE  280 (514)
Q Consensus       216 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~---------------g~~~~a~~~~~~m~~~~~~~p~~~  280 (514)
                      ..|-..|++.+|...|.+.+.         |...|..|-..               .+.-.|-.+|++.    |..    
T Consensus       975 R~YEn~g~v~~Av~FfTrAqa---------fsnAIRlcKEnd~~d~L~nlal~s~~~d~v~aArYyEe~----g~~---- 1037 (1416)
T KOG3617|consen  975 RMYENDGDVVKAVKFFTRAQA---------FSNAIRLCKENDMKDRLANLALMSGGSDLVSAARYYEEL----GGY---- 1037 (1416)
T ss_pred             HHhhhhHHHHHHHHHHHHHHH---------HHHHHHHHHhcCHHHHHHHHHhhcCchhHHHHHHHHHHc----chh----
Confidence            889999999999999987653         33334333322               2333444455433    211    


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhC-------------CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-------
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNM-------------HAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMI-------  340 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m-------------~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-------  340 (514)
                       ...-+..|-++|.+.+|+++--+-             ....|+...+.-..-+..+.++++|..++-...+.       
T Consensus      1038 -~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~ar~~~~AlqlC 1116 (1416)
T KOG3617|consen 1038 -AHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLAREFSGALQLC 1116 (1416)
T ss_pred             -hhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             223455688888888887753211             12245666666666667777777776655333221       


Q ss_pred             ---------------CCCC---------cchHHHHHHHHHHccChhHHHHHHH
Q 040365          341 ---------------DPNN---------MGAYVILSNTYAAARRWKDAASLRV  369 (514)
Q Consensus       341 ---------------~p~~---------~~~~~~l~~~~~~~g~~~~a~~~~~  369 (514)
                                     -|..         ......++..|.++|.|..|.+-|.
T Consensus      1117 ~~~nv~vtee~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~AtKKfT 1169 (1416)
T KOG3617|consen 1117 KNRNVRVTEEFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHAATKKFT 1169 (1416)
T ss_pred             hcCCCchhHHHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHHHHHHHh
Confidence                           0110         1356678888999998888776654

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.33  E-value=7.2e-05  Score=68.77  Aligned_cols=181  Identities=16%  Similarity=0.032  Sum_probs=125.4

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCc---HHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C-Ch---hH
Q 040365          140 PRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDN---MFIASSLLDMYAKCGNIRLARCIFDKMDL--H-DI---VS  210 (514)
Q Consensus       140 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~-d~---~~  210 (514)
                      .....+......+...|+++.|...++.+++.. +.+   ...+..+...|.+.|++++|...|+++.+  | +.   .+
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a  109 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYA  109 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHH
Confidence            345567777888899999999999999998764 222   24667788999999999999999999852  2 22   24


Q ss_pred             HHHHHHHHHhC--------CChHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhH
Q 040365          211 WTAVIMGNALH--------GNAHDAISLFEQMEKDGVKPNSV-AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEH  281 (514)
Q Consensus       211 ~~~li~~~~~~--------g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~  281 (514)
                      +..+..++.+.        |+.++|.+.|+++...  .|+.. ....+.... .   .      .... .        ..
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~~-~---~------~~~~-~--------~~  168 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRMD-Y---L------RNRL-A--------GK  168 (235)
T ss_pred             HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHHH-H---H------HHHH-H--------HH
Confidence            55555666654        7899999999999875  45542 221111110 0   0      0000 0        11


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhCC----CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          282 YAAVADLLGRAGKLQEAYEFISNMH----AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       282 ~~~li~~~~~~g~~~~A~~~~~~m~----~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      ...+...|.+.|++++|...+++..    ..| ....|..+..++...|++++|...++.+....|
T Consensus       169 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~~  234 (235)
T TIGR03302       169 ELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANYP  234 (235)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            2256677889999999999888763    122 356888999999999999999998888766544

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).

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.32  E-value=5.4e-05  Score=74.30  Aligned_cols=246  Identities=13%  Similarity=0.057  Sum_probs=177.8

Q ss_pred             HHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHH
Q 040365          116 GCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRL  195 (514)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~  195 (514)
                      -+.++|++.+|.-.|+...+.. +-+...|.-|-..-+..++-..|...+.+.++.. +.|..+.-+|.-.|...|.-..
T Consensus       294 ~lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q~~  371 (579)
T KOG1125|consen  294 NLMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQNQ  371 (579)
T ss_pred             HHHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhHHH
Confidence            3567888999998898887764 3455667777777777788888888888888875 5677788888888999999999


Q ss_pred             HHHHHHhCCCC-ChhHHHHHH---------HHHHhCCChHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040365          196 ARCIFDKMDLH-DIVSWTAVI---------MGNALHGNAHDAISLFEQMEK-DGVKPNSVAFVAVLTACSHAGLIDKAWS  264 (514)
Q Consensus       196 A~~~~~~m~~~-d~~~~~~li---------~~~~~~g~~~~A~~l~~~m~~-~g~~p~~~t~~~ll~a~~~~g~~~~a~~  264 (514)
                      |.+.|+.-..- -...|...-         ..+..........++|-++.. .+.++|......|.-.|--.|++++|..
T Consensus       372 Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiD  451 (579)
T KOG1125|consen  372 ALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVD  451 (579)
T ss_pred             HHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHH
Confidence            99888875210 000000000         122222334556677777654 4544566666666667888999999999


Q ss_pred             HHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040365          265 YFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNM-HAGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMID  341 (514)
Q Consensus       265 ~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  341 (514)
                      .|+...   .++| |...||.|...++...+.++|+.-|.+. ..+|+ +.++..|.-+|...|.+++|...|-.++.+.
T Consensus       452 cf~~AL---~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq  528 (579)
T KOG1125|consen  452 CFEAAL---QVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSMQ  528 (579)
T ss_pred             HHHHHH---hcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHhh
Confidence            999886   4578 7899999999999999999999999886 45676 5678889999999999999999998888765


Q ss_pred             CC-----C-----cchHHHHHHHHHHccChhHHHH
Q 040365          342 PN-----N-----MGAYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       342 p~-----~-----~~~~~~l~~~~~~~g~~~~a~~  366 (514)
                      +.     .     ...|..|=.++...++.|-+.+
T Consensus       529 ~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~  563 (579)
T KOG1125|consen  529 RKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQE  563 (579)
T ss_pred             hcccccccCCcchHHHHHHHHHHHHHcCCchHHHH
Confidence            32     1     1356666666666666654443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.32  E-value=9.6e-06  Score=68.03  Aligned_cols=99  Identities=12%  Similarity=-0.064  Sum_probs=87.5

Q ss_pred             CCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          275 IAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-A-GPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       275 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~-~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      +.|+  .+..+...+...|++++|...|+... . +.+...|..+..++...|++++|...|+++.+++|+++.++..++
T Consensus        22 ~~p~--~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg   99 (144)
T PRK15359         22 VDPE--TVYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTG   99 (144)
T ss_pred             cCHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHH
Confidence            3454  35567888899999999999999863 3 357889999999999999999999999999999999999999999


Q ss_pred             HHHHHccChhHHHHHHHHHHhCC
Q 040365          353 NTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       353 ~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      .++...|++++|...++...+..
T Consensus       100 ~~l~~~g~~~eAi~~~~~Al~~~  122 (144)
T PRK15359        100 VCLKMMGEPGLAREAFQTAIKMS  122 (144)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC
Confidence            99999999999999999887654

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.31  E-value=0.00089  Score=67.59  Aligned_cols=52  Identities=12%  Similarity=-0.062  Sum_probs=32.2

Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      +..+-++.|..+.+-..+..  -+....-+..-+...|++++|.+.+-+..+.+
T Consensus       974 ~d~~afd~afdlari~~k~k--~~~vhlk~a~~ledegk~edaskhyveaikln 1025 (1636)
T KOG3616|consen  974 ADNCAFDFAFDLARIAAKDK--MGEVHLKLAMFLEDEGKFEDASKHYVEAIKLN 1025 (1636)
T ss_pred             hcccchhhHHHHHHHhhhcc--CccchhHHhhhhhhccchhhhhHhhHHHhhcc
Confidence            33444555555444433322  23455667777788999999998887776654

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.30  E-value=0.00027  Score=69.00  Aligned_cols=345  Identities=12%  Similarity=0.033  Sum_probs=203.7

Q ss_pred             HHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHH
Q 040365           15 GLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVED   94 (514)
Q Consensus        15 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~   94 (514)
                      +....|+++.|+.+|-+.+... ++|.+.|+.-..+++..|++++|.+=-...++.. |.=..-|+-+..++.-.|++++
T Consensus        11 aa~s~~d~~~ai~~~t~ai~l~-p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~-p~w~kgy~r~Gaa~~~lg~~~e   88 (539)
T KOG0548|consen   11 AAFSSGDFETAIRLFTEAIMLS-PTNHVLYSNRSAAYASLGSYEKALKDATKTRRLN-PDWAKGYSRKGAALFGLGDYEE   88 (539)
T ss_pred             hhcccccHHHHHHHHHHHHccC-CCccchhcchHHHHHHHhhHHHHHHHHHHHHhcC-CchhhHHHHhHHHHHhcccHHH
Confidence            4556799999999999888765 5577889988999999999999887777666653 2234567777788888899999


Q ss_pred             HHHHHccCCCC---ChhHHHHHHHHHHHCCChhHHHHHHHH----HHHCCCC-----CCHHHHHHHHHHHhcc-------
Q 040365           95 SHRLFCLLPVK---DAISWNSIIAGCVQNGLFDEGLKFFRQ----MLIAKIK-----PRHVSFSSIMPACAHL-------  155 (514)
Q Consensus        95 A~~~f~~~~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~----m~~~g~~-----p~~~t~~~ll~~~~~~-------  155 (514)
                      |..-|.+-.+.   |...++-+..++....   ++.+.|..    +...+.+     ....+|..++...-+.       
T Consensus        89 A~~ay~~GL~~d~~n~~L~~gl~~a~~~~~---~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~~  165 (539)
T KOG0548|consen   89 AILAYSEGLEKDPSNKQLKTGLAQAYLEDY---AADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKLY  165 (539)
T ss_pred             HHHHHHHHhhcCCchHHHHHhHHHhhhHHH---HhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhcc
Confidence            99999876543   4556666666661110   11111110    0000000     0111232333222110       


Q ss_pred             CChHHHHHHHHHHHHc--------C-------CCC------------c----------HHHHHHHHHHHHhcCCHHHHHH
Q 040365          156 TTLHLGKQLHGCIIRN--------G-------FDD------------N----------MFIASSLLDMYAKCGNIRLARC  198 (514)
Q Consensus       156 ~~~~~a~~~~~~~~~~--------~-------~~~------------~----------~~~~~~li~~y~k~g~~~~A~~  198 (514)
                      .+.+...+.+..+...        +       ..|            |          ..-...|.++.-+..+++.|.+
T Consensus       166 l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~q  245 (539)
T KOG0548|consen  166 LNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAIQ  245 (539)
T ss_pred             cccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHH
Confidence            0111111111111100        0       011            0          0112345566666667777776


Q ss_pred             HHHhCC--CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC--C----HHHHHHHHHHHHccCCHHHHHHHHHHhH
Q 040365          199 IFDKMD--LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP--N----SVAFVAVLTACSHAGLIDKAWSYFNSMT  270 (514)
Q Consensus       199 ~~~~m~--~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p--~----~~t~~~ll~a~~~~g~~~~a~~~~~~m~  270 (514)
                      -+....  ..++.-++....+|...|.+.++...-....+.|-.-  +    ...+..+..++.+.++.+.++.+|....
T Consensus       246 ~y~~a~el~~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~kaL  325 (539)
T KOG0548|consen  246 HYAKALELATDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGNAYTKREDYEGAIKYYQKAL  325 (539)
T ss_pred             HHHHHHhHhhhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHHHh
Confidence            666554  2333445555666777777777666666655544211  1    1122234446666777888888888765


Q ss_pred             HhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchH
Q 040365          271 KDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPTEN-VWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAY  348 (514)
Q Consensus       271 ~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~  348 (514)
                      ..+ ..|+         .+.+....+++....+... ..|+.. --..=...+.+.|++..|...+.+++..+|+|+..|
T Consensus       326 te~-Rt~~---------~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~P~Da~lY  395 (539)
T KOG0548|consen  326 TEH-RTPD---------LLSKLKEAEKALKEAERKAYINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRDPEDARLY  395 (539)
T ss_pred             hhh-cCHH---------HHHHHHHHHHHHHHHHHHHhhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCchhHHH
Confidence            542 2232         2334444455555444332 234331 122335678899999999999999999999999999


Q ss_pred             HHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          349 VILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       349 ~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ...+-+|.+.|.+..|++--+.-.+.
T Consensus       396 sNRAac~~kL~~~~~aL~Da~~~ieL  421 (539)
T KOG0548|consen  396 SNRAACYLKLGEYPEALKDAKKCIEL  421 (539)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            99999999999999999876655444

>PLN02789 farnesyltranstransferase

Probab=98.29  E-value=0.00079  Score=64.28  Aligned_cols=207  Identities=10%  Similarity=-0.019  Sum_probs=124.0

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHccCCCC---ChhHHHHHHHHHHHCC-ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHh
Q 040365           78 IGSSLINMYAKCARVEDSHRLFCLLPVK---DAISWNSIIAGCVQNG-LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACA  153 (514)
Q Consensus        78 ~~~~li~~~~~~g~~~~A~~~f~~~~~~---d~~~~~~li~~~~~~g-~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~  153 (514)
                      ++..+-..+...++.++|+.+.+.+.+.   +..+|+.--..+...| .+++++..++++.+.. +-+...|.---..+.
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~l~  117 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWLAE  117 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHHHH
Confidence            4556666777788999999999887643   4456776666667777 6799999999998864 233344554433444


Q ss_pred             ccCCh--HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhC---CCh-
Q 040365          154 HLTTL--HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALH---GNA-  224 (514)
Q Consensus       154 ~~~~~--~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~---g~~-  224 (514)
                      +.+..  +.+..+.+.+++.. +-|..+|+...-.+.+.|++++|.+.++++.   ..|..+|+.....+.+.   |.. 
T Consensus       118 ~l~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~N~sAW~~R~~vl~~~~~l~~~~  196 (320)
T PLN02789        118 KLGPDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITRSPLLGGLE  196 (320)
T ss_pred             HcCchhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCchhHHHHHHHHHHhcccccccc
Confidence            45542  55667777777665 5566777777777777777777777777765   34556677665555443   222 


Q ss_pred             ---HHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHcc----CCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHh
Q 040365          225 ---HDAISLFEQMEKDGVKP-NSVAFVAVLTACSHA----GLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGR  291 (514)
Q Consensus       225 ---~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~----g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~  291 (514)
                         +++++...++...  .| |...|+.+...+...    +...+|..++.....   ..| +......|++.|+.
T Consensus       197 ~~~e~el~y~~~aI~~--~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~---~~~~s~~al~~l~d~~~~  267 (320)
T PLN02789        197 AMRDSELKYTIDAILA--NPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLS---KDSNHVFALSDLLDLLCE  267 (320)
T ss_pred             ccHHHHHHHHHHHHHh--CCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhc---ccCCcHHHHHHHHHHHHh
Confidence               3455555455543  23 334555555555441    233445555554432   223 34444555555543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.28  E-value=1.4e-06  Score=53.20  Aligned_cols=35  Identities=29%  Similarity=0.625  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCH
Q 040365          209 VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNS  243 (514)
Q Consensus       209 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~  243 (514)
                      ++||++|.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999973

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.27  E-value=1.5e-06  Score=52.73  Aligned_cols=34  Identities=24%  Similarity=0.446  Sum_probs=31.2

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKP   39 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p   39 (514)
                      +.+||++|.+|++.|+++.|+++|+.|.+.|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            4689999999999999999999999999999887

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

Probab=98.25  E-value=0.00013  Score=73.52  Aligned_cols=212  Identities=11%  Similarity=-0.043  Sum_probs=163.9

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CCChhHHHHHHHHHHhCC
Q 040365          145 FSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD--LHDIVSWTAVIMGNALHG  222 (514)
Q Consensus       145 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~d~~~~~~li~~~~~~g  222 (514)
                      -..+...+...|-...|..+++++.         .+.-.|.+|...|+..+|..+..+-.  +||...|..+.+......
T Consensus       401 q~~laell~slGitksAl~I~Erle---------mw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s  471 (777)
T KOG1128|consen  401 QRLLAELLLSLGITKSALVIFERLE---------MWDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPS  471 (777)
T ss_pred             HHHHHHHHHHcchHHHHHHHHHhHH---------HHHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChH
Confidence            3345556667777888888887654         45568889999999999988876554  567788888888887788


Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEF  301 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~  301 (514)
                      -+++|.++++.....       .-..+.....+.++++++.+.|+.-.   .+.| ...+|-.+.-+..+.++++.|.+.
T Consensus       472 ~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl---~~nplq~~~wf~~G~~ALqlek~q~av~a  541 (777)
T KOG1128|consen  472 LYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSL---EINPLQLGTWFGLGCAALQLEKEQAAVKA  541 (777)
T ss_pred             HHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHh---hcCccchhHHHhccHHHHHHhhhHHHHHH
Confidence            899999998875432       11111222234789999999998654   4455 567888888888899999999998


Q ss_pred             HHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          302 ISNM-HAGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       302 ~~~m-~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      |..- ...|| ...||+|-.+|.+.++..+|...+.++++-+-.+...|....-...+.|.|++|.+.+.++.+..
T Consensus       542 F~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~rll~~~  617 (777)
T KOG1128|consen  542 FHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDLR  617 (777)
T ss_pred             HHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHHHHHhh
Confidence            8764 34554 67899999999999999999999999999887777777777777889999999999999887543

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

Probab=98.24  E-value=0.00046  Score=73.49  Aligned_cols=240  Identities=10%  Similarity=0.055  Sum_probs=146.3

Q ss_pred             CCCC-hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHH
Q 040365           37 LKPD-SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIA  115 (514)
Q Consensus        37 ~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~  115 (514)
                      ..|+ ...+..++..+...+++++|.++.+..++.. +.....|-.+...|...++.+++..+             .++.
T Consensus        26 ~~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~-P~~i~~yy~~G~l~~q~~~~~~~~lv-------------~~l~   91 (906)
T PRK14720         26 YSLSKFKELDDLIDAYKSENLTDEAKDICEEHLKEH-KKSISALYISGILSLSRRPLNDSNLL-------------NLID   91 (906)
T ss_pred             CCcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CcceehHHHHHHHHHhhcchhhhhhh-------------hhhh
Confidence            4444 3467778888878888888888888666553 33333444444466666665554443             3444


Q ss_pred             HHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHH
Q 040365          116 GCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRL  195 (514)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~  195 (514)
                      ......++.-...+...|...  .-+...+-.+..+|.+.|+.+++.++++++++.. +.|+.+.|.+...|+.. ++++
T Consensus        92 ~~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~K  167 (906)
T PRK14720         92 SFSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEK  167 (906)
T ss_pred             hcccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHH
Confidence            444455554444444455543  3344567778888888899999999999988887 77788888888888888 8888


Q ss_pred             HHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCC
Q 040365          196 ARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGI  275 (514)
Q Consensus       196 A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~  275 (514)
                      |.+++.+.           +..|...+++.++.++|.++...  .|+.+.+               -.++.+.+....+.
T Consensus       168 A~~m~~KA-----------V~~~i~~kq~~~~~e~W~k~~~~--~~~d~d~---------------f~~i~~ki~~~~~~  219 (906)
T PRK14720        168 AITYLKKA-----------IYRFIKKKQYVGIEEIWSKLVHY--NSDDFDF---------------FLRIERKVLGHREF  219 (906)
T ss_pred             HHHHHHHH-----------HHHHHhhhcchHHHHHHHHHHhc--CcccchH---------------HHHHHHHHHhhhcc
Confidence            88877654           33367777888888888888874  3443322               12222223222222


Q ss_pred             CCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHH
Q 040365          276 APSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACR  322 (514)
Q Consensus       276 ~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~  322 (514)
                      .--..++-.+...|-..++++++..+++.+-  .+.|.....-|+..|.
T Consensus       220 ~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        220 TRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKAREELIRFYK  268 (906)
T ss_pred             chhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHHHHHHHHH
Confidence            2233444445555666666667766666653  1223334444444443

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.23  E-value=0.00091  Score=64.83  Aligned_cols=175  Identities=18%  Similarity=0.124  Sum_probs=123.4

Q ss_pred             HHHHHHHHHhCC------CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040365          193 IRLARCIFDKMD------LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYF  266 (514)
Q Consensus       193 ~~~A~~~~~~m~------~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  266 (514)
                      +.+++..-+.++      .++.......+.+.........+..++. +... -.-...-|...+ .....|.+++|+..+
T Consensus       253 Ia~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~~~~~~~~~~~~~~~-~~~~-~~~~aa~YG~A~-~~~~~~~~d~A~~~l  329 (484)
T COG4783         253 IADLRNRAEQSPPYNKLDSPDFQLARARIRAKYEALPNQQAADLLA-KRSK-RGGLAAQYGRAL-QTYLAGQYDEALKLL  329 (484)
T ss_pred             HHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhccccccchHHHHH-HHhC-ccchHHHHHHHH-HHHHhcccchHHHHH
Confidence            455555666665      2344455555554433332222322222 2222 011222343333 345678999999999


Q ss_pred             HHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          267 NSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       267 ~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      +.+.+.   .| |+.......+.+.+.++..+|.+.++++. ..|+ ...+-.+..++.+.|++.+|+++++.....+|+
T Consensus       330 ~~L~~~---~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~p~  406 (484)
T COG4783         330 QPLIAA---QPDNPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDPE  406 (484)
T ss_pred             HHHHHh---CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCC
Confidence            998754   45 66677778899999999999999999874 4466 677888899999999999999999999999999


Q ss_pred             CcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          344 NMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       344 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      |+..|..|..+|...|+..++...+.++-.
T Consensus       407 dp~~w~~LAqay~~~g~~~~a~~A~AE~~~  436 (484)
T COG4783         407 DPNGWDLLAQAYAELGNRAEALLARAEGYA  436 (484)
T ss_pred             CchHHHHHHHHHHHhCchHHHHHHHHHHHH
Confidence            999999999999999998888887776643

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.22  E-value=0.00022  Score=74.97  Aligned_cols=141  Identities=12%  Similarity=0.070  Sum_probs=117.0

Q ss_pred             CChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHH
Q 040365          206 HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYA  283 (514)
Q Consensus       206 ~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~  283 (514)
                      .++..+-.|.....+.|++++|..+++...+  +.||. .....+...+.+.+.+++|....++...   ..| +.....
T Consensus        84 ~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~---~~p~~~~~~~  158 (694)
T PRK15179         84 HTELFQVLVARALEAAHRSDEGLAVWRGIHQ--RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFS---GGSSSAREIL  158 (694)
T ss_pred             ccHHHHHHHHHHHHHcCCcHHHHHHHHHHHh--hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhh---cCCCCHHHHH
Confidence            3577888888889999999999999999988  57775 4567788889999999999999998864   366 577788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          284 AVADLLGRAGKLQEAYEFISNMH-AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m~-~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      .+..++.+.|++++|.++|++.. ..|+ ..+|.++..++...|+.++|...|+++++...+-...|+.+
T Consensus       159 ~~a~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~  228 (694)
T PRK15179        159 LEAKSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRR  228 (694)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHH
Confidence            88889999999999999999875 3344 78899999999999999999999999998875555555543

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.18  E-value=0.00049  Score=71.80  Aligned_cols=338  Identities=15%  Similarity=0.123  Sum_probs=174.3

Q ss_pred             hhHHHHHHHHHhhCCCCCC-hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHc
Q 040365           22 YEEALNIVRQMGNVNLKPD-SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFC  100 (514)
Q Consensus        22 ~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~  100 (514)
                      ...|+..|-+..+..  |+ ...|..+...|....+...|.+.|..+.+.+ +.|...+.++.+.|++..+++.|..+.-
T Consensus       474 ~~~al~ali~alrld--~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~~~we~a~~I~l  550 (1238)
T KOG1127|consen  474 SALALHALIRALRLD--VSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEESTWEEAFEICL  550 (1238)
T ss_pred             HHHHHHHHHHHHhcc--cchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhccccHHHHHHHHH
Confidence            444555444443321  22 1245556666665556666667776666654 4555666666777777776666665532


Q ss_pred             ------------------------------------cCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC
Q 040365          101 ------------------------------------LLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR  141 (514)
Q Consensus       101 ------------------------------------~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~  141 (514)
                                                          ...   ..|...|..+..+|...|++.-|+++|.+...  +.|+
T Consensus       551 ~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~--LrP~  628 (1238)
T KOG1127|consen  551 RAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASL--LRPL  628 (1238)
T ss_pred             HHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHh--cCcH
Confidence                                                211   12556777888888888888888888877655  3454


Q ss_pred             HHHHHHHHH--HHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh-------cCCHHHHHHHHHhCC--------
Q 040365          142 HVSFSSIMP--ACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK-------CGNIRLARCIFDKMD--------  204 (514)
Q Consensus       142 ~~t~~~ll~--~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k-------~g~~~~A~~~~~~m~--------  204 (514)
                      .. |.....  .-+..|.+.++...++.++... .......+.|...+.+       .|-..+|...|+.-.        
T Consensus       629 s~-y~~fk~A~~ecd~GkYkeald~l~~ii~~~-s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~f~~~l~  706 (1238)
T KOG1127|consen  629 SK-YGRFKEAVMECDNGKYKEALDALGLIIYAF-SLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIESFIVSLI  706 (1238)
T ss_pred             hH-HHHHHHHHHHHHhhhHHHHHHHHHHHHHHH-HHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHH
Confidence            32 222211  2345677777777777665432 1112222333333322       222233333333221        


Q ss_pred             ---CCChhHHHHHHHHHHh---CC--ChH-HHH-HHHHHHHHcCCCCCHH--------------------HHHHHHHHHH
Q 040365          205 ---LHDIVSWTAVIMGNAL---HG--NAH-DAI-SLFEQMEKDGVKPNSV--------------------AFVAVLTACS  254 (514)
Q Consensus       205 ---~~d~~~~~~li~~~~~---~g--~~~-~A~-~l~~~m~~~g~~p~~~--------------------t~~~ll~a~~  254 (514)
                         ..+...|-.+-.++.-   ..  -+. -.+ -++.+....+.-|+..                    +|..+...|.
T Consensus       707 h~~~~~~~~Wi~asdac~~f~q~e~~~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~~hlsl~~~~~~WyNLGinyl  786 (1238)
T KOG1127|consen  707 HSLQSDRLQWIVASDACYIFSQEEPSIVNMHYLIILSKQLEKTGALKKNDLLFLGYECGIAHLSLAIHMYPWYNLGINYL  786 (1238)
T ss_pred             HhhhhhHHHHHHHhHHHHHHHHhcccchHHHHHHHHHHHHHhcccCcchhHHHHHHHHhhHHHHHhhccchHHHHhHHHH
Confidence               1122333333222111   00  000 000 1111122222222111                    1111111111


Q ss_pred             c----cC----CHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhC--CCCCCHHHHHHHHHHHHh
Q 040365          255 H----AG----LIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNM--HAGPTENVWLTLLSACRV  323 (514)
Q Consensus       255 ~----~g----~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m--~~~p~~~~~~~ll~~~~~  323 (514)
                      +    .+    +...|+..+...++   +.. +...|+.|.-+ ...|.+.-|..-|-.-  ..+....+|..+...|.+
T Consensus       787 r~f~~l~et~~~~~~Ai~c~KkaV~---L~ann~~~WnaLGVl-sg~gnva~aQHCfIks~~sep~~~~~W~NlgvL~l~  862 (1238)
T KOG1127|consen  787 RYFLLLGETMKDACTAIRCCKKAVS---LCANNEGLWNALGVL-SGIGNVACAQHCFIKSRFSEPTCHCQWLNLGVLVLE  862 (1238)
T ss_pred             HHHHHcCCcchhHHHHHHHHHHHHH---HhhccHHHHHHHHHh-hccchhhhhhhhhhhhhhccccchhheeccceeEEe
Confidence            1    11    11234444433322   122 33344443332 4445555555444322  123456778888888888


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHH
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVF  370 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~  370 (514)
                      ..|++-|...|.+...++|.|...|......-...|+.-++..+|..
T Consensus       863 n~d~E~A~~af~~~qSLdP~nl~~WlG~Ali~eavG~ii~~~~lfaH  909 (1238)
T KOG1127|consen  863 NQDFEHAEPAFSSVQSLDPLNLVQWLGEALIPEAVGRIIERLILFAH  909 (1238)
T ss_pred             cccHHHhhHHHHhhhhcCchhhHHHHHHHHhHHHHHHHHHHHHHHHh
Confidence            89999999999999999999999998888888888888888888775

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.16  E-value=0.00059  Score=71.86  Aligned_cols=141  Identities=11%  Similarity=0.122  Sum_probs=116.0

Q ss_pred             CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CC-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH-HHHH
Q 040365          173 FDDNMFIASSLLDMYAKCGNIRLARCIFDKMD--LH-DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV-AFVA  248 (514)
Q Consensus       173 ~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~  248 (514)
                      ++.++..+-.|.......|.+++|..+++...  .| +...+..+...+.+.+++++|+..+++....  .|+.. ....
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~  159 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILL  159 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHH
Confidence            56678888889999999999999999999886  34 5677888999999999999999999999884  56654 5566


Q ss_pred             HHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHH
Q 040365          249 VLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLL  318 (514)
Q Consensus       249 ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll  318 (514)
                      +..++.+.|++++|..+|+++...   .| +...+..+..++-+.|+.++|...|+...  ..|-..-|+.++
T Consensus       160 ~a~~l~~~g~~~~A~~~y~~~~~~---~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~~  229 (694)
T PRK15179        160 EAKSWDEIGQSEQADACFERLSRQ---HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRRL  229 (694)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHhc---CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHHH
Confidence            667888999999999999999752   44 47888899999999999999999999874  234555555544

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.14  E-value=4e-06  Score=50.73  Aligned_cols=34  Identities=26%  Similarity=0.576  Sum_probs=30.2

Q ss_pred             hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCC
Q 040365          107 AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKP  140 (514)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  140 (514)
                      +.+||++|.+|++.|+++.|.++|++|.+.|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            3689999999999999999999999999998887

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

Probab=98.13  E-value=5.1e-05  Score=62.95  Aligned_cols=100  Identities=19%  Similarity=0.212  Sum_probs=73.3

Q ss_pred             CCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          275 IAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       275 ~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      ..| +......+...+...|++++|.+.++...  .+.+...|..+...+...|+++.|...++++.+.+|+++..+..+
T Consensus        12 ~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l   91 (135)
T TIGR02552        12 LDSEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHA   91 (135)
T ss_pred             CChhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHH
Confidence            344 34455566666777778888877777652  223566777777778788888888888888888888888888888


Q ss_pred             HHHHHHccChhHHHHHHHHHHhC
Q 040365          352 SNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       352 ~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +.+|...|++++|.+.++...+.
T Consensus        92 a~~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        92 AECLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHh
Confidence            88888888888888888777654

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=98.13  E-value=0.00015  Score=70.65  Aligned_cols=122  Identities=16%  Similarity=0.145  Sum_probs=101.6

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHh
Q 040365          246 FVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRV  323 (514)
Q Consensus       246 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~  323 (514)
                      ..+++..+...++++.|..+|+++.+.   .|+  ....++..+...++-.+|.+++++.. ..| |...+..-...|..
T Consensus       172 v~~Ll~~l~~t~~~~~ai~lle~L~~~---~pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~  246 (395)
T PF09295_consen  172 VDTLLKYLSLTQRYDEAIELLEKLRER---DPE--VAVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLS  246 (395)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHhc---CCc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence            446677777788999999999998654   355  44557888888888899999888763 233 56666666777899


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      .++++.|..+++++.+..|.+..+|..|+.+|.+.|++++|+-.++.+.
T Consensus       247 k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  247 KKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             cCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            9999999999999999999999999999999999999999999999885

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

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.10  E-value=0.00056  Score=60.98  Aligned_cols=158  Identities=14%  Similarity=0.078  Sum_probs=116.8

Q ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040365           75 NVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPA  151 (514)
Q Consensus        75 ~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~  151 (514)
                      |..+ ..+-..+--.|+-+.+..+.....   ..|....+..+....+.|++.+|+..|++...- -++|..+|+.+.-+
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaa  143 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAA  143 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHH
Confidence            4444 556666777777777777766643   235556666888888888888888888887664 36788888888888


Q ss_pred             HhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHH
Q 040365          152 CAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAI  228 (514)
Q Consensus       152 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~  228 (514)
                      |.+.|+++.|+.-|.+..+.. +-+....|.|.-.|.-.|+++.|+.++....   ..|...-..+.......|++++|.
T Consensus       144 ldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~  222 (257)
T COG5010         144 LDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAE  222 (257)
T ss_pred             HHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHH
Confidence            888888888888888888764 4455666777777778888888888887653   336667777777778888888888


Q ss_pred             HHHHHHH
Q 040365          229 SLFEQME  235 (514)
Q Consensus       229 ~l~~~m~  235 (514)
                      ++-.+-.
T Consensus       223 ~i~~~e~  229 (257)
T COG5010         223 DIAVQEL  229 (257)
T ss_pred             hhccccc
Confidence            8766543

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

Probab=98.09  E-value=0.0013  Score=70.16  Aligned_cols=238  Identities=7%  Similarity=-0.035  Sum_probs=154.7

Q ss_pred             CCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhh-HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHH
Q 040365            3 VSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFT-LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSS   81 (514)
Q Consensus         3 ~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~   81 (514)
                      ..+...|-.||..|...+++++|.++.+...+.  .|+... |-.+...+.+.++...+..+  .+...  .+...-++.
T Consensus        28 p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~--~~~~~~~~~  101 (906)
T PRK14720         28 LSKFKELDDLIDAYKSENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLL--NLIDS--FSQNLKWAI  101 (906)
T ss_pred             cchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhh--hhhhh--cccccchhH
Confidence            346778999999999999999999999977664  466543 32222355566666665555  23222  122112222


Q ss_pred             HHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHH
Q 040365           82 LINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLG  161 (514)
Q Consensus        82 li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a  161 (514)
                      .-..|...|++.           .+..++-.+..+|-+.|+.++|..+++++.+.. +-|....+.+...++.. ++++|
T Consensus       102 ve~~~~~i~~~~-----------~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA  168 (906)
T PRK14720        102 VEHICDKILLYG-----------ENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKA  168 (906)
T ss_pred             HHHHHHHHHhhh-----------hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHH
Confidence            222222222211           123367788899999999999999999999876 55777888888888888 99999


Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHc-CCC
Q 040365          162 KQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKD-GVK  240 (514)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~  240 (514)
                      .++..++++.               |...+++..+.+++.++..-++.-             .+.-..+.+.+... |..
T Consensus       169 ~~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~~~~~d-------------~d~f~~i~~ki~~~~~~~  220 (906)
T PRK14720        169 ITYLKKAIYR---------------FIKKKQYVGIEEIWSKLVHYNSDD-------------FDFFLRIERKVLGHREFT  220 (906)
T ss_pred             HHHHHHHHHH---------------HHhhhcchHHHHHHHHHHhcCccc-------------chHHHHHHHHHHhhhccc
Confidence            9999887764               667778888888888875433322             22223333333332 223


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHH
Q 040365          241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLG  290 (514)
Q Consensus       241 p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~  290 (514)
                      --..++..+-..|....+++++..+++.+.+   ..| |.....-+++.|.
T Consensus       221 ~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~---~~~~n~~a~~~l~~~y~  268 (906)
T PRK14720        221 RLVGLLEDLYEPYKALEDWDEVIYILKKILE---HDNKNNKAREELIRFYK  268 (906)
T ss_pred             hhHHHHHHHHHHHhhhhhhhHHHHHHHHHHh---cCCcchhhHHHHHHHHH
Confidence            3345566666777888889999999988863   355 4455555555554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.09  E-value=0.0031  Score=61.23  Aligned_cols=109  Identities=12%  Similarity=0.019  Sum_probs=52.7

Q ss_pred             ccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CCC-hhHHHHHHHHHHhCCChHHHHHH
Q 040365          154 HLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD--LHD-IVSWTAVIMGNALHGNAHDAISL  230 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~d-~~~~~~li~~~~~~g~~~~A~~l  230 (514)
                      ..++++.|+..+..+++.- +.|+.......+.+.+.|+..+|.+.|+++.  .|+ ...+-.+..+|.+.|++.+|+.+
T Consensus       318 ~~~~~d~A~~~l~~L~~~~-P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~  396 (484)
T COG4783         318 LAGQYDEALKLLQPLIAAQ-PDNPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRI  396 (484)
T ss_pred             HhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHH
Confidence            3445555555555544432 3344444444555555555555555555543  222 23344444555555555555555


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040365          231 FEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWS  264 (514)
Q Consensus       231 ~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~  264 (514)
                      +++.... .+-|...|..|..+|...|+..++..
T Consensus       397 L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~a~~  429 (484)
T COG4783         397 LNRYLFN-DPEDPNGWDLLAQAYAELGNRAEALL  429 (484)
T ss_pred             HHHHhhc-CCCCchHHHHHHHHHHHhCchHHHHH
Confidence            5554443 22344455555555555555544443

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.08  E-value=0.00053  Score=61.17  Aligned_cols=152  Identities=16%  Similarity=0.125  Sum_probs=80.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccC
Q 040365          181 SSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAG  257 (514)
Q Consensus       181 ~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g  257 (514)
                      ..+-..|.-.|+-+.+..+.....   ..|....+..+....+.|++.+|+..|++.... -+||..+++.+.-+|.+.|
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~G  148 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQLG  148 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHcc
Confidence            334444555555555555554432   224344444555566666666666666665543 2445556666666666666


Q ss_pred             CHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHHHHHHHH
Q 040365          258 LIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMHAG--PTENVWLTLLSACRVHKNVELAGKVA  334 (514)
Q Consensus       258 ~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~ll~~~~~~~~~~~a~~~~  334 (514)
                      ++++|..-|.+..+   +.| ++..++.|.-.|.-.|+++.|..++......  .|..+-..|.-+....|++++|+.+.
T Consensus       149 r~~~Ar~ay~qAl~---L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~  225 (257)
T COG5010         149 RFDEARRAYRQALE---LAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIA  225 (257)
T ss_pred             ChhHHHHHHHHHHH---hccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhc
Confidence            66666666655543   233 3344455555555556666666655554311  24455555555555666666665554


Q ss_pred             HH
Q 040365          335 EK  336 (514)
Q Consensus       335 ~~  336 (514)
                      ..
T Consensus       226 ~~  227 (257)
T COG5010         226 VQ  227 (257)
T ss_pred             cc
Confidence            44

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.08  E-value=0.0036  Score=65.66  Aligned_cols=128  Identities=15%  Similarity=0.168  Sum_probs=86.0

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHh-----CC--CCCCHHH
Q 040365          242 NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISN-----MH--AGPTENV  313 (514)
Q Consensus       242 ~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~-----m~--~~p~~~~  313 (514)
                      +..+|..+.-.|....+++.|...|....   .+.| +...|..........|+.-++..+|..     +.  .-|+..-
T Consensus       849 ~~~~W~NlgvL~l~n~d~E~A~~af~~~q---SLdP~nl~~WlG~Ali~eavG~ii~~~~lfaHs~el~~~~gka~~f~Y  925 (1238)
T KOG1127|consen  849 CHCQWLNLGVLVLENQDFEHAEPAFSSVQ---SLDPLNLVQWLGEALIPEAVGRIIERLILFAHSDELCSKEGKAKKFQY  925 (1238)
T ss_pred             chhheeccceeEEecccHHHhhHHHHhhh---hcCchhhHHHHHHHHhHHHHHHHHHHHHHHHhhHHhhccccccchhhH
Confidence            34455555555666778888888888764   5666 556665555555667888888887764     11  1256666


Q ss_pred             HHHHHHHHHhcCCHHHHHHHH----------HHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          314 WLTLLSACRVHKNVELAGKVA----------EKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       314 ~~~ll~~~~~~~~~~~a~~~~----------~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      |..-..-...+|+.++-+...          ++...-.|+...+|...+...-+.+.+++|.....+..
T Consensus       926 w~c~te~h~~Ng~~e~~I~t~~ki~sAs~al~~yf~~~p~~~fAy~~~gstlEhL~ey~~a~ela~Rli  994 (1238)
T KOG1127|consen  926 WLCATEIHLQNGNIEESINTARKISSASLALSYYFLGHPQLCFAYAANGSTLEHLEEYRAALELATRLI  994 (1238)
T ss_pred             HHHHHHHHHhccchHHHHHHhhhhhhhHHHHHHHHhcCcchhHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence            666555566677666554443          44444568888899998888888888888888776653

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

Probab=98.06  E-value=0.00017  Score=70.18  Aligned_cols=127  Identities=14%  Similarity=0.124  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccC
Q 040365          178 FIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAG  257 (514)
Q Consensus       178 ~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g  257 (514)
                      ....+|+..+...++++.|..+|+++.+.+...+..++..+...++..+|++++++..... +-|...+..-...|.+.+
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~~pev~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~k~  248 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcC
Confidence            3445566677778899999999999987777677778888888888899999999888642 224455555556688889


Q ss_pred             CHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCCCC
Q 040365          258 LIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMHAG  308 (514)
Q Consensus       258 ~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  308 (514)
                      +.+.|..+.+++.   ...| +..+|..|..+|...|++++|+..++.+|..
T Consensus       249 ~~~lAL~iAk~av---~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm~  297 (395)
T PF09295_consen  249 KYELALEIAKKAV---ELSPSEFETWYQLAECYIQLGDFENALLALNSCPML  297 (395)
T ss_pred             CHHHHHHHHHHHH---HhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcCC
Confidence            9999999999886   4467 5678999999999999999999999988744

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

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

Probab=98.05  E-value=0.00086  Score=68.60  Aligned_cols=240  Identities=15%  Similarity=0.131  Sum_probs=138.2

Q ss_pred             CchhHHHHHHH--HHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHC-C--------CCCCH
Q 040365           74 ANVCIGSSLIN--MYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIA-K--------IKPRH  142 (514)
Q Consensus        74 ~~~~~~~~li~--~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g--------~~p~~  142 (514)
                      -|..+--++++  .|..-|++|.|.+-.+.+.  +...|..|.+.+.+..+.+-|.-.+-.|... |        -.|+ 
T Consensus       724 Cd~~TRkaml~FSfyvtiG~MD~AfksI~~Ik--S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-  800 (1416)
T KOG3617|consen  724 CDESTRKAMLDFSFYVTIGSMDAAFKSIQFIK--SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-  800 (1416)
T ss_pred             cCHHHHHhhhceeEEEEeccHHHHHHHHHHHh--hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-
Confidence            35555555553  4566677777776666554  3456777777777777776666555554321 0        1122 


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC-ChhHHHHHHHHHHhC
Q 040365          143 VSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH-DIVSWTAVIMGNALH  221 (514)
Q Consensus       143 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~-d~~~~~~li~~~~~~  221 (514)
                      .+=.-+.-....+|.+++|+.++.+..+..         .|=..|-..|.+++|.++-+.=..- =..||.....-+-..
T Consensus       801 e~eakvAvLAieLgMlEeA~~lYr~ckR~D---------LlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear  871 (1416)
T KOG3617|consen  801 EDEAKVAVLAIELGMLEEALILYRQCKRYD---------LLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEAR  871 (1416)
T ss_pred             chhhHHHHHHHHHhhHHHHHHHHHHHHHHH---------HHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhh
Confidence            111122222346777888888887766543         3345566677888877765432211 113455555555556


Q ss_pred             CChHHHHHHHHHH----------HHcC---------CCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHH
Q 040365          222 GNAHDAISLFEQM----------EKDG---------VKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHY  282 (514)
Q Consensus       222 g~~~~A~~l~~~m----------~~~g---------~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~  282 (514)
                      ++.+.|++.|++-          ....         -+.|..-|..-....-..|+.+.|+.++... ++         |
T Consensus       872 ~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A-~D---------~  941 (1416)
T KOG3617|consen  872 RDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSA-KD---------Y  941 (1416)
T ss_pred             ccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHh-hh---------h
Confidence            6777777666542          2211         1123344444555556678888888888766 32         4


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040365          283 AAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIF  338 (514)
Q Consensus       283 ~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  338 (514)
                      -+++...+-.|+.++|-++-++-.   |......|..-|...|++.+|..+|-++.
T Consensus       942 fs~VrI~C~qGk~~kAa~iA~esg---d~AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  942 FSMVRIKCIQGKTDKAARIAEESG---DKAACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             hhheeeEeeccCchHHHHHHHhcc---cHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            566666666777777776666543   45555556666777777777766665543

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

Probab=98.04  E-value=5.6e-06  Score=48.86  Aligned_cols=31  Identities=32%  Similarity=0.659  Sum_probs=28.2

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCC
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNL   37 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~   37 (514)
                      ++||+||++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            5899999999999999999999999998774

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.03  E-value=0.0057  Score=54.77  Aligned_cols=134  Identities=11%  Similarity=0.036  Sum_probs=67.2

Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH
Q 040365          165 HGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV  244 (514)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~  244 (514)
                      .+.+.......+......-...|.+.|++++|.+.......-+....  =+..+.+..+.+-|...+++|.+-   -+..
T Consensus        96 ~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~~lE~~Al--~VqI~lk~~r~d~A~~~lk~mq~i---ded~  170 (299)
T KOG3081|consen   96 YELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGENLEAAAL--NVQILLKMHRFDLAEKELKKMQQI---DEDA  170 (299)
T ss_pred             HHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccchHHHHHH--HHHHHHHHHHHHHHHHHHHHHHcc---chHH
Confidence            33343333333333333334456667777777776666332222222  233344555666677777777652   2445


Q ss_pred             HHHHHHHHHHc----cCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          245 AFVAVLTACSH----AGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       245 t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      |.+.|..++.+    .+.+..|.-+|++|..  ...|++.+.+...-+....|++++|..++++.
T Consensus       171 tLtQLA~awv~la~ggek~qdAfyifeE~s~--k~~~T~~llnG~Av~~l~~~~~eeAe~lL~ea  233 (299)
T KOG3081|consen  171 TLTQLAQAWVKLATGGEKIQDAFYIFEELSE--KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEA  233 (299)
T ss_pred             HHHHHHHHHHHHhccchhhhhHHHHHHHHhc--ccCCChHHHccHHHHHHHhcCHHHHHHHHHHH
Confidence            55555555432    3345556666665532  23445544444444445555555555555544

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

Probab=97.98  E-value=0.017  Score=55.07  Aligned_cols=104  Identities=14%  Similarity=0.183  Sum_probs=61.3

Q ss_pred             HHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040365          184 LDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAW  263 (514)
Q Consensus       184 i~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  263 (514)
                      |.-+...|+...|.++-.+..-||..-|...+.+|+..++|++-..+...      +-.++-|..++.+|...|...+|.
T Consensus       184 i~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~~~~~~~eA~  257 (319)
T PF04840_consen  184 IRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACLKYGNKKEAS  257 (319)
T ss_pred             HHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHHHCCCHHHHH
Confidence            34445566666676666666666666677777777777776655544321      112355666666666666666666


Q ss_pred             HHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          264 SYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       264 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  304 (514)
                      .+...+           .+..-+.+|.++|++.+|.+.--+
T Consensus       258 ~yI~k~-----------~~~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  258 KYIPKI-----------PDEERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             HHHHhC-----------ChHHHHHHHHHCCCHHHHHHHHHH
Confidence            665542           113445666666666666555433

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

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

Probab=97.89  E-value=1.6e-05  Score=46.85  Aligned_cols=31  Identities=26%  Similarity=0.638  Sum_probs=24.5

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHHHHcCC
Q 040365          209 VSWTAVIMGNALHGNAHDAISLFEQMEKDGV  239 (514)
Q Consensus       209 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~  239 (514)
                      ++||++|++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4688888888888888888888888887664

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.87  E-value=0.051  Score=56.82  Aligned_cols=68  Identities=18%  Similarity=0.171  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHhcCCH---HHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCC
Q 040365          313 VWLTLLSACRVHKNV---ELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTP  380 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~---~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~  380 (514)
                      +-+.|+..|++.++.   -+|+-+++......|.|..+-..|+.+|.-.|-...|.++++.|.-+.|..+.
T Consensus       438 av~~Lid~~rktnd~~~l~eaI~LLE~glt~s~hnf~~KLlLiriY~~lGa~p~a~~~y~tLdIK~IQ~DT  508 (932)
T KOG2053|consen  438 AVNHLIDLWRKTNDLTDLFEAITLLENGLTKSPHNFQTKLLLIRIYSYLGAFPDAYELYKTLDIKNIQTDT  508 (932)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHhhcCCccHHHHHHHHHHHHHhcCChhHHHHHHhcchHHhhhcc
Confidence            346778889888875   45677777777888999999999999999999999999999999777766554

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.85  E-value=0.0034  Score=56.17  Aligned_cols=244  Identities=11%  Similarity=0.002  Sum_probs=143.0

Q ss_pred             HHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCH
Q 040365          114 IAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNI  193 (514)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~  193 (514)
                      |+-+.-.|.+..++..-......  +-+..+-.-+-++|...|......   ..+.... .|.......+......-++.
T Consensus        15 iRn~fY~Gnyq~~ine~~~~~~~--~~~~e~d~y~~raylAlg~~~~~~---~eI~~~~-~~~lqAvr~~a~~~~~e~~~   88 (299)
T KOG3081|consen   15 IRNYFYLGNYQQCINEAEKFSSS--KTDVELDVYMYRAYLALGQYQIVI---SEIKEGK-ATPLQAVRLLAEYLELESNK   88 (299)
T ss_pred             HHHHHHhhHHHHHHHHHHhhccc--cchhHHHHHHHHHHHHcccccccc---ccccccc-CChHHHHHHHHHHhhCcchh
Confidence            34445567777776654443322  233344444556666666543221   1222222 23333322222222223333


Q ss_pred             HHH-HHHHHhCCCCCh---hHHH-HHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040365          194 RLA-RCIFDKMDLHDI---VSWT-AVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNS  268 (514)
Q Consensus       194 ~~A-~~~~~~m~~~d~---~~~~-~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~  268 (514)
                      ++- .++.+.+..+..   .+|. .-...|...|++++|++..+...      +......=+....+..+++-|.+.++.
T Consensus        89 ~~~~~~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~~~lk~  162 (299)
T KOG3081|consen   89 KSILASLYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAEKELKK  162 (299)
T ss_pred             HHHHHHHHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            332 233344432221   1222 22345778899999998887621      222222223345567788889998888


Q ss_pred             hHHhcCCCCCHhHHHHHHHHH----HhcCCHHHHHHHHHhCCC--CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          269 MTKDYGIAPSFEHYAAVADLL----GRAGKLQEAYEFISNMHA--GPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       269 m~~~~~~~p~~~~~~~li~~~----~~~g~~~~A~~~~~~m~~--~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      |..   + .+-.+.+-|..++    .-.+.+.+|.-+|++|..  .|+..+.+-...++...|++++|+.+++.++..++
T Consensus       163 mq~---i-ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~  238 (299)
T KOG3081|consen  163 MQQ---I-DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDA  238 (299)
T ss_pred             HHc---c-chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccC
Confidence            853   2 2334455454444    445678899999999864  48888888888899999999999999999999999


Q ss_pred             CCcchHHHHHHHHHHccChhHH-HHHHHHHHh
Q 040365          343 NNMGAYVILSNTYAAARRWKDA-ASLRVFMRN  373 (514)
Q Consensus       343 ~~~~~~~~l~~~~~~~g~~~~a-~~~~~~m~~  373 (514)
                      .++.+...++-.-...|.-.++ .+...+++.
T Consensus       239 ~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~  270 (299)
T KOG3081|consen  239 KDPETLANLIVLALHLGKDAEVTERNLSQLKL  270 (299)
T ss_pred             CCHHHHHHHHHHHHHhCCChHHHHHHHHHHHh
Confidence            8888888888877777776544 344555543

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

Probab=97.85  E-value=0.00053  Score=56.76  Aligned_cols=87  Identities=8%  Similarity=-0.101  Sum_probs=38.3

Q ss_pred             HHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChH
Q 040365          149 MPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAH  225 (514)
Q Consensus       149 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~  225 (514)
                      ...+...|++++|.+.+..+...+ +.+...+..+...|.+.|++++|...|+...   ..+...|..+...|...|+++
T Consensus        24 a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~~  102 (135)
T TIGR02552        24 AYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEPE  102 (135)
T ss_pred             HHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCHH
Confidence            333444444444444444444432 2334444444444444444444444444332   223333444444444444555


Q ss_pred             HHHHHHHHHHH
Q 040365          226 DAISLFEQMEK  236 (514)
Q Consensus       226 ~A~~l~~~m~~  236 (514)
                      +|+..|++..+
T Consensus       103 ~A~~~~~~al~  113 (135)
T TIGR02552       103 SALKALDLAIE  113 (135)
T ss_pred             HHHHHHHHHHH
Confidence            55554444444

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

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

Probab=97.83  E-value=0.00084  Score=56.41  Aligned_cols=114  Identities=20%  Similarity=0.124  Sum_probs=55.6

Q ss_pred             cCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCCCC-CCH----HHHHHHHHHHHhcCCHHH
Q 040365          256 AGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMHAG-PTE----NVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       256 ~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~----~~~~~ll~~~~~~~~~~~  329 (514)
                      .++...+...++.+.++++-.| .....-.+...+...|++++|...|+..... ||.    .....|...+...|++++
T Consensus        24 ~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~  103 (145)
T PF09976_consen   24 AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDE  103 (145)
T ss_pred             CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHH
Confidence            4555555555555544422221 1222223344455556666665555554311 222    123334455556666666


Q ss_pred             HHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHH
Q 040365          330 AGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVF  370 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~  370 (514)
                      |+..++.. ...+..+..+..++++|.+.|++++|...|+.
T Consensus       104 Al~~L~~~-~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen  104 ALATLQQI-PDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHhc-cCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            66655442 11222344555666666666666666666653

>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=97.82  E-value=0.00026  Score=53.79  Aligned_cols=92  Identities=22%  Similarity=0.260  Sum_probs=72.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHcc
Q 040365          282 YAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR  359 (514)
Q Consensus       282 ~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  359 (514)
                      +..+...+...|++++|.+.+++.. ..| +...+..+...+...++++.|...+++.....|.+...+..++.++...|
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKLG   82 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHH
Confidence            4456666777888888888887753 223 44667777888888888999999999988888888888888888999999


Q ss_pred             ChhHHHHHHHHHHh
Q 040365          360 RWKDAASLRVFMRN  373 (514)
Q Consensus       360 ~~~~a~~~~~~m~~  373 (514)
                      ++++|...+....+
T Consensus        83 ~~~~a~~~~~~~~~   96 (100)
T cd00189          83 KYEEALEAYEKALE   96 (100)
T ss_pred             hHHHHHHHHHHHHc
Confidence            99999888877654

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.81  E-value=0.002  Score=57.14  Aligned_cols=181  Identities=16%  Similarity=0.118  Sum_probs=124.9

Q ss_pred             cCCHHHHHHHHHhCC--------CCChh-HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHH-HHHHHccCCH
Q 040365          190 CGNIRLARCIFDKMD--------LHDIV-SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAV-LTACSHAGLI  259 (514)
Q Consensus       190 ~g~~~~A~~~~~~m~--------~~d~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l-l~a~~~~g~~  259 (514)
                      ..+.++..+++.++.        .++.. .|-.++-+....|+.+.|...++++... + |.+.-...+ ..-+-..|.+
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~-f-p~S~RV~~lkam~lEa~~~~  102 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDR-F-PGSKRVGKLKAMLLEATGNY  102 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHh-C-CCChhHHHHHHHHHHHhhch
Confidence            356777777777764        22332 3444455566778888888888888775 2 443221111 1123456888


Q ss_pred             HHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040365          260 DKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEK  336 (514)
Q Consensus       260 ~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  336 (514)
                      ++|.++++.+..+   .| |..+|-.=+.+.-..|+--+|++-+.+..  +..|...|.-|...|...|+++.|.-.+++
T Consensus       103 ~~A~e~y~~lL~d---dpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE  179 (289)
T KOG3060|consen  103 KEAIEYYESLLED---DPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEE  179 (289)
T ss_pred             hhHHHHHHHHhcc---CcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHH
Confidence            8999999888765   35 56666666666666777667776655542  346888899999999999999999999999


Q ss_pred             HHhcCCCCcchHHHHHHHHHHcc---ChhHHHHHHHHHHhCC
Q 040365          337 IFMIDPNNMGAYVILSNTYAAAR---RWKDAASLRVFMRNKG  375 (514)
Q Consensus       337 ~~~~~p~~~~~~~~l~~~~~~~g---~~~~a~~~~~~m~~~g  375 (514)
                      ++-..|.++..+..++..+.-.|   +.+-|++.+.+..+..
T Consensus       180 ~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~  221 (289)
T KOG3060|consen  180 LLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLN  221 (289)
T ss_pred             HHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhC
Confidence            98888988888888888876555   4666777777766543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.73  E-value=0.00084  Score=53.97  Aligned_cols=100  Identities=15%  Similarity=0.089  Sum_probs=50.5

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC----HHHHHHHHHH
Q 040365          247 VAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT----ENVWLTLLSA  320 (514)
Q Consensus       247 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~----~~~~~~ll~~  320 (514)
                      ..+...+...|++++|...|..+...+.-.| ....+..+...+.+.|++++|.+.++.+. ..|+    ..++..+..+
T Consensus         6 ~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~   85 (119)
T TIGR02795         6 YDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMS   85 (119)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHH
Confidence            3344444555555555555555543321111 12334445555555555555555555442 1122    3345555556


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcc
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMG  346 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~  346 (514)
                      +...|+.+.|...++++++..|++..
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~p~~~~  111 (119)
T TIGR02795        86 LQELGDKEKAKATLQQVIKRYPGSSA  111 (119)
T ss_pred             HHHhCChHHHHHHHHHHHHHCcCChh
Confidence            66666666666666666666665543

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.72  E-value=0.00013  Score=52.33  Aligned_cols=64  Identities=23%  Similarity=0.219  Sum_probs=58.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHcc-ChhHHHHHHHHHHh
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR-RWKDAASLRVFMRN  373 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g-~~~~a~~~~~~m~~  373 (514)
                      ++.+|..+...+...|++++|+..|+++++.+|+++..|..++.+|...| ++++|.+.+++..+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            56788999999999999999999999999999999999999999999999 79999999987654

...

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.69  E-value=7.3e-05  Score=56.18  Aligned_cols=78  Identities=15%  Similarity=0.215  Sum_probs=48.1

Q ss_pred             cCCHHHHHHHHHhCC-CCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHH
Q 040365          292 AGKLQEAYEFISNMH-AGP---TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASL  367 (514)
Q Consensus       292 ~g~~~~A~~~~~~m~-~~p---~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~  367 (514)
                      .|++++|+.+++++. ..|   +...|..+..++.+.|++++|..++++ .+.+|.+......++.+|.+.|++++|.++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPSNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHCHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            355666666666552 112   344555566777777777777777776 555555555666667777777777777777


Q ss_pred             HHH
Q 040365          368 RVF  370 (514)
Q Consensus       368 ~~~  370 (514)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            764

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.68  E-value=0.011  Score=52.54  Aligned_cols=191  Identities=18%  Similarity=0.206  Sum_probs=138.7

Q ss_pred             ccCChHHHHHHHHHHHH---cC-CCCcH-HHHHHHHHHHHhcCCHHHHHHHHHhCCCC-----ChhHHHHHHHHHHhCCC
Q 040365          154 HLTTLHLGKQLHGCIIR---NG-FDDNM-FIASSLLDMYAKCGNIRLARCIFDKMDLH-----DIVSWTAVIMGNALHGN  223 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~---~~-~~~~~-~~~~~li~~y~k~g~~~~A~~~~~~m~~~-----d~~~~~~li~~~~~~g~  223 (514)
                      ...+.++..+++..++.   .| ..++. .++..++-+...+|+.+.|...++.+..+     -+.-..+|  -+-..|+
T Consensus        24 ~~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam--~lEa~~~  101 (289)
T KOG3060|consen   24 TVRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAM--LLEATGN  101 (289)
T ss_pred             cccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHH--HHHHhhc
Confidence            44567888888887764   24 44554 45666777788899999999999887522     22222222  2345799


Q ss_pred             hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          224 AHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFIS  303 (514)
Q Consensus       224 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~  303 (514)
                      +++|+++++.+.+.. +.|.+++.-=+...-..|+--+|++-+....+.  +..|.+.|.-+.+.|...|++++|.--++
T Consensus       102 ~~~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  102 YKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK--FMNDQEAWHELAEIYLSEGDFEKAAFCLE  178 (289)
T ss_pred             hhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH--hcCcHHHHHHHHHHHHhHhHHHHHHHHHH
Confidence            999999999999875 446677776666666677777888888877663  46689999999999999999999999999


Q ss_pred             hCC-CCC-CHHHHHHHHHHHH---hcCCHHHHHHHHHHHHhcCCCCcchHH
Q 040365          304 NMH-AGP-TENVWLTLLSACR---VHKNVELAGKVAEKIFMIDPNNMGAYV  349 (514)
Q Consensus       304 ~m~-~~p-~~~~~~~ll~~~~---~~~~~~~a~~~~~~~~~~~p~~~~~~~  349 (514)
                      ++. ..| +...+..+...+-   ...+.+.+...+.+.+++.|.+...+.
T Consensus       179 E~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~~~~ral~  229 (289)
T KOG3060|consen  179 ELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNPKNLRALF  229 (289)
T ss_pred             HHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhChHhHHHHH
Confidence            874 345 5555666666543   344788899999999999986554433

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

Probab=97.67  E-value=0.0027  Score=53.34  Aligned_cols=123  Identities=11%  Similarity=0.118  Sum_probs=79.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChh---hHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCch--hHHHHH
Q 040365            8 SWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSF---TLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANV--CIGSSL   82 (514)
Q Consensus         8 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~---t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~--~~~~~l   82 (514)
                      .|..++..+. .++...+...++.+.... +.+.+   ..-.+...+...|++++|...++.++.....++.  ...-.|
T Consensus        14 ~y~~~~~~~~-~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   14 LYEQALQALQ-AGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHHH-CCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            4666666664 677777777777777653 22212   2223445666778888888888888776522221  234446


Q ss_pred             HHHHHHCCCHHHHHHHHccCCCC--ChhHHHHHHHHHHHCCChhHHHHHHHH
Q 040365           83 INMYAKCARVEDSHRLFCLLPVK--DAISWNSIIAGCVQNGLFDEGLKFFRQ  132 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~~~--d~~~~~~li~~~~~~g~~~~A~~l~~~  132 (514)
                      ...+...|++++|+..++..+.+  ....+......|.+.|+.++|...|++
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            67777788888888888765433  334555667777788888888877765

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.62  E-value=0.00099  Score=53.55  Aligned_cols=96  Identities=18%  Similarity=0.081  Sum_probs=81.0

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---cchHHHH
Q 040365          280 EHYAAVADLLGRAGKLQEAYEFISNMH-AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN---MGAYVIL  351 (514)
Q Consensus       280 ~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~---~~~~~~l  351 (514)
                      ..+..++..+.+.|++++|.+.++.+. ..|+    ...+..+..++...|+++.|...++.+....|++   +.++..+
T Consensus         3 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         3 EAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            456677888899999999999998874 2233    3467778899999999999999999999988775   4578889


Q ss_pred             HHHHHHccChhHHHHHHHHHHhCC
Q 040365          352 SNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       352 ~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      +.++.+.|++++|.+.++.+.+..
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHHHHHC
Confidence            999999999999999999998764

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.

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=97.60  E-value=0.061  Score=50.09  Aligned_cols=289  Identities=13%  Similarity=0.109  Sum_probs=203.9

Q ss_pred             HHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHH---HHHHHCCChhHHHHHHHHHHHCCCCCCHHHHH-HHHHHHhccC
Q 040365           81 SLINMYAKCARVEDSHRLFCLLPVKDAISWNSII---AGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFS-SIMPACAHLT  156 (514)
Q Consensus        81 ~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li---~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~-~ll~~~~~~~  156 (514)
                      -|-+.+...|++.+|+.-|....+-|+..|-++.   ..|...|+..-|+.=|.+..+  ++||-..-. .-...+.+.|
T Consensus        43 ElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVle--lKpDF~~ARiQRg~vllK~G  120 (504)
T KOG0624|consen   43 ELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLE--LKPDFMAARIQRGVVLLKQG  120 (504)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHh--cCccHHHHHHHhchhhhhcc
Confidence            3445556678888888888888777777776664   467778888888888887776  467744322 1123456788


Q ss_pred             ChHHHHHHHHHHHHcCCCC--cHH------------HHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHH
Q 040365          157 TLHLGKQLHGCIIRNGFDD--NMF------------IASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNA  219 (514)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~--~~~------------~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~  219 (514)
                      .++.|..=|+.+++.....  ...            .....+..+...|+...|+.....+.   .-|+..+..-..+|.
T Consensus       121 ele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~Wda~l~~~Rakc~i  200 (504)
T KOG0624|consen  121 ELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQPWDASLRQARAKCYI  200 (504)
T ss_pred             cHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCcchhHHHHHHHHHHH
Confidence            8888888888888764211  111            11223345667889999988888775   447788888889999


Q ss_pred             hCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHh----HHHHH---H------
Q 040365          220 LHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFE----HYAAV---A------  286 (514)
Q Consensus       220 ~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~----~~~~l---i------  286 (514)
                      ..|++..|+.=++...+.. .-|..++--+-..+...|+.+.++...++-.   .+.|+-.    +|-.|   +      
T Consensus       201 ~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECL---KldpdHK~Cf~~YKklkKv~K~les~  276 (504)
T KOG0624|consen  201 AEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECL---KLDPDHKLCFPFYKKLKKVVKSLESA  276 (504)
T ss_pred             hcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHH---ccCcchhhHHHHHHHHHHHHHHHHHH
Confidence            9999999988777665532 2244566666677788899988888777664   4566532    22221   1      


Q ss_pred             HHHHhcCCHHHHHHHHHh-CCCCCCH-----HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          287 DLLGRAGKLQEAYEFISN-MHAGPTE-----NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       287 ~~~~~~g~~~~A~~~~~~-m~~~p~~-----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      ....+.+++.++.+-.+. |...|..     ..+..+-.+++..+++.+|++...++++.+|+|..++.--+.+|.-...
T Consensus       277 e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~d~~dv~~l~dRAeA~l~dE~  356 (504)
T KOG0624|consen  277 EQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDIDPDDVQVLCDRAEAYLGDEM  356 (504)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhHH
Confidence            123455677777666654 3444542     2344555677889999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHhCC
Q 040365          361 WKDAASLRVFMRNKG  375 (514)
Q Consensus       361 ~~~a~~~~~~m~~~g  375 (514)
                      |++|..-|+...+-+
T Consensus       357 YD~AI~dye~A~e~n  371 (504)
T KOG0624|consen  357 YDDAIHDYEKALELN  371 (504)
T ss_pred             HHHHHHHHHHHHhcC
Confidence            999999999887654

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.53  E-value=0.00034  Score=49.51  Aligned_cols=58  Identities=19%  Similarity=0.155  Sum_probs=43.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          317 LLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       317 ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +...+...|++++|+..++++++..|.++..+..++.++...|++++|...+++..+.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3456677788888888888888888888888888888888888888888888777543

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.53  E-value=0.013  Score=58.75  Aligned_cols=233  Identities=14%  Similarity=0.139  Sum_probs=131.2

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCCCC-----------ChhhHHHHHHHHhCCCChHHHH--HHHHHHHHhCCC
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKP-----------DSFTLSSVLPIFADYVDVIKGK--EIHGYAIRHGLD   73 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-----------~~~t~~~ll~~~~~~~~~~~a~--~~~~~~~~~g~~   73 (514)
                      +.+.+=+--|...|.+++|..+--    .|+.-           +.-.++..=++|.+..+..--+  .-++++.+.|-.
T Consensus       557 vp~~~~m~q~Ieag~f~ea~~iac----lgVv~~DW~~LA~~ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~  632 (1081)
T KOG1538|consen  557 VPQSAPMYQYIERGLFKEAYQIAC----LGVTDTDWRELAMEALEALDFETARKAYIRVRDLRYLELISELEERKKRGET  632 (1081)
T ss_pred             ccccccchhhhhccchhhhhcccc----cceecchHHHHHHHHHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCC
Confidence            344444556777787777765421    11111           1222344445555555544322  223455566655


Q ss_pred             CchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHh
Q 040365           74 ANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACA  153 (514)
Q Consensus        74 ~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~  153 (514)
                      |+...   +...++-.|.+.+|-++|.                  ++|....|+++|..|+--.          ...-+.
T Consensus       633 P~~iL---lA~~~Ay~gKF~EAAklFk------------------~~G~enRAlEmyTDlRMFD----------~aQE~~  681 (1081)
T KOG1538|consen  633 PNDLL---LADVFAYQGKFHEAAKLFK------------------RSGHENRALEMYTDLRMFD----------YAQEFL  681 (1081)
T ss_pred             chHHH---HHHHHHhhhhHHHHHHHHH------------------HcCchhhHHHHHHHHHHHH----------HHHHHh
Confidence            66543   4455666788888888875                  4566667777776664311          122333


Q ss_pred             ccCChHHHHHHHHHHHHc--C-CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHH
Q 040365          154 HLTTLHLGKQLHGCIIRN--G-FDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISL  230 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~--~-~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l  230 (514)
                      ..|+.++-+.+..+-.+-  . -+|.     +-..++...|+.++|..+                  .+.+|..+-++++
T Consensus       682 ~~g~~~eKKmL~RKRA~WAr~~kePk-----aAAEmLiSaGe~~KAi~i------------------~~d~gW~d~lidI  738 (1081)
T KOG1538|consen  682 GSGDPKEKKMLIRKRADWARNIKEPK-----AAAEMLISAGEHVKAIEI------------------CGDHGWVDMLIDI  738 (1081)
T ss_pred             hcCChHHHHHHHHHHHHHhhhcCCcH-----HHHHHhhcccchhhhhhh------------------hhcccHHHHHHHH
Confidence            444444444333322111  0 1222     234566677888877654                  3456666666666


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCC-CC
Q 040365          231 FEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHA-GP  309 (514)
Q Consensus       231 ~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p  309 (514)
                      -+++-.    .+..+...+..-+-+...+..|-++|..|-.          ...++++....+++++|..+-++.|. .|
T Consensus       739 ~rkld~----~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD----------~ksiVqlHve~~~W~eAFalAe~hPe~~~  804 (1081)
T KOG1538|consen  739 ARKLDK----AEREPLLLCATYLKKLDSPGLAAEIFLKMGD----------LKSLVQLHVETQRWDEAFALAEKHPEFKD  804 (1081)
T ss_pred             Hhhcch----hhhhHHHHHHHHHhhccccchHHHHHHHhcc----------HHHHhhheeecccchHhHhhhhhCccccc
Confidence            665533    2445555566666667777888888887732          24577888888999999998888873 34


Q ss_pred             CH
Q 040365          310 TE  311 (514)
Q Consensus       310 ~~  311 (514)
                      |+
T Consensus       805 dV  806 (1081)
T KOG1538|consen  805 DV  806 (1081)
T ss_pred             cc
Confidence            54

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.51  E-value=0.12  Score=51.17  Aligned_cols=159  Identities=12%  Similarity=0.136  Sum_probs=99.2

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHH
Q 040365          210 SWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADL  288 (514)
Q Consensus       210 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~  288 (514)
                      +|-..+..-.+..-...|..+|.+..+.+..+ +.....+++.-++ .++.+.|.++|+.=.+.+|-.  +.--...++-
T Consensus       368 v~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d~--p~yv~~Yldf  444 (656)
T KOG1914|consen  368 VYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGDS--PEYVLKYLDF  444 (656)
T ss_pred             ehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCCC--hHHHHHHHHH
Confidence            45556666566666777888888888777766 4455555555443 467778888887666654433  3344566777


Q ss_pred             HHhcCCHHHHHHHHHhCCCC---C--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC----cchHHHHHHHHHHcc
Q 040365          289 LGRAGKLQEAYEFISNMHAG---P--TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN----MGAYVILSNTYAAAR  359 (514)
Q Consensus       289 ~~~~g~~~~A~~~~~~m~~~---p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~----~~~~~~l~~~~~~~g  359 (514)
                      +...++-..|..+|++....   |  ...+|..+|.--..-|+...+..+-++....-|.+    ...-..++..|.-.+
T Consensus       445 L~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d  524 (656)
T KOG1914|consen  445 LSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILD  524 (656)
T ss_pred             HHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhcc
Confidence            77778777888888776322   2  34678888887788888888877777766554411    112334555565555


Q ss_pred             ChhHHHHHHHHH
Q 040365          360 RWKDAASLRVFM  371 (514)
Q Consensus       360 ~~~~a~~~~~~m  371 (514)
                      .+..-..-++.|
T Consensus       525 ~~~c~~~elk~l  536 (656)
T KOG1914|consen  525 LYPCSLDELKFL  536 (656)
T ss_pred             cccccHHHHHhh
Confidence            554444444333

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.50  E-value=0.00091  Score=65.31  Aligned_cols=105  Identities=16%  Similarity=0.129  Sum_probs=86.3

Q ss_pred             HHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcC
Q 040365          249 VLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHK  325 (514)
Q Consensus       249 ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~  325 (514)
                      -...+...|++++|+..|+.+.+   ..| +...|..+..+|.+.|++++|+..++++. ..| +...|..+..+|...|
T Consensus         8 ~a~~a~~~~~~~~Ai~~~~~Al~---~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg   84 (356)
T PLN03088          8 KAKEAFVDDDFALAVDLYTQAID---LDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLE   84 (356)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhC
Confidence            35566778999999999999875   355 57788888899999999999999998863 334 6778888999999999


Q ss_pred             CHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          326 NVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                      ++++|+..++++++++|+++.....+..+..
T Consensus        85 ~~~eA~~~~~~al~l~P~~~~~~~~l~~~~~  115 (356)
T PLN03088         85 EYQTAKAALEKGASLAPGDSRFTKLIKECDE  115 (356)
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            9999999999999999998877666655433

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.46  E-value=0.0053  Score=53.25  Aligned_cols=130  Identities=18%  Similarity=0.220  Sum_probs=83.3

Q ss_pred             ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHH
Q 040365          207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN--SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYA  283 (514)
Q Consensus       207 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~  283 (514)
                      ....+..+...+...|++++|+..|++.......|+  ...+..+...+.+.|++++|...+.....   ..| +...+.
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~  110 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE---LNPKQPSALN  110 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcccHHHHH
Confidence            344566677777778888888888888776433332  34666777777788888888888877754   234 455555


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          284 AVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      .+...+...|+...+..-++...                  ..++.|.++++++...+|++   |..+...+...|+
T Consensus       111 ~lg~~~~~~g~~~~a~~~~~~A~------------------~~~~~A~~~~~~a~~~~p~~---~~~~~~~~~~~~~  166 (172)
T PRK02603        111 NIAVIYHKRGEKAEEAGDQDEAE------------------ALFDKAAEYWKQAIRLAPNN---YIEAQNWLKTTGR  166 (172)
T ss_pred             HHHHHHHHcCChHhHhhCHHHHH------------------HHHHHHHHHHHHHHhhCchh---HHHHHHHHHhcCc
Confidence            66666666666655543322211                  12677888888888888875   5555555555443

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.46  E-value=0.0025  Score=62.22  Aligned_cols=100  Identities=14%  Similarity=0.108  Sum_probs=79.0

Q ss_pred             HHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcC
Q 040365          215 IMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAG  293 (514)
Q Consensus       215 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g  293 (514)
                      ...+...|++++|+++|++.++.. +-+...|..+..++.+.|++++|+..++.+..   +.| +...|..+..+|...|
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~---l~P~~~~a~~~lg~~~~~lg   84 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIE---LDPSLAKAYLRKGTACMKLE   84 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---hCcCCHHHHHHHHHHHHHhC
Confidence            455677899999999999999853 22456788888899999999999999998864   456 6778888999999999


Q ss_pred             CHHHHHHHHHhCC-CCCCHHHHHHHH
Q 040365          294 KLQEAYEFISNMH-AGPTENVWLTLL  318 (514)
Q Consensus       294 ~~~~A~~~~~~m~-~~p~~~~~~~ll  318 (514)
                      ++++|...|++.. ..|+......++
T Consensus        85 ~~~eA~~~~~~al~l~P~~~~~~~~l  110 (356)
T PLN03088         85 EYQTAKAALEKGASLAPGDSRFTKLI  110 (356)
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            9999999998863 445544433333

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.40  E-value=0.0069  Score=57.00  Aligned_cols=133  Identities=14%  Similarity=0.202  Sum_probs=97.9

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHH
Q 040365          209 VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTA-CSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       209 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a-~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  287 (514)
                      .+|-.++...-+.+..+.|..+|.+..+.+ ..+...|...... +...++.+.|..+|+...+.+  ..+...|...++
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f--~~~~~~~~~Y~~   78 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKF--PSDPDFWLEYLD   78 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHH--TT-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHH
Confidence            357777877777778888888898887542 2233444444333 334577777999999998764  346677888999


Q ss_pred             HHHhcCCHHHHHHHHHhCCCC-CC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040365          288 LLGRAGKLQEAYEFISNMHAG-PT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN  344 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~~~-p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~  344 (514)
                      .+.+.|+.+.|..+|++.... |.    ..+|...+.--.+.|+.+....+.+++.+.-|.+
T Consensus        79 ~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~~  140 (280)
T PF05843_consen   79 FLIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPED  140 (280)
T ss_dssp             HHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTTS
T ss_pred             HHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhh
Confidence            999999999999999986422 33    3589999999999999999999999999887764

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.

>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=97.39  E-value=0.0017  Score=56.56  Aligned_cols=98  Identities=15%  Similarity=0.268  Sum_probs=77.1

Q ss_pred             HHHHHhC--CCCChhHHHHHHHHHHh-----CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcc-------------
Q 040365          197 RCIFDKM--DLHDIVSWTAVIMGNAL-----HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHA-------------  256 (514)
Q Consensus       197 ~~~~~~m--~~~d~~~~~~li~~~~~-----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~-------------  256 (514)
                      ...|+..  ..+|..+|..++..|.+     .|..+=....++.|.+-|+.-|..+|+.||..+=+.             
T Consensus        34 ~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~  113 (228)
T PF06239_consen   34 EELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFM  113 (228)
T ss_pred             HHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhc
Confidence            4556655  46677788888887765     467778888889999999999999999999876542             


Q ss_pred             ---CCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCH
Q 040365          257 ---GLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKL  295 (514)
Q Consensus       257 ---g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  295 (514)
                         .+-+-|++++++| +++|+-||.+++..|++.+++.+..
T Consensus       114 hyp~Qq~c~i~lL~qM-E~~gV~Pd~Et~~~ll~iFG~~s~p  154 (228)
T PF06239_consen  114 HYPRQQECAIDLLEQM-ENNGVMPDKETEQMLLNIFGRKSHP  154 (228)
T ss_pred             cCcHHHHHHHHHHHHH-HHcCCCCcHHHHHHHHHHhccccHH
Confidence               2356789999999 6679999999999999999877653

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

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

Probab=97.39  E-value=0.0025  Score=49.29  Aligned_cols=79  Identities=13%  Similarity=0.020  Sum_probs=67.2

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHhhCCC-CCChhhHHHHHHHHhCCC--------ChHHHHHHHHHHHHhCCCCchhHHH
Q 040365           10 NTVIVGLARNGLYEEALNIVRQMGNVNL-KPDSFTLSSVLPIFADYV--------DVIKGKEIHGYAIRHGLDANVCIGS   80 (514)
Q Consensus        10 ~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~~~t~~~ll~~~~~~~--------~~~~a~~~~~~~~~~g~~~~~~~~~   80 (514)
                      ...|..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        ++-..+.+++.|+..++.|+..+|+
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            4556677777999999999999999999 999999999999987653        2446778999999999999999999


Q ss_pred             HHHHHHHH
Q 040365           81 SLINMYAK   88 (514)
Q Consensus        81 ~li~~~~~   88 (514)
                      .++..+.+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            99987754

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 [, , ].

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.36  E-value=0.029  Score=55.36  Aligned_cols=125  Identities=14%  Similarity=0.113  Sum_probs=59.4

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--CC-hhHHHHHHHHHH
Q 040365          144 SFSSIMPACAHLTTLHLGKQLHGCIIRNGFDD-NMFIASSLLDMYAKCGNIRLARCIFDKMDL--HD-IVSWTAVIMGNA  219 (514)
Q Consensus       144 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d-~~~~~~li~~~~  219 (514)
                      +|...++.--+..-+..|+.+|.++.+.+..+ ++.++++++.-|+ .++..-|.++|+--.+  +| ..--+..+.-+.
T Consensus       368 v~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d~p~yv~~YldfL~  446 (656)
T KOG1914|consen  368 VYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGDSPEYVLKYLDFLS  446 (656)
T ss_pred             ehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence            34444555555555555555555555554444 5555555555444 3445555555543321  12 222233344444


Q ss_pred             hCCChHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          220 LHGNAHDAISLFEQMEKDGVKPNS--VAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       220 ~~g~~~~A~~l~~~m~~~g~~p~~--~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      ..++-..|..+|++....++.||.  ..|..+|.--+.-|++..+.++-+++
T Consensus       447 ~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~  498 (656)
T KOG1914|consen  447 HLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRR  498 (656)
T ss_pred             HhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence            445555555555555544444332  34445555445555555544444444

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.34  E-value=0.0033  Score=54.50  Aligned_cols=82  Identities=11%  Similarity=0.017  Sum_probs=57.9

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC---C-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHH
Q 040365          279 FEHYAAVADLLGRAGKLQEAYEFISNMH-AGP---T-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSN  353 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p---~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~  353 (514)
                      ...+..+...+...|++++|...|++.. ..|   + ...|..+...+...|+++.|...++++++..|.+...+..++.
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~  114 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAV  114 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHH
Confidence            3445556666666677777777666542 112   1 3567777788888888888888888888888888888888888


Q ss_pred             HHHHccC
Q 040365          354 TYAAARR  360 (514)
Q Consensus       354 ~~~~~g~  360 (514)
                      +|...|+
T Consensus       115 ~~~~~g~  121 (172)
T PRK02603        115 IYHKRGE  121 (172)
T ss_pred             HHHHcCC
Confidence            8877666

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.34  E-value=0.012  Score=60.30  Aligned_cols=64  Identities=17%  Similarity=0.110  Sum_probs=42.1

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +..+|.++.-.....|++++|...++++++++| +..+|..++..|...|+.++|...+++....
T Consensus       419 ~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~p-s~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L  482 (517)
T PRK10153        419 LPRIYEILAVQALVKGKTDEAYQAINKAIDLEM-SWLNYVLLGKVYELKGDNRLAADAYSTAFNL  482 (517)
T ss_pred             ChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            445565555555556777777777777777776 4566777777777777777777777665543

>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=97.33  E-value=0.0031  Score=47.58  Aligned_cols=58  Identities=14%  Similarity=0.114  Sum_probs=27.1

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      |..+...+...|++++|...|++..+.. +.+...+..+...+...+++++|.+.|+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~   60 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKA   60 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3344445555555555555555554431 112233444444444445555555555444

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.32  E-value=0.00039  Score=49.67  Aligned_cols=53  Identities=19%  Similarity=0.257  Sum_probs=42.9

Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ...|++++|+..++++.+.+|++...+..++.+|.+.|++++|.++++.+...
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~   54 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQ   54 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred             hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            45688888888888888888888888888888888888888888888866554

...

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

Probab=97.31  E-value=0.17  Score=48.34  Aligned_cols=111  Identities=15%  Similarity=0.112  Sum_probs=87.4

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRV  323 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~  323 (514)
                      .+.+..+.-|...|....|.++-...    .+ |+...|-..+.+|+..|++++-.++...   +.++.-|..++.+|..
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~F----kv-~dkrfw~lki~aLa~~~~w~eL~~fa~s---kKsPIGyepFv~~~~~  249 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEF----KV-PDKRFWWLKIKALAENKDWDELEKFAKS---KKSPIGYEPFVEACLK  249 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHc----CC-cHHHHHHHHHHHHHhcCCHHHHHHHHhC---CCCCCChHHHHHHHHH
Confidence            34556667777888888877775544    54 7888899999999999999998887654   3456789999999999


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                      .|+..+|.....++         .+..-+.+|.++|+|.+|.+.--+.
T Consensus       250 ~~~~~eA~~yI~k~---------~~~~rv~~y~~~~~~~~A~~~A~~~  288 (319)
T PF04840_consen  250 YGNKKEASKYIPKI---------PDEERVEMYLKCGDYKEAAQEAFKE  288 (319)
T ss_pred             CCCHHHHHHHHHhC---------ChHHHHHHHHHCCCHHHHHHHHHHc
Confidence            99999998888772         2356788899999999998875544

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

>PRK15331 chaperone protein SicA; Provisional

Probab=97.31  E-value=0.0031  Score=52.72  Aligned_cols=88  Identities=16%  Similarity=0.148  Sum_probs=77.0

Q ss_pred             HHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhH
Q 040365          286 ADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKD  363 (514)
Q Consensus       286 i~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  363 (514)
                      .--+-..|++++|..+|+-+-  ..-|..-|..|..+|...++++.|...|.....++++|+.++.....+|...|+.+.
T Consensus        44 Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~~  123 (165)
T PRK15331         44 AYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAK  123 (165)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHH
Confidence            334557899999999998653  334677789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHh
Q 040365          364 AASLRVFMRN  373 (514)
Q Consensus       364 a~~~~~~m~~  373 (514)
                      |...|+...+
T Consensus       124 A~~~f~~a~~  133 (165)
T PRK15331        124 ARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHh
Confidence            9999998876

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=97.29  E-value=0.0047  Score=51.90  Aligned_cols=69  Identities=23%  Similarity=0.288  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH-----hCCCccCC
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR-----NKGMKKTP  380 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~-----~~g~~~~~  380 (514)
                      .+...++..+...|+++.|...+++++..+|.+...|..++.+|...|+..+|.++|+.+.     +.|+.|++
T Consensus        63 ~~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~  136 (146)
T PF03704_consen   63 DALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSP  136 (146)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----H
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCH
Confidence            3556677888899999999999999999999999999999999999999999999999885     34887665

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

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

Probab=97.28  E-value=0.0041  Score=48.09  Aligned_cols=81  Identities=15%  Similarity=0.118  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHHCCChhHHHHHHHHHHHCCC-CCCHHHHHHHHHHHhccC--------ChHHHHHHHHHHHHcCCCCcHHH
Q 040365          109 SWNSIIAGCVQNGLFDEGLKFFRQMLIAKI-KPRHVSFSSIMPACAHLT--------TLHLGKQLHGCIIRNGFDDNMFI  179 (514)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~~~t~~~ll~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~  179 (514)
                      |-...|..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        ++-....+++.|+..++.|+..+
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~et  106 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDET  106 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHH
Confidence            334567777778999999999999999999 899999999999877653        24456778889999999999999


Q ss_pred             HHHHHHHHHh
Q 040365          180 ASSLLDMYAK  189 (514)
Q Consensus       180 ~~~li~~y~k  189 (514)
                      |+.++..+.+
T Consensus       107 Ynivl~~Llk  116 (120)
T PF08579_consen  107 YNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHH
Confidence            9999887765

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 [, , ].

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.28  E-value=0.0035  Score=54.11  Aligned_cols=93  Identities=9%  Similarity=-0.148  Sum_probs=72.4

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHH
Q 040365          279 FEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSN  353 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~  353 (514)
                      ...|..+...+...|++++|...|++.. ..|+    ..+|..+...+...|++++|+..+++++...|....++..++.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~  114 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAV  114 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHH
Confidence            4556666777778888888888887752 2222    3578888899999999999999999999999988888888888


Q ss_pred             HHH-------HccChhHHHHHHHHH
Q 040365          354 TYA-------AARRWKDAASLRVFM  371 (514)
Q Consensus       354 ~~~-------~~g~~~~a~~~~~~m  371 (514)
                      +|.       ..|++++|...+++-
T Consensus       115 i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        115 ICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHHhhHHHHHcccHHHHHHHHHHH
Confidence            888       778888776666544

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.27  E-value=0.0054  Score=57.74  Aligned_cols=139  Identities=11%  Similarity=0.110  Sum_probs=101.2

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHH-HhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPI-FADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~-~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      .+|-.++...-+.+..+.|..+|.+.++.+ .-+...|...... +...++.+.|..+|+..++. ++.+...|..-++.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            578899999999999999999999998643 2233334333333 33356777799999999887 57788889999999


Q ss_pred             HHHCCCHHHHHHHHccCCCC------ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040365           86 YAKCARVEDSHRLFCLLPVK------DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIM  149 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~~------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (514)
                      +.+.|+.+.|+.+|++....      -...|...+.-=.+.|+.+.+.++.+++.+.  -|+..++..++
T Consensus        80 l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~  147 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFS  147 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHH
Confidence            99999999999999987632      3357999999888999999999999888774  44544444443

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.

>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=97.27  E-value=0.011  Score=51.63  Aligned_cols=105  Identities=20%  Similarity=0.271  Sum_probs=76.0

Q ss_pred             CCCHHHHHHHHHHHhc-----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHH
Q 040365          139 KPRHVSFSSIMPACAH-----LTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTA  213 (514)
Q Consensus       139 ~p~~~t~~~ll~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~  213 (514)
                      ..|..+|..++..+.+     .|..+-....+..|.+.|+..|..+|+.|++.+=| |.+- -..+|+.+          
T Consensus        44 ~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK-g~fv-p~n~fQ~~----------  111 (228)
T PF06239_consen   44 AKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK-GKFV-PRNFFQAE----------  111 (228)
T ss_pred             cccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC-CCcc-cccHHHHH----------
Confidence            4566777777777653     46677777888888999999999999999988765 3321 11111111          


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCC
Q 040365          214 VIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGL  258 (514)
Q Consensus       214 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~  258 (514)
                       ..-  ...+-+-|++++++|...|+.||..|+..+++.+.+.+.
T Consensus       112 -F~h--yp~Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  112 -FMH--YPRQQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             -hcc--CcHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence             111  134567899999999999999999999999999977654

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

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.26  E-value=0.0011  Score=49.78  Aligned_cols=80  Identities=21%  Similarity=0.310  Sum_probs=46.1

Q ss_pred             CCChHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHH
Q 040365          221 HGNAHDAISLFEQMEKDGV-KPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~-~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A  298 (514)
                      .|+++.|+.+|+++.+... .|+...+..+..++.+.|++++|..+++..    ...| +....-.+..++.+.|++++|
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~----~~~~~~~~~~~l~a~~~~~l~~y~eA   77 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKL----KLDPSNPDIHYLLARCLLKLGKYEEA   77 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCH----THHHCHHHHHHHHHHHHHHTT-HHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHh----CCCCCCHHHHHHHHHHHHHhCCHHHH
Confidence            4677777777777776432 123444444667777777777777777652    2222 223333446666777777777


Q ss_pred             HHHHHh
Q 040365          299 YEFISN  304 (514)
Q Consensus       299 ~~~~~~  304 (514)
                      .+.+++
T Consensus        78 i~~l~~   83 (84)
T PF12895_consen   78 IKALEK   83 (84)
T ss_dssp             HHHHHH
T ss_pred             HHHHhc
Confidence            776654

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.25  E-value=0.0029  Score=57.69  Aligned_cols=96  Identities=17%  Similarity=0.122  Sum_probs=66.9

Q ss_pred             HHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHH
Q 040365          253 CSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT-ENVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       253 ~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~-~~~~~~ll~~~~~~~~~~~  329 (514)
                      ..+.+++++|+..|...+   .+.| |..-|..=..+|.+.|.++.|++=.+... ..|. ..+|..|..+|...|++++
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 LMKNKDYQEAVDKYTEAI---ELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHhhhHHHHHHHHHHHH---hcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHH
Confidence            445677777777777665   4566 45555556777777787777776665542 3343 4678888888888888888


Q ss_pred             HHHHHHHHHhcCCCCcchHHHH
Q 040365          330 AGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      |++.|++.++++|++......|
T Consensus       168 A~~aykKaLeldP~Ne~~K~nL  189 (304)
T KOG0553|consen  168 AIEAYKKALELDPDNESYKSNL  189 (304)
T ss_pred             HHHHHHhhhccCCCcHHHHHHH
Confidence            8888888888888887444344

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.22  E-value=0.0013  Score=47.79  Aligned_cols=58  Identities=14%  Similarity=0.097  Sum_probs=49.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          318 LSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       318 l~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      -..+.+.++++.|..++++++.++|+++..+...+.+|.+.|++++|.+.++...+.+
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            3567788899999999999999999999999999999999999999999998887554

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.20  E-value=0.0067  Score=55.66  Aligned_cols=103  Identities=17%  Similarity=0.186  Sum_probs=86.3

Q ss_pred             CC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHh---cCCHHHHHHHHHHHHhcCCCCcchHH
Q 040365          276 AP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRV---HKNVELAGKVAEKIFMIDPNNMGAYV  349 (514)
Q Consensus       276 ~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~~~p~~~~~~~  349 (514)
                      .| |.+.|-.|...|.+.|+++.|..-|.+..  ..++...+..+..++..   .....++..++++++.++|.|..+..
T Consensus       152 nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~  231 (287)
T COG4235         152 NPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALS  231 (287)
T ss_pred             CCCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHH
Confidence            45 78999999999999999999999998763  23566677666666533   34568899999999999999999999


Q ss_pred             HHHHHHHHccChhHHHHHHHHHHhCCCcc
Q 040365          350 ILSNTYAAARRWKDAASLRVFMRNKGMKK  378 (514)
Q Consensus       350 ~l~~~~~~~g~~~~a~~~~~~m~~~g~~~  378 (514)
                      .|...+...|++.+|...++.|.+..-.-
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~lp~~  260 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDLLPAD  260 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhcCCCC
Confidence            99999999999999999999999875443

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.20  E-value=0.017  Score=55.09  Aligned_cols=159  Identities=15%  Similarity=0.066  Sum_probs=112.0

Q ss_pred             HHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHH---HH-------
Q 040365          216 MGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYA---AV-------  285 (514)
Q Consensus       216 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~---~l-------  285 (514)
                      .++...|++++|...-....+.. ..+......--.++...++.+.|...|++.+   .+.|+-..-.   .+       
T Consensus       177 ~cl~~~~~~~~a~~ea~~ilkld-~~n~~al~vrg~~~yy~~~~~ka~~hf~qal---~ldpdh~~sk~~~~~~k~le~~  252 (486)
T KOG0550|consen  177 ECLAFLGDYDEAQSEAIDILKLD-ATNAEALYVRGLCLYYNDNADKAINHFQQAL---RLDPDHQKSKSASMMPKKLEVK  252 (486)
T ss_pred             hhhhhcccchhHHHHHHHHHhcc-cchhHHHHhcccccccccchHHHHHHHhhhh---ccChhhhhHHhHhhhHHHHHHH
Confidence            34666788888887766665532 1122222112223445678888988888764   3445422111   11       


Q ss_pred             ---HHHHHhcCCHHHHHHHHHhCC------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          286 ---ADLLGRAGKLQEAYEFISNMH------AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       286 ---i~~~~~~g~~~~A~~~~~~m~------~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                         .....+.|++.+|.+.+.+..      .+|++..|.....+..+.|+..+|+.--+++..++|.-...|..-++++.
T Consensus       253 k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~syikall~ra~c~l  332 (486)
T KOG0550|consen  253 KERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSSYIKALLRRANCHL  332 (486)
T ss_pred             HhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHHHHHHHHHHHHHHH
Confidence               223457899999999998763      33667778888888999999999999999999999887778888889999


Q ss_pred             HccChhHHHHHHHHHHhCCCcc
Q 040365          357 AARRWKDAASLRVFMRNKGMKK  378 (514)
Q Consensus       357 ~~g~~~~a~~~~~~m~~~g~~~  378 (514)
                      ..++|++|.+-++...+..-.+
T Consensus       333 ~le~~e~AV~d~~~a~q~~~s~  354 (486)
T KOG0550|consen  333 ALEKWEEAVEDYEKAMQLEKDC  354 (486)
T ss_pred             HHHHHHHHHHHHHHHHhhcccc
Confidence            9999999999999876654333

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

Probab=97.20  E-value=0.0067  Score=59.64  Aligned_cols=119  Identities=13%  Similarity=0.096  Sum_probs=78.8

Q ss_pred             CCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC-C-----ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHH
Q 040365           72 LDANVCIGSSLINMYAKCARVEDSHRLFCLLPV-K-----DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSF  145 (514)
Q Consensus        72 ~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~-~-----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~  145 (514)
                      .+.+......+++......+++.+..++-+... |     -..|..++|+.|.+.|..++++.+++.=...|+-||.+|+
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            344555555666666666667777776655542 1     1224457778888888888888877777777778888888


Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc
Q 040365          146 SSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKC  190 (514)
Q Consensus       146 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~  190 (514)
                      +.++..+.+.|++..|.++...|...+...+..++..-+..+.+.
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            888888888888887777777776666555555554444444444

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 [].

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.18  E-value=0.0016  Score=46.05  Aligned_cols=61  Identities=21%  Similarity=0.260  Sum_probs=47.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          285 VADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      +...+.+.|++++|.+.|++.. ..| +...|..+..++...|++++|...++++++.+|+++
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~~p   65 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPDNP   65 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCC
Confidence            4456778888888888888864 335 567788888899999999999999999999988764

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.18  E-value=0.0046  Score=58.60  Aligned_cols=256  Identities=14%  Similarity=0.100  Sum_probs=146.8

Q ss_pred             HHHHCCChhHHHHHHHHHHHCCCCCCHH----HHHHHHHHHhccCChHHHHHHHHHHH--Hc--CCC-CcHHHHHHHHHH
Q 040365          116 GCVQNGLFDEGLKFFRQMLIAKIKPRHV----SFSSIMPACAHLTTLHLGKQLHGCII--RN--GFD-DNMFIASSLLDM  186 (514)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~--~~--~~~-~~~~~~~~li~~  186 (514)
                      -+++.|+....+.+|+...+.|. -|..    .|..+-.+|.-++++++|.++|..=+  ..  |-. -.......|.+.
T Consensus        26 RLck~gdcraGv~ff~aA~qvGT-eDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLGNt  104 (639)
T KOG1130|consen   26 RLCKMGDCRAGVDFFKAALQVGT-EDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLGNT  104 (639)
T ss_pred             HHHhccchhhhHHHHHHHHHhcc-hHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccccccccch
Confidence            35677777777777777777662 3333    34445556666677777777764321  11  100 000111112223


Q ss_pred             HHhcCCHHHHHHHHH-hCC------CC--ChhHHHHHHHHHHhCCC--------------------hHHHHHHHHHHH--
Q 040365          187 YAKCGNIRLARCIFD-KMD------LH--DIVSWTAVIMGNALHGN--------------------AHDAISLFEQME--  235 (514)
Q Consensus       187 y~k~g~~~~A~~~~~-~m~------~~--d~~~~~~li~~~~~~g~--------------------~~~A~~l~~~m~--  235 (514)
                      +--.|.+++|.-.-. .+.      .+  ....+..+...|...|+                    ++.|.++|.+=.  
T Consensus       105 lKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~fy~eNL~l  184 (639)
T KOG1130|consen  105 LKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVKFYMENLEL  184 (639)
T ss_pred             hhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHHHHHHHHHH
Confidence            333455555433221 111      00  11233334444433321                    233444443321  


Q ss_pred             --HcCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHH---hHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhC---
Q 040365          236 --KDGVK-PNSVAFVAVLTACSHAGLIDKAWSYFNS---MTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNM---  305 (514)
Q Consensus       236 --~~g~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~---m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m---  305 (514)
                        ..|-. .-...|..|.+.|.-.|+++.|+..++.   +.+++|-.. ....+..|..++.-.|+++.|.+.++..   
T Consensus       185 ~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~L  264 (639)
T KOG1130|consen  185 SEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNL  264 (639)
T ss_pred             HHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHH
Confidence              11111 1123455666666777899999887763   223444433 3456777888888899999999888753   


Q ss_pred             ----CC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc----C--CCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          306 ----HA-GPTENVWLTLLSACRVHKNVELAGKVAEKIFMI----D--PNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       306 ----~~-~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~--p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                          .. .....+..+|..+|....+++.|+..+.+-+.+    +  .....++.+|.++|...|..+.|+...+.-.
T Consensus       265 Aielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  265 AIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHL  342 (639)
T ss_pred             HHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence                11 134556778899999999999999888776543    2  3346789999999999999999988776554

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

Probab=97.15  E-value=0.0044  Score=60.87  Aligned_cols=118  Identities=10%  Similarity=0.061  Sum_probs=66.2

Q ss_pred             CCChhhHHHHHHHHhCCCChHHHHHHHHHHHHh--CCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC----CCChhHHH
Q 040365           38 KPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRH--GLDANVCIGSSLINMYAKCARVEDSHRLFCLLP----VKDAISWN  111 (514)
Q Consensus        38 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~--g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~----~~d~~~~~  111 (514)
                      +.+...+..++..+....+++.++.++-.....  ....-..+..++|+.|.+.|..+.+..++..=.    -||..++|
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            444555555666666555666665555554443  122223344566666666666666666665432    25666666


Q ss_pred             HHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc
Q 040365          112 SIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHL  155 (514)
Q Consensus       112 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~  155 (514)
                      .||+.+.+.|++..|.++...|...+...+..|+...+.+|.+.
T Consensus       143 ~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  143 LLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            66666666666666666666665555555556665555555443

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 [].

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.12  E-value=0.019  Score=47.90  Aligned_cols=95  Identities=11%  Similarity=0.050  Sum_probs=51.1

Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCH-HHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHH
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRH-VSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL  184 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  184 (514)
                      +....-.+..-+.+.|++++|..+|+-+...  .|.. .-|-.+..+|-..|++++|...+....... +.|...+-.+.
T Consensus        34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~--Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag  110 (157)
T PRK15363         34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIY--DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAA  110 (157)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHH
Confidence            3334444445555666666666666665553  2322 233344444555566666666666665554 34444455555


Q ss_pred             HHHHhcCCHHHHHHHHHhC
Q 040365          185 DMYAKCGNIRLARCIFDKM  203 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m  203 (514)
                      .+|.+.|+.+.|++.|+..
T Consensus       111 ~c~L~lG~~~~A~~aF~~A  129 (157)
T PRK15363        111 ECYLACDNVCYAIKALKAV  129 (157)
T ss_pred             HHHHHcCCHHHHHHHHHHH
Confidence            5666666666666655543

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.11  E-value=0.012  Score=49.87  Aligned_cols=100  Identities=20%  Similarity=0.237  Sum_probs=51.9

Q ss_pred             CCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC--CcchH
Q 040365          274 GIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH---AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN--NMGAY  348 (514)
Q Consensus       274 ~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~--~~~~~  348 (514)
                      .+.|++.+--.|..++.+.|+..||...|++..   ...|....-.+..+....+++..|...++.+.+-.|.  .+.+.
T Consensus        84 ~~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~  163 (251)
T COG4700          84 AIAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH  163 (251)
T ss_pred             hhchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch
Confidence            344555555555555555555555555555432   2234455555555555555555555555555554432  33444


Q ss_pred             HHHHHHHHHccChhHHHHHHHHHHh
Q 040365          349 VILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       349 ~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..+...|...|++++|+..|+....
T Consensus       164 Ll~aR~laa~g~~a~Aesafe~a~~  188 (251)
T COG4700         164 LLFARTLAAQGKYADAESAFEVAIS  188 (251)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHH
Confidence            4555555555555555555555443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.06  E-value=0.23  Score=51.15  Aligned_cols=106  Identities=15%  Similarity=0.229  Sum_probs=78.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHH
Q 040365          183 LLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKA  262 (514)
Q Consensus       183 li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  262 (514)
                      -+.-+..-|+..+|.++-.+..-||-..|-.-+.+++..+++++-+++-+.+.      ...-|.-...+|.+.|+.++|
T Consensus       690 Tv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~kweeLekfAkskk------sPIGy~PFVe~c~~~~n~~EA  763 (829)
T KOG2280|consen  690 TVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIKKWEELEKFAKSKK------SPIGYLPFVEACLKQGNKDEA  763 (829)
T ss_pred             HHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhhhHHHHHHHHhccC------CCCCchhHHHHHHhcccHHHH
Confidence            34445667888888888888888888888888888888888887766655543      135566678888888999888


Q ss_pred             HHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          263 WSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       263 ~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  304 (514)
                      ..++.+..   |..       -.+.+|.+.|++.+|.++--+
T Consensus       764 ~KYiprv~---~l~-------ekv~ay~~~~~~~eAad~A~~  795 (829)
T KOG2280|consen  764 KKYIPRVG---GLQ-------EKVKAYLRVGDVKEAADLAAE  795 (829)
T ss_pred             hhhhhccC---ChH-------HHHHHHHHhccHHHHHHHHHH
Confidence            88887552   211       467788888888888766543

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.05  E-value=0.037  Score=49.59  Aligned_cols=167  Identities=9%  Similarity=0.013  Sum_probs=109.9

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHccCCC--CCh--------hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHH
Q 040365           79 GSSLINMYAKCARVEDSHRLFCLLPV--KDA--------ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSI  148 (514)
Q Consensus        79 ~~~li~~~~~~g~~~~A~~~f~~~~~--~d~--------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l  148 (514)
                      +++|...|.-..-+.+-...|+.-..  ..+        ..-+.++..+.-.|.+.-.+.++.+.++...+-++.....+
T Consensus       139 qesLdRl~~L~~~V~~ii~~~e~~~~~ESsv~lW~KRl~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~L  218 (366)
T KOG2796|consen  139 QESLDRLHKLKTVVSKILANLEQGLAEESSIRLWRKRLGRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGL  218 (366)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHH
Confidence            35555555544444555555544322  122        23456777777788888888888888887666677777788


Q ss_pred             HHHHhccCChHHHHHHHHHHHHcC-----CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC---CChhHHHHHHHHHHh
Q 040365          149 MPACAHLTTLHLGKQLHGCIIRNG-----FDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL---HDIVSWTAVIMGNAL  220 (514)
Q Consensus       149 l~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~---~d~~~~~~li~~~~~  220 (514)
                      .+.-.+.|+.+.|...++.+.+..     ...+..+.-.....|.-.+++..|...|++++.   +|++.-|.-.-+..-
T Consensus       219 gr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllY  298 (366)
T KOG2796|consen  219 GRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLY  298 (366)
T ss_pred             HHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHH
Confidence            888888899998888888776643     233333333444456667788888888887763   455666665555566


Q ss_pred             CCChHHHHHHHHHHHHcCCCCCHHHHH
Q 040365          221 HGNAHDAISLFEQMEKDGVKPNSVAFV  247 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~~p~~~t~~  247 (514)
                      .|+..+|++.++.|.+.  .|...+-+
T Consensus       299 lg~l~DAiK~~e~~~~~--~P~~~l~e  323 (366)
T KOG2796|consen  299 LGKLKDALKQLEAMVQQ--DPRHYLHE  323 (366)
T ss_pred             HHHHHHHHHHHHHHhcc--CCccchhh
Confidence            78888888888888874  44444333

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.04  E-value=0.062  Score=49.35  Aligned_cols=174  Identities=10%  Similarity=0.050  Sum_probs=98.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCCCC--C-hhH---HHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc-
Q 040365          183 LLDMYAKCGNIRLARCIFDKMDLH--D-IVS---WTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSH-  255 (514)
Q Consensus       183 li~~y~k~g~~~~A~~~~~~m~~~--d-~~~---~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~-  255 (514)
                      ....+.+.|++++|.+.|+.+...  + ...   .-.+..+|.+.+++++|...|++..+.-..-...-+...+.+.+. 
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~  117 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNM  117 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhh
Confidence            344456677888888877777522  1 111   233455667777788888887777764211112333333333321 


Q ss_pred             -cC---------------C---HHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHH
Q 040365          256 -AG---------------L---IDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLT  316 (514)
Q Consensus       256 -~g---------------~---~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~  316 (514)
                       .+               +   ...|+..|+.++                +-|-.+.-..+|...+..+..+--.. --.
T Consensus       118 ~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li----------------~~yP~S~ya~~A~~rl~~l~~~la~~-e~~  180 (243)
T PRK10866        118 ALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLV----------------RGYPNSQYTTDATKRLVFLKDRLAKY-ELS  180 (243)
T ss_pred             hcchhhhhhccCCCccccCHHHHHHHHHHHHHHH----------------HHCcCChhHHHHHHHHHHHHHHHHHH-HHH
Confidence             10               1   112233333333                33333333444444333332110000 113


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCc---chHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          317 LLSACRVHKNVELAGKVAEKIFMIDPNNM---GAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       317 ll~~~~~~~~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      +..-|.+.|.+..|..-++.+++.-|+.+   .+...+..+|...|..++|.++...+..
T Consensus       181 ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~~  240 (243)
T PRK10866        181 VAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIAA  240 (243)
T ss_pred             HHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHhc
Confidence            44558889999999999999999887654   4566888999999999999998876643

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.04  E-value=0.087  Score=49.75  Aligned_cols=89  Identities=13%  Similarity=0.153  Sum_probs=36.9

Q ss_pred             HHHHhC-CChHHHHHHHHHHHH----cCCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCC----CCCH-hHHH
Q 040365          216 MGNALH-GNAHDAISLFEQMEK----DGVKPN--SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGI----APSF-EHYA  283 (514)
Q Consensus       216 ~~~~~~-g~~~~A~~l~~~m~~----~g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~----~p~~-~~~~  283 (514)
                      ..|-.. |++++|++.|++..+    .| .|.  ...+..+...+.+.|++++|.++|+++....--    ..+. ..+.
T Consensus       122 ~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l  200 (282)
T PF14938_consen  122 EIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFL  200 (282)
T ss_dssp             HHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHH
Confidence            334444 555555555555432    12 111  123444555555556666666666555432110    1111 1222


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhC
Q 040365          284 AVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      ..+-++...|++..|.+.+++.
T Consensus       201 ~a~l~~L~~~D~v~A~~~~~~~  222 (282)
T PF14938_consen  201 KAILCHLAMGDYVAARKALERY  222 (282)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH
Confidence            2333444455666665555553

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=96.99  E-value=0.021  Score=49.30  Aligned_cols=80  Identities=9%  Similarity=-0.002  Sum_probs=42.7

Q ss_pred             hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCC--CHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHH
Q 040365          108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKP--RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLD  185 (514)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  185 (514)
                      ..|..+...+...|++++|+..|++.......|  ...++..+...+...|++++|...+....+.. +.....++.+..
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~  114 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAV  114 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHH
Confidence            345556666666677777777776665432121  12345555556666666666666666665542 222333444444


Q ss_pred             HHH
Q 040365          186 MYA  188 (514)
Q Consensus       186 ~y~  188 (514)
                      .|.
T Consensus       115 i~~  117 (168)
T CHL00033        115 ICH  117 (168)
T ss_pred             HHH
Confidence            444

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=96.99  E-value=0.00059  Score=40.93  Aligned_cols=33  Identities=30%  Similarity=0.480  Sum_probs=30.6

Q ss_pred             HHHHHhcCCCCcchHHHHHHHHHHccChhHHHH
Q 040365          334 AEKIFMIDPNNMGAYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       334 ~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~  366 (514)
                      ++++++++|+++.+|..|+.+|...|++++|.+
T Consensus         2 y~kAie~~P~n~~a~~nla~~~~~~g~~~~A~~   34 (34)
T PF13431_consen    2 YKKAIELNPNNAEAYNNLANLYLNQGDYEEAIA   34 (34)
T ss_pred             hHHHHHHCCCCHHHHHHHHHHHHHCcCHHhhcC
Confidence            678899999999999999999999999999863

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=96.98  E-value=0.093  Score=50.66  Aligned_cols=161  Identities=19%  Similarity=0.169  Sum_probs=105.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCCCC---Ch----hHHHHHHHHHHh---CCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040365          182 SLLDMYAKCGNIRLARCIFDKMDLH---DI----VSWTAVIMGNAL---HGNAHDAISLFEQMEKDGVKPNSVAFVAVLT  251 (514)
Q Consensus       182 ~li~~y~k~g~~~~A~~~~~~m~~~---d~----~~~~~li~~~~~---~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  251 (514)
                      .|+-.|-...+++...++.+.+...   ++    ..--...-++.+   .|+.++|++++..+......++..||..+..
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            4455688899999999999988743   21    112233445556   7899999999999776666778888877776


Q ss_pred             HHHc---------cCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHH----HHHHHH---HhC-----CCC--
Q 040365          252 ACSH---------AGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQ----EAYEFI---SNM-----HAG--  308 (514)
Q Consensus       252 a~~~---------~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~----~A~~~~---~~m-----~~~--  308 (514)
                      .|-.         ....++|+..|.+.   +.+.|+..+--.++.++.-.|...    +..++-   ...     ...  
T Consensus       226 IyKD~~~~s~~~d~~~ldkAi~~Y~kg---Fe~~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~  302 (374)
T PF13281_consen  226 IYKDLFLESNFTDRESLDKAIEWYRKG---FEIEPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKM  302 (374)
T ss_pred             HHHHHHHHcCccchHHHHHHHHHHHHH---HcCCccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhcccccc
Confidence            6532         23467788877744   566676544334444444444322    222222   111     011  


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          309 PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      .|--.+.+++.++.-.|+.+.|.+.++++..+.|+.-
T Consensus       303 ~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~~~W  339 (374)
T PF13281_consen  303 QDYWDVATLLEASVLAGDYEKAIQAAEKAFKLKPPAW  339 (374)
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcCCcch
Confidence            3444557899999999999999999999999987653

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.96  E-value=0.037  Score=44.36  Aligned_cols=91  Identities=16%  Similarity=0.239  Sum_probs=65.0

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHH
Q 040365          214 VIMGNALHGNAHDAISLFEQMEKDGVKPNS--VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLG  290 (514)
Q Consensus       214 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~--~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~  290 (514)
                      +..++-..|+.++|+.+|++....|.....  ..+..+.+++...|++++|..+|+.....+.-.+ +......+..++.
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHH
Confidence            345667789999999999999988876553  4567788888899999999999998876532211 1222223445677


Q ss_pred             hcCCHHHHHHHHHh
Q 040365          291 RAGKLQEAYEFISN  304 (514)
Q Consensus       291 ~~g~~~~A~~~~~~  304 (514)
                      ..|+.++|++.+-.
T Consensus        87 ~~gr~~eAl~~~l~  100 (120)
T PF12688_consen   87 NLGRPKEALEWLLE  100 (120)
T ss_pred             HCCCHHHHHHHHHH
Confidence            88999998887644

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.95  E-value=0.0031  Score=57.51  Aligned_cols=86  Identities=21%  Similarity=0.127  Sum_probs=76.5

Q ss_pred             HHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHH
Q 040365          288 LLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAA  365 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~  365 (514)
                      -+.+.+++++|+..|.+.. .. .|.+.|..=..+|.+.|.++.|.+-.+..+.++|....+|..|..+|...|++++|.
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A~  169 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEAI  169 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHHH
Confidence            3567899999999998864 34 477778888999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHh
Q 040365          366 SLRVFMRN  373 (514)
Q Consensus       366 ~~~~~m~~  373 (514)
                      +.|++..+
T Consensus       170 ~aykKaLe  177 (304)
T KOG0553|consen  170 EAYKKALE  177 (304)
T ss_pred             HHHHhhhc
Confidence            99886654

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.93  E-value=0.0035  Score=44.81  Aligned_cols=64  Identities=22%  Similarity=0.258  Sum_probs=49.1

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhcCC
Q 040365          279 FEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHK-NVELAGKVAEKIFMIDP  342 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~-~~~~a~~~~~~~~~~~p  342 (514)
                      ...|..+...+...|++++|+..|++.. ..| +...|..+..++...| ++++|+..++++++++|
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P   69 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP   69 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence            4567777777888888888888887652 233 5667888888888888 78899999988888876

...

>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=96.92  E-value=0.0018  Score=46.18  Aligned_cols=49  Identities=20%  Similarity=0.260  Sum_probs=26.9

Q ss_pred             ccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          255 HAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH  306 (514)
Q Consensus       255 ~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~  306 (514)
                      ..|++++|..+|+.+...   .| +...+..+..+|.+.|++++|.++++++.
T Consensus         3 ~~~~~~~A~~~~~~~l~~---~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~   52 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQR---NPDNPEARLLLAQCYLKQGQYDEAEELLERLL   52 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHH---TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCH
T ss_pred             hccCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            345666666666665443   33 44555555666666666666666665553

...

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=96.88  E-value=0.076  Score=54.42  Aligned_cols=59  Identities=15%  Similarity=0.178  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      ..|..+.......|++++|...+++..   .+.|+...|..+...+...|+.++|.+.+++.
T Consensus       421 ~~~~ala~~~~~~g~~~~A~~~l~rAl---~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A  479 (517)
T PRK10153        421 RIYEILAVQALVKGKTDEAYQAINKAI---DLEMSWLNYVLLGKVYELKGDNRLAADAYSTA  479 (517)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHH---HcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            445444444445566666666666664   33456666666666666666666666666553

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.84  E-value=0.036  Score=44.43  Aligned_cols=90  Identities=13%  Similarity=0.050  Sum_probs=50.7

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCCCC--HHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCC---cHHHHHHHHHHH
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIAKIKPR--HVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDD---NMFIASSLLDMY  187 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~li~~y  187 (514)
                      +..++-..|+.++|+.+|++....|...+  ...+..+.+.+...|++++|..+++...... +.   +..+...+.-++
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~-p~~~~~~~l~~f~Al~L   85 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF-PDDELNAALRVFLALAL   85 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCccccHHHHHHHHHHH
Confidence            34455667777777777777777765543  2344455566667777777777777665542 11   122222223344


Q ss_pred             HhcCCHHHHHHHHHhC
Q 040365          188 AKCGNIRLARCIFDKM  203 (514)
Q Consensus       188 ~k~g~~~~A~~~~~~m  203 (514)
                      ...|+.++|.+.+-..
T Consensus        86 ~~~gr~~eAl~~~l~~  101 (120)
T PF12688_consen   86 YNLGRPKEALEWLLEA  101 (120)
T ss_pred             HHCCCHHHHHHHHHHH
Confidence            5556666655555443

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=96.84  E-value=0.066  Score=50.56  Aligned_cols=117  Identities=21%  Similarity=0.231  Sum_probs=72.2

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcc-CCHHHHHHHHHHhHHhcCCCCC----HhHHHHHH
Q 040365          212 TAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHA-GLIDKAWSYFNSMTKDYGIAPS----FEHYAAVA  286 (514)
Q Consensus       212 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~-g~~~~a~~~~~~m~~~~~~~p~----~~~~~~li  286 (514)
                      ...+..|...|++..|-.++.++               ...|... |++++|.++|+....-+.-...    ...+..+.
T Consensus        98 ~~A~~~y~~~G~~~~aA~~~~~l---------------A~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A  162 (282)
T PF14938_consen   98 EKAIEIYREAGRFSQAAKCLKEL---------------AEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAA  162 (282)
T ss_dssp             HHHHHHHHHCT-HHHHHHHHHHH---------------HHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHH---------------HHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHH
Confidence            33456666677776666555554               4456666 7888888888877554322222    34566777


Q ss_pred             HHHHhcCCHHHHHHHHHhCCC---C-C----CHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          287 DLLGRAGKLQEAYEFISNMHA---G-P----TEN-VWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       287 ~~~~~~g~~~~A~~~~~~m~~---~-p----~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      ..+.+.|++++|.++|++...   . +    +.. .+-..+-.+...||+..|...+++....+|.
T Consensus       163 ~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~  228 (282)
T PF14938_consen  163 DLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPS  228 (282)
T ss_dssp             HHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTT
T ss_pred             HHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            888999999999999987531   1 1    111 2223333566678899999999998888764

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.70  E-value=0.25  Score=50.44  Aligned_cols=251  Identities=14%  Similarity=0.050  Sum_probs=132.0

Q ss_pred             HHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHH-CCCCCCH--HHHH--HH--HHHHhccCChHHHHHH
Q 040365           92 VEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLI-AKIKPRH--VSFS--SI--MPACAHLTTLHLGKQL  164 (514)
Q Consensus        92 ~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~-~g~~p~~--~t~~--~l--l~~~~~~~~~~~a~~~  164 (514)
                      +++|.+..+.  .|.+..|..+.....+.-.++-|...|-+... .|++.-.  .|..  .+  ...-+--|.+++|+++
T Consensus       679 ledA~qfiEd--nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~~g~feeaek~  756 (1189)
T KOG2041|consen  679 LEDAIQFIED--NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAFYGEFEEAEKL  756 (1189)
T ss_pred             hHHHHHHHhc--CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhhhcchhHhhhh
Confidence            5556665554  34556777777666666666666666655433 1221100  0000  00  1112234778888888


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC--C---hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCC
Q 040365          165 HGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH--D---IVSWTAVIMGNALHGNAHDAISLFEQMEKDGV  239 (514)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~--d---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~  239 (514)
                      +-.+-++.         .-|.++.+.|++-...++++.-...  |   ..+|+.+...++....+++|.+.|..-..   
T Consensus       757 yld~drrD---------LAielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~---  824 (1189)
T KOG2041|consen  757 YLDADRRD---------LAIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD---  824 (1189)
T ss_pred             hhccchhh---------hhHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc---
Confidence            77665543         2467788888888877777654321  1   24677777777777777777776664321   


Q ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHH
Q 040365          240 KPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLS  319 (514)
Q Consensus       240 ~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~  319 (514)
                         .   ...+.++.+..++++-..+-..+      +-+....-.+.+++.+.|.-++|.+.+-+-.. |     .+.+.
T Consensus       825 ---~---e~~~ecly~le~f~~LE~la~~L------pe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~-p-----kaAv~  886 (1189)
T KOG2041|consen  825 ---T---ENQIECLYRLELFGELEVLARTL------PEDSELLPVMADMFTSVGMCDQAVEAYLRRSL-P-----KAAVH  886 (1189)
T ss_pred             ---h---HhHHHHHHHHHhhhhHHHHHHhc------CcccchHHHHHHHHHhhchHHHHHHHHHhccC-c-----HHHHH
Confidence               1   12344455555555444443333      22344455566677777777777665544431 1     22344


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCC-----------CcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          320 ACRVHKNVELAGKVAEKIFMIDPN-----------NMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~p~-----------~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +|...+++.+|.++.++..--.-.           ......--+..+-++|+.-+|.+++.+|.++
T Consensus       887 tCv~LnQW~~avelaq~~~l~qv~tliak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae~  952 (1189)
T KOG2041|consen  887 TCVELNQWGEAVELAQRFQLPQVQTLIAKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAER  952 (1189)
T ss_pred             HHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhHH
Confidence            455555555555444332100000           0011122345566667777777777766544

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.66  E-value=0.01  Score=57.97  Aligned_cols=63  Identities=19%  Similarity=-0.029  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc---hHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG---AYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~---~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ...|+.+..+|...|++++|+..+++.++++|++..   +|..++.+|...|+.++|...+++..+
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444444444445555555555554444444442   244444445555555555444444443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.59  E-value=0.017  Score=53.47  Aligned_cols=92  Identities=13%  Similarity=0.023  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhCC-CCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---cchHHHHHH
Q 040365          282 YAAVADLLGRAGKLQEAYEFISNMH-AGPTE----NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN---MGAYVILSN  353 (514)
Q Consensus       282 ~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~---~~~~~~l~~  353 (514)
                      |..-+..+.+.|++++|...|+.+. ..|+.    ..+.-+..++...|+++.|...|+++....|++   +.++..++.
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~  225 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGV  225 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHH
Confidence            3333333334445555554444432 11221    234444555555555555555555555554443   233333445


Q ss_pred             HHHHccChhHHHHHHHHHHh
Q 040365          354 TYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       354 ~~~~~g~~~~a~~~~~~m~~  373 (514)
                      +|...|++++|.++++.+.+
T Consensus       226 ~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        226 IMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            55555555555555555543

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.59  E-value=0.59  Score=42.94  Aligned_cols=64  Identities=14%  Similarity=0.065  Sum_probs=35.6

Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHH-HH---HHHHHHHhccCChHHHHHHHHHHHHc
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHV-SF---SSIMPACAHLTTLHLGKQLHGCIIRN  171 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~---~~ll~~~~~~~~~~~a~~~~~~~~~~  171 (514)
                      +...+-.....+.+.|++++|.+.|+++...-  |+.. ..   -.+..++-+.++++.|...++..++.
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~y--P~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~   98 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRY--PFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL   98 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            33333344455566777777777777776642  3222 11   23344556666666666666666654

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.57  E-value=0.19  Score=45.27  Aligned_cols=229  Identities=12%  Similarity=-0.037  Sum_probs=120.8

Q ss_pred             hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH-hccCC-hH-HHHHHHHHHHHc-CCCCcHHHHHH
Q 040365          107 AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPAC-AHLTT-LH-LGKQLHGCIIRN-GFDDNMFIASS  182 (514)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~-~~~~~-~~-~a~~~~~~~~~~-~~~~~~~~~~~  182 (514)
                      ...|+.-+..+++....++|..-+....+-. .||- -|...=..+ .+.|. .. ..+.+|..+... |.     -+++
T Consensus        69 lq~wT~r~~~l~kLR~~~~a~~EL~~f~~lD-~pdl-~Yey~p~iyp~rrGSmVPFsmR~lhAe~~~~lgn-----pqes  141 (366)
T KOG2796|consen   69 LQLWTVRLALLVKLRLFQNAEMELEPFGNLD-QPDL-YYEYYPHVYPGRRGSMVPFSMRILHAELQQYLGN-----PQES  141 (366)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHhhhhhhccCC-Ccce-eeeeccccCCCCcCccccHHHHHHHHHHHHhcCC-----cHHH
Confidence            3456666777777777777765554443321 1211 010000000 11222 11 123344444332 22     2455


Q ss_pred             HHHHHHhcCCHHHHHHHHHhCCC--C--------ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040365          183 LLDMYAKCGNIRLARCIFDKMDL--H--------DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTA  252 (514)
Q Consensus       183 li~~y~k~g~~~~A~~~~~~m~~--~--------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a  252 (514)
                      |...|.-..-+++-...|+.-..  .        -....+.++..+.-+|.+.-.+.++++.++...+-+..-...+.+.
T Consensus       142 LdRl~~L~~~V~~ii~~~e~~~~~ESsv~lW~KRl~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~  221 (366)
T KOG2796|consen  142 LDRLHKLKTVVSKILANLEQGLAEESSIRLWRKRLGRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRI  221 (366)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHH
Confidence            55555544444444444443321  1        2234456666666678888888888888886555566677777777


Q ss_pred             HHccCCHHHHHHHHHHhHHhcCCCCCHhHHHH-----HHHHHHhcCCHHHHHHHHHhCCCC--CCHHHHHHHHHHHHhcC
Q 040365          253 CSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAA-----VADLLGRAGKLQEAYEFISNMHAG--PTENVWLTLLSACRVHK  325 (514)
Q Consensus       253 ~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~-----li~~~~~~g~~~~A~~~~~~m~~~--p~~~~~~~ll~~~~~~~  325 (514)
                      -.+.|+.+.|..+|+...+..+ ..+....+.     ....|.-++++.+|...+.+++..  .|+...|.-.-+..-.|
T Consensus       222 ~MQ~GD~k~a~~yf~~vek~~~-kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg  300 (366)
T KOG2796|consen  222 SMQIGDIKTAEKYFQDVEKVTQ-KLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLG  300 (366)
T ss_pred             HHhcccHHHHHHHHHHHHHHHh-hhhccchhHHHHhhhhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHH
Confidence            7888899888888887754422 122222222     223344556666666666666422  23333333333334456


Q ss_pred             CHHHHHHHHHHHHhcCCC
Q 040365          326 NVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~  343 (514)
                      +...|.+..+.+.+..|.
T Consensus       301 ~l~DAiK~~e~~~~~~P~  318 (366)
T KOG2796|consen  301 KLKDALKQLEAMVQQDPR  318 (366)
T ss_pred             HHHHHHHHHHHHhccCCc
Confidence            666666666666666654

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.54  E-value=0.0055  Score=39.28  Aligned_cols=42  Identities=24%  Similarity=0.445  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHH
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSN  353 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~  353 (514)
                      .+|..+..++...|++++|+++++++++.+|+|+..+..|+.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La~   43 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALAQ   43 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhhh
Confidence            367888999999999999999999999999999988877653

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.51  E-value=0.048  Score=50.55  Aligned_cols=101  Identities=14%  Similarity=0.129  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCCC-CC----CHHHHHHHH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMHA-GP----TENVWLTLL  318 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p----~~~~~~~ll  318 (514)
                      .|...+....+.|++++|...|+.+.+.+.-.+ ....+-.+...|...|++++|...|+.+.. .|    ....+..+.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg  224 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVG  224 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHH
Confidence            344444444455677777777777665532221 124455666677777777777777766531 12    234455556


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          319 SACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      ..+...|+.+.|...++++++..|++.
T Consensus       225 ~~~~~~g~~~~A~~~~~~vi~~yP~s~  251 (263)
T PRK10803        225 VIMQDKGDTAKAKAVYQQVIKKYPGTD  251 (263)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCcCCH
Confidence            667778888888888888888888754

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.49  E-value=0.84  Score=43.66  Aligned_cols=282  Identities=14%  Similarity=0.113  Sum_probs=179.3

Q ss_pred             HHHHHHHHH--HCCCHHHHHHHHccCC---CCChhHHHHHHHH--HHHCCChhHHHHHHHHHHHCCCCCCHHH--HHHHH
Q 040365           79 GSSLINMYA--KCARVEDSHRLFCLLP---VKDAISWNSIIAG--CVQNGLFDEGLKFFRQMLIAKIKPRHVS--FSSIM  149 (514)
Q Consensus        79 ~~~li~~~~--~~g~~~~A~~~f~~~~---~~d~~~~~~li~~--~~~~g~~~~A~~l~~~m~~~g~~p~~~t--~~~ll  149 (514)
                      |.+|-.++.  -.|+-..|+++-.+-.   ..|....-.++.+  -.-.|+++.|.+-|+.|...   |....  +..|.
T Consensus        85 yqALStGliAagAGda~lARkmt~~~~~llssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLRgLy  161 (531)
T COG3898          85 YQALSTGLIAAGAGDASLARKMTARASKLLSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLRGLY  161 (531)
T ss_pred             HHHHhhhhhhhccCchHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHHHHH
Confidence            344444433  3567777777655433   2343333333332  33468999999999999762   32221  22333


Q ss_pred             HHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC-----CCChh--HHHHHHHHHHh--
Q 040365          150 PACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD-----LHDIV--SWTAVIMGNAL--  220 (514)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~-----~~d~~--~~~~li~~~~~--  220 (514)
                      -..-+.|+.+.|++.-+..-..- +.-...+.+++...+..|+++.|+++.+.-.     ++|+.  .-..|+.+-+.  
T Consensus       162 leAqr~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~  240 (531)
T COG3898         162 LEAQRLGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSL  240 (531)
T ss_pred             HHHHhcccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHH
Confidence            33456788888888877765543 3334567788999999999999999998754     44442  22333333221  


Q ss_pred             -CCChHHHHHHHHHHHHcCCCCCHHH-HHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040365          221 -HGNAHDAISLFEQMEKDGVKPNSVA-FVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       221 -~g~~~~A~~l~~~m~~~g~~p~~~t-~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  298 (514)
                       .-+...|.+.-.+..+  +.||.+- -.....++.+.|++.++-.+++.+.+.   .|.+..+...+  +.|.|+....
T Consensus       241 ldadp~~Ar~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~---ePHP~ia~lY~--~ar~gdta~d  313 (531)
T COG3898         241 LDADPASARDDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKILETAWKA---EPHPDIALLYV--RARSGDTALD  313 (531)
T ss_pred             hcCChHHHHHHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhHHHHHHhc---CCChHHHHHHH--HhcCCCcHHH
Confidence             2345556555554443  5677543 334456788999999999999988654   67776654444  3455553221


Q ss_pred             --H--HHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc-cChhHHHHHHHHHHh
Q 040365          299 --Y--EFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA-RRWKDAASLRVFMRN  373 (514)
Q Consensus       299 --~--~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~-g~~~~a~~~~~~m~~  373 (514)
                        .  +-++.|+ +.+..+--++..+-...|++..|..-.+.+....|. .+.|..|.++-... |+-.++...+.+-.+
T Consensus       314 RlkRa~~L~slk-~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~~pr-es~~lLlAdIeeAetGDqg~vR~wlAqav~  391 (531)
T COG3898         314 RLKRAKKLESLK-PNNAESSLAVAEAALDAGEFSAARAKAEAAAREAPR-ESAYLLLADIEEAETGDQGKVRQWLAQAVK  391 (531)
T ss_pred             HHHHHHHHHhcC-ccchHHHHHHHHHHHhccchHHHHHHHHHHhhhCch-hhHHHHHHHHHhhccCchHHHHHHHHHHhc
Confidence              1  1233443 345667777888888999999999999998888886 46888888876544 888888887776554

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.38  E-value=0.54  Score=40.19  Aligned_cols=99  Identities=15%  Similarity=0.022  Sum_probs=55.1

Q ss_pred             CCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC-----CChhHHHH
Q 040365          139 KPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL-----HDIVSWTA  213 (514)
Q Consensus       139 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~-----~d~~~~~~  213 (514)
                      .|+...-..+..+....|+..+|...+++....-+..|..+.-.+.++....++...|...++.+-+     +...+.-.
T Consensus        86 ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll  165 (251)
T COG4700          86 APTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLL  165 (251)
T ss_pred             chhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHH
Confidence            4555555555566666666666666666665554555555555566666666666666665555431     12223333


Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHc
Q 040365          214 VIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       214 li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      +...|.-.|++.+|..-|+.....
T Consensus       166 ~aR~laa~g~~a~Aesafe~a~~~  189 (251)
T COG4700         166 FARTLAAQGKYADAESAFEVAISY  189 (251)
T ss_pred             HHHHHHhcCCchhHHHHHHHHHHh
Confidence            445555566666666666665553

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.28  E-value=0.036  Score=50.15  Aligned_cols=102  Identities=15%  Similarity=0.124  Sum_probs=83.8

Q ss_pred             HHHHHHHHhCC--CCChhHHHHHHHHHHhC-----CChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccC---------
Q 040365          194 RLARCIFDKMD--LHDIVSWTAVIMGNALH-----GNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAG---------  257 (514)
Q Consensus       194 ~~A~~~~~~m~--~~d~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g---------  257 (514)
                      -..++.|...+  ++|-.+|-+++..|..+     +..+-....++.|.+.|+.-|..+|..||+.+-+..         
T Consensus        51 v~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~  130 (406)
T KOG3941|consen   51 VHVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQK  130 (406)
T ss_pred             cchhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHH
Confidence            34466777776  78899999999988764     567778888999999999999999999998775532         


Q ss_pred             -------CHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHH
Q 040365          258 -------LIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       258 -------~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  296 (514)
                             +-+=++.++++| +.+|+.||-++-..|+.++++.+..-
T Consensus       131 ~F~HYP~QQ~C~I~vLeqM-E~hGVmPdkE~e~~lvn~FGr~~~p~  175 (406)
T KOG3941|consen  131 VFLHYPQQQNCAIKVLEQM-EWHGVMPDKEIEDILVNAFGRWNFPT  175 (406)
T ss_pred             HHhhCchhhhHHHHHHHHH-HHcCCCCchHHHHHHHHHhccccccH
Confidence                   234578999999 77899999999999999999988643

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.25  E-value=1.8  Score=44.96  Aligned_cols=327  Identities=16%  Similarity=0.080  Sum_probs=173.2

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCCh--HHHHHHHHHHHHhCCCCchhHHHHHHHHHH
Q 040365           10 NTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDV--IKGKEIHGYAIRHGLDANVCIGSSLINMYA   87 (514)
Q Consensus        10 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~--~~a~~~~~~~~~~g~~~~~~~~~~li~~~~   87 (514)
                      ..+|.-++..+.+..|+++-..|...-..- ...|.....-..+..+.  +.+.+....=+.... .+-..|..+..---
T Consensus       441 ~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~-~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~~-~~~iSy~~iA~~Ay  518 (829)
T KOG2280|consen  441 EVVIDRLVDRHLYSVAIQVAKLLNLPESQG-DRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAKL-TPGISYAAIARRAY  518 (829)
T ss_pred             hhhhHHHHhcchhHHHHHHHHHhCCccccc-cHHHHHHHHHHHhccCccchHHHHHHHHHhcccC-CCceeHHHHHHHHH
Confidence            345666666677777777766664322111 34444444444433221  111111111111111 23344555555555


Q ss_pred             HCCCHHHHHHHHccCCCC--------ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChH
Q 040365           88 KCARVEDSHRLFCLLPVK--------DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLH  159 (514)
Q Consensus        88 ~~g~~~~A~~~f~~~~~~--------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~  159 (514)
                      .+|+.+-|.++++.=+..        +..-+...+.-..+.|+.+-...++..|...   .+...|...      ..+..
T Consensus       519 ~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~---~~~s~l~~~------l~~~p  589 (829)
T KOG2280|consen  519 QEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNK---LNRSSLFMT------LRNQP  589 (829)
T ss_pred             hcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHH---HHHHHHHHH------HHhch
Confidence            677777777777653321        1122334444455556665555555554432   111111111      12233


Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHh-C------CCCChhHHHHHHHHHHhCCC---------
Q 040365          160 LGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDK-M------DLHDIVSWTAVIMGNALHGN---------  223 (514)
Q Consensus       160 ~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~-m------~~~d~~~~~~li~~~~~~g~---------  223 (514)
                      .|..++.+..+..-.      ..|-+.|-...+.. +...|.. -      .++-.........++++...         
T Consensus       590 ~a~~lY~~~~r~~~~------~~l~d~y~q~dn~~-~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~~s~e~ka~e  662 (829)
T KOG2280|consen  590 LALSLYRQFMRHQDR------ATLYDFYNQDDNHQ-ALASFHLQASYAAETIEGRIPALKTAANAFAKSKEKSFEAKALE  662 (829)
T ss_pred             hhhHHHHHHHHhhch------hhhhhhhhcccchh-hhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhhhhhHHHHHH
Confidence            344444444332100      11222333322222 2222211 1      01111222223333333322         


Q ss_pred             -hHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHH
Q 040365          224 -AHDAISLFEQMEK-DGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEF  301 (514)
Q Consensus       224 -~~~A~~l~~~m~~-~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~  301 (514)
                       ..+-+.+++.+.. .|..-...|.+--+.-+...|+..+|.++-....     -|+...|-.-+.+++..+++++-+++
T Consensus       663 d~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk-----ipdKr~~wLk~~aLa~~~kweeLekf  737 (829)
T KOG2280|consen  663 DQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK-----IPDKRLWWLKLTALADIKKWEELEKF  737 (829)
T ss_pred             HHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC-----CcchhhHHHHHHHHHhhhhHHHHHHH
Confidence             1122233333332 2333445566667777888899999998877662     47888888889999999999999888


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHH
Q 040365          302 ISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVF  370 (514)
Q Consensus       302 ~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~  370 (514)
                      -+..+   .+.-|.-+..+|.+.|+.++|...+.+.-.        +.-...+|.+.|++.+|.++--+
T Consensus       738 Akskk---sPIGy~PFVe~c~~~~n~~EA~KYiprv~~--------l~ekv~ay~~~~~~~eAad~A~~  795 (829)
T KOG2280|consen  738 AKSKK---SPIGYLPFVEACLKQGNKDEAKKYIPRVGG--------LQEKVKAYLRVGDVKEAADLAAE  795 (829)
T ss_pred             HhccC---CCCCchhHHHHHHhcccHHHHhhhhhccCC--------hHHHHHHHHHhccHHHHHHHHHH
Confidence            87765   356678889999999999999988776422        22578899999999999887543

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=96.21  E-value=2.1  Score=45.39  Aligned_cols=219  Identities=11%  Similarity=0.060  Sum_probs=150.7

Q ss_pred             HHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHH--hCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCH
Q 040365           15 GLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIF--ADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARV   92 (514)
Q Consensus        15 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~--~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~   92 (514)
                      .....+++.+|+....++.+.  .||. .|..+++++  .+.|+.++|..+++.....+ ..|..+...+-..|-..|+.
T Consensus        18 d~ld~~qfkkal~~~~kllkk--~Pn~-~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~-~~D~~tLq~l~~~y~d~~~~   93 (932)
T KOG2053|consen   18 DLLDSSQFKKALAKLGKLLKK--HPNA-LYAKVLKALSLFRLGKGDEALKLLEALYGLK-GTDDLTLQFLQNVYRDLGKL   93 (932)
T ss_pred             HHhhhHHHHHHHHHHHHHHHH--CCCc-HHHHHHHHHHHHHhcCchhHHHHHhhhccCC-CCchHHHHHHHHHHHHHhhh
Confidence            345568899999999988775  3553 466677766  57899999998887766555 44888999999999999999


Q ss_pred             HHHHHHHccCCC--CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC----------hHH
Q 040365           93 EDSHRLFCLLPV--KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTT----------LHL  160 (514)
Q Consensus        93 ~~A~~~f~~~~~--~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~----------~~~  160 (514)
                      ++|..++++...  |+......+..+|++-+.+.+-.+.=-+|.+ .++-+.+.|-++++...+.-.          +..
T Consensus        94 d~~~~~Ye~~~~~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK-~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~L  172 (932)
T KOG2053|consen   94 DEAVHLYERANQKYPSEELLYHLFMAYVREKSYKKQQKAALQLYK-NFPKRAYYFWSVISLILQSIFSENELLDPILLAL  172 (932)
T ss_pred             hHHHHHHHHHHhhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hCCcccchHHHHHHHHHHhccCCcccccchhHHH
Confidence            999999999874  4545555667778887776554333333333 356677888888877654321          344


Q ss_pred             HHHHHHHHHHcC-CCCcHHHHHHHHHHHHhcCCHHHHHHHHHh-----CCCCChhHHHHHHHHHHhCCChHHHHHHHHHH
Q 040365          161 GKQLHGCIIRNG-FDDNMFIASSLLDMYAKCGNIRLARCIFDK-----MDLHDIVSWTAVIMGNALHGNAHDAISLFEQM  234 (514)
Q Consensus       161 a~~~~~~~~~~~-~~~~~~~~~~li~~y~k~g~~~~A~~~~~~-----m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m  234 (514)
                      |....+.+++.+ -..+..=.-.-.......|.+++|.+++..     ...-+...-+--+.-+...+++.+..++-.++
T Consensus       173 A~~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~L  252 (932)
T KOG2053|consen  173 AEKMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRL  252 (932)
T ss_pred             HHHHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            666677776654 111111111123344567889999998833     23445556666777888899999999999998


Q ss_pred             HHcC
Q 040365          235 EKDG  238 (514)
Q Consensus       235 ~~~g  238 (514)
                      ...|
T Consensus       253 l~k~  256 (932)
T KOG2053|consen  253 LEKG  256 (932)
T ss_pred             HHhC
Confidence            8875

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.20  E-value=0.35  Score=43.09  Aligned_cols=50  Identities=12%  Similarity=-0.003  Sum_probs=37.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCcc---hHHHHHHHHHHccChhHHHH
Q 040365          317 LLSACRVHKNVELAGKVAEKIFMIDPNNMG---AYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       317 ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~---~~~~l~~~~~~~g~~~~a~~  366 (514)
                      +..-|.+.|.+..|..-++.+++.-|+...   +...|+.+|.+.|..+.+..
T Consensus       147 ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a~~  199 (203)
T PF13525_consen  147 IARFYYKRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAADT  199 (203)
T ss_dssp             HHHHHHCTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHHHH
Confidence            455688899999999999999999887653   45678888999998885443

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.19  E-value=0.023  Score=41.03  Aligned_cols=62  Identities=16%  Similarity=0.170  Sum_probs=47.6

Q ss_pred             HHHHhcCCHHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchH
Q 040365          287 DLLGRAGKLQEAYEFISNMH-A-GPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAY  348 (514)
Q Consensus       287 ~~~~~~g~~~~A~~~~~~m~-~-~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~  348 (514)
                      ..|.+.+++++|.+.++.+. . +.+...|......+...|+++.|...+++.++..|+++...
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~~~~~   66 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELSPDDPDAR   66 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCcHHHH
Confidence            45777888888888888763 2 23566777788888889999999999999998888766443

>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=96.19  E-value=0.075  Score=43.03  Aligned_cols=51  Identities=18%  Similarity=0.258  Sum_probs=34.8

Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHH
Q 040365          238 GVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADL  288 (514)
Q Consensus       238 g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~  288 (514)
                      ...|+..+..+++.+++..|++..|.++.+...+.|+++-+...|..|+.-
T Consensus        47 pl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   47 PLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             CCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            355677777777777777777777777777777777766566666666543

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.16  E-value=1.9  Score=44.39  Aligned_cols=55  Identities=13%  Similarity=0.146  Sum_probs=31.7

Q ss_pred             CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHH
Q 040365          173 FDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFE  232 (514)
Q Consensus       173 ~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~  232 (514)
                      ++.+....-.+.+|+...|.-++|.+.|-+-..|..     -+..|...+++.+|.++-+
T Consensus       848 Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~pka-----Av~tCv~LnQW~~avelaq  902 (1189)
T KOG2041|consen  848 LPEDSELLPVMADMFTSVGMCDQAVEAYLRRSLPKA-----AVHTCVELNQWGEAVELAQ  902 (1189)
T ss_pred             cCcccchHHHHHHHHHhhchHHHHHHHHHhccCcHH-----HHHHHHHHHHHHHHHHHHH
Confidence            455666666777777777777777777666544421     2233344444555554443

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.10  E-value=0.012  Score=43.16  Aligned_cols=61  Identities=16%  Similarity=0.101  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcC----C---CCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMID----P---NNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~----p---~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      .+++.+...+...|++++|+..+++.+++.    +   ....++..++.+|...|++++|.+.+++..
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            345566666666666666666666665431    1   124566777778888888888888777653

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.10  E-value=0.35  Score=48.97  Aligned_cols=176  Identities=11%  Similarity=0.086  Sum_probs=102.9

Q ss_pred             HHHHHHHHHhcCCh--hHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHH
Q 040365            9 WNTVIVGLARNGLY--EEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMY   86 (514)
Q Consensus         9 ~~~li~~~~~~g~~--~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~   86 (514)
                      ++..=.+|.+-.+.  -+-+.-+++|++.|-.|+....   ...|+-.|.+.+|-++|.   +.|.+      |..+.+|
T Consensus       601 f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~iLl---A~~~Ay~gKF~EAAklFk---~~G~e------nRAlEmy  668 (1081)
T KOG1538|consen  601 FETARKAYIRVRDLRYLELISELEERKKRGETPNDLLL---ADVFAYQGKFHEAAKLFK---RSGHE------NRALEMY  668 (1081)
T ss_pred             hHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchHHHH---HHHHHhhhhHHHHHHHHH---HcCch------hhHHHHH
Confidence            34444556654443  2344456777888877887654   345667788999888875   44533      4456677


Q ss_pred             HHCCCHHHHHHHHccCCC---------CChhHHH-----HHHHHHHHCCChhHHHHHHHH------HHHCCC---CCCHH
Q 040365           87 AKCARVEDSHRLFCLLPV---------KDAISWN-----SIIAGCVQNGLFDEGLKFFRQ------MLIAKI---KPRHV  143 (514)
Q Consensus        87 ~~~g~~~~A~~~f~~~~~---------~d~~~~~-----~li~~~~~~g~~~~A~~l~~~------m~~~g~---~p~~~  143 (514)
                      .....+|.|.++...-..         +-..+++     +....+...|+.++|..+.-+      +.+-+-   ..+..
T Consensus       669 TDlRMFD~aQE~~~~g~~~eKKmL~RKRA~WAr~~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere  748 (1081)
T KOG1538|consen  669 TDLRMFDYAQEFLGSGDPKEKKMLIRKRADWARNIKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAERE  748 (1081)
T ss_pred             HHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhhhcCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhh
Confidence            666777777776654321         1111111     233445556666666654321      111111   22334


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC
Q 040365          144 SFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL  205 (514)
Q Consensus       144 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~  205 (514)
                      +...+..-+-+...+..|.++|..|-+.         .+++++....+++++|..+-++.++
T Consensus       749 ~l~~~a~ylk~l~~~gLAaeIF~k~gD~---------ksiVqlHve~~~W~eAFalAe~hPe  801 (1081)
T KOG1538|consen  749 PLLLCATYLKKLDSPGLAAEIFLKMGDL---------KSLVQLHVETQRWDEAFALAEKHPE  801 (1081)
T ss_pred             HHHHHHHHHhhccccchHHHHHHHhccH---------HHHhhheeecccchHhHhhhhhCcc
Confidence            4555555555666777777777766432         2577788888888888888888774

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=96.07  E-value=0.047  Score=52.04  Aligned_cols=254  Identities=13%  Similarity=0.040  Sum_probs=151.5

Q ss_pred             HHHhcCChhHHHHHHHHHhhCCCCCChh----hHHHHHHHHhCCCChHHHHHHHHHHHH--h--CCC-CchhHHHHHHHH
Q 040365           15 GLARNGLYEEALNIVRQMGNVNLKPDSF----TLSSVLPIFADYVDVIKGKEIHGYAIR--H--GLD-ANVCIGSSLINM   85 (514)
Q Consensus        15 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~~--~--g~~-~~~~~~~~li~~   85 (514)
                      -+++.|+.+..+.+|+..++.|. -|-.    .|..+-.+|.-.+++++|++.|..=+-  .  |-. -.......|-+.
T Consensus        26 RLck~gdcraGv~ff~aA~qvGT-eDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLGNt  104 (639)
T KOG1130|consen   26 RLCKMGDCRAGVDFFKAALQVGT-EDLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLGNT  104 (639)
T ss_pred             HHHhccchhhhHHHHHHHHHhcc-hHHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccccccccch
Confidence            47889999999999999999873 3433    456666777788899999998764321  1  100 011112223333


Q ss_pred             HHHCCCHHHHHHHHcc-CC------CC--ChhHHHHHHHHHHHCCC--------------------hhHHHHHHHHHHH-
Q 040365           86 YAKCARVEDSHRLFCL-LP------VK--DAISWNSIIAGCVQNGL--------------------FDEGLKFFRQMLI-  135 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~-~~------~~--d~~~~~~li~~~~~~g~--------------------~~~A~~l~~~m~~-  135 (514)
                      +--.|.+++|...-.+ +.      .+  ...++..+...|...|+                    ++.|.++|.+=.+ 
T Consensus       105 lKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~fy~eNL~l  184 (639)
T KOG1130|consen  105 LKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVKFYMENLEL  184 (639)
T ss_pred             hhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHHHHHHHHHH
Confidence            3345666665433221 11      00  12234445555554443                    1223333332111 


Q ss_pred             ---CCC-CCCHHHHHHHHHHHhccCChHHHHHHHHHHHH----cCC-CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--
Q 040365          136 ---AKI-KPRHVSFSSIMPACAHLTTLHLGKQLHGCIIR----NGF-DDNMFIASSLLDMYAKCGNIRLARCIFDKMD--  204 (514)
Q Consensus       136 ---~g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~----~~~-~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--  204 (514)
                         .|- -.-...|..+-..|--+|+++.|...|+.-+.    .|- ......+..|.++|.-.|+++.|.+.|..-.  
T Consensus       185 ~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~L  264 (639)
T KOG1130|consen  185 SEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNL  264 (639)
T ss_pred             HHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHH
Confidence               110 01112344444445556789999888876433    221 1234566778889999999999988887542  


Q ss_pred             -----CCC--hhHHHHHHHHHHhCCChHHHHHHHHHHHHc-----CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          205 -----LHD--IVSWTAVIMGNALHGNAHDAISLFEQMEKD-----GVKPNSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       205 -----~~d--~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                           .+.  ..+..+|...|.-..++++|+.++.+-..-     ...-....+-+|..++...|..++|..+...-
T Consensus       265 Aielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~h  341 (639)
T KOG1130|consen  265 AIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELH  341 (639)
T ss_pred             HHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHH
Confidence                 333  346777888888888899999988775431     12224467888999999999999998776654

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=95.88  E-value=0.71  Score=37.04  Aligned_cols=140  Identities=17%  Similarity=0.184  Sum_probs=81.7

Q ss_pred             HhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040365          219 ALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       219 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  298 (514)
                      ...|..++..++..+....   .+..-++.++--....-+-+-..+.++.+-+-+.+.              .+|++...
T Consensus        13 ildG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis--------------~C~NlKrV   75 (161)
T PF09205_consen   13 ILDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDIS--------------KCGNLKRV   75 (161)
T ss_dssp             HHTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GG--------------G-S-THHH
T ss_pred             HHhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhhhcCch--------------hhcchHHH
Confidence            3456777777777776653   234455555544444444455555555553333222              23333333


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCc
Q 040365          299 YEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       299 ~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  377 (514)
                      ..-+-.+.  .+.......++.....|+-+.-.+++..+...+..++....-++++|.+.|+..++..++.+.-++|++
T Consensus        76 i~C~~~~n--~~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   76 IECYAKRN--KLSEYVDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHTT-----HHHHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHhc--chHHHHHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            33333322  233444566778888999999999999988766667889999999999999999999999999999975

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.87  E-value=1.9  Score=41.74  Aligned_cols=160  Identities=16%  Similarity=-0.007  Sum_probs=95.6

Q ss_pred             CCHHHHHHHH-HHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHH--HHHHhcCCHHHHHHHHHhCCCCChh-------
Q 040365          140 PRHVSFSSIM-PACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL--DMYAKCGNIRLARCIFDKMDLHDIV-------  209 (514)
Q Consensus       140 p~~~t~~~ll-~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li--~~y~k~g~~~~A~~~~~~m~~~d~~-------  209 (514)
                      |.-.++-.+- ..+...++.+.|.++-..+++.. ..+  .+..++  .++--.++.+.|..-|++...-|..       
T Consensus       166 pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld-~~n--~~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~~  242 (486)
T KOG0550|consen  166 PACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD-ATN--AEALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKSA  242 (486)
T ss_pred             chhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc-cch--hHHHHhcccccccccchHHHHHHHhhhhccChhhhhHHhH
Confidence            3334444332 23466788888887777776653 112  111222  2233457778888888877532221       


Q ss_pred             --------HHHHHHHHHHhCCChHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC
Q 040365          210 --------SWTAVIMGNALHGNAHDAISLFEQMEKD---GVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS  278 (514)
Q Consensus       210 --------~~~~li~~~~~~g~~~~A~~l~~~m~~~---g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~  278 (514)
                              .|..=..-..+.|++.+|.+.|.+.+..   .++|+...|........+.|+.++|+.--+...   .+.|.
T Consensus       243 ~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al---~iD~s  319 (486)
T KOG0550|consen  243 SMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEAL---KIDSS  319 (486)
T ss_pred             hhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhh---hcCHH
Confidence                    2222333456788899999999888762   345556667777777788888888888776554   33442


Q ss_pred             -HhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          279 -FEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       279 -~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                       +..|..-..++.-.+++++|.+-++..
T Consensus       320 yikall~ra~c~l~le~~e~AV~d~~~a  347 (486)
T KOG0550|consen  320 YIKALLRRANCHLALEKWEEAVEDYEKA  347 (486)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             233333344455567788888877764

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=95.80  E-value=0.14  Score=41.54  Aligned_cols=63  Identities=17%  Similarity=0.284  Sum_probs=32.7

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHhH--------------HhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          242 NSVAFVAVLTACSHAGLIDKAWSYFNSMT--------------KDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       242 ~~~t~~~ll~a~~~~g~~~~a~~~~~~m~--------------~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  304 (514)
                      |..++..++.++++.|+++....+.+..-              ....+.|+..+..+++.+|+..|++..|+++++.
T Consensus         1 de~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~   77 (126)
T PF12921_consen    1 DEELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDF   77 (126)
T ss_pred             ChHHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHH
Confidence            34556666666666666666666655331              1123334445555555555555555555554443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=95.69  E-value=0.026  Score=41.39  Aligned_cols=59  Identities=19%  Similarity=0.180  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC-----C---CCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNMH-----A---GPT-ENVWLTLLSACRVHKNVELAGKVAEKIFM  339 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m~-----~---~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  339 (514)
                      +|+.+...|.+.|++++|++.+++..     .   .|+ ..++..+...+...|++++|++.+++.++
T Consensus         7 ~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    7 AYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44445555555555555555554331     0   122 34566667777777777777777776654

...

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=95.68  E-value=2.1  Score=41.05  Aligned_cols=285  Identities=16%  Similarity=0.111  Sum_probs=169.5

Q ss_pred             HHHHHHHHHhc--CChhHHHHHHHHHhhCCCCCChhhHHHHHHHHh--CCCChHHHHHHHHHHHHhCCCCchhH--HHHH
Q 040365            9 WNTVIVGLARN--GLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFA--DYVDVIKGKEIHGYAIRHGLDANVCI--GSSL   82 (514)
Q Consensus         9 ~~~li~~~~~~--g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~--~~~~~~~a~~~~~~~~~~g~~~~~~~--~~~l   82 (514)
                      |.+|-.++...  |+-..|.++-.+-.+. +..|...+..++.+-.  -.|+.+.|++-|+-|..   .|....  ...|
T Consensus        85 yqALStGliAagAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~---dPEtRllGLRgL  160 (531)
T COG3898          85 YQALSTGLIAAGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLD---DPETRLLGLRGL  160 (531)
T ss_pred             HHHHhhhhhhhccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhc---ChHHHHHhHHHH
Confidence            55555555543  5556665555544321 3456666666665543  45888899998888874   222221  1222


Q ss_pred             HHHHHHCCCHHHHHHHHccCCCC---ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCC-CCCCHHHH--HHHHHHHhc--
Q 040365           83 INMYAKCARVEDSHRLFCLLPVK---DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAK-IKPRHVSF--SSIMPACAH--  154 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~--~~ll~~~~~--  154 (514)
                      .-.--+.|+.+.|...-+...+.   =...|.+.+...+..|+++.|+++++.-++.. +.++..--  ..|+.+-+.  
T Consensus       161 yleAqr~GareaAr~yAe~Aa~~Ap~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~  240 (531)
T COG3898         161 YLEAQRLGAREAARHYAERAAEKAPQLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSL  240 (531)
T ss_pred             HHHHHhcccHHHHHHHHHHHHhhccCCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHH
Confidence            22334567777777766554421   23567888999999999999999998776543 44544322  233333221  


Q ss_pred             -cCChHHHHHHHHHHHHcCCCCcHHHHH-HHHHHHHhcCCHHHHHHHHHhCCC--CChhHHHHHHHHHHhCCChHHHHHH
Q 040365          155 -LTTLHLGKQLHGCIIRNGFDDNMFIAS-SLLDMYAKCGNIRLARCIFDKMDL--HDIVSWTAVIMGNALHGNAHDAISL  230 (514)
Q Consensus       155 -~~~~~~a~~~~~~~~~~~~~~~~~~~~-~li~~y~k~g~~~~A~~~~~~m~~--~d~~~~~~li~~~~~~g~~~~A~~l  230 (514)
                       ..+...|+..-.+..+.  .||..-.. .-..+|.+.|++.++-.+++.+-+  |....|.  +-.+++.|  +.++.-
T Consensus       241 ldadp~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~ia~--lY~~ar~g--dta~dR  314 (531)
T COG3898         241 LDADPASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPDIAL--LYVRARSG--DTALDR  314 (531)
T ss_pred             hcCChHHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChHHHH--HHHHhcCC--CcHHHH
Confidence             12455555555555543  34432211 224678889999999998888853  3333332  22233444  445555


Q ss_pred             HHHHHH-cCCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHh-cCCHHHHHHHHHhCC
Q 040365          231 FEQMEK-DGVKPNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGR-AGKLQEAYEFISNMH  306 (514)
Q Consensus       231 ~~~m~~-~g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~-~g~~~~A~~~~~~m~  306 (514)
                      +++... ..++||. .+...+..+-...|++..|..--+...   ...|....|..|.+.-.. .|+-.++...+.+..
T Consensus       315 lkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~---r~~pres~~lLlAdIeeAetGDqg~vR~wlAqav  390 (531)
T COG3898         315 LKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAA---REAPRESAYLLLADIEEAETGDQGKVRQWLAQAV  390 (531)
T ss_pred             HHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHh---hhCchhhHHHHHHHHHhhccCchHHHHHHHHHHh
Confidence            554433 3356664 566677777778888888877666553   457888888877776543 488888888777653

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=95.53  E-value=1.7  Score=38.75  Aligned_cols=59  Identities=12%  Similarity=0.053  Sum_probs=28.2

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCC--CCHHHHHHHHHHHhccCChHHHHHHHHHHHHc
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIAKIK--PRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN  171 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~g~~--p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  171 (514)
                      ....+.+.|++.+|.+.|+++...-..  --....-.+..++-+.|+++.|...++..++.
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344455666666666666666553110  01112223444555556666666555555543

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.49  E-value=0.33  Score=44.83  Aligned_cols=98  Identities=12%  Similarity=0.014  Sum_probs=51.5

Q ss_pred             CCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc--C-CHHHHHHHHHhCC---CCChhHHH
Q 040365          139 KPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKC--G-NIRLARCIFDKMD---LHDIVSWT  212 (514)
Q Consensus       139 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~--g-~~~~A~~~~~~m~---~~d~~~~~  212 (514)
                      +-|...|..|..+|...++++.|..-|....+.. +++...+..+..++...  | .-.++..+|+++.   ..|+.+-.
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~  231 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALS  231 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHH
Confidence            3345555555555555555555555555555542 33333333333332221  1 2345556666554   22445555


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          213 AVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       213 ~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      .+...+.+.|++.+|...|+.|...
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~  256 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDL  256 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhc
Confidence            5556666777777777777777664

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.48  E-value=0.17  Score=48.48  Aligned_cols=64  Identities=19%  Similarity=0.073  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ..++..|..++.+.+++..|++..++.++++|+|.-....=..+|...|.++.|+..|+++.+.
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~  320 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKL  320 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence            3467778888999999999999999999999999999999999999999999999999998764

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.41  E-value=0.92  Score=45.53  Aligned_cols=157  Identities=10%  Similarity=0.058  Sum_probs=100.8

Q ss_pred             HHhcCChhHHHHHHH-HHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHH
Q 040365           16 LARNGLYEEALNIVR-QMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVED   94 (514)
Q Consensus        16 ~~~~g~~~~A~~l~~-~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~   94 (514)
                      ..-+|+++++..+.+ .-.-..++  ..-...++.-+-+.|..+.|+++-..         +   ..-.+...++|+++.
T Consensus       271 av~~~d~~~v~~~i~~~~ll~~i~--~~~~~~i~~fL~~~G~~e~AL~~~~D---------~---~~rFeLAl~lg~L~~  336 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLPNIP--KDQGQSIARFLEKKGYPELALQFVTD---------P---DHRFELALQLGNLDI  336 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS----------H---HHHHHHHHHCT-HHH
T ss_pred             HHHcCChhhhhhhhhhhhhcccCC--hhHHHHHHHHHHHCCCHHHHHhhcCC---------h---HHHhHHHHhcCCHHH
Confidence            344677888776665 21111222  34467778888888888888776432         2   234566778999999


Q ss_pred             HHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCC
Q 040365           95 SHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFD  174 (514)
Q Consensus        95 A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  174 (514)
                      |.++-++..  +...|..|.....+.|+++-|.+.|.+...         |..++-.|.-.|+.+.-.++.......| .
T Consensus       337 A~~~a~~~~--~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~~-~  404 (443)
T PF04053_consen  337 ALEIAKELD--DPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEERG-D  404 (443)
T ss_dssp             HHHHCCCCS--THHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT--
T ss_pred             HHHHHHhcC--cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHcc-C
Confidence            999988776  667899999999999999999999987543         4556666777888888888887777766 2


Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKM  203 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m  203 (514)
                           +|.-..++.-.|++++..+++.+-
T Consensus       405 -----~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  405 -----INIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             -----HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             -----HHHHHHHHHHcCCHHHHHHHHHHc
Confidence                 344444555567777777666543

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.

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.22  E-value=0.53  Score=47.22  Aligned_cols=132  Identities=15%  Similarity=0.205  Sum_probs=79.5

Q ss_pred             HHhCCChHHHHHHHHHHH-HcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHH
Q 040365          218 NALHGNAHDAISLFEQME-KDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       218 ~~~~g~~~~A~~l~~~m~-~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  296 (514)
                      ....|+++++.++.+.=. -..++  ..-...++.-+.+.|..+.|+++-..-.             .-.++..++|+++
T Consensus       271 av~~~d~~~v~~~i~~~~ll~~i~--~~~~~~i~~fL~~~G~~e~AL~~~~D~~-------------~rFeLAl~lg~L~  335 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLPNIP--KDQGQSIARFLEKKGYPELALQFVTDPD-------------HRFELALQLGNLD  335 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS-HH-------------HHHHHHHHCT-HH
T ss_pred             HHHcCChhhhhhhhhhhhhcccCC--hhHHHHHHHHHHHCCCHHHHHhhcCChH-------------HHhHHHHhcCCHH
Confidence            345677777665554111 11122  2335666777777788888777654322             1234556788888


Q ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          297 EAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       297 ~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      .|.++.++..   +...|..|.......|+++.|+..+.+        ..-+..|+-.|...|+.+.-.++-+....+|
T Consensus       336 ~A~~~a~~~~---~~~~W~~Lg~~AL~~g~~~lAe~c~~k--------~~d~~~L~lLy~~~g~~~~L~kl~~~a~~~~  403 (443)
T PF04053_consen  336 IALEIAKELD---DPEKWKQLGDEALRQGNIELAEECYQK--------AKDFSGLLLLYSSTGDREKLSKLAKIAEERG  403 (443)
T ss_dssp             HHHHHCCCCS---THHHHHHHHHHHHHTTBHHHHHHHHHH--------CT-HHHHHHHHHHCT-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhcC---cHHHHHHHHHHHHHcCCHHHHHHHHHh--------hcCccccHHHHHHhCCHHHHHHHHHHHHHcc
Confidence            8887766554   677888888888888888888888887        3456677778888888777777776666655

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.

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.21  E-value=0.3  Score=46.91  Aligned_cols=95  Identities=16%  Similarity=0.083  Sum_probs=77.8

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH
Q 040365          280 EHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA  357 (514)
Q Consensus       280 ~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  357 (514)
                      ..+..|.-++.+.+++.+|++.-+...  .++|+...-.=..++...|+++.|+..|+++++++|.|-.+-..|+.+-.+
T Consensus       258 ~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~k  337 (397)
T KOG0543|consen  258 ACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQK  337 (397)
T ss_pred             HHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence            456677788899999999998877652  346777777778899999999999999999999999998888888888877


Q ss_pred             ccChhHH-HHHHHHHHhC
Q 040365          358 ARRWKDA-ASLRVFMRNK  374 (514)
Q Consensus       358 ~g~~~~a-~~~~~~m~~~  374 (514)
                      ...+.+. .++|..|-.+
T Consensus       338 ~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  338 IREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHhhc
Confidence            7766555 7788888654

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=94.98  E-value=1.2  Score=43.83  Aligned_cols=64  Identities=13%  Similarity=-0.005  Sum_probs=42.4

Q ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CCC-h---hHHHHHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          174 DDNMFIASSLLDMYAKCGNIRLARCIFDKMD--LHD-I---VSWTAVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       174 ~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~d-~---~~~~~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      +.+...++.+..+|.+.|++++|...|++..  .|+ .   .+|..+..+|...|+.++|++.+++..+.
T Consensus        72 P~~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         72 VKTAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3455666777777777777777777776643  333 2   34777777777777777777777776663

>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=94.92  E-value=0.12  Score=43.17  Aligned_cols=57  Identities=16%  Similarity=0.144  Sum_probs=28.8

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHH
Q 040365           10 NTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYA   67 (514)
Q Consensus        10 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~   67 (514)
                      ..++..+...|++++|+.+.+.+.... +-|...|..+|.++...|+...|.++|..+
T Consensus        66 ~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~  122 (146)
T PF03704_consen   66 ERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERY  122 (146)
T ss_dssp             HHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence            334444555555555555555555432 334445555555555555555555555544

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=94.86  E-value=3.3  Score=38.41  Aligned_cols=141  Identities=17%  Similarity=0.092  Sum_probs=64.5

Q ss_pred             HHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHH
Q 040365          217 GNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       217 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  296 (514)
                      .....|++.+|..+|.......-. +...-..+..++...|+++.|..++..+..+.. .........-+..+.+.....
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~~~-~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~-~~~~~~l~a~i~ll~qaa~~~  220 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAAPE-NSEAKLLLAECLLAAGDVEAAQAILAALPLQAQ-DKAAHGLQAQIELLEQAAATP  220 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhCcc-cchHHHHHHHHHHHcCChHHHHHHHHhCcccch-hhHHHHHHHHHHHHHHHhcCC
Confidence            344556666666666666553211 223344455556666666666666665532100 000111112233344444444


Q ss_pred             HHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CCCcchHHHHHHHHHHcc
Q 040365          297 EAYEFISNMHAGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMID--PNNMGAYVILSNTYAAAR  359 (514)
Q Consensus       297 ~A~~~~~~m~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--p~~~~~~~~l~~~~~~~g  359 (514)
                      +..++-.+.-..| |...-..|...+...|+.+.|...+-.++..+  -.|...-..|+..+...|
T Consensus       221 ~~~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g  286 (304)
T COG3118         221 EIQDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFG  286 (304)
T ss_pred             CHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcC
Confidence            3333433333333 34444445555555555555555544444432  233444445555555444

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.82  E-value=2.9  Score=37.58  Aligned_cols=200  Identities=13%  Similarity=0.116  Sum_probs=110.1

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCC--hhHHHHHHHHHHhCC
Q 040365          145 FSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHD--IVSWTAVIMGNALHG  222 (514)
Q Consensus       145 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d--~~~~~~li~~~~~~g  222 (514)
                      |.-...+|-...++++++..+.+..+. .+.+...|.       ....++.|.-+.++|.+-+  +..++--...|.++|
T Consensus        34 yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfh-------AAKayEqaamLake~~klsEvvdl~eKAs~lY~E~G  105 (308)
T KOG1585|consen   34 YEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFH-------AAKAYEQAAMLAKELSKLSEVVDLYEKASELYVECG  105 (308)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHH-------HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhC
Confidence            334445666677777777766655532 122222221       1223344444555554222  234566667788888


Q ss_pred             ChHHHHHHHHHHHH--cCCCCCHH--HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040365          223 NAHDAISLFEQMEK--DGVKPNSV--AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       223 ~~~~A~~l~~~m~~--~g~~p~~~--t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  298 (514)
                      .++-|-..+++.-+  +++.|+..  .|..-+......++...|.                +.|......|.+..++++|
T Consensus       106 spdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~----------------el~gk~sr~lVrl~kf~Ea  169 (308)
T KOG1585|consen  106 SPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAF----------------ELYGKCSRVLVRLEKFTEA  169 (308)
T ss_pred             CcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHH----------------HHHHHhhhHhhhhHHhhHH
Confidence            87777776666543  34555532  1222222222222222222                3344455567777777777


Q ss_pred             HHHHHhCC-------CCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHhc----CCCCcchHHHHHHHHHHccChhHHHH
Q 040365          299 YEFISNMH-------AGPTE-NVWLTLLSACRVHKNVELAGKVAEKIFMI----DPNNMGAYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       299 ~~~~~~m~-------~~p~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~----~p~~~~~~~~l~~~~~~~g~~~~a~~  366 (514)
                      -..|.+-.       .-|+. ..+-+.+-.+.-..|+..|+..++.-.+.    .|++..+...|+.+| ..|+.+++.+
T Consensus       170 a~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~E~~~k  248 (308)
T KOG1585|consen  170 ATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDIEEIKK  248 (308)
T ss_pred             HHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCHHHHHH
Confidence            66554432       11332 23455555666667888899888886554    366777888888887 4677777776


Q ss_pred             HHH
Q 040365          367 LRV  369 (514)
Q Consensus       367 ~~~  369 (514)
                      +..
T Consensus       249 vl~  251 (308)
T KOG1585|consen  249 VLS  251 (308)
T ss_pred             HHc
Confidence            654

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=94.70  E-value=2.9  Score=37.00  Aligned_cols=194  Identities=19%  Similarity=0.135  Sum_probs=111.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCC-----CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMD-----LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLT  251 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~-----~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  251 (514)
                      ..........+...+.+..+...+....     ......+......+...+....+.+.+.........+. ........
T Consensus        59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  137 (291)
T COG0457          59 AGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALALDPDPD-LAEALLAL  137 (291)
T ss_pred             hHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCcc-hHHHHHHH
Confidence            3444555555666666666666555543     22334455555555556666666666666665332221 11111222


Q ss_pred             -HHHccCCHHHHHHHHHHhHHhcCCCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC--CHHHHHHHHHHHHh
Q 040365          252 -ACSHAGLIDKAWSYFNSMTKDYGIAP----SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP--TENVWLTLLSACRV  323 (514)
Q Consensus       252 -a~~~~g~~~~a~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p--~~~~~~~ll~~~~~  323 (514)
                       ++...|+++.+...+.....   ..|    ....+......+...++.++|...+.... ..+  ....+..+...+..
T Consensus       138 ~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  214 (291)
T COG0457         138 GALYELGDYEEALELYEKALE---LDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLK  214 (291)
T ss_pred             HHHHHcCCHHHHHHHHHHHHh---cCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhhCcccchHHHHHhhHHHHH
Confidence             56667777777777776632   222    22333333444556677777777766653 222  25666777777777


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .++.+.+...+.......|.....+..+...+...|.++++...+......
T Consensus       215 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         215 LGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             cccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            777777777777777777764555556666666666677777777666543

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=94.64  E-value=0.33  Score=44.21  Aligned_cols=112  Identities=8%  Similarity=0.040  Sum_probs=82.4

Q ss_pred             HHHHHHHHccCC--CCChhHHHHHHHHHHHC-----CChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccC--------
Q 040365           92 VEDSHRLFCLLP--VKDAISWNSIIAGCVQN-----GLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLT--------  156 (514)
Q Consensus        92 ~~~A~~~f~~~~--~~d~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~--------  156 (514)
                      +-..++.|...+  ++|-.+|-+++..|...     +..+-....++.|.+.|+.-|..+|..||..+-+-.        
T Consensus        50 Lv~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ  129 (406)
T KOG3941|consen   50 LVHVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQ  129 (406)
T ss_pred             ccchhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHH
Confidence            334566777776  67888898888888654     456666677889999999999999999998765432        


Q ss_pred             --------ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCH-HHHHHHHHhC
Q 040365          157 --------TLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNI-RLARCIFDKM  203 (514)
Q Consensus       157 --------~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~-~~A~~~~~~m  203 (514)
                              +-+-+..++++|...|+-||-.+-..|++++++.|-. .+..+..--|
T Consensus       130 ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWm  185 (406)
T KOG3941|consen  130 KVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWM  185 (406)
T ss_pred             HHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhh
Confidence                    2345778888888889999988888888888877753 3334443334

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.64  E-value=2.1  Score=35.29  Aligned_cols=83  Identities=14%  Similarity=0.235  Sum_probs=37.3

Q ss_pred             HHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhH
Q 040365           46 SVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDE  125 (514)
Q Consensus        46 ~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~  125 (514)
                      .++..+...+........++.+.+.+ ..+....|.++..|++.+. ......+..  ..+.......++.|.+.+.+++
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~~-~~ll~~l~~--~~~~yd~~~~~~~c~~~~l~~~   87 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYDP-QKEIERLDN--KSNHYDIEKVGKLCEKAKLYEE   87 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHCH-HHHHHHHHh--ccccCCHHHHHHHHHHcCcHHH
Confidence            34444444455555555555555554 3445555666666655432 222233331  1122222334444444444444


Q ss_pred             HHHHHHH
Q 040365          126 GLKFFRQ  132 (514)
Q Consensus       126 A~~l~~~  132 (514)
                      +.-++.+
T Consensus        88 ~~~l~~k   94 (140)
T smart00299       88 AVELYKK   94 (140)
T ss_pred             HHHHHHh
Confidence            4444444

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=94.59  E-value=4.1  Score=39.58  Aligned_cols=30  Identities=23%  Similarity=0.128  Sum_probs=21.4

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHhHH
Q 040365          242 NSVAFVAVLTACSHAGLIDKAWSYFNSMTK  271 (514)
Q Consensus       242 ~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  271 (514)
                      |--.+.+++.++.-.|+.+.|.+..+.|.+
T Consensus       304 dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~  333 (374)
T PF13281_consen  304 DYWDVATLLEASVLAGDYEKAIQAAEKAFK  333 (374)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHhh
Confidence            444556677777778888888888887753

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=94.54  E-value=5.2  Score=39.27  Aligned_cols=128  Identities=16%  Similarity=0.128  Sum_probs=93.9

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcC-CCCCHhHHHHHHHHHHhcCCHHHHHHHHHh-CCCCCCHHHH-HHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYG-IAPSFEHYAAVADLLGRAGKLQEAYEFISN-MHAGPTENVW-LTLLSA  320 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~-~~p~~~~~~~li~~~~~~g~~~~A~~~~~~-m~~~p~~~~~-~~ll~~  320 (514)
                      ..|...+++-.+..-++.|+.+|-...+. + +.+++..+++++.-++ .|+..-|..+|+- |..-||...| +-.+.-
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~-~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~d~~~y~~kyl~f  475 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKE-GIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFPDSTLYKEKYLLF  475 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhcc-CCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            45667777878888899999999999665 5 5678889999988665 5778889999875 4444666554 445666


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCC--CCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          321 CRVHKNVELAGKVAEKIFMIDP--NNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p--~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      +...++-+.|..+|+...+.-.  .-...|.-++.--..-|+...|..+-++|.+
T Consensus       476 Li~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         476 LIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            7778888899999986654321  1245788888888888888777777666654

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.45  E-value=0.36  Score=44.03  Aligned_cols=95  Identities=20%  Similarity=0.208  Sum_probs=61.6

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHH
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKDGVKP--NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVAD  287 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p--~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~  287 (514)
                      |+.-+.. .+.|++.+|...|...++....-  ..-.+-.|..++...|+++.|..+|..+.++++-.|. ++.+--|..
T Consensus       145 Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~  223 (262)
T COG1729         145 YNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGV  223 (262)
T ss_pred             HHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHH
Confidence            5554443 34566777777777777642110  1123445777777788888888888877777666663 466666777


Q ss_pred             HHHhcCCHHHHHHHHHhCC
Q 040365          288 LLGRAGKLQEAYEFISNMH  306 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~  306 (514)
                      ...+.|+.++|...+++..
T Consensus       224 ~~~~l~~~d~A~atl~qv~  242 (262)
T COG1729         224 SLGRLGNTDEACATLQQVI  242 (262)
T ss_pred             HHHHhcCHHHHHHHHHHHH
Confidence            7777777777777776654

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=94.42  E-value=0.83  Score=43.23  Aligned_cols=44  Identities=11%  Similarity=0.182  Sum_probs=20.6

Q ss_pred             HHCCChhHHHHHHHHHHHC--CCCCCHHHHHHHHHHHhccCChHHH
Q 040365          118 VQNGLFDEGLKFFRQMLIA--KIKPRHVSFSSIMPACAHLTTLHLG  161 (514)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~--g~~p~~~t~~~ll~~~~~~~~~~~a  161 (514)
                      .+..+.++|+..+.+-...  ...---.+|..+..+.++.|.++++
T Consensus        17 y~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~m   62 (518)
T KOG1941|consen   17 YQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEM   62 (518)
T ss_pred             hcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHH
Confidence            3455666666666554432  0111123444555555555555444

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=94.38  E-value=1.2  Score=44.20  Aligned_cols=68  Identities=16%  Similarity=0.114  Sum_probs=43.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCC--CcchHHHHHHHHHHccChhHHHHHHHHHHhCCCccCCc
Q 040365          314 WLTLLSACRVHKNVELAGKVAEKIFMIDPN--NMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPA  381 (514)
Q Consensus       314 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~--~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~  381 (514)
                      =..|..++.+.|+.++|++.++++++..|.  +......|+.++...+++.++..++.+-.+-...+...
T Consensus       262 KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAt  331 (539)
T PF04184_consen  262 KRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSAT  331 (539)
T ss_pred             HHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHH
Confidence            345666667777777777777777665543  33456677777777777777777777654444444443

The molecular function of this protein is uncertain.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=94.26  E-value=4.2  Score=41.42  Aligned_cols=161  Identities=14%  Similarity=0.095  Sum_probs=106.6

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHc-CCCCCH-----HHHHHHHHHHHc----cCCHHHHHHHHHHhHHhcCCCCCHh
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKD-GVKPNS-----VAFVAVLTACSH----AGLIDKAWSYFNSMTKDYGIAPSFE  280 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~-----~t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~p~~~  280 (514)
                      ...+++...-.|+-+.+++++.+-.+. ++.-..     .+|..++..+..    ....+.+.+++..+.+.   -|+..
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            334555555677778888777776552 232211     223333333332    45788899999999765   46655


Q ss_pred             HHHHH-HHHHHhcCCHHHHHHHHHhCCC-C-----CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHH-HHH
Q 040365          281 HYAAV-ADLLGRAGKLQEAYEFISNMHA-G-----PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYV-ILS  352 (514)
Q Consensus       281 ~~~~l-i~~~~~~g~~~~A~~~~~~m~~-~-----p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~-~l~  352 (514)
                      .|... ...+...|++++|.+.|++... +     -....+--+...+....++++|...|.++.+.+.-+...|. ..+
T Consensus       268 lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~WSka~Y~Y~~a  347 (468)
T PF10300_consen  268 LFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKWSKAFYAYLAA  347 (468)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhccccHHHHHHHHHH
Confidence            55433 4567788999999999997542 1     12234445666778889999999999999998766556666 445


Q ss_pred             HHHHHccCh-------hHHHHHHHHHHhC
Q 040365          353 NTYAAARRW-------KDAASLRVFMRNK  374 (514)
Q Consensus       353 ~~~~~~g~~-------~~a~~~~~~m~~~  374 (514)
                      .+|...|+.       ++|.+++.+....
T Consensus       348 ~c~~~l~~~~~~~~~~~~a~~l~~~vp~l  376 (468)
T PF10300_consen  348 ACLLMLGREEEAKEHKKEAEELFRKVPKL  376 (468)
T ss_pred             HHHHhhccchhhhhhHHHHHHHHHHHHHH
Confidence            556778888       8888888877543

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.

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=94.19  E-value=0.1  Score=30.92  Aligned_cols=32  Identities=19%  Similarity=0.200  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      .+|..+..++...|++++|+..++++++++|+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence            46788888888888888888888888888885

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=94.17  E-value=0.61  Score=37.32  Aligned_cols=89  Identities=19%  Similarity=0.102  Sum_probs=66.8

Q ss_pred             HHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC-CCC---cchHHHHHHHHHHccCh
Q 040365          288 LLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMID-PNN---MGAYVILSNTYAAARRW  361 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-p~~---~~~~~~l~~~~~~~g~~  361 (514)
                      +++..|+++.|++.|.+..  .+.....||.-..+++-.|+.++|..-+++++++. |..   -.+|+.-...|-..|+-
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~d  131 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGND  131 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCch
Confidence            4677888888888887652  23456778888888888888888888888888875 332   13566667778888888


Q ss_pred             hHHHHHHHHHHhCCC
Q 040365          362 KDAASLRVFMRNKGM  376 (514)
Q Consensus       362 ~~a~~~~~~m~~~g~  376 (514)
                      +.|+.=|+...+.|-
T Consensus       132 d~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  132 DAARADFEAAAQLGS  146 (175)
T ss_pred             HHHHHhHHHHHHhCC
Confidence            888888888777663

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=94.02  E-value=0.16  Score=29.91  Aligned_cols=33  Identities=36%  Similarity=0.371  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN  344 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~  344 (514)
                      ..|..+...+...|++++|++.++++++++|+|
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~~   34 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPNN   34 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcCC
Confidence            356777788888888888888888888888764

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=94.02  E-value=3  Score=34.44  Aligned_cols=39  Identities=10%  Similarity=-0.042  Sum_probs=17.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCCCC---ChhHHHHHHHHHHhC
Q 040365          183 LLDMYAKCGNIRLARCIFDKMDLH---DIVSWTAVIMGNALH  221 (514)
Q Consensus       183 li~~y~k~g~~~~A~~~~~~m~~~---d~~~~~~li~~~~~~  221 (514)
                      ++..+.+.+........++.+...   +....|.++..|++.
T Consensus        13 vv~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~   54 (140)
T smart00299       13 VVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKY   54 (140)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHH
Confidence            344444444444554444444321   233444444444443

>PRK11906 transcriptional regulator; Provisional

Probab=93.99  E-value=1.1  Score=44.39  Aligned_cols=78  Identities=8%  Similarity=-0.018  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          295 LQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       295 ~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      ..+|.++.+...  .+.|......+..+....++++.|...|+++..++|+.+.+|...+....-.|+.++|.+.+++-.
T Consensus       320 ~~~a~~~A~rAveld~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~al  399 (458)
T PRK11906        320 AQKALELLDYVSDITTVDGKILAIMGLITGLSGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEKIEEARICIDKSL  399 (458)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            445555555442  234666666666666777778888888888888888888888888888888888888888877643

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.89  E-value=13  Score=41.25  Aligned_cols=82  Identities=22%  Similarity=0.140  Sum_probs=41.1

Q ss_pred             HHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 040365          249 VLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVE  328 (514)
Q Consensus       249 ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~  328 (514)
                      .+.+|...|+|++|..+..++..  +-.--..+-..|+.-+...++.-+|-++..+.-..|..     .+..+++...++
T Consensus       971 Al~a~~~~~dWr~~l~~a~ql~~--~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd~~~-----av~ll~ka~~~~ 1043 (1265)
T KOG1920|consen  971 ALKAYKECGDWREALSLAAQLSE--GKDELVILAEELVSRLVEQRKHYEAAKILLEYLSDPEE-----AVALLCKAKEWE 1043 (1265)
T ss_pred             HHHHHHHhccHHHHHHHHHhhcC--CHHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcCHHH-----HHHHHhhHhHHH
Confidence            34555666666666666655521  11111222345566666666666666666655433321     223334444566


Q ss_pred             HHHHHHHHH
Q 040365          329 LAGKVAEKI  337 (514)
Q Consensus       329 ~a~~~~~~~  337 (514)
                      +|.++....
T Consensus      1044 eAlrva~~~ 1052 (1265)
T KOG1920|consen 1044 EALRVASKA 1052 (1265)
T ss_pred             HHHHHHHhc
Confidence            666555543

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=93.80  E-value=2.1  Score=41.91  Aligned_cols=145  Identities=11%  Similarity=0.095  Sum_probs=95.3

Q ss_pred             hhhHHHHHHHHhCCCChHHHHHHHHHHHHhC-CCCchhHHHHHHHHHHHCCCHHHHHHHHccCC--CCChhHH-HHHHHH
Q 040365           41 SFTLSSVLPIFADYVDVIKGKEIHGYAIRHG-LDANVCIGSSLINMYAKCARVEDSHRLFCLLP--VKDAISW-NSIIAG  116 (514)
Q Consensus        41 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g-~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~--~~d~~~~-~~li~~  116 (514)
                      .+.|...+.+..+...++.|+.+|..+.+.| ..+++.++++++.-|+ .|+...|-++|+.-.  -+|+..| +-.+.-
T Consensus       397 t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~d~~~y~~kyl~f  475 (660)
T COG5107         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFPDSTLYKEKYLLF  475 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            3556667777777777888888888888887 5678888888887665 567777888887533  3444433 445566


Q ss_pred             HHHCCChhHHHHHHHHHHHCCCCCC--HHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh
Q 040365          117 CVQNGLFDEGLKFFRQMLIAKIKPR--HVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK  189 (514)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~--~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k  189 (514)
                      +...++-+.|..+|+..... +..+  ...|..+|.--+..|++..+..+-+.+...  -|-..+.....+.|+-
T Consensus       476 Li~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~--~pQen~~evF~Sry~i  547 (660)
T COG5107         476 LIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL--VPQENLIEVFTSRYAI  547 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH--cCcHhHHHHHHHHHhh
Confidence            66777888888888754432 2223  456777787777888887777776666554  2333333444445543

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=93.79  E-value=2.9  Score=34.36  Aligned_cols=61  Identities=16%  Similarity=0.162  Sum_probs=31.8

Q ss_pred             HHHhCCChHHHHHHHHHHHHcCC--CCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC
Q 040365          217 GNALHGNAHDAISLFEQMEKDGV--KPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP  277 (514)
Q Consensus       217 ~~~~~g~~~~A~~l~~~m~~~g~--~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p  277 (514)
                      ...+.|++++|.+.|+.+...=.  +-....-..++.++.+.+++++|...+++.++-+.-.|
T Consensus        19 ~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp   81 (142)
T PF13512_consen   19 EALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHP   81 (142)
T ss_pred             HHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCC
Confidence            33455666666666666655310  01223444555666666666666666666655433333

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=93.68  E-value=2.9  Score=39.51  Aligned_cols=134  Identities=12%  Similarity=0.190  Sum_probs=74.9

Q ss_pred             hhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhc--cC----ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHH
Q 040365          123 FDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH--LT----TLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLA  196 (514)
Q Consensus       123 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~--~~----~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A  196 (514)
                      +++.+.+++.|.+.|++-+..+|.+.......  ..    ....+..+|+.|.+.-.-.                     
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fL---------------------  136 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFL---------------------  136 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccc---------------------
Confidence            34556788888999998888888765444333  11    2344556666665542100                     


Q ss_pred             HHHHHhCCCCChhHHHHHHHHHHhCCC----hHHHHHHHHHHHHcCCCCCH--HHHHHHHHHHHccCC--HHHHHHHHHH
Q 040365          197 RCIFDKMDLHDIVSWTAVIMGNALHGN----AHDAISLFEQMEKDGVKPNS--VAFVAVLTACSHAGL--IDKAWSYFNS  268 (514)
Q Consensus       197 ~~~~~~m~~~d~~~~~~li~~~~~~g~----~~~A~~l~~~m~~~g~~p~~--~t~~~ll~a~~~~g~--~~~a~~~~~~  268 (514)
                             ..++-.++..|+..  ..++    .+.+..+|+.+...|+..+.  .....+|..+.....  +..+..+++.
T Consensus       137 -------Ts~~D~~~a~lLA~--~~~~~e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~  207 (297)
T PF13170_consen  137 -------TSPEDYPFAALLAM--TSEDVEELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNA  207 (297)
T ss_pred             -------cCccchhHHHHHhc--ccccHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHH
Confidence                   01222333333322  1111    35667778888887776643  334444443333222  4477788888


Q ss_pred             hHHhcCCCCCHhHHHHHHH
Q 040365          269 MTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       269 m~~~~~~~p~~~~~~~li~  287 (514)
                      +.+ .|+++...+|..+.-
T Consensus       208 l~~-~~~kik~~~yp~lGl  225 (297)
T PF13170_consen  208 LKK-NGVKIKYMHYPTLGL  225 (297)
T ss_pred             HHH-cCCccccccccHHHH
Confidence            854 488888888766543

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=93.64  E-value=5.4  Score=39.80  Aligned_cols=98  Identities=10%  Similarity=0.135  Sum_probs=67.7

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCC--CCCH--HHHHHHHHHHH
Q 040365          247 VAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHA--GPTE--NVWLTLLSACR  322 (514)
Q Consensus       247 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~p~~--~~~~~ll~~~~  322 (514)
                      ..+..++-+.|+.++|++.|++|.+++...........|+..|...+.+.++..++.+...  -|..  ..|++.+--.+
T Consensus       263 rRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaR  342 (539)
T PF04184_consen  263 RRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKAR  342 (539)
T ss_pred             HHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHH
Confidence            3466667788999999999999987644333455677899999999999999999988752  1433  45666554444


Q ss_pred             hcCCH---------------HHHHHHHHHHHhcCCCC
Q 040365          323 VHKNV---------------ELAGKVAEKIFMIDPNN  344 (514)
Q Consensus       323 ~~~~~---------------~~a~~~~~~~~~~~p~~  344 (514)
                      ..++.               ..|.++..++.+.+|.-
T Consensus       343 av~d~fs~e~a~rRGls~ae~~aveAi~RAvefNPHV  379 (539)
T PF04184_consen  343 AVGDKFSPEAASRRGLSPAEMNAVEAIHRAVEFNPHV  379 (539)
T ss_pred             hhccccCchhhhhcCCChhHHHHHHHHHHHHHhCCCC
Confidence            44431               23456777877777653

The molecular function of this protein is uncertain.

>PRK09687 putative lyase; Provisional

Probab=93.44  E-value=6.9  Score=36.78  Aligned_cols=235  Identities=10%  Similarity=0.008  Sum_probs=103.2

Q ss_pred             CCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCCh----hHHHHHHHHHHHCCCCCCHHHHHHH
Q 040365           73 DANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLF----DEGLKFFRQMLIAKIKPRHVSFSSI  148 (514)
Q Consensus        73 ~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~----~~A~~l~~~m~~~g~~p~~~t~~~l  148 (514)
                      .+|..+....+..+...|..+....+......+|...-...+.++.+.|+.    .+++.++..+...  .|+...-...
T Consensus        34 d~d~~vR~~A~~aL~~~~~~~~~~~l~~ll~~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR~~A  111 (280)
T PRK09687         34 DHNSLKRISSIRVLQLRGGQDVFRLAIELCSSKNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVRASA  111 (280)
T ss_pred             CCCHHHHHHHHHHHHhcCcchHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHHHHH
Confidence            344445555555555555433333333323344555555555566666653    3456666655332  3455555455


Q ss_pred             HHHHhccCChHH--HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCC-ChH
Q 040365          149 MPACAHLTTLHL--GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHG-NAH  225 (514)
Q Consensus       149 l~~~~~~~~~~~--a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g-~~~  225 (514)
                      +.+++..+....  ..+....+...-..++..+-...+.++++.|+-+....+..-+..+|...-..-+.++.+.+ ...
T Consensus       112 ~~aLG~~~~~~~~~~~~a~~~l~~~~~D~~~~VR~~a~~aLg~~~~~~ai~~L~~~L~d~~~~VR~~A~~aLg~~~~~~~  191 (280)
T PRK09687        112 INATGHRCKKNPLYSPKIVEQSQITAFDKSTNVRFAVAFALSVINDEAAIPLLINLLKDPNGDVRNWAAFALNSNKYDNP  191 (280)
T ss_pred             HHHHhcccccccccchHHHHHHHHHhhCCCHHHHHHHHHHHhccCCHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCCCCH
Confidence            555544432110  11122222221123345555555666666665433333333333444433333344444432 133


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          226 DAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       226 ~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      .+...+..+..   .+|...-...+.++.+.++. .+...+-...+.    ++  .....+.+++..|.. +|...+..+
T Consensus       192 ~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~----~~--~~~~a~~ALg~ig~~-~a~p~L~~l  260 (280)
T PRK09687        192 DIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKK----GT--VGDLIIEAAGELGDK-TLLPVLDTL  260 (280)
T ss_pred             HHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcC----Cc--hHHHHHHHHHhcCCH-hHHHHHHHH
Confidence            45555554442   34555555555566665553 333333333221    11  123445555555553 344444443


Q ss_pred             C-CCCCHHHHHHHHHH
Q 040365          306 H-AGPTENVWLTLLSA  320 (514)
Q Consensus       306 ~-~~p~~~~~~~ll~~  320 (514)
                      . ..||..+-...+.+
T Consensus       261 ~~~~~d~~v~~~a~~a  276 (280)
T PRK09687        261 LYKFDDNEIITKAIDK  276 (280)
T ss_pred             HhhCCChhHHHHHHHH
Confidence            3 23444444433333

>PRK11906 transcriptional regulator; Provisional

Probab=93.44  E-value=8.7  Score=38.19  Aligned_cols=174  Identities=11%  Similarity=0.156  Sum_probs=110.5

Q ss_pred             CCHHHHHHHHHhCCCCCh---hHH--HHHHHHHHhC-----CChHHHHHHHHHHHH-cCCCCCHH-HHHHHHHHHHc---
Q 040365          191 GNIRLARCIFDKMDLHDI---VSW--TAVIMGNALH-----GNAHDAISLFEQMEK-DGVKPNSV-AFVAVLTACSH---  255 (514)
Q Consensus       191 g~~~~A~~~~~~m~~~d~---~~~--~~li~~~~~~-----g~~~~A~~l~~~m~~-~g~~p~~~-t~~~ll~a~~~---  255 (514)
                      ..+..++. -...+..+.   ..|  ..++.|....     ...+.|+.+|.+... ..+.|+-. .|..+..++..   
T Consensus       232 ~~~~~~E~-~~r~~~~~l~~~~a~~~d~ylrg~~~~~~~t~~~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~  310 (458)
T PRK11906        232 QTVHKPER-SVRLAKQDQGYKNHYLSDEMLAGKKELYDFTPESIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLAL  310 (458)
T ss_pred             hhhhhhhh-hhcCCCCCcccccchhhHHHHHHHHHhhccCHHHHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHH
Confidence            44444444 233334455   567  6677665542     235688889999883 33677643 33333322211   


Q ss_pred             ------cCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCC
Q 040365          256 ------AGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT-ENVWLTLLSACRVHKN  326 (514)
Q Consensus       256 ------~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~-~~~~~~ll~~~~~~~~  326 (514)
                            .....+|.++-+...   .+.| |......+..++.-.|+++.|..+|++.. ..|| ..+|......+.-.|+
T Consensus       311 ~g~~~~~~~~~~a~~~A~rAv---eld~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~  387 (458)
T PRK11906        311 HGKSELELAAQKALELLDYVS---DITTVDGKILAIMGLITGLSGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEK  387 (458)
T ss_pred             hcCCCchHHHHHHHHHHHHHH---hcCCCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCC
Confidence                  233455666666554   4455 67777777777788888999999999874 3454 5667777777788999


Q ss_pred             HHHHHHHHHHHHhcCCCCcchHH--HHHHHHHHccChhHHHHHHH
Q 040365          327 VELAGKVAEKIFMIDPNNMGAYV--ILSNTYAAARRWKDAASLRV  369 (514)
Q Consensus       327 ~~~a~~~~~~~~~~~p~~~~~~~--~l~~~~~~~g~~~~a~~~~~  369 (514)
                      .++|.+.+++.++++|.....-.  ..++.|... ..++|.+++-
T Consensus       388 ~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  431 (458)
T PRK11906        388 IEEARICIDKSLQLEPRRRKAVVIKECVDMYVPN-PLKNNIKLYY  431 (458)
T ss_pred             HHHHHHHHHHHhccCchhhHHHHHHHHHHHHcCC-chhhhHHHHh
Confidence            99999999999999997544332  333455544 4566666653

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=93.29  E-value=6.3  Score=35.85  Aligned_cols=143  Identities=16%  Similarity=0.172  Sum_probs=83.3

Q ss_pred             hhHHHHHHHHHHhCCChHHHHHHHHHHHHcC-CC-CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHH
Q 040365          208 IVSWTAVIMGNALHGNAHDAISLFEQMEKDG-VK-PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAV  285 (514)
Q Consensus       208 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~l  285 (514)
                      +..|-.-+..-.+.|++++|.+.|+.+...- .. -...+...++.++.+.++.++|+...++..+.++-.|+.. |...
T Consensus        34 ~~~LY~~g~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~d-Y~~Y  112 (254)
T COG4105          34 ASELYNEGLTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNAD-YAYY  112 (254)
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChh-HHHH
Confidence            3344444555567788888888888877531 11 1345666677777778888888888888777766666642 3333


Q ss_pred             HHHHHhcCCHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc-----------------ch
Q 040365          286 ADLLGRAGKLQEAYEFISNMH-AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM-----------------GA  347 (514)
Q Consensus       286 i~~~~~~g~~~~A~~~~~~m~-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~-----------------~~  347 (514)
                      +.+++          .|..+. ...|..             -...|..-|+.++..-|++.                 .-
T Consensus       113 lkgLs----------~~~~i~~~~rDq~-------------~~~~A~~~f~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~  169 (254)
T COG4105         113 LKGLS----------YFFQIDDVTRDQS-------------AARAAFAAFKELVQRYPNSRYAPDAKARIVKLNDALAGH  169 (254)
T ss_pred             HHHHH----------HhccCCccccCHH-------------HHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHHHHH
Confidence            44433          111111 001110             11223333444444444432                 11


Q ss_pred             HHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          348 YVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       348 ~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      =....+-|.+.|.|..|..-++.|.+.
T Consensus       170 Em~IaryY~kr~~~~AA~nR~~~v~e~  196 (254)
T COG4105         170 EMAIARYYLKRGAYVAAINRFEEVLEN  196 (254)
T ss_pred             HHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence            235677899999999999999999876

>PRK15331 chaperone protein SicA; Provisional

Probab=92.99  E-value=1.2  Score=37.51  Aligned_cols=18  Identities=39%  Similarity=0.634  Sum_probs=8.7

Q ss_pred             HHCCChhHHHHHHHHHHH
Q 040365          118 VQNGLFDEGLKFFRQMLI  135 (514)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~  135 (514)
                      -+.|++++|..+|+-+..
T Consensus        48 y~~Gk~~eA~~~F~~L~~   65 (165)
T PRK15331         48 YNQGRLDEAETFFRFLCI   65 (165)
T ss_pred             HHCCCHHHHHHHHHHHHH
Confidence            344555555555544443

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=92.80  E-value=0.62  Score=43.17  Aligned_cols=62  Identities=18%  Similarity=0.191  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      .++..++..+...|+.+.+...++++++.+|-+...|..|+.+|.+.|+...|...++.+.+
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence            45566777888888899999999999999999989999999999999999999999988865

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=92.76  E-value=10  Score=36.85  Aligned_cols=150  Identities=12%  Similarity=0.008  Sum_probs=76.8

Q ss_pred             CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC--CH
Q 040365          205 LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP---NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP--SF  279 (514)
Q Consensus       205 ~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p---~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p--~~  279 (514)
                      .....+|..+...+.+.|+++.|...+.++...+..+   +......-....-..|+.++|+..++...+. .+..  +.
T Consensus       143 ~~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~-~~~~~~~~  221 (352)
T PF02259_consen  143 EELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKC-RLSKNIDS  221 (352)
T ss_pred             hHHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHH-Hhhhcccc
Confidence            3345678888888888888888888888877643211   2223333344455667778888877776552 1111  11


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHH-HHhCCCCCCHHHHHHHHHHHHhc------CCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          280 EHYAAVADLLGRAGKLQEAYEF-ISNMHAGPTENVWLTLLSACRVH------KNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       280 ~~~~~li~~~~~~g~~~~A~~~-~~~m~~~p~~~~~~~ll~~~~~~------~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      .....+...+..  ..+..... ......+.-..++..+..-+...      ++.+.+...|+.+.+..|.....|..++
T Consensus       222 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~a~~~l~~a~w~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~k~~~~~a  299 (352)
T PF02259_consen  222 ISNAELKSGLLE--SLEVISSTNLDKESKELKAKAFLLLAKWLDELYSKLSSESSDEILKYYKEATKLDPSWEKAWHSWA  299 (352)
T ss_pred             ccHHHHhhcccc--ccccccccchhhhhHHHHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHHHhChhHHHHHHHHH
Confidence            111111111000  00000000 00000000012233333333333      7788889999999999888777777666


Q ss_pred             HHHHH
Q 040365          353 NTYAA  357 (514)
Q Consensus       353 ~~~~~  357 (514)
                      ..+.+
T Consensus       300 ~~~~~  304 (352)
T PF02259_consen  300 LFNDK  304 (352)
T ss_pred             HHHHH
Confidence            65543

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=92.66  E-value=13  Score=37.94  Aligned_cols=178  Identities=17%  Similarity=0.154  Sum_probs=105.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCCCCCh---hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCC--CCHHHHHHHHH
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMDLHDI---VSWTAVIMGNALHGNAHDAISLFEQMEKDGVK--PNSVAFVAVLT  251 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~---~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~--p~~~t~~~ll~  251 (514)
                      ..+|...++.-.+.|+.+.+.-+|++...|-.   .-|--.+.-....|+.+-|-.++....+--++  |....+.+.  
T Consensus       297 l~nw~~yLdf~i~~g~~~~~~~l~ercli~cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~i~L~~a~--  374 (577)
T KOG1258|consen  297 LKNWRYYLDFEITLGDFSRVFILFERCLIPCALYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPIIHLLEAR--  374 (577)
T ss_pred             HHHHHHHhhhhhhcccHHHHHHHHHHHHhHHhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcHHHHHHHH--
Confidence            44555555555566666666666655543321   22333333333346666555555544442222  222222222  


Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCCCH-hHHHHHHHHHHhcCCHHHHH---HHHHhCC-CCCCHHHHHHHHH-----HH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAPSF-EHYAAVADLLGRAGKLQEAY---EFISNMH-AGPTENVWLTLLS-----AC  321 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p~~-~~~~~li~~~~~~g~~~~A~---~~~~~m~-~~p~~~~~~~ll~-----~~  321 (514)
                      -+-..|+++.|..+++.+..++   |+. ..-..-+....+.|..+.+.   +++.... .+-+..+...+.-     -+
T Consensus       375 f~e~~~n~~~A~~~lq~i~~e~---pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~~~~~~~i~~~l~~~~~r~~~  451 (577)
T KOG1258|consen  375 FEESNGNFDDAKVILQRIESEY---PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYEGKENNGILEKLYVKFARLRY  451 (577)
T ss_pred             HHHhhccHHHHHHHHHHHHhhC---CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhcccccCcchhHHHHHHHHHHHH
Confidence            2455789999999999997653   643 33334456677888888887   5554432 2223222222222     24


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHcc
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR  359 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  359 (514)
                      ...++.+.|..++.++.+..|++...|..+++.....+
T Consensus       452 ~i~~d~~~a~~~l~~~~~~~~~~k~~~~~~~~~~~~~~  489 (577)
T KOG1258|consen  452 KIREDADLARIILLEANDILPDCKVLYLELIRFELIQP  489 (577)
T ss_pred             HHhcCHHHHHHHHHHhhhcCCccHHHHHHHHHHHHhCC
Confidence            56688999999999999999999999999988877665

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.26  E-value=5.1  Score=37.74  Aligned_cols=112  Identities=18%  Similarity=0.149  Sum_probs=57.6

Q ss_pred             cCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH--HHH--HHHHHHHccCCHHHH
Q 040365          190 CGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV--AFV--AVLTACSHAGLIDKA  262 (514)
Q Consensus       190 ~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~--t~~--~ll~a~~~~g~~~~a  262 (514)
                      .|+..+|-..++++.   +.|..+|+--=.+|...|+...-...+++.... -.||..  +|.  .+..++...|-+++|
T Consensus       116 ~g~~h~a~~~wdklL~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y~dA  194 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIYDDA  194 (491)
T ss_pred             cccccHHHHHHHHHHHhCchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccchhH
Confidence            455555555555554   335566666666666666666666666665542 123321  222  222233445666666


Q ss_pred             HHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          263 WSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       263 ~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      .+.-++..   .+.| |.-.-.++...+--.|++.++.+++.+-
T Consensus       195 Ek~A~ral---qiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~t  235 (491)
T KOG2610|consen  195 EKQADRAL---QINRFDCWASHAKAHVLEMNGRHKEGKEFMYKT  235 (491)
T ss_pred             HHHHHhhc---cCCCcchHHHHHHHHHHHhcchhhhHHHHHHhc
Confidence            65555432   3333 3333444555555666666666666554

>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=92.19  E-value=5.1  Score=32.38  Aligned_cols=65  Identities=14%  Similarity=0.042  Sum_probs=43.1

Q ss_pred             hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCC
Q 040365          108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGF  173 (514)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  173 (514)
                      ...+..+....+.|.-+.-.+++..+.+. -.|++.....+..||.+.|+..++.+++.++-+.|+
T Consensus        87 e~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   87 EYVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence            34455667777888888877888777653 367777777888888888888888888888877774

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=91.98  E-value=14  Score=36.57  Aligned_cols=198  Identities=17%  Similarity=0.171  Sum_probs=110.3

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHH-------HHHHHHHhc----CCHHHHHHHHHhCCCCChhH-
Q 040365          143 VSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIAS-------SLLDMYAKC----GNIRLARCIFDKMDLHDIVS-  210 (514)
Q Consensus       143 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-------~li~~y~k~----g~~~~A~~~~~~m~~~d~~~-  210 (514)
                      .+|..++..+.+.++...|.+.+..+.-.  .|+..+..       +|.++.+.-    -++.+=..+++.....|+.. 
T Consensus       299 ~~F~~~Ls~~Vk~~~T~~a~q~l~lL~~l--dp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~DiDrq  376 (549)
T PF07079_consen  299 DRFGNLLSFKVKQVQTEEAKQYLALLKIL--DPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDIDRQ  376 (549)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHHHhc--CCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcccHH
Confidence            46777888888888888888887766543  34333222       222222210    11222233444444333321 


Q ss_pred             --HHHHH---HHHHhCCC-hHHHHHHHHHHHHcCCCCCH-----HHHHHHHHHHHcc---CCHHHHHHHHHHhHHhcCCC
Q 040365          211 --WTAVI---MGNALHGN-AHDAISLFEQMEKDGVKPNS-----VAFVAVLTACSHA---GLIDKAWSYFNSMTKDYGIA  276 (514)
Q Consensus       211 --~~~li---~~~~~~g~-~~~A~~l~~~m~~~g~~p~~-----~t~~~ll~a~~~~---g~~~~a~~~~~~m~~~~~~~  276 (514)
                        -..|+   .-+-+.|. -++|+++++...+  +.|..     .++..+=.+|.+.   ..+.+-..+-+-+ ++-|+.
T Consensus       377 QLvh~L~~~Ak~lW~~g~~dekalnLLk~il~--ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi-~e~gl~  453 (549)
T PF07079_consen  377 QLVHYLVFGAKHLWEIGQCDEKALNLLKLILQ--FTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFI-TEVGLT  453 (549)
T ss_pred             HHHHHHHHHHHHHHhcCCccHHHHHHHHHHHH--hccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHH-HhcCCC
Confidence              11122   22445555 7888888888876  33332     2333333344332   3344444444433 455877


Q ss_pred             C----CHhHHHHHHHH--HHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHH
Q 040365          277 P----SFEHYAAVADL--LGRAGKLQEAYEFISNM-HAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYV  349 (514)
Q Consensus       277 p----~~~~~~~li~~--~~~~g~~~~A~~~~~~m-~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~  349 (514)
                      |    +.+.-|.|.++  +...|++.++.-.-.-. ...|++.+|+-+.-+.....++++|-..+..+    |++..++.
T Consensus       454 ~i~i~e~eian~LaDAEyLysqgey~kc~~ys~WL~~iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~L----P~n~~~~d  529 (549)
T PF07079_consen  454 PITISEEEIANFLADAEYLYSQGEYHKCYLYSSWLTKIAPSPQAYRLLGLCLMENKRYQEAWEYLQKL----PPNERMRD  529 (549)
T ss_pred             cccccHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHhhHHHHHHHHHhC----CCchhhHH
Confidence            7    34666777666  55778888876543322 34578888888888888888888888877664    44444444

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.91  E-value=3.9  Score=37.49  Aligned_cols=101  Identities=17%  Similarity=0.183  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCC-CHHHHHHHH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNM----HAGP-TENVWLTLL  318 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p-~~~~~~~ll  318 (514)
                      -|...+..+ +.|++..|.+-|...++.|.-.+ ....+--|...+...|++++|...|..+    |..| -+...--|.
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            465555443 55668888888888877643322 3445556777777888888877777655    2222 224555566


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCcc
Q 040365          319 SACRVHKNVELAGKVAEKIFMIDPNNMG  346 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~p~~~~  346 (514)
                      ......|+.++|...++++.+..|..+.
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~YP~t~a  250 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKRYPGTDA  250 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHCCCCHH
Confidence            6677777777777777777777776543

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=91.66  E-value=10  Score=34.50  Aligned_cols=179  Identities=15%  Similarity=0.116  Sum_probs=109.1

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCC------hhHHHHHHHHHHhCCChHHHHHHHHHHHHc-CCCCCHHHHH
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMDLHD------IVSWTAVIMGNALHGNAHDAISLFEQMEKD-GVKPNSVAFV  247 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~t~~  247 (514)
                      |-...|+.-+. -.+.|++++|.+.|+.+..+.      ..+--.++-++-+.+++++|+..+++.... +-.||. -|.
T Consensus        33 p~~~LY~~g~~-~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~-dY~  110 (254)
T COG4105          33 PASELYNEGLT-ELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNA-DYA  110 (254)
T ss_pred             CHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCCh-hHH
Confidence            44455655443 457899999999999997432      234445666778899999999999998774 334443 344


Q ss_pred             HHHHHHH---cc----CCHH---HHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHH--HH
Q 040365          248 AVLTACS---HA----GLID---KAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENV--WL  315 (514)
Q Consensus       248 ~ll~a~~---~~----g~~~---~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~--~~  315 (514)
                      ..|.+.+   ..    .+..   +|..-|+.++.++   |+             +.-...|..-+..+.   |...  =.
T Consensus       111 ~YlkgLs~~~~i~~~~rDq~~~~~A~~~f~~~i~ry---Pn-------------S~Ya~dA~~~i~~~~---d~LA~~Em  171 (254)
T COG4105         111 YYLKGLSYFFQIDDVTRDQSAARAAFAAFKELVQRY---PN-------------SRYAPDAKARIVKLN---DALAGHEM  171 (254)
T ss_pred             HHHHHHHHhccCCccccCHHHHHHHHHHHHHHHHHC---CC-------------CcchhhHHHHHHHHH---HHHHHHHH
Confidence            4444443   21    1222   2333333333322   21             111112211111111   1111  12


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc---hHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNNMG---AYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~---~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++..-|.+.|.+..|..-++++++.-|+...   .+..|.++|...|..++|.+.-+-+...
T Consensus       172 ~IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N  233 (254)
T COG4105         172 AIARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVLGAN  233 (254)
T ss_pred             HHHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhc
Confidence            3456688999999999999999988766554   4556778899999999999988877654

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=91.51  E-value=12  Score=34.87  Aligned_cols=116  Identities=13%  Similarity=0.089  Sum_probs=66.2

Q ss_pred             HHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCCh-hHHH---HHHHHHHhCCChH
Q 040365          150 PACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDI-VSWT---AVIMGNALHGNAH  225 (514)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~-~~~~---~li~~~~~~g~~~  225 (514)
                      ......+++..+..++....... +-+....-.|...|...|+.+.|..++..++.... ..|-   +-|..+.+.....
T Consensus       142 ~~~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~  220 (304)
T COG3118         142 KELIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATP  220 (304)
T ss_pred             hhhhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCC
Confidence            34567788889999888887764 33455666788899999999999999999873321 1121   1222233333322


Q ss_pred             HHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          226 DAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       226 ~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      +...+-++.-.   .| |...-..+...+...|+.++|.+.+-.+
T Consensus       221 ~~~~l~~~~aa---dPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~  262 (304)
T COG3118         221 EIQDLQRRLAA---DPDDVEAALALADQLHLVGRNEAALEHLLAL  262 (304)
T ss_pred             CHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            22222222222   34 3333334444555566666665544443

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=91.41  E-value=4.6  Score=38.24  Aligned_cols=126  Identities=9%  Similarity=0.062  Sum_probs=79.4

Q ss_pred             hHHHHHHHHHHHHhCCCCchhHHHHHHHHHHH--CC----CHHHHHHHHccCCC-------CChhHHHHHHHHHHHCCC-
Q 040365           57 VIKGKEIHGYAIRHGLDANVCIGSSLINMYAK--CA----RVEDSHRLFCLLPV-------KDAISWNSIIAGCVQNGL-  122 (514)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~--~g----~~~~A~~~f~~~~~-------~d~~~~~~li~~~~~~g~-  122 (514)
                      +++...+++.+.+.|+..+.+++-+..-....  ..    .+..|..+|+.|++       ++..++.+|+..  ..++ 
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            45667899999999998888777664433333  22    35678888888873       355566666655  3333 


Q ss_pred             ---hhHHHHHHHHHHHCCCCCCHH--HHHHHHHHHhccCC--hHHHHHHHHHHHHcCCCCcHHHHHHHH
Q 040365          123 ---FDEGLKFFRQMLIAKIKPRHV--SFSSIMPACAHLTT--LHLGKQLHGCIIRNGFDDNMFIASSLL  184 (514)
Q Consensus       123 ---~~~A~~l~~~m~~~g~~p~~~--t~~~ll~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~li  184 (514)
                         .+++..+|+.+...|+..+..  ..+.++..+.....  ...+.++++.+.+.|+++....|..+.
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lG  224 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLG  224 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHH
Confidence               355677888888877665433  23333333332222  346777888888888877776666554

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=91.40  E-value=16  Score=36.14  Aligned_cols=343  Identities=13%  Similarity=0.069  Sum_probs=184.0

Q ss_pred             HhcCChhHHHHHHHHHhhC--CCCC------------ChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCC----CchhH
Q 040365           17 ARNGLYEEALNIVRQMGNV--NLKP------------DSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLD----ANVCI   78 (514)
Q Consensus        17 ~~~g~~~~A~~l~~~m~~~--g~~p------------~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~----~~~~~   78 (514)
                      -+.+.+..|++.|.....+  +..|            |-+.=+..+..+...|.+.+|+.+++++...=++    -+..+
T Consensus        90 Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~  169 (549)
T PF07079_consen   90 YKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDM  169 (549)
T ss_pred             HHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHH
Confidence            3567888999888877654  3222            1112234456677899999999999888765443    68889


Q ss_pred             HHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCC-------------------------------hhHHH
Q 040365           79 GSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGL-------------------------------FDEGL  127 (514)
Q Consensus        79 ~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~-------------------------------~~~A~  127 (514)
                      |+.++-++++.=-++--......+    ..-|.-||..|.+.=+                               ..--+
T Consensus       170 yd~~vlmlsrSYfLEl~e~~s~dl----~pdyYemilfY~kki~~~d~~~Y~k~~peeeL~s~imqhlfi~p~e~l~~~m  245 (549)
T PF07079_consen  170 YDRAVLMLSRSYFLELKESMSSDL----YPDYYEMILFYLKKIHAFDQRPYEKFIPEEELFSTIMQHLFIVPKERLPPLM  245 (549)
T ss_pred             HHHHHHHHhHHHHHHHHHhccccc----ChHHHHHHHHHHHHHHHHhhchHHhhCcHHHHHHHHHHHHHhCCHhhccHHH
Confidence            999888887653222211111111    1123334433332211                               11111


Q ss_pred             HHHHHHHHCCCCCCHHHH-HHHHHHHhccCChHHHHHHHHHHHHcCCC----CcHHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          128 KFFRQMLIAKIKPRHVSF-SSIMPACAHLTTLHLGKQLHGCIIRNGFD----DNMFIASSLLDMYAKCGNIRLARCIFDK  202 (514)
Q Consensus       128 ~l~~~m~~~g~~p~~~t~-~~ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~li~~y~k~g~~~~A~~~~~~  202 (514)
                      +++..-...-+.|+.... ..+......  +.+++..+-+.+....+.    .=+..+..++....+.++...|.+.+.-
T Consensus       246 q~l~~We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~l  323 (549)
T PF07079_consen  246 QILENWENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYLAL  323 (549)
T ss_pred             HHHHHHHhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence            222222222234443222 222222222  444544444444333211    1134566667777778888887776665


Q ss_pred             CC--CCChh-------HHHHHHHHHH----hCCChHHHHHHHHHHHHcCCCCCHHHHH-HHHH---HHHccCC-HHHHHH
Q 040365          203 MD--LHDIV-------SWTAVIMGNA----LHGNAHDAISLFEQMEKDGVKPNSVAFV-AVLT---ACSHAGL-IDKAWS  264 (514)
Q Consensus       203 m~--~~d~~-------~~~~li~~~~----~~g~~~~A~~l~~~m~~~g~~p~~~t~~-~ll~---a~~~~g~-~~~a~~  264 (514)
                      +.  .|+..       +-..+-+..+    ..-+..+-+.+|.......+  |..-.. .++.   -+-+.|. -+.|++
T Consensus       324 L~~ldp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~Di--DrqQLvh~L~~~Ak~lW~~g~~dekaln  401 (549)
T PF07079_consen  324 LKILDPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDI--DRQQLVHYLVFGAKHLWEIGQCDEKALN  401 (549)
T ss_pred             HHhcCCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcc--cHHHHHHHHHHHHHHHHhcCCccHHHHH
Confidence            43  33221       1111222222    11233444556666655433  222111 1221   2333444 788888


Q ss_pred             HHHHhHHhcCCCC-CHhHHHHHHH----HHHhc---CCHH---HHHHHHHhCCCCC----CHHHHHHHHHH--HHhcCCH
Q 040365          265 YFNSMTKDYGIAP-SFEHYAAVAD----LLGRA---GKLQ---EAYEFISNMHAGP----TENVWLTLLSA--CRVHKNV  327 (514)
Q Consensus       265 ~~~~m~~~~~~~p-~~~~~~~li~----~~~~~---g~~~---~A~~~~~~m~~~p----~~~~~~~ll~~--~~~~~~~  327 (514)
                      +++.+.+   +.| |.+.-+.+..    .|..+   ..+.   .-+.++++....|    +...-|.|..|  +..+|++
T Consensus       402 LLk~il~---ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEyLysqgey  478 (549)
T PF07079_consen  402 LLKLILQ---FTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLADAEYLYSQGEY  478 (549)
T ss_pred             HHHHHHH---hccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHhcccH
Confidence            8887753   344 3333332221    12111   1122   2233444444332    44556666665  5789999


Q ss_pred             HHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          328 ELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       328 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                      .++...-.-+.+..| ++.+|..++-......++++|..++..+
T Consensus       479 ~kc~~ys~WL~~iaP-S~~~~RLlGl~l~e~k~Y~eA~~~l~~L  521 (549)
T PF07079_consen  479 HKCYLYSSWLTKIAP-SPQAYRLLGLCLMENKRYQEAWEYLQKL  521 (549)
T ss_pred             HHHHHHHHHHHHhCC-cHHHHHHHHHHHHHHhhHHHHHHHHHhC
Confidence            999999999999999 7899999999999999999999999865

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=91.34  E-value=6.5  Score=32.38  Aligned_cols=57  Identities=18%  Similarity=0.191  Sum_probs=35.6

Q ss_pred             HHhcCCHHHHHHHHHhCCCC----C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          289 LGRAGKLQEAYEFISNMHAG----P-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       289 ~~~~g~~~~A~~~~~~m~~~----p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      ..+.|++++|.+.|+.+..+    | ....--.|+.++.+.+++++|...+++.+++.|.++
T Consensus        20 ~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp   81 (142)
T PF13512_consen   20 ALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHP   81 (142)
T ss_pred             HHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCC
Confidence            34556666666666665311    1 223445566777777777777777777777776654

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.90  E-value=13  Score=39.54  Aligned_cols=141  Identities=16%  Similarity=0.059  Sum_probs=67.2

Q ss_pred             HHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040365          184 LDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAW  263 (514)
Q Consensus       184 i~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  263 (514)
                      .+-+.+.|++++|...|-+-...-..  ..+|.-|....+..+-..+++.+.+.|+.- ...-..|+.+|.+.++.+.-.
T Consensus       375 gd~Ly~Kgdf~~A~~qYI~tI~~le~--s~Vi~kfLdaq~IknLt~YLe~L~~~gla~-~dhttlLLncYiKlkd~~kL~  451 (933)
T KOG2114|consen  375 GDYLYGKGDFDEATDQYIETIGFLEP--SEVIKKFLDAQRIKNLTSYLEALHKKGLAN-SDHTTLLLNCYIKLKDVEKLT  451 (933)
T ss_pred             HHHHHhcCCHHHHHHHHHHHcccCCh--HHHHHHhcCHHHHHHHHHHHHHHHHccccc-chhHHHHHHHHHHhcchHHHH
Confidence            33444566666666555443211111  123444445555555556666666666542 222234666666666666655


Q ss_pred             HHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040365          264 SYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEK  336 (514)
Q Consensus       264 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  336 (514)
                      ++.+.-. + |.-  ..-....+..+.+.+-+++|.-+-.....  +......   .+...+++++|.+.++.
T Consensus       452 efI~~~~-~-g~~--~fd~e~al~Ilr~snyl~~a~~LA~k~~~--he~vl~i---lle~~~ny~eAl~yi~s  515 (933)
T KOG2114|consen  452 EFISKCD-K-GEW--FFDVETALEILRKSNYLDEAELLATKFKK--HEWVLDI---LLEDLHNYEEALRYISS  515 (933)
T ss_pred             HHHhcCC-C-cce--eeeHHHHHHHHHHhChHHHHHHHHHHhcc--CHHHHHH---HHHHhcCHHHHHHHHhc
Confidence            5554331 1 111  11123345555566666666655554432  1222222   23345566666665554

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=90.89  E-value=2.1  Score=39.77  Aligned_cols=76  Identities=14%  Similarity=0.212  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHH-----cCCCCCHHHHHH
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEK-----DGVKPNSVAFVA  248 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~-----~g~~p~~~t~~~  248 (514)
                      ..++..++..+..+|+.+.+.+.++++.   .-|...|..++.+|.+.|+...|+..|+++..     .|+.|...+...
T Consensus       153 ~~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         153 IKALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            3466778888999999999888888775   34677899999999999999999999888765     466776655544


Q ss_pred             HHHH
Q 040365          249 VLTA  252 (514)
Q Consensus       249 ll~a  252 (514)
                      ...+
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            4433

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=90.88  E-value=11  Score=33.38  Aligned_cols=161  Identities=14%  Similarity=0.088  Sum_probs=90.0

Q ss_pred             hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHH
Q 040365          208 IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVA  286 (514)
Q Consensus       208 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li  286 (514)
                      ...||-+.--+...|+++.|.+.|+...+.  .|. ..+...-.-++.-.|++..|.+-|...-..-.-.|-...|--++
T Consensus        99 ~~vfNyLG~Yl~~a~~fdaa~eaFds~~EL--Dp~y~Ya~lNRgi~~YY~gR~~LAq~d~~~fYQ~D~~DPfR~LWLYl~  176 (297)
T COG4785          99 PEVFNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGRYKLAQDDLLAFYQDDPNDPFRSLWLYLN  176 (297)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHhhhHhcc--CCcchHHHhccceeeeecCchHhhHHHHHHHHhcCCCChHHHHHHHHH
Confidence            456777777777888888888888887764  332 22222222234456777777766655533312222222332222


Q ss_pred             HHHHhcCCHHHHHH-HHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-------cchHHHHHHHHHHc
Q 040365          287 DLLGRAGKLQEAYE-FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN-------MGAYVILSNTYAAA  358 (514)
Q Consensus       287 ~~~~~~g~~~~A~~-~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~-------~~~~~~l~~~~~~~  358 (514)
                      .   +.-++.+|.. +.++.. +.|..-|..-|-.+--..-.+  +.+++++.....++       ..+|.-|..-|...
T Consensus       177 E---~k~dP~~A~tnL~qR~~-~~d~e~WG~~iV~~yLgkiS~--e~l~~~~~a~a~~n~~~Ae~LTEtyFYL~K~~l~~  250 (297)
T COG4785         177 E---QKLDPKQAKTNLKQRAE-KSDKEQWGWNIVEFYLGKISE--ETLMERLKADATDNTSLAEHLTETYFYLGKYYLSL  250 (297)
T ss_pred             H---hhCCHHHHHHHHHHHHH-hccHhhhhHHHHHHHHhhccH--HHHHHHHHhhccchHHHHHHHHHHHHHHHHHHhcc
Confidence            1   2334555554 333332 445556665554443222111  22333433322222       35888999999999


Q ss_pred             cChhHHHHHHHHHHhCCC
Q 040365          359 RRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       359 g~~~~a~~~~~~m~~~g~  376 (514)
                      |+.++|..+|+......+
T Consensus       251 G~~~~A~~LfKLaiannV  268 (297)
T COG4785         251 GDLDEATALFKLAVANNV  268 (297)
T ss_pred             ccHHHHHHHHHHHHHHhH
Confidence            999999999998776554

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.84  E-value=12  Score=33.78  Aligned_cols=201  Identities=13%  Similarity=0.084  Sum_probs=93.4

Q ss_pred             hHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCC--hhHHHHHHHHHHHC
Q 040365           43 TLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKD--AISWNSIIAGCVQN  120 (514)
Q Consensus        43 t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d--~~~~~~li~~~~~~  120 (514)
                      .|.-...+|....++++|+..+..+.+. .+.+...|.+       ...++.|-.+..++..-+  +..|+--...|.++
T Consensus        33 ~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfhA-------AKayEqaamLake~~klsEvvdl~eKAs~lY~E~  104 (308)
T KOG1585|consen   33 LYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFHA-------AKAYEQAAMLAKELSKLSEVVDLYEKASELYVEC  104 (308)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHHH-------HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHh
Confidence            3555556666777777777766655532 2333332221       223344444444444322  22355566667777


Q ss_pred             CChhHHHHHHHHHHH--CCCCCCHH--HHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHH
Q 040365          121 GLFDEGLKFFRQMLI--AKIKPRHV--SFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLA  196 (514)
Q Consensus       121 g~~~~A~~l~~~m~~--~g~~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A  196 (514)
                      |.++-|-..+++.-+  +++.|+..  .|.-.+...-..++...+.++               +..+-..|.+...+++|
T Consensus       105 GspdtAAmaleKAak~lenv~Pd~AlqlYqralavve~~dr~~ma~el---------------~gk~sr~lVrl~kf~Ea  169 (308)
T KOG1585|consen  105 GSPDTAAMALEKAAKALENVKPDDALQLYQRALAVVEEDDRDQMAFEL---------------YGKCSRVLVRLEKFTEA  169 (308)
T ss_pred             CCcchHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHhccchHHHHHHH---------------HHHhhhHhhhhHHhhHH
Confidence            776666555554422  22344321  122222222222222222222               22233344455555555


Q ss_pred             HHHHHhCCC--------CCh-hHHHHHHHHHHhCCChHHHHHHHHHHHHcC--CCC-CHHHHHHHHHHHHccCCHHHHHH
Q 040365          197 RCIFDKMDL--------HDI-VSWTAVIMGNALHGNAHDAISLFEQMEKDG--VKP-NSVAFVAVLTACSHAGLIDKAWS  264 (514)
Q Consensus       197 ~~~~~~m~~--------~d~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--~~p-~~~t~~~ll~a~~~~g~~~~a~~  264 (514)
                      -..|.+-..        ++. ..+-+.|-.|.-..++..|...+++--+.+  ..| +..+...||.+| ..|+.++...
T Consensus       170 a~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~E~~~k  248 (308)
T KOG1585|consen  170 ATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDIEEIKK  248 (308)
T ss_pred             HHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCHHHHHH
Confidence            444433220        111 123344444555566777777776644322  122 345666666665 4466666666


Q ss_pred             HHH
Q 040365          265 YFN  267 (514)
Q Consensus       265 ~~~  267 (514)
                      ++.
T Consensus       249 vl~  251 (308)
T KOG1585|consen  249 VLS  251 (308)
T ss_pred             HHc
Confidence            544

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=90.79  E-value=3.2  Score=33.40  Aligned_cols=87  Identities=10%  Similarity=-0.092  Sum_probs=50.4

Q ss_pred             HHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC----CChh---HHHHHHHHHHHCCC
Q 040365           50 IFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPV----KDAI---SWNSIIAGCVQNGL  122 (514)
Q Consensus        50 ~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~----~d~~---~~~~li~~~~~~g~  122 (514)
                      +.+..|+++.|++.|.+.+..- +....+||.-..+|--.|+.++|+.-+++..+    +.-.   +|---...|...|+
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~-P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~trtacqa~vQRg~lyRl~g~  130 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLA-PERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQTRTACQAFVQRGLLYRLLGN  130 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhc-ccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHhCc
Confidence            4556667777777777666553 45566667666666666766666665554431    1111   12222334556677


Q ss_pred             hhHHHHHHHHHHHCC
Q 040365          123 FDEGLKFFRQMLIAK  137 (514)
Q Consensus       123 ~~~A~~l~~~m~~~g  137 (514)
                      -+.|..=|....+.|
T Consensus       131 dd~AR~DFe~AA~LG  145 (175)
T KOG4555|consen  131 DDAARADFEAAAQLG  145 (175)
T ss_pred             hHHHHHhHHHHHHhC
Confidence            777777676665554

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=90.64  E-value=9.8  Score=32.41  Aligned_cols=134  Identities=12%  Similarity=0.120  Sum_probs=83.6

Q ss_pred             HHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCc-hhHHHHHHHHHHHC-CCHHHHHHHHccCC
Q 040365           26 LNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDAN-VCIGSSLINMYAKC-ARVEDSHRLFCLLP  103 (514)
Q Consensus        26 ~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~-~~~~~~li~~~~~~-g~~~~A~~~f~~~~  103 (514)
                      ++.++.+.+.+++|+...+..++..+.+.|.+..-.+    ++..++-+| ..+...|++.-.+. .-..-|..++.++.
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~q----llq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~   89 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQ----LLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLG   89 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHH----HHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhh
Confidence            4566677778999999999999999999998765443    444454444 44444444332211 01334555555554


Q ss_pred             CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHc
Q 040365          104 VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN  171 (514)
Q Consensus       104 ~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~  171 (514)
                          ..+..++..+...|++-+|+++.+.....    +......++.+..+.++...-..++....+.
T Consensus        90 ----~~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~  149 (167)
T PF07035_consen   90 ----TAYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEER  149 (167)
T ss_pred             ----hhHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence                34667788899999999999988775322    2222344566666666666555555555443

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.48  E-value=3.5  Score=34.98  Aligned_cols=48  Identities=15%  Similarity=0.104  Sum_probs=21.5

Q ss_pred             hcCCHHHHHHHHHhCCCC-C---hhHHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          189 KCGNIRLARCIFDKMDLH-D---IVSWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       189 k~g~~~~A~~~~~~m~~~-d---~~~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      ..|.+++.....+-+..+ +   ...-.+|.-+-.+.|++.+|...|.++..
T Consensus       144 D~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         144 DNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             ccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            345555544444444311 1   12233343444455555555555555544

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=90.39  E-value=0.59  Score=27.48  Aligned_cols=31  Identities=19%  Similarity=0.190  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      +|..+...+...|++++|...|++.++++|+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~~   33 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALELNPD   33 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            5666777777777777777777777777663

...

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=90.31  E-value=12  Score=32.83  Aligned_cols=197  Identities=17%  Similarity=0.107  Sum_probs=116.8

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHc-CCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--CC-hhHHHHHHH-H
Q 040365          143 VSFSSIMPACAHLTTLHLGKQLHGCIIRN-GFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--HD-IVSWTAVIM-G  217 (514)
Q Consensus       143 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d-~~~~~~li~-~  217 (514)
                      ..+......+...+.+..+...+...... ........+..+...+...+++..+.+.+.....  ++ ......... .
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  139 (291)
T COG0457          60 GLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALALDPDPDLAEALLALGA  139 (291)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCcchHHHHHHHHH
Confidence            34444444444555555555444444431 2233344444555555555666666666665542  11 122222233 5


Q ss_pred             HHhCCChHHHHHHHHHHHHcCCCC----CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhc
Q 040365          218 NALHGNAHDAISLFEQMEKDGVKP----NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRA  292 (514)
Q Consensus       218 ~~~~g~~~~A~~l~~~m~~~g~~p----~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~  292 (514)
                      +...|+++.|...|.+...  ..|    ....+......+...++.+.+...+....+.  ... ....+..+...+...
T Consensus       140 ~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  215 (291)
T COG0457         140 LYELGDYEEALELYEKALE--LDPELNELAEALLALGALLEALGRYEEALELLEKALKL--NPDDDAEALLNLGLLYLKL  215 (291)
T ss_pred             HHHcCCHHHHHHHHHHHHh--cCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhh--CcccchHHHHHhhHHHHHc
Confidence            7777888888888887754  233    2333444444466778888888888877542  222 356677777788888


Q ss_pred             CCHHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          293 GKLQEAYEFISNMH-AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       293 g~~~~A~~~~~~m~-~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      +.+++|...+.... ..|+ ...+..+...+...+..+.+...+.+.....|.
T Consensus       216 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (291)
T COG0457         216 GKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALELDPD  268 (291)
T ss_pred             ccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHhCcc
Confidence            88888888887764 2343 445555555555667788888888888888775

>PRK11619 lytic murein transglycosylase; Provisional

Probab=90.06  E-value=29  Score=36.95  Aligned_cols=80  Identities=9%  Similarity=-0.012  Sum_probs=49.9

Q ss_pred             hHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccC
Q 040365           77 CIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLT  156 (514)
Q Consensus        77 ~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~  156 (514)
                      ..-...+..+++.+++....+.+.. +..+...-.....+....|+.++|....+.+=..| ...+.....++..+.+.|
T Consensus       100 ~Lr~~~l~~La~~~~w~~~~~~~~~-~p~~~~~~c~~~~A~~~~G~~~~A~~~a~~lW~~g-~~~p~~cd~l~~~~~~~g  177 (644)
T PRK11619        100 SLQSRFVNELARREDWRGLLAFSPE-KPKPVEARCNYYYAKWATGQQQEAWQGAKELWLTG-KSLPNACDKLFSVWQQSG  177 (644)
T ss_pred             HHHHHHHHHHHHccCHHHHHHhcCC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-CCCChHHHHHHHHHHHcC
Confidence            3444455566777888888873333 23455555667777888888887877777765554 334556666666666555


Q ss_pred             Ch
Q 040365          157 TL  158 (514)
Q Consensus       157 ~~  158 (514)
                      .+
T Consensus       178 ~l  179 (644)
T PRK11619        178 KQ  179 (644)
T ss_pred             CC
Confidence            43

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=89.87  E-value=0.56  Score=28.25  Aligned_cols=26  Identities=15%  Similarity=0.072  Sum_probs=21.3

Q ss_pred             hHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          347 AYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       347 ~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      +|..|..+|.+.|+|++|.+++++..
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            46788999999999999999998843

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=89.72  E-value=26  Score=35.80  Aligned_cols=160  Identities=9%  Similarity=0.004  Sum_probs=69.8

Q ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCch------hHHHHHHHHHHH----CCCHHHHHHHHccCCC--CChhHHH
Q 040365           44 LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANV------CIGSSLINMYAK----CARVEDSHRLFCLLPV--KDAISWN  111 (514)
Q Consensus        44 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~------~~~~~li~~~~~----~g~~~~A~~~f~~~~~--~d~~~~~  111 (514)
                      +..++...+-.||.+.+.+.+....+.+--..+      ..|...+..+..    ..+.+.|.++++.+..  |+...|.
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~yP~s~lfl  270 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRYPNSALFL  270 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhCCCcHHHH
Confidence            344555555555666666555555443211111      112222222221    3345556666655543  4444443


Q ss_pred             HH-HHHHHHCCChhHHHHHHHHHHHCC---CCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHH-HHHHH
Q 040365          112 SI-IAGCVQNGLFDEGLKFFRQMLIAK---IKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIAS-SLLDM  186 (514)
Q Consensus       112 ~l-i~~~~~~g~~~~A~~l~~~m~~~g---~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~li~~  186 (514)
                      .. .+.+...|++++|++.|++.....   -+.....+--+.-.+.-..++++|...+..+.+.. .....+|. ....+
T Consensus       271 ~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~a~c  349 (468)
T PF10300_consen  271 FFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLAAAC  349 (468)
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHHHHH
Confidence            32 233444556666666665443211   01111222233334455556666666666655543 11222222 22333


Q ss_pred             HHhcCCH-------HHHHHHHHhCC
Q 040365          187 YAKCGNI-------RLARCIFDKMD  204 (514)
Q Consensus       187 y~k~g~~-------~~A~~~~~~m~  204 (514)
                      |...|+.       ++|.++|.+++
T Consensus       350 ~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  350 LLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHhhccchhhhhhHHHHHHHHHHHH
Confidence            4445555       55666665553

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.

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=89.59  E-value=0.65  Score=27.96  Aligned_cols=28  Identities=18%  Similarity=0.063  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFMI  340 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~  340 (514)
                      +|..|...|...|++++|+.++++.+.+
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~l   28 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALAL   28 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4677788888888888888888885543

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=89.33  E-value=2  Score=36.06  Aligned_cols=53  Identities=11%  Similarity=0.068  Sum_probs=28.8

Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ...++.+.++.++..+.-+.|..+..-..-...+...|+|.+|.++++.+.+.
T Consensus        21 l~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRVLRPEFPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             HccCChHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            34445555555555555555555555555555555555555555555555443

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.27  E-value=7.6  Score=39.63  Aligned_cols=148  Identities=18%  Similarity=0.105  Sum_probs=103.2

Q ss_pred             hcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHccCCHHHHHHHHH
Q 040365          189 KCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV-AFVAVLTACSHAGLIDKAWSYFN  267 (514)
Q Consensus       189 k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~a~~~~g~~~~a~~~~~  267 (514)
                      -.|+++.|..++..++++   .-+.++.-+.+.|..++|+++         .||.. -|..    ..+.|+++.|.++..
T Consensus       598 mrrd~~~a~~vLp~I~k~---~rt~va~Fle~~g~~e~AL~~---------s~D~d~rFel----al~lgrl~iA~~la~  661 (794)
T KOG0276|consen  598 LRRDLEVADGVLPTIPKE---IRTKVAHFLESQGMKEQALEL---------STDPDQRFEL----ALKLGRLDIAFDLAV  661 (794)
T ss_pred             hhccccccccccccCchh---hhhhHHhHhhhccchHhhhhc---------CCChhhhhhh----hhhcCcHHHHHHHHH
Confidence            357788887777766633   334455556667777777653         33332 2322    346789999988776


Q ss_pred             HhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcch
Q 040365          268 SMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGA  347 (514)
Q Consensus       268 ~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~  347 (514)
                      +.       -+..-|..|.++....|++..|.+.|....      -|..|+-.+...|+.+....+.....+.+..|   
T Consensus       662 e~-------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~------d~~~LlLl~t~~g~~~~l~~la~~~~~~g~~N---  725 (794)
T KOG0276|consen  662 EA-------NSEVKWRQLGDAALSAGELPLASECFLRAR------DLGSLLLLYTSSGNAEGLAVLASLAKKQGKNN---  725 (794)
T ss_pred             hh-------cchHHHHHHHHHHhhcccchhHHHHHHhhc------chhhhhhhhhhcCChhHHHHHHHHHHhhcccc---
Confidence            54       256678999999999999999999987754      26778888888888776666666666655544   


Q ss_pred             HHHHHHHHHHccChhHHHHHHHH
Q 040365          348 YVILSNTYAAARRWKDAASLRVF  370 (514)
Q Consensus       348 ~~~l~~~~~~~g~~~~a~~~~~~  370 (514)
                        ....+|...|+++++.+++..
T Consensus       726 --~AF~~~~l~g~~~~C~~lLi~  746 (794)
T KOG0276|consen  726 --LAFLAYFLSGDYEECLELLIS  746 (794)
T ss_pred             --hHHHHHHHcCCHHHHHHHHHh
Confidence              344567889999999888764

>PRK09687 putative lyase; Provisional

Probab=89.15  E-value=20  Score=33.72  Aligned_cols=231  Identities=11%  Similarity=-0.022  Sum_probs=131.4

Q ss_pred             CCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCH----HHHHHHHccC--CCCChhHHH
Q 040365           38 KPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARV----EDSHRLFCLL--PVKDAISWN  111 (514)
Q Consensus        38 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~----~~A~~~f~~~--~~~d~~~~~  111 (514)
                      .+|.......+.++...|..+-... ...+.+   .+|..+-...+.+++..|+-    +++...+..+  .++|...-.
T Consensus        34 d~d~~vR~~A~~aL~~~~~~~~~~~-l~~ll~---~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~D~d~~VR~  109 (280)
T PRK09687         34 DHNSLKRISSIRVLQLRGGQDVFRL-AIELCS---SKNPIERDIGADILSQLGMAKRCQDNVFNILNNLALEDKSACVRA  109 (280)
T ss_pred             CCCHHHHHHHHHHHHhcCcchHHHH-HHHHHh---CCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhcCCCHHHHH
Confidence            3566666667777777665432222 222322   45666777777777777763    4566666654  356655555


Q ss_pred             HHHHHHHHCCCh-----hHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 040365          112 SIIAGCVQNGLF-----DEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDM  186 (514)
Q Consensus       112 ~li~~~~~~g~~-----~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  186 (514)
                      ..+.++...+..     .++...+.....   .++...-...+.++++.++ +.+...+-.+++   .+|..+-..-+.+
T Consensus       110 ~A~~aLG~~~~~~~~~~~~a~~~l~~~~~---D~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L~---d~~~~VR~~A~~a  182 (280)
T PRK09687        110 SAINATGHRCKKNPLYSPKIVEQSQITAF---DKSTNVRFAVAFALSVIND-EAAIPLLINLLK---DPNGDVRNWAAFA  182 (280)
T ss_pred             HHHHHHhcccccccccchHHHHHHHHHhh---CCCHHHHHHHHHHHhccCC-HHHHHHHHHHhc---CCCHHHHHHHHHH
Confidence            555555554321     233444433333   2355555566777777776 345555555554   3444555556666


Q ss_pred             HHhcC-CHHHHHHHH-HhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040365          187 YAKCG-NIRLARCIF-DKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWS  264 (514)
Q Consensus       187 y~k~g-~~~~A~~~~-~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~  264 (514)
                      +++.+ +-..+...+ ..+..+|...-..-+.++.+.|+ ..|+..+-+..+.+   +  ....++.++...|.. +|..
T Consensus       183 Lg~~~~~~~~~~~~L~~~L~D~~~~VR~~A~~aLg~~~~-~~av~~Li~~L~~~---~--~~~~a~~ALg~ig~~-~a~p  255 (280)
T PRK09687        183 LNSNKYDNPDIREAFVAMLQDKNEEIRIEAIIGLALRKD-KRVLSVLIKELKKG---T--VGDLIIEAAGELGDK-TLLP  255 (280)
T ss_pred             HhcCCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHccCC-hhHHHHHHHHHcCC---c--hHHHHHHHHHhcCCH-hHHH
Confidence            66543 123444443 34446677777777778888777 45666666665542   2  234677778888885 6777


Q ss_pred             HHHHhHHhcCCCCCHhHHHHHHHHH
Q 040365          265 YFNSMTKDYGIAPSFEHYAAVADLL  289 (514)
Q Consensus       265 ~~~~m~~~~~~~p~~~~~~~li~~~  289 (514)
                      .+..+...   .||...-...+.++
T Consensus       256 ~L~~l~~~---~~d~~v~~~a~~a~  277 (280)
T PRK09687        256 VLDTLLYK---FDDNEIITKAIDKL  277 (280)
T ss_pred             HHHHHHhh---CCChhHHHHHHHHH
Confidence            77777543   45665555555544

>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=89.02  E-value=12  Score=32.34  Aligned_cols=57  Identities=21%  Similarity=0.184  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCCCCC------hhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMDLHD------IVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~~~d------~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      .+..+.+.|.+.|+++.|.+.|.++.+..      +..+-.+|......|++..+.....+..
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            44556666666666666666666654332      1234444555555555555555555443

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.

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=88.61  E-value=9.2  Score=29.19  Aligned_cols=87  Identities=13%  Similarity=0.098  Sum_probs=58.9

Q ss_pred             hHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHC
Q 040365           57 VIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIA  136 (514)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (514)
                      .++|.-+-+.+...+-. ...+--.-+..+...|++++|..+.+.+..||...|-+|-..  +.|..+++..-+.+|...
T Consensus        21 HqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce~--rlGl~s~l~~rl~rla~s   97 (115)
T TIGR02508        21 HQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCEW--RLGLGSALESRLNRLAAS   97 (115)
T ss_pred             HHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHHH--hhccHHHHHHHHHHHHhC
Confidence            45666666665544311 222222333456778999999999999999999999887654  677777777777788777


Q ss_pred             CCCCCHHHHHH
Q 040365          137 KIKPRHVSFSS  147 (514)
Q Consensus       137 g~~p~~~t~~~  147 (514)
                      | .|...+|..
T Consensus        98 g-~p~lq~Faa  107 (115)
T TIGR02508        98 G-DPRLQTFVA  107 (115)
T ss_pred             C-CHHHHHHHH
Confidence            6 565555543

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>PRK12798 chemotaxis protein; Reviewed

Probab=88.31  E-value=27  Score=34.29  Aligned_cols=182  Identities=18%  Similarity=0.214  Sum_probs=118.9

Q ss_pred             cCCHHHHHHHHHhCCC----CChhHHHHHHHHH-HhCCChHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHHccCCHH
Q 040365          190 CGNIRLARCIFDKMDL----HDIVSWTAVIMGN-ALHGNAHDAISLFEQMEKDGVKPNS----VAFVAVLTACSHAGLID  260 (514)
Q Consensus       190 ~g~~~~A~~~~~~m~~----~d~~~~~~li~~~-~~~g~~~~A~~l~~~m~~~g~~p~~----~t~~~ll~a~~~~g~~~  260 (514)
                      .|+.++|.+.+..+..    +.+..+-+|+.+- ....++.+|+++|++..-.  -|-.    ....--+....+.|+.+
T Consensus       125 ~Gr~~~a~~~La~i~~~~l~~~lg~~laLv~a~l~~~~dP~~Al~~lD~aRLl--aPGTLvEEAALRRsi~la~~~g~~~  202 (421)
T PRK12798        125 SGRGREARKLLAGVAPEYLPAELGAYLALVQGNLMVATDPATALKLLDQARLL--APGTLVEEAALRRSLFIAAQLGDAD  202 (421)
T ss_pred             cCCHHHHHHHhhcCChhhcCchhhhHHHHHHHHHhcccCHHHHHHHHHHHHHh--CCchHHHHHHHHHhhHHHHhcCcHH
Confidence            6888888888888863    3455677777664 4466899999999987763  4433    33444555678899999


Q ss_pred             HHHHHHHHhHHhcCCCCCHhHHH-HHHHHHHh---cCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040365          261 KAWSYFNSMTKDYGIAPSFEHYA-AVADLLGR---AGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEK  336 (514)
Q Consensus       261 ~a~~~~~~m~~~~~~~p~~~~~~-~li~~~~~---~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~  336 (514)
                      ++..+-.....+|.-.|-...|. .++..+.+   .-..+.-..++..|...--..+|..+...-...|+.+.|....++
T Consensus       203 rf~~la~~Y~rRF~~S~YA~~F~~~F~~~~~~~~d~~~~~~l~~~ls~~d~~~q~~lYL~iAR~Ali~Gk~~lA~~As~~  282 (421)
T PRK12798        203 KFEALARNYLRRFRHSPYASQFAQRFVDLVVRLDDEIRDARLVEILSFMDPERQRELYLRIARAALIDGKTELARFASER  282 (421)
T ss_pred             HHHHHHHHHHHHhccCchHHHHHHHHHHHHHhccccccHHHHHHHHHhcCchhHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            98877777667666677443333 23333333   334555666777775333456888899999999999999999999


Q ss_pred             HHhcCCCCcchHHHHHHHHHH-----ccChhHHHHHHHHHHhC
Q 040365          337 IFMIDPNNMGAYVILSNTYAA-----ARRWKDAASLRVFMRNK  374 (514)
Q Consensus       337 ~~~~~p~~~~~~~~l~~~~~~-----~g~~~~a~~~~~~m~~~  374 (514)
                      +..+... ...-...+..|..     ..+.+++.+.+..+...
T Consensus       283 A~~L~~~-~~~~~~ra~LY~aaa~v~s~~~~~al~~L~~I~~~  324 (421)
T PRK12798        283 ALKLADP-DSADAARARLYRGAALVASDDAESALEELSQIDRD  324 (421)
T ss_pred             HHHhccC-CCcchHHHHHHHHHHccCcccHHHHHHHHhcCChh
Confidence            9987632 2222333333332     23466666666655443

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=88.25  E-value=3.4  Score=34.14  Aligned_cols=53  Identities=11%  Similarity=0.026  Sum_probs=36.3

Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          323 VHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ..++.+.++.++..+.-+.|..+..-..-...+...|+|++|.++++...+.+
T Consensus        22 ~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~   74 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILRELLSSA   74 (153)
T ss_pred             hcCCHHHHHHHHHHHHHhCCCccccchhHHHHHHHcCCHHHHHHHHHhhhccC
Confidence            36666777777777777777766666666666677777777777777766654

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.15  E-value=39  Score=35.88  Aligned_cols=90  Identities=16%  Similarity=0.360  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHHHcCCCC-----CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHH
Q 040365          225 HDAISLFEQMEKDGVKP-----NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAY  299 (514)
Q Consensus       225 ~~A~~l~~~m~~~g~~p-----~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~  299 (514)
                      +..+++|.+.-...+-|     ........+..|.+.|-+++-.-++.+|    |     .++.+|.-.--+.+++++|.
T Consensus       611 dk~I~LYAEyDrk~LLPFLr~s~~Y~lekA~eiC~q~~~~~E~VYlLgrm----G-----n~k~AL~lII~el~die~AI  681 (846)
T KOG2066|consen  611 DKQIELYAEYDRKKLLPFLRKSQNYNLEKALEICSQKNFYEELVYLLGRM----G-----NAKEALKLIINELRDIEKAI  681 (846)
T ss_pred             hHHHHHHHHHhHhhhhHHHHhcCCCCHHHHHHHHHhhCcHHHHHHHHHhh----c-----chHHHHHHHHHHhhCHHHHH
Confidence            45566666654443333     1223445566677777777766666666    2     23444444445566777777


Q ss_pred             HHHHhCCCCCCHHHHHHHHHHHHhcCC
Q 040365          300 EFISNMHAGPTENVWLTLLSACRVHKN  326 (514)
Q Consensus       300 ~~~~~m~~~p~~~~~~~ll~~~~~~~~  326 (514)
                      ++.++-   .|...|..||.-+...-.
T Consensus       682 efvKeq---~D~eLWe~LI~~~ldkPe  705 (846)
T KOG2066|consen  682 EFVKEQ---DDSELWEDLINYSLDKPE  705 (846)
T ss_pred             HHHHhc---CCHHHHHHHHHHhhcCcH
Confidence            776553   478888888877665543

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=88.09  E-value=9  Score=29.23  Aligned_cols=87  Identities=17%  Similarity=0.180  Sum_probs=59.7

Q ss_pred             hHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          158 LHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                      .++|..|-+.+...+-. ...+.-.-+..+...|++++|..+.+.+..||+..|-++-.  .+.|..+++..-+.+|..+
T Consensus        21 HqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce--~rlGl~s~l~~rl~rla~s   97 (115)
T TIGR02508        21 HQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCE--WRLGLGSALESRLNRLAAS   97 (115)
T ss_pred             HHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHH--HhhccHHHHHHHHHHHHhC
Confidence            46666666666554421 23333333556778899999999999999999999988755  4667777777777788777


Q ss_pred             CCCCCHHHHHH
Q 040365          238 GVKPNSVAFVA  248 (514)
Q Consensus       238 g~~p~~~t~~~  248 (514)
                      | .|...+|..
T Consensus        98 g-~p~lq~Faa  107 (115)
T TIGR02508        98 G-DPRLQTFVA  107 (115)
T ss_pred             C-CHHHHHHHH
Confidence            6 555555543

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>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=87.93  E-value=7.6  Score=33.64  Aligned_cols=61  Identities=15%  Similarity=0.043  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCCh--hhHHHHHHHHhCCCChHHHHHHHHHHH
Q 040365            8 SWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDS--FTLSSVLPIFADYVDVIKGKEIHGYAI   68 (514)
Q Consensus         8 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~~~   68 (514)
                      .|..+...|.+.|+.+.|++.|.++......|..  ..+-.++..+...+++..+.....++.
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            4555666666666666666666666654333332  234445555555566665555554443

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.

>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=87.91  E-value=24  Score=33.14  Aligned_cols=16  Identities=25%  Similarity=-0.080  Sum_probs=9.2

Q ss_pred             HHhcCCHHHHHHHHHH
Q 040365          321 CRVHKNVELAGKVAEK  336 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~  336 (514)
                      +.+.++++.|...++-
T Consensus       256 ~~~~k~y~~A~~w~~~  271 (278)
T PF08631_consen  256 HYKAKNYDEAIEWYEL  271 (278)
T ss_pred             HHhhcCHHHHHHHHHH
Confidence            4455566666666553

It is also involved in sporulation [].

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=87.87  E-value=1.9  Score=27.25  Aligned_cols=28  Identities=21%  Similarity=0.344  Sum_probs=16.4

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhC
Q 040365            8 SWNTVIVGLARNGLYEEALNIVRQMGNV   35 (514)
Q Consensus         8 ~~~~li~~~~~~g~~~~A~~l~~~m~~~   35 (514)
                      +|..+...|.+.|++++|.++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3555555666666666666666666554

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=87.63  E-value=0.84  Score=27.13  Aligned_cols=31  Identities=23%  Similarity=0.197  Sum_probs=19.3

Q ss_pred             HHHHHhCCCCchhHHHHHHHHHHHCCCHHHHH
Q 040365           65 GYAIRHGLDANVCIGSSLINMYAKCARVEDSH   96 (514)
Q Consensus        65 ~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~   96 (514)
                      .++++.. |.+..+|+.|...|...|++++|+
T Consensus         3 ~kAie~~-P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    3 KKAIELN-PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHHC-CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            3444443 556666777777777777777664

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.40  E-value=5.5  Score=37.20  Aligned_cols=98  Identities=15%  Similarity=0.227  Sum_probs=72.3

Q ss_pred             cCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC-C--------ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC
Q 040365          171 NGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL-H--------DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP  241 (514)
Q Consensus       171 ~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~-~--------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  241 (514)
                      .|.+....+...+++.-....+++++...+-++.. +        ..++|-.++.    .=++++++.++..=.+.|+-|
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlll----ky~pq~~i~~l~npIqYGiF~  133 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLL----KYDPQKAIYTLVNPIQYGIFP  133 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHH----ccChHHHHHHHhCcchhcccc
Confidence            34455555666667666667788888888777652 2        2344444433    336779999988888999999


Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHhHHh
Q 040365          242 NSVAFVAVLTACSHAGLIDKAWSYFNSMTKD  272 (514)
Q Consensus       242 ~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~  272 (514)
                      |..|+..+++.+.+.+++.+|.++.-.|..+
T Consensus       134 dqf~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  134 DQFTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             chhhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            9999999999999999999998887777554

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=87.27  E-value=5  Score=30.34  Aligned_cols=63  Identities=14%  Similarity=0.197  Sum_probs=48.4

Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  287 (514)
                      +.-++.+-++.+....+-|+.....+.|.||.+.+++..|.++|+....+.|  .+...|..+++
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~--~~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCG--AHKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--CchhhHHHHHH
Confidence            4556677777777778899999999999999999999999999998854433  24456666654

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.

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=87.15  E-value=2.9  Score=36.30  Aligned_cols=87  Identities=15%  Similarity=0.108  Sum_probs=66.8

Q ss_pred             HHhcCCHHHHHHHHHhCC-CCC------CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccCh
Q 040365          289 LGRAGKLQEAYEFISNMH-AGP------TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRW  361 (514)
Q Consensus       289 ~~~~g~~~~A~~~~~~m~-~~p------~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  361 (514)
                      +.+.|++++|..-|.+.. .-|      -.+.|..-..+..+.+..+.|+.-..+.++++|....+...-+.+|.+..++
T Consensus       105 ~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pty~kAl~RRAeayek~ek~  184 (271)
T KOG4234|consen  105 LFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNPTYEKALERRAEAYEKMEKY  184 (271)
T ss_pred             hhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCchhHHHHHHHHHHHHhhhhH
Confidence            556777777777666542 111      1244555566788899999999999999999998777777778899999999


Q ss_pred             hHHHHHHHHHHhCC
Q 040365          362 KDAASLRVFMRNKG  375 (514)
Q Consensus       362 ~~a~~~~~~m~~~g  375 (514)
                      ++|+.=++++.+..
T Consensus       185 eealeDyKki~E~d  198 (271)
T KOG4234|consen  185 EEALEDYKKILESD  198 (271)
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999987754

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=87.10  E-value=45  Score=35.43  Aligned_cols=69  Identities=25%  Similarity=0.258  Sum_probs=43.3

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCC-------hHHHHHHHHHHHHhCCCCchh
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVD-------VIKGKEIHGYAIRHGLDANVC   77 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~-------~~~a~~~~~~~~~~g~~~~~~   77 (514)
                      ..| ++|--+.|.|++++|.++....... .......|...+..+....+       -++...-+.+..+.....|++
T Consensus       113 p~W-a~Iyy~LR~G~~~~A~~~~~~~~~~-~~~~~~~f~~~l~~~~~s~~~~l~~~~~~~l~~ey~~~~r~~~~~Dpy  188 (613)
T PF04097_consen  113 PIW-ALIYYCLRCGDYDEALEVANENRNQ-FQKIERSFPTYLKAYASSPDRRLPPELRDKLKLEYNQRIRNSTDGDPY  188 (613)
T ss_dssp             EHH-HHHHHHHTTT-HHHHHHHHHHTGGG-S-TTTTHHHHHHHHCTTTTSS---TCCCHHHHHHHHHHTTT-TTS-HH
T ss_pred             ccH-HHHHHHHhcCCHHHHHHHHHHhhhh-hcchhHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhcCCCCCChH
Confidence            345 4788899999999999999666543 45666778888998877533       234445555555543322443

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>KOG4279 consensus Serine/threonine protein kinase [Signal transduction mechanisms]

Probab=86.93  E-value=11  Score=39.42  Aligned_cols=186  Identities=16%  Similarity=0.242  Sum_probs=111.0

Q ss_pred             hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHH----------HHHHHHHHHhccCChHHHHHHHHHHHHc-C-CCC
Q 040365          108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHV----------SFSSIMPACAHLTTLHLGKQLHGCIIRN-G-FDD  175 (514)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~----------t~~~ll~~~~~~~~~~~a~~~~~~~~~~-~-~~~  175 (514)
                      .+-..|+-.|....+++..+++.+.++.-   ||..          .|...++---+-|+-++|..+.--+++. | +.|
T Consensus       202 d~V~nlmlSyRDvQdY~amirLVe~Lk~i---P~t~~vve~~nv~f~YaFALNRRNr~GDRakAL~~~l~lve~eg~vap  278 (1226)
T KOG4279|consen  202 DTVSNLMLSYRDVQDYDAMIRLVEDLKRI---PDTLKVVETHNVRFHYAFALNRRNRPGDRAKALNTVLPLVEKEGPVAP  278 (1226)
T ss_pred             HHHHHHHhhhccccchHHHHHHHHHHHhC---cchhhhhccCceEEEeeehhcccCCCccHHHHHHHHHHHHHhcCCCCC
Confidence            34556777788888899999998888763   4332          2333333334456777777766655543 3 344


Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHH---HHHHHHH
Q 040365          176 NMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVA---FVAVLTA  252 (514)
Q Consensus       176 ~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t---~~~ll~a  252 (514)
                      |         +||-||++      |..|-         +-+.|...+..+.|.+.|++.-+  +.|+..+   +..|+.+
T Consensus       279 D---------m~Cl~GRI------YKDmF---------~~S~ytDa~s~~~a~~WyrkaFe--veP~~~sGIN~atLL~a  332 (1226)
T KOG4279|consen  279 D---------MYCLCGRI------YKDMF---------IASNYTDAESLNHAIEWYRKAFE--VEPLEYSGINLATLLRA  332 (1226)
T ss_pred             c---------eeeeechh------hhhhh---------hccCCcchhhHHHHHHHHHHHhc--cCchhhccccHHHHHHH
Confidence            4         67777763      33332         11234445566778888887766  5676543   4444433


Q ss_pred             HHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 040365          253 CSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGK  332 (514)
Q Consensus       253 ~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~  332 (514)
                      -.+  .++...+    +.         ..--.|-..++|.|.++...++++-.          ..+.+-.-.+|+..|.+
T Consensus       333 aG~--~Fens~E----lq---------~IgmkLn~LlgrKG~leklq~YWdV~----------~y~~asVLAnd~~kaiq  387 (1226)
T KOG4279|consen  333 AGE--HFENSLE----LQ---------QIGMKLNSLLGRKGALEKLQEYWDVA----------TYFEASVLANDYQKAIQ  387 (1226)
T ss_pred             hhh--hccchHH----HH---------HHHHHHHHHhhccchHHHHHHHHhHH----------HhhhhhhhccCHHHHHH
Confidence            221  1111111    10         11123445678999998888777532          23455666789999999


Q ss_pred             HHHHHHhcCCCCcch
Q 040365          333 VAEKIFMIDPNNMGA  347 (514)
Q Consensus       333 ~~~~~~~~~p~~~~~  347 (514)
                      +.+.|.++.|+....
T Consensus       388 Aae~mfKLk~P~WYL  402 (1226)
T KOG4279|consen  388 AAEMMFKLKPPVWYL  402 (1226)
T ss_pred             HHHHHhccCCceehH
Confidence            999999999876433

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=86.85  E-value=31  Score=33.38  Aligned_cols=69  Identities=14%  Similarity=0.181  Sum_probs=56.3

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC----CCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCc
Q 040365          309 PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDP----NNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p----~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  377 (514)
                      ....+|..+...+++.|+++.|...+.++...++    ..+.....-+......|+.++|...++...+..+.
T Consensus       144 ~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~~~~  216 (352)
T PF02259_consen  144 ELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKCRLS  216 (352)
T ss_pred             HHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHHHhh
Confidence            4557899999999999999999999999988652    24566677788899999999999999888774333

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=86.73  E-value=5.7  Score=37.11  Aligned_cols=99  Identities=11%  Similarity=0.136  Sum_probs=69.4

Q ss_pred             hCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC-C--------ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCC
Q 040365           70 HGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPV-K--------DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKP  140 (514)
Q Consensus        70 ~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~-~--------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  140 (514)
                      .|.+....+...++..-....+++++...+-.+.. |        ...+|   ++.+. .-++++++.++..=.+.|+-|
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~---irlll-ky~pq~~i~~l~npIqYGiF~  133 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTW---IRLLL-KYDPQKAIYTLVNPIQYGIFP  133 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHH---HHHHH-ccChHHHHHHHhCcchhcccc
Confidence            34455555666677666667778888877766542 2        22233   33322 336778888888888889999


Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHHcC
Q 040365          141 RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNG  172 (514)
Q Consensus       141 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  172 (514)
                      |.+|+..+++.+.+.+++..|.++...|+...
T Consensus       134 dqf~~c~l~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  134 DQFTFCLLMDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             chhhHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            99999999999999998888888877776654

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=86.64  E-value=5.8  Score=30.37  Aligned_cols=63  Identities=14%  Similarity=0.157  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHH
Q 040365          224 AHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADL  288 (514)
Q Consensus       224 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~  288 (514)
                      .-+..+-+..+....+-|+.....+.|.||.+.+++..|.++|+.+..+.|  +....|..+++-
T Consensus        26 ~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~--~~~~~Y~~~lqE   88 (108)
T PF02284_consen   26 GWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG--NKKEIYPYILQE   88 (108)
T ss_dssp             HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT--T-TTHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--ChHHHHHHHHHH
Confidence            335566666666777889999999999999999999999999998865544  333377776653

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 ....

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=86.17  E-value=1.7  Score=25.42  Aligned_cols=27  Identities=7%  Similarity=0.156  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          210 SWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       210 ~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      +|..+...|...|++++|+..|++.++
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            466666666666777777777666665

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=85.99  E-value=20  Score=30.25  Aligned_cols=88  Identities=15%  Similarity=0.097  Sum_probs=49.6

Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHhcCCHHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRAGKLQEAYEFISNMHAG-PTENVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~~~~~~~ll~~~~~~~~~~~  329 (514)
                      .-...++.+++..++..+.   -+.|. ...-..-.-.+.+.|++.+|..+|+++... |....-.+|+..|.....-..
T Consensus        19 ~al~~~~~~D~e~lL~ALr---vLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~CL~~~~D~~   95 (160)
T PF09613_consen   19 VALRLGDPDDAEALLDALR---VLRPEFPELDLFDGWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALCLYALGDPS   95 (160)
T ss_pred             HHHccCChHHHHHHHHHHH---HhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHHcCChH
Confidence            3345667777777777764   44553 222233344466778888888888887533 444444556666654443333


Q ss_pred             HHHHHHHHHhcCC
Q 040365          330 AGKVAEKIFMIDP  342 (514)
Q Consensus       330 a~~~~~~~~~~~p  342 (514)
                      =....+++++.++
T Consensus        96 Wr~~A~evle~~~  108 (160)
T PF09613_consen   96 WRRYADEVLESGA  108 (160)
T ss_pred             HHHHHHHHHhcCC
Confidence            3444444555443

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=85.76  E-value=21  Score=30.41  Aligned_cols=131  Identities=16%  Similarity=0.095  Sum_probs=60.5

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCC-CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC
Q 040365          128 KFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGF-DDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH  206 (514)
Q Consensus       128 ~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~  206 (514)
                      ++++.+.+.+++|+...+..++..+.+.|.+..-.++.    ..++ +++..+...|++.-.   ....+.++=-.|..+
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~qll----q~~Vi~DSk~lA~~LLs~~~---~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQLL----QYHVIPDSKPLACQLLSLGN---QYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHH----hhcccCCcHHHHHHHHHhHc---cChHHHHHHHHHHHH
Confidence            44555556667777777777777777766655443332    2232 222333322322211   112222222222222


Q ss_pred             ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       207 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      =-..+..++..+...|++-+|+++.++....    +...-..++.+-.+.++...-..+|+-.
T Consensus        88 L~~~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff  146 (167)
T PF07035_consen   88 LGTAYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFF  146 (167)
T ss_pred             hhhhHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            2223445556666677777777766654221    1111233455555555544444444433

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=85.57  E-value=95  Score=37.71  Aligned_cols=309  Identities=10%  Similarity=0.050  Sum_probs=165.2

Q ss_pred             HHhCCCChHHHHHHHHHHHHhCC--CCchhHHHHHHHHHHHCCCHHHHHHHHc-cCCCCChhHHHHHHHHHHHCCChhHH
Q 040365           50 IFADYVDVIKGKEIHGYAIRHGL--DANVCIGSSLINMYAKCARVEDSHRLFC-LLPVKDAISWNSIIAGCVQNGLFDEG  126 (514)
Q Consensus        50 ~~~~~~~~~~a~~~~~~~~~~g~--~~~~~~~~~li~~~~~~g~~~~A~~~f~-~~~~~d~~~~~~li~~~~~~g~~~~A  126 (514)
                      +-.+.+.+..|...++.-.....  ......+-.|...|+.-++.|...-+.. ....+++   ..-|.-....|++..|
T Consensus      1392 aSfrc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a~~sl---~~qil~~e~~g~~~da 1468 (2382)
T KOG0890|consen 1392 ASFRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFADPSL---YQQILEHEASGNWADA 1468 (2382)
T ss_pred             HHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhcCccH---HHHHHHHHhhccHHHH
Confidence            44455666667666665210000  1122234445557888888777666665 3333432   2344555678899999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHH-HHHHHhcCCHHHHHHHHHhCCC
Q 040365          127 LKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSL-LDMYAKCGNIRLARCIFDKMDL  205 (514)
Q Consensus       127 ~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l-i~~y~k~g~~~~A~~~~~~m~~  205 (514)
                      ...|+++.+.+ ++...+++.++..--..+.++...-..+-.... ..+...-++++ +.+-.+.++++.-.....   .
T Consensus      1469 ~~Cye~~~q~~-p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~-~se~~~~~~s~~~eaaW~l~qwD~~e~~l~---~ 1543 (2382)
T KOG0890|consen 1469 AACYERLIQKD-PDKEKHHSGVLKSMLAIQHLSTEILHLDGLIIN-RSEEVDELNSLGVEAAWRLSQWDLLESYLS---D 1543 (2382)
T ss_pred             HHHHHHhhcCC-CccccchhhHHHhhhcccchhHHHhhhcchhhc-cCHHHHHHHHHHHHHHhhhcchhhhhhhhh---c
Confidence            99999988764 334677777777666666666655543333322 23333333333 455567777777766655   5


Q ss_pred             CChhHHHHH-HH-HHHhC--CChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh----------HH
Q 040365          206 HDIVSWTAV-IM-GNALH--GNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSM----------TK  271 (514)
Q Consensus       206 ~d~~~~~~l-i~-~~~~~--g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m----------~~  271 (514)
                      ++..+|.+. +. .+.+.  .+.-.-.++.+-+++.-+.|        +.+|+..|.+..+.++.-.+          ..
T Consensus      1544 ~n~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~--------lsa~s~~~Sy~~~Y~~~~kLH~l~el~~~~~~ 1615 (2382)
T KOG0890|consen 1544 RNIEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIEN--------LSACSIEGSYVRSYEILMKLHLLLELENSIEE 1615 (2382)
T ss_pred             ccccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhh--------HHHhhccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566666665 22 22221  12212223333333321111        22333333322222221111          11


Q ss_pred             hcCCCCCH------hHHHHH---HHHHHhcCCHHHHHH-HHHhCCCC-----CCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 040365          272 DYGIAPSF------EHYAAV---ADLLGRAGKLQEAYE-FISNMHAG-----PTENVWLTLLSACRVHKNVELAGKVAEK  336 (514)
Q Consensus       272 ~~~~~p~~------~~~~~l---i~~~~~~g~~~~A~~-~~~~m~~~-----p~~~~~~~ll~~~~~~~~~~~a~~~~~~  336 (514)
                      ..+..++.      ..|-.-   .+-+.+....=-|.+ .+......     .-..+|-.....++..|.++.|....-.
T Consensus      1616 l~~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~~q~A~nall~ 1695 (2382)
T KOG0890|consen 1616 LKKVSYDEDSANNSDNWKNRLERTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGHLQRAQNALLN 1695 (2382)
T ss_pred             hhccCccccccccchhHHHHHHHhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcccHHHHHHHHHh
Confidence            11233321      111111   111222111111111 11111112     2346899999999999999999998888


Q ss_pred             HHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCC
Q 040365          337 IFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       337 ~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  376 (514)
                      +.+..+  +..+.-.+......|+-..|..+++...+...
T Consensus      1696 A~e~r~--~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~~~ 1733 (2382)
T KOG0890|consen 1696 AKESRL--PEIVLERAKLLWQTGDELNALSVLQEILSKNF 1733 (2382)
T ss_pred             hhhccc--chHHHHHHHHHHhhccHHHHHHHHHHHHHhhc
Confidence            877774  46888899999999999999999998886544

>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional

Probab=85.43  E-value=68  Score=35.94  Aligned_cols=254  Identities=11%  Similarity=-0.075  Sum_probs=119.2

Q ss_pred             HHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCc
Q 040365           97 RLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDN  176 (514)
Q Consensus        97 ~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~  176 (514)
                      .+...+..+|...--..+..+.+.+. .++...+.+....   +|...-...+.++.+.+........+..+++   .+|
T Consensus       625 ~L~~~L~D~d~~VR~~Av~~L~~~~~-~~~~~~L~~aL~D---~d~~VR~~Aa~aL~~l~~~~~~~~~L~~~L~---~~d  697 (897)
T PRK13800        625 ELAPYLADPDPGVRRTAVAVLTETTP-PGFGPALVAALGD---GAAAVRRAAAEGLRELVEVLPPAPALRDHLG---SPD  697 (897)
T ss_pred             HHHHHhcCCCHHHHHHHHHHHhhhcc-hhHHHHHHHHHcC---CCHHHHHHHHHHHHHHHhccCchHHHHHHhc---CCC
Confidence            44444556666666666666666654 3344444444432   3333333444444433221111122223332   245


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcc
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHA  256 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~  256 (514)
                      ..+-...++++...+.- ....+...+..+|...-...+.++.+.+..+.    +....   -.+|...-.....++...
T Consensus       698 ~~VR~~A~~aL~~~~~~-~~~~l~~~L~D~d~~VR~~Av~aL~~~~~~~~----l~~~l---~D~~~~VR~~aa~aL~~~  769 (897)
T PRK13800        698 PVVRAAALDVLRALRAG-DAALFAAALGDPDHRVRIEAVRALVSVDDVES----VAGAA---TDENREVRIAVAKGLATL  769 (897)
T ss_pred             HHHHHHHHHHHHhhccC-CHHHHHHHhcCCCHHHHHHHHHHHhcccCcHH----HHHHh---cCCCHHHHHHHHHHHHHh
Confidence            55555555555544321 12234445556666555555666665544322    11222   234555555555555555


Q ss_pred             CCHHH-HHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          257 GLIDK-AWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAE  335 (514)
Q Consensus       257 g~~~~-a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~  335 (514)
                      +..+. +...+..+.+    .++...-...+.++++.|..+.+...+..+...+|..+-...+.++...+.. ++...+.
T Consensus       770 ~~~~~~~~~~L~~ll~----D~d~~VR~aA~~aLg~~g~~~~~~~~l~~aL~d~d~~VR~~Aa~aL~~l~~~-~a~~~L~  844 (897)
T PRK13800        770 GAGGAPAGDAVRALTG----DPDPLVRAAALAALAELGCPPDDVAAATAALRASAWQVRQGAARALAGAAAD-VAVPALV  844 (897)
T ss_pred             ccccchhHHHHHHHhc----CCCHHHHHHHHHHHHhcCCcchhHHHHHHHhcCCChHHHHHHHHHHHhcccc-chHHHHH
Confidence            54332 2333434432    3556666677777777776655444444443345655555566666666543 3434433


Q ss_pred             HHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          336 KIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       336 ~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      .+++ +| +...-...+.++.+.+.-..+...+....
T Consensus       845 ~~L~-D~-~~~VR~~A~~aL~~~~~~~~a~~~L~~al  879 (897)
T PRK13800        845 EALT-DP-HLDVRKAAVLALTRWPGDPAARDALTTAL  879 (897)
T ss_pred             HHhc-CC-CHHHHHHHHHHHhccCCCHHHHHHHHHHH
Confidence            3332 12 23344444455544322234444444433

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=84.23  E-value=77  Score=35.56  Aligned_cols=174  Identities=13%  Similarity=0.122  Sum_probs=96.2

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHC-----CCCCCHH--HHHHHHHHHhccC--ChHHHHHHHHHHHHcC--------CCC
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIA-----KIKPRHV--SFSSIMPACAHLT--TLHLGKQLHGCIIRNG--------FDD  175 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~-----g~~p~~~--t~~~ll~~~~~~~--~~~~a~~~~~~~~~~~--------~~~  175 (514)
                      ++-+-..+.++.+-+-+++++++.     .++.|.+  -|...+...+..|  -+++.+.+   +.+.|        +.|
T Consensus       857 l~VAq~SqkDPkEyLP~L~el~~m~~~~rkF~ID~~L~ry~~AL~hLs~~~~~~~~e~~n~---I~kh~Ly~~aL~ly~~  933 (1265)
T KOG1920|consen  857 LLVAQKSQKDPKEYLPFLNELKKMETLLRKFKIDDYLKRYEDALSHLSECGETYFPECKNY---IKKHGLYDEALALYKP  933 (1265)
T ss_pred             HHHHHHhccChHHHHHHHHHHhhchhhhhheeHHHHHHHHHHHHHHHHHcCccccHHHHHH---HHhcccchhhhheecc
Confidence            334445566777777777776531     1112211  2334444444444  33333333   33333        245


Q ss_pred             cHHHHHHHHHH----HHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHH--HHHH
Q 040365          176 NMFIASSLLDM----YAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVA--FVAV  249 (514)
Q Consensus       176 ~~~~~~~li~~----y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t--~~~l  249 (514)
                      +...+.-...+    +...+.+++|--.|+..-+     ..--+.+|...|+|.+|+.+-.+|..   .-|...  -..|
T Consensus       934 ~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gk-----lekAl~a~~~~~dWr~~l~~a~ql~~---~~de~~~~a~~L 1005 (1265)
T KOG1920|consen  934 DSEKQKVIYEAYADHLREELMSDEAALMYERCGK-----LEKALKAYKECGDWREALSLAAQLSE---GKDELVILAEEL 1005 (1265)
T ss_pred             CHHHHHHHHHHHHHHHHHhccccHHHHHHHHhcc-----HHHHHHHHHHhccHHHHHHHHHhhcC---CHHHHHHHHHHH
Confidence            55444444433    4455666777666655431     12235667777888888887777643   112222  2456


Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH  306 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  306 (514)
                      ..-+...++.-+|-++..+...    .|     .-.+..|++...+++|..+-....
T Consensus      1006 ~s~L~e~~kh~eAa~il~e~~s----d~-----~~av~ll~ka~~~~eAlrva~~~~ 1053 (1265)
T KOG1920|consen 1006 VSRLVEQRKHYEAAKILLEYLS----DP-----EEAVALLCKAKEWEEALRVASKAK 1053 (1265)
T ss_pred             HHHHHHcccchhHHHHHHHHhc----CH-----HHHHHHHhhHhHHHHHHHHHHhcc
Confidence            7777788888888777765532    22     334566788888888888776554

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=83.97  E-value=37  Score=31.66  Aligned_cols=58  Identities=12%  Similarity=-0.041  Sum_probs=52.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      .....|...|.+.+|.++.++++.++|-+...+..|...|+..|+--.|.+-++.+.+
T Consensus       284 kva~~yle~g~~neAi~l~qr~ltldpL~e~~nk~lm~~la~~gD~is~~khyerya~  341 (361)
T COG3947         284 KVARAYLEAGKPNEAIQLHQRALTLDPLSEQDNKGLMASLATLGDEISAIKHYERYAE  341 (361)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHhhcChhhhHHHHHHHHHHHHhccchhhhhHHHHHHH
Confidence            3446789999999999999999999999999999999999999998888888888754

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=83.87  E-value=0.53  Score=39.14  Aligned_cols=54  Identities=11%  Similarity=0.135  Sum_probs=33.4

Q ss_pred             HHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          148 IMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFD  201 (514)
Q Consensus       148 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~  201 (514)
                      ++..+.+.+.++...++++.+.+.+...+..+.+.|+..|++.++.++..++++
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            445555566666666677777666555566777777777777766555555555

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.54  E-value=42  Score=31.96  Aligned_cols=150  Identities=13%  Similarity=0.006  Sum_probs=96.1

Q ss_pred             HCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHc---CCCCcHHHHHHHHHHHHhcCCHHH
Q 040365          119 QNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN---GFDDNMFIASSLLDMYAKCGNIRL  195 (514)
Q Consensus       119 ~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~li~~y~k~g~~~~  195 (514)
                      .+|...+|-..++++.+. .+.|...+...=.+|...|+.+.-+..+++++..   ++|-...+-..+.-++..||-+++
T Consensus       115 ~~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~d  193 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDD  193 (491)
T ss_pred             ccccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchh
Confidence            467777777778887765 5667777777778888888888888888877654   222233444444555668899999


Q ss_pred             HHHHHHhCCCC---ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          196 ARCIFDKMDLH---DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP---NSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       196 A~~~~~~m~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p---~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      |++.-++..+-   |..+-.+....+-..|+..++.+...+-...=-..   -...|-...-.+...+.++.|.++|+.-
T Consensus       194 AEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~e  273 (491)
T KOG2610|consen  194 AEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDRE  273 (491)
T ss_pred             HHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHHH
Confidence            98888876533   44455556666667888888888776543210000   0111222233344567888888888743

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=83.45  E-value=6.4  Score=38.94  Aligned_cols=122  Identities=16%  Similarity=0.222  Sum_probs=85.8

Q ss_pred             HHhCCChHHHH-HHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHH
Q 040365          218 NALHGNAHDAI-SLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       218 ~~~~g~~~~A~-~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~  296 (514)
                      -...|+.-.|- ++|.-+....-.|+.+-..+.|  ..+.|.++.+.+.+....+  -+.....+-.+++....+.|+++
T Consensus       299 ~~~~gd~~aas~~~~~~lr~~~~~p~~i~l~~~i--~~~lg~ye~~~~~~s~~~~--~~~s~~~~~~~~~r~~~~l~r~~  374 (831)
T PRK15180        299 QLADGDIIAASQQLFAALRNQQQDPVLIQLRSVI--FSHLGYYEQAYQDISDVEK--IIGTTDSTLRCRLRSLHGLARWR  374 (831)
T ss_pred             HhhccCHHHHHHHHHHHHHhCCCCchhhHHHHHH--HHHhhhHHHHHHHhhchhh--hhcCCchHHHHHHHhhhchhhHH
Confidence            34456665554 4555566665677777666665  5678999999998887643  34446677888999999999999


Q ss_pred             HHHHHHHhCCCC--CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          297 EAYEFISNMHAG--PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       297 ~A~~~~~~m~~~--p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      +|..+-+.|...  .+..+.........+.|-++++...+++++.++|+
T Consensus       375 ~a~s~a~~~l~~eie~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~~~  423 (831)
T PRK15180        375 EALSTAEMMLSNEIEDEEVLTVAAGSADALQLFDKSYHYWKRVLLLNPE  423 (831)
T ss_pred             HHHHHHHHHhccccCChhheeeecccHHHHhHHHHHHHHHHHHhccCCh
Confidence            999988877421  34444444445566778889999999999888755

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=83.43  E-value=0.57  Score=38.92  Aligned_cols=84  Identities=14%  Similarity=0.252  Sum_probs=54.2

Q ss_pred             HHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHH
Q 040365           47 VLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEG  126 (514)
Q Consensus        47 ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A  126 (514)
                      +++.+.+.+.+.....+++.+.+.+...+....+.|+..|++.++.+...++++....   .-...++..+.+.|.+++|
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~l~~~a   89 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN---YDLDKALRLCEKHGLYEEA   89 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTTSHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc---cCHHHHHHHHHhcchHHHH
Confidence            4556666677777777777777666556677788888888888777777777774332   2233456666666666666


Q ss_pred             HHHHHHH
Q 040365          127 LKFFRQM  133 (514)
Q Consensus       127 ~~l~~~m  133 (514)
                      .-++.++
T Consensus        90 ~~Ly~~~   96 (143)
T PF00637_consen   90 VYLYSKL   96 (143)
T ss_dssp             HHHHHCC
T ss_pred             HHHHHHc
Confidence            6666554

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=82.35  E-value=13  Score=32.63  Aligned_cols=67  Identities=7%  Similarity=-0.085  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC-------CCChhHHHHHHHHHHHCCChhHH
Q 040365           59 KGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP-------VKDAISWNSIIAGCVQNGLFDEG  126 (514)
Q Consensus        59 ~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~-------~~d~~~~~~li~~~~~~g~~~~A  126 (514)
                      .|++.|-.+...+.-.++...-+|...|. ..+.+.|..++....       ..|+..+.+|++.|.+.|+++.|
T Consensus       124 ~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  124 EALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            35555555554444445555555555554 334444444443321       33555566666666666666555

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=82.34  E-value=3.2  Score=23.85  Aligned_cols=27  Identities=11%  Similarity=0.054  Sum_probs=13.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          317 LLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       317 ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      +..++...|+.++|...++++++..|+
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~~P~   32 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKRYPD   32 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence            334444555555555555555555443

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=82.12  E-value=2.4  Score=26.01  Aligned_cols=28  Identities=29%  Similarity=0.285  Sum_probs=21.6

Q ss_pred             chHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          346 GAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       346 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      .+++.|+..|...|++++|..++++..+
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4677888888888888888888887754

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=81.78  E-value=13  Score=32.61  Aligned_cols=72  Identities=19%  Similarity=-0.001  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHc---CCCCcHHHHHHHHHHHHhcCCHHHH
Q 040365          124 DEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN---GFDDNMFIASSLLDMYAKCGNIRLA  196 (514)
Q Consensus       124 ~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~li~~y~k~g~~~~A  196 (514)
                      ++|++.|-++...+.--++.....+...| ...+.+++.+++..+++.   +-.+|+.++.+|++.|-+.|+++.|
T Consensus       123 ~~A~~~fL~~E~~~~l~t~elq~aLAtyY-~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  123 QEALRRFLQLEGTPELETAELQYALATYY-TKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            45566665555554333333333333333 345566666666655543   2245566666666666666666655

>PF09477 Type_III_YscG: Bacterial type II secretion system chaperone protein (type_III_yscG); InterPro: IPR013348 YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion)

Probab=81.56  E-value=23  Score=27.50  Aligned_cols=89  Identities=11%  Similarity=0.070  Sum_probs=57.6

Q ss_pred             CCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHH
Q 040365           54 YVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQM  133 (514)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m  133 (514)
                      ....++|..+.+.+...+- ....+--.-+..+...|++++|...=.....||...|-+|-.  .+.|..+++...+.++
T Consensus        19 ~HcH~EA~tIa~wL~~~~~-~~E~v~lIr~~sLmNrG~Yq~ALl~~~~~~~pdL~p~~AL~a--~klGL~~~~e~~l~rl   95 (116)
T PF09477_consen   19 HHCHQEANTIADWLEQEGE-MEEVVALIRLSSLMNRGDYQEALLLPQCHCYPDLEPWAALCA--WKLGLASALESRLTRL   95 (116)
T ss_dssp             TT-HHHHHHHHHHHHHTTT-THHHHHHHHHHHHHHTT-HHHHHHHHTTS--GGGHHHHHHHH--HHCT-HHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHhhHHHHHHHHhcccCCCccHHHHHHHHH--HhhccHHHHHHHHHHH
Confidence            3456788888888877763 334444445556778899999966666666789999877655  4788888888888887


Q ss_pred             HHCCCCCCHHHHH
Q 040365          134 LIAKIKPRHVSFS  146 (514)
Q Consensus       134 ~~~g~~p~~~t~~  146 (514)
                      ..+| .|....|.
T Consensus        96 a~~g-~~~~q~Fa  107 (116)
T PF09477_consen   96 ASSG-SPELQAFA  107 (116)
T ss_dssp             CT-S-SHHHHHHH
T ss_pred             HhCC-CHHHHHHH
Confidence            7665 45444443

The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia, and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens.; GO: 0009405 pathogenesis; PDB: 3PH0_D 2UWJ_G 2P58_C.

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=81.36  E-value=44  Score=30.72  Aligned_cols=218  Identities=18%  Similarity=0.245  Sum_probs=120.6

Q ss_pred             HHHHHHHHHCCChhHHHHHHHHHHHC---CC--CCCHHHHHHHHHHHhccCChHHHHHHHHHHHHc-----CCCCcHHHH
Q 040365          111 NSIIAGCVQNGLFDEGLKFFRQMLIA---KI--KPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN-----GFDDNMFIA  180 (514)
Q Consensus       111 ~~li~~~~~~g~~~~A~~l~~~m~~~---g~--~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~  180 (514)
                      -.+|..+.+.|++++.++.|.+|...   .+  .-+..+.++++..-+...+.+.-..+++..++.     +-..--.+-
T Consensus        69 KQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVTrNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTN  148 (440)
T KOG1464|consen   69 KQMIKINFRLGNYKEMMERYKQLLTYIKSAVTRNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTN  148 (440)
T ss_pred             HHHHHHHhccccHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeecc
Confidence            34566666777777777776666431   11  124455666766666666666655555543321     101111223


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhCCC--------CC-------hhHHHHHHHHHHhCCChHHHHHHHHHHHH-cCCCCCHH
Q 040365          181 SSLLDMYAKCGNIRLARCIFDKMDL--------HD-------IVSWTAVIMGNALHGNAHDAISLFEQMEK-DGVKPNSV  244 (514)
Q Consensus       181 ~~li~~y~k~g~~~~A~~~~~~m~~--------~d-------~~~~~~li~~~~~~g~~~~A~~l~~~m~~-~g~~p~~~  244 (514)
                      +-|...|...|++.+-.+++.++..        .|       ...|..=|..|....+-.+-..+|++... ...-|...
T Consensus       149 tKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPl  228 (440)
T KOG1464|consen  149 TKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPL  228 (440)
T ss_pred             chHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchH
Confidence            4566777778888887777777641        11       24577777888888877777778887654 22334443


Q ss_pred             HHHHHHHHHH-----ccCCHHHHHHHHHHhHHhcCCC--CC---HhHHHHHHHHHHhcCC----HHHHHHHHHhCCCCCC
Q 040365          245 AFVAVLTACS-----HAGLIDKAWSYFNSMTKDYGIA--PS---FEHYAAVADLLGRAGK----LQEAYEFISNMHAGPT  310 (514)
Q Consensus       245 t~~~ll~a~~-----~~g~~~~a~~~~~~m~~~~~~~--p~---~~~~~~li~~~~~~g~----~~~A~~~~~~m~~~p~  310 (514)
                       ...++.-|.     +.|.+++|-.-|-+..+.+.-.  |.   ---|..|..++.++|-    -++|.    -....|.
T Consensus       229 -ImGvIRECGGKMHlreg~fe~AhTDFFEAFKNYDEsGspRRttCLKYLVLANMLmkS~iNPFDsQEAK----PyKNdPE  303 (440)
T KOG1464|consen  229 -IMGVIRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAK----PYKNDPE  303 (440)
T ss_pred             -HHhHHHHcCCccccccchHHHHHhHHHHHHhcccccCCcchhHHHHHHHHHHHHHHcCCCCCcccccC----CCCCCHH
Confidence             334555553     4577887765444443544322  22   2345566677766652    11211    0012255


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHH
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVA  334 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~  334 (514)
                      ....+.|+.+|..+ +..+-++++
T Consensus       304 IlAMTnlv~aYQ~N-dI~eFE~Il  326 (440)
T KOG1464|consen  304 ILAMTNLVAAYQNN-DIIEFERIL  326 (440)
T ss_pred             HHHHHHHHHHHhcc-cHHHHHHHH
Confidence            66778888888654 444433333

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=81.29  E-value=11  Score=28.84  Aligned_cols=48  Identities=23%  Similarity=0.220  Sum_probs=31.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       305 m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      +..-|++.+..+.+.+|++.+|+..|.++++-+...-.+....|..++
T Consensus        39 ~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~l   86 (108)
T PF02284_consen   39 YDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYIL   86 (108)
T ss_dssp             SSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHH
T ss_pred             cccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHH
Confidence            334588888899999999999999999999888765443333555443

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 ....

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=81.23  E-value=2.3  Score=23.30  Aligned_cols=23  Identities=22%  Similarity=0.111  Sum_probs=17.1

Q ss_pred             hHHHHHHHHHHccChhHHHHHHH
Q 040365          347 AYVILSNTYAAARRWKDAASLRV  369 (514)
Q Consensus       347 ~~~~l~~~~~~~g~~~~a~~~~~  369 (514)
                      ....|..++...|++++|..+++
T Consensus         3 a~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    3 ARLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHh
Confidence            45667777888888888877764

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=81.06  E-value=11  Score=28.68  Aligned_cols=47  Identities=23%  Similarity=0.221  Sum_probs=32.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       305 m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      +..-|++.+..+-+.||++.+|+..|.++++-+...-.++...|-.+
T Consensus        36 ~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~   82 (103)
T cd00923          36 YDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYI   82 (103)
T ss_pred             cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHH
Confidence            34457888888888888888888888888887764433333345443

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.

>PHA02875 ankyrin repeat protein; Provisional

Probab=80.81  E-value=64  Score=32.21  Aligned_cols=209  Identities=12%  Similarity=0.055  Sum_probs=108.2

Q ss_pred             HHHHhcCChhHHHHHHHHHhhCCCCCChhh--HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchh--HHHHHHHHHHHC
Q 040365           14 VGLARNGLYEEALNIVRQMGNVNLKPDSFT--LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVC--IGSSLINMYAKC   89 (514)
Q Consensus        14 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t--~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~--~~~~li~~~~~~   89 (514)
                      ...++.|+.+-+    +.+.+.|..|+...  ..+.+..++..|+.+    +.+.+++.|..++..  ...+.+...++.
T Consensus         7 ~~A~~~g~~~iv----~~Ll~~g~~~n~~~~~g~tpL~~A~~~~~~~----~v~~Ll~~ga~~~~~~~~~~t~L~~A~~~   78 (413)
T PHA02875          7 CDAILFGELDIA----RRLLDIGINPNFEIYDGISPIKLAMKFRDSE----AIKLLMKHGAIPDVKYPDIESELHDAVEE   78 (413)
T ss_pred             HHHHHhCCHHHH----HHHHHCCCCCCccCCCCCCHHHHHHHcCCHH----HHHHHHhCCCCccccCCCcccHHHHHHHC
Confidence            344556766444    44445676665432  233455555667765    445566677655432  123445566788


Q ss_pred             CCHHHHHHHHccCCCCC----hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHH--HHHHHHHhccCChHHHHH
Q 040365           90 ARVEDSHRLFCLLPVKD----AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSF--SSIMPACAHLTTLHLGKQ  163 (514)
Q Consensus        90 g~~~~A~~~f~~~~~~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~--~~ll~~~~~~~~~~~a~~  163 (514)
                      |+.+.+..+++.-...+    ..-++. +...+..|+.    ++++.+.+.|..|+....  .+.+...+..|+.+.++.
T Consensus        79 g~~~~v~~Ll~~~~~~~~~~~~~g~tp-L~~A~~~~~~----~iv~~Ll~~gad~~~~~~~g~tpLh~A~~~~~~~~v~~  153 (413)
T PHA02875         79 GDVKAVEELLDLGKFADDVFYKDGMTP-LHLATILKKL----DIMKLLIARGADPDIPNTDKFSPLHLAVMMGDIKGIEL  153 (413)
T ss_pred             CCHHHHHHHHHcCCcccccccCCCCCH-HHHHHHhCCH----HHHHHHHhCCCCCCCCCCCCCCHHHHHHHcCCHHHHHH
Confidence            99999888887643221    111222 3333455655    344555566766654321  233444556677665544


Q ss_pred             HHHHHHHcCCCCcHH--HHHHHHHHHHhcCCHHHHHHHHHhCCCCChhH---HHHHHHHHHhCCChHHHHHHHHHHHHcC
Q 040365          164 LHGCIIRNGFDDNMF--IASSLLDMYAKCGNIRLARCIFDKMDLHDIVS---WTAVIMGNALHGNAHDAISLFEQMEKDG  238 (514)
Q Consensus       164 ~~~~~~~~~~~~~~~--~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~---~~~li~~~~~~g~~~~A~~l~~~m~~~g  238 (514)
                      ++    +.|..++..  ...+.+...+..|+.+-+.-+++.-..++...   ..+.+...+..|+.+    +.+-+.+.|
T Consensus       154 Ll----~~g~~~~~~d~~g~TpL~~A~~~g~~eiv~~Ll~~ga~~n~~~~~~~~t~l~~A~~~~~~~----iv~~Ll~~g  225 (413)
T PHA02875        154 LI----DHKACLDIEDCCGCTPLIIAMAKGDIAICKMLLDSGANIDYFGKNGCVAALCYAIENNKID----IVRLFIKRG  225 (413)
T ss_pred             HH----hcCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHhCCCCCCcCCCCCCchHHHHHHHcCCHH----HHHHHHHCC
Confidence            43    444333211  12233444566788877777776554443221   223444334556553    444455567


Q ss_pred             CCCCH
Q 040365          239 VKPNS  243 (514)
Q Consensus       239 ~~p~~  243 (514)
                      ..|+.
T Consensus       226 ad~n~  230 (413)
T PHA02875        226 ADCNI  230 (413)
T ss_pred             cCcch
Confidence            77664

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=80.67  E-value=4  Score=24.96  Aligned_cols=28  Identities=14%  Similarity=0.229  Sum_probs=16.8

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          209 VSWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       209 ~~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      .+++.+...|...|++++|+.++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            3556666666666666666666666543

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=80.14  E-value=3.5  Score=23.92  Aligned_cols=28  Identities=14%  Similarity=0.151  Sum_probs=23.9

Q ss_pred             chHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          346 GAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       346 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..+..++..|...|++++|.+.+++..+
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            4678899999999999999999998765

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

---

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	514
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-09
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	9e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 59.1 bits (141), Expect = 2e-09
 Identities = 22/183 (12%), Positives = 51/183 (27%), Gaps = 7/183 (3%)

Query: 136 AKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRL 195
           A   P     + ++       +L + +   G   +           +          + L
Sbjct: 86  APESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPL 145

Query: 196 ARCIFDKM-------DLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVA 248
           A  +            L  +  + AV++G A  G   + + +   ++  G+ P+ +++ A
Sbjct: 146 AHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAA 205

Query: 249 VLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAG 308
            L                       G+       A +     RA  L+  ++        
Sbjct: 206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLP 265

Query: 309 PTE 311
           P  
Sbjct: 266 PQL 268

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 47.5 bits (111), Expect = 9e-06
 Identities = 19/177 (10%), Positives = 53/177 (29%), Gaps = 8/177 (4%)

Query: 38  KPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHR 97
            P    L+ +L      + +   +   G   +  L        +         ++  +H 
Sbjct: 89  SPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLPLAHH 148

Query: 98  LFCLL-------PVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMP 150
           L  +         +     +N+++ G  + G F E +     +  A + P  +S+++ + 
Sbjct: 149 LLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ 208

Query: 151 ACAHLT-TLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH 206
                       ++    + + G        + LL    +   ++    +     L 
Sbjct: 209 CMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLP 265

>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 = 55.2 bits (132), Expect = 3e-08
 Identities = 67/487 (13%), Positives = 137/487 (28%), Gaps = 169/487 (34%)

Query: 5   DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKP--DSFTLSS-VLPI-----FADYVD 56
            + S    +  L ++  YE  L ++    NV      ++F LS  +L         D++ 
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLL---NVQNAKAWNAFNLSCKILLTTRFKQVTDFLS 282

Query: 57  VIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA--RVEDSHRLFCLLPVKDAISWN--- 111
                 I        L         + ++  K    R +D       LP ++ ++ N   
Sbjct: 283 AATTTHISLDHHSMTLTP-----DEVKSLLLKYLDCRPQD-------LP-REVLTTNPRR 329

Query: 112 -SIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPAC-AHLTTLHLGKQLHGCII 169
            SIIA  +++GL       ++ +   K        ++I+ +    L      K      +
Sbjct: 330 LSIIAESIRDGL--ATWDNWKHVNCDK-------LTTIIESSLNVLEPAEYRKMFDRLSV 380

Query: 170 RNGFDDNMFIASSLL-------------DMYAKCGNIRLARCIFDKM--DLHDIVSWTAV 214
              F  +  I + LL              +  K     L      +    +  I      
Sbjct: 381 ---FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI------ 431

Query: 215 IMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG 274
                        + L  ++E +                 H  ++D  ++   +   D  
Sbjct: 432 ------------YLELKVKLENEYAL--------------HRSIVDH-YNIPKTFDSDDL 464

Query: 275 IAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVH-KNVELAGKV 333
           I P  + Y                Y  I   H                 H KN+E   ++
Sbjct: 465 IPPYLDQYF---------------YSHI--GH-----------------HLKNIEHPERM 490

Query: 334 AE--KIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSW------- 384
                +F+                            R F+  K    + A +        
Sbjct: 491 TLFRMVFL--------------------------DFR-FLEQKIRHDSTAWNASGSILNT 523

Query: 385 -IEVKN-KAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDTKEVLHDVEEEQKKNL 442
             ++K  K Y       + P Y R+  A+ + L ++E+        ++L  +    +   
Sbjct: 524 LQQLKFYKPYIC----DNDPKYERLVNAILDFLPKIEENLICSKYTDLLR-IALMAEDEA 578

Query: 443 LYYHSER 449
           ++  + +
Sbjct: 579 IFEEAHK 585

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	514
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.97
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.96
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.96
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.93
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.92
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.9
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.89
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.89
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.86
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.85
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.83
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.83
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.81
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.8
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.78
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.78
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.78
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.78
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.76
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.76
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.75
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.75
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.75
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.74
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.73
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.73
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.73
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.73
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.72
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.65
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.64
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.63
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.62
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.61
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.61
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.6
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.56
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.55
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.55
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.54
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.54
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.54
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.54
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.54
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.54
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.53
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.52
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.52
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.5
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.49
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.49
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.48
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.48
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.48
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.47
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.47
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.45
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.43
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.41
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.4
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.39
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.39
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.37
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.36
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.34
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.33
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.33
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.32
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.29
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.29
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.27
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.27
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.25
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.24
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.24
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.18
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.18
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.18
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.18
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.1
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.08
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.04
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.03
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.03
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.03
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.97
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.97
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.95
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.95
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	98.94
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.93
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.91
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.9
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.88
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.86
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.8
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.79
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.79
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.78
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.77
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.76
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.76
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.75
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.74
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.72
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.72
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.72
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.7
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.7
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.7
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.69
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.68
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.68
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.65
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.65
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.64
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.62
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.62
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.62
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.62
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.61
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.6
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.58
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.56
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.54
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.53
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.53
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.51
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.49
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.48
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.45
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.42
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.42
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.42
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.41
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.41
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.41
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.39
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.38
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.37
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.36
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.36
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.35
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.33
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.33
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.32
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.32
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.31
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.31
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.31
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.3
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.27
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.27
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.27
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.27
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.24
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.23
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.22
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.22
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.21
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.21
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.19
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.18
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.16
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.12
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.07
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.07
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.06
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.05
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.04
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.04
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.03
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.02
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.01
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.01
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.0
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.99
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.99
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.98
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.94
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.94
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.91
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.89
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.89
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.83
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.83
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.82
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.82
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.81
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.81
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.79
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.75
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.67
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.65
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.64
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.54
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.42
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.39
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.36
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.31
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.22
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.21
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.19
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.17
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.16
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.14
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.06
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.84
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.83
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.79
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.77
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.69
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.67
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.65
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.59
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.55
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.49
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.09
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.85
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.73
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.71
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.59
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.13
1pc2_A	152	Mitochondria fission protein; unknown function; NM	94.52
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	94.5
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	94.42
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	93.35
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	93.31
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	93.25
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	93.0
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	92.94
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	92.19
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	91.92
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	91.32
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	91.21
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	90.97
2p58_C	116	Putative type III secretion protein YSCG; type III	90.26
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	90.15
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	89.9
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	89.89
2p58_C	116	Putative type III secretion protein YSCG; type III	89.86
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	89.32
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	88.54
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	87.86
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	87.59
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	87.53
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	86.25
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	86.15
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	84.11
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	83.41
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	83.03
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	82.99
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	82.83
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	82.67
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	81.19
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	80.03

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=4.5e-35  Score=307.10  Aligned_cols=366  Identities=11%  Similarity=-0.014  Sum_probs=322.7

Q ss_pred             CCCCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHH
Q 040365            2 PVSDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSS   81 (514)
Q Consensus         2 ~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~   81 (514)
                      |.+++..|+.++..|.+.|++++|+.+|++|..  ..|+..++..++.+|...|++++|.++++.+...  +++..+++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~  155 (597)
T 2xpi_A           80 SLSREDYLRLWRHDALMQQQYKCAAFVGEKVLD--ITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYL  155 (597)
T ss_dssp             --CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHccCchHHHHHHHHHHh--hCCCchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHH
Confidence            457889999999999999999999999999985  4688899999999999999999999999988644  788999999


Q ss_pred             HHHHHHHCCCHHHHHHHHccCCCC-------------------ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCC----
Q 040365           82 LINMYAKCARVEDSHRLFCLLPVK-------------------DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKI----  138 (514)
Q Consensus        82 li~~~~~~g~~~~A~~~f~~~~~~-------------------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~----  138 (514)
                      ++.+|.++|++++|.++|+++...                   +..+|+.++.+|.+.|++++|+++|++|.+.+.    
T Consensus       156 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~  235 (597)
T 2xpi_A          156 AAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYE  235 (597)
T ss_dssp             HHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhH
Confidence            999999999999999999965433                   478999999999999999999999999865431    


Q ss_pred             ------------------------------------------------------------------CCCHHHHHHHHHHH
Q 040365          139 ------------------------------------------------------------------KPRHVSFSSIMPAC  152 (514)
Q Consensus       139 ------------------------------------------------------------------~p~~~t~~~ll~~~  152 (514)
                                                                                        +++..++..++.++
T Consensus       236 ~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~  315 (597)
T 2xpi_A          236 AFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTL  315 (597)
T ss_dssp             HHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHH
Confidence                                                                              26777888888999


Q ss_pred             hccCChHHHHHHHHHHHHcCC---------------------------------CCcHHHHHHHHHHHHhcCCHHHHHHH
Q 040365          153 AHLTTLHLGKQLHGCIIRNGF---------------------------------DDNMFIASSLLDMYAKCGNIRLARCI  199 (514)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~~---------------------------------~~~~~~~~~li~~y~k~g~~~~A~~~  199 (514)
                      .+.|++++|.++++.+.+.+.                                 +.+..+++.++.+|.++|++++|.++
T Consensus       316 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  395 (597)
T 2xpi_A          316 FVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRY  395 (597)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHH
Confidence            999999999999998876531                                 34577888899999999999999999


Q ss_pred             HHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCC
Q 040365          200 FDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA  276 (514)
Q Consensus       200 ~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~  276 (514)
                      |+++.   ..+..+|+.++.+|.+.|++++|+++|+++.+.+ +++..++..++.+|.+.|++++|.++|+.+.+.  .+
T Consensus       396 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~  472 (597)
T 2xpi_A          396 FSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILLANEYLQSSYAL--FQ  472 (597)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CC
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CC
Confidence            99874   4578899999999999999999999999998863 347789999999999999999999999999754  23


Q ss_pred             CCHhHHHHHHHHHHhcCCHHHHHHHHHhC-------CCCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcch
Q 040365          277 PSFEHYAAVADLLGRAGKLQEAYEFISNM-------HAGPT--ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGA  347 (514)
Q Consensus       277 p~~~~~~~li~~~~~~g~~~~A~~~~~~m-------~~~p~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~  347 (514)
                      .+..+|..++.+|.+.|++++|.++|+++       +..|+  ..+|..++.+|...|++++|...++++.+.+|+++.+
T Consensus       473 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~  552 (597)
T 2xpi_A          473 YDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDANV  552 (597)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHH
T ss_pred             CChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHH
Confidence            36889999999999999999999999987       33677  7899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          348 YVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       348 ~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      |..++.+|.+.|++++|.+.++++.+.
T Consensus       553 ~~~l~~~~~~~g~~~~A~~~~~~~l~~  579 (597)
T 2xpi_A          553 HTAIALVYLHKKIPGLAITHLHESLAI  579 (597)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            999999999999999999999999875

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.3e-31  Score=278.96  Aligned_cols=297  Identities=9%  Similarity=-0.026  Sum_probs=239.9

Q ss_pred             CChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHH
Q 040365           55 VDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFR  131 (514)
Q Consensus        55 ~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~  131 (514)
                      |++++|.++++.+.+.  +++..+++.++.+|.+.|++++|.++|+++.   ..+..+|+.++.+|.+.|++++|.++|+
T Consensus       286 g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  363 (597)
T 2xpi_A          286 DELRRAEDYLSSINGL--EKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISN  363 (597)
T ss_dssp             HHHHHHHHHHHTSTTG--GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHhhcC--CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            3334444444433332  3455566666666666666666666666553   2345556666666666666666666666


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCCh
Q 040365          132 QMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDI  208 (514)
Q Consensus       132 ~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~  208 (514)
                      ++.+. .+.+..++..+...|.+.|++++|.++++.+.+.. +.+..+++.++.+|.+.|++++|.++|+++.   ..+.
T Consensus       364 ~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  441 (597)
T 2xpi_A          364 DLVDR-HPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTH  441 (597)
T ss_dssp             HHHHH-CTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCS
T ss_pred             HHHhh-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccch
Confidence            66543 24567889999999999999999999999998865 5678899999999999999999999999875   4578


Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhc---CCCCC--HhHHH
Q 040365          209 VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDY---GIAPS--FEHYA  283 (514)
Q Consensus       209 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~---~~~p~--~~~~~  283 (514)
                      .+|+.++.+|.+.|++++|+++|+++.+.. +.+..+|..++..|.+.|++++|.++|+.+.+..   +..|+  ..+|.
T Consensus       442 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~  520 (597)
T 2xpi_A          442 LPYLFLGMQHMQLGNILLANEYLQSSYALF-QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWA  520 (597)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHH
Confidence            999999999999999999999999999863 3478899999999999999999999999996643   66787  78999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          284 AVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                      .++.+|.+.|++++|.++++++.  .+.+..+|..+..+|...|++++|...++++++++|+++..+..|.++|.
T Consensus       521 ~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~  595 (597)
T 2xpi_A          521 NLGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAISPNEIMASDLLKRALE  595 (597)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTC
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCChHHHHHHHHHHh
Confidence            99999999999999999999874  23588999999999999999999999999999999999999999988774

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.97  E-value=6.4e-30  Score=259.24  Aligned_cols=212  Identities=13%  Similarity=0.134  Sum_probs=169.5

Q ss_pred             hHHHHHHHHHhhCCCCCChh-hHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHcc
Q 040365           23 EEALNIVRQMGNVNLKPDSF-TLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCL  101 (514)
Q Consensus        23 ~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~  101 (514)
                      ..+..+.+.+.+.++.+.+. .++.+|.+|++.|++++|.++|++|.+.|+.||..+||+||.+|++.+...++      
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~------   80 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATES------   80 (501)
T ss_dssp             -----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSS------
T ss_pred             chHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhh------
Confidence            44566777888777766544 58888999999999999999999999999999999999999999887754321      


Q ss_pred             CCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHH
Q 040365          102 LPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIAS  181 (514)
Q Consensus       102 ~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  181 (514)
                                      .+.+..++|.++|++|...|+.||..||+++|.+|++.|++++|.+++++|.+.|+.||..+||
T Consensus        81 ----------------~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn  144 (501)
T 4g26_A           81 ----------------SPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYG  144 (501)
T ss_dssp             ----------------SCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHH
T ss_pred             ----------------hhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceeh
Confidence                            1345578899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcc
Q 040365          182 SLLDMYAKCGNIRLARCIFDKMD----LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHA  256 (514)
Q Consensus       182 ~li~~y~k~g~~~~A~~~~~~m~----~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~  256 (514)
                      +||.+|++.|++++|.++|++|.    .||..+|++||.+|++.|+.++|.++|++|.+.|..|+..||+.++..+...
T Consensus       145 ~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          145 PALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            99999999988888888888885    6788888888888888888888888888888888888888888888877653

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.97  E-value=1.6e-29  Score=256.25  Aligned_cols=197  Identities=14%  Similarity=0.170  Sum_probs=175.4

Q ss_pred             HHHHHccCCCC-----ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC---------hHH
Q 040365           95 SHRLFCLLPVK-----DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTT---------LHL  160 (514)
Q Consensus        95 A~~~f~~~~~~-----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~---------~~~  160 (514)
                      +..+++.+.++     ....++.+|++|++.|++++|+++|++|.+.|++||..||+++|.+|++.+.         ++.
T Consensus         9 ~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~   88 (501)
T 4g26_A            9 SENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSR   88 (501)
T ss_dssp             ---------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHH
T ss_pred             HHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHH
Confidence            44444555432     2346888999999999999999999999999999999999999999987654         688


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD----LHDIVSWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~----~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      |.++|++|.+.|+.||..+||+||++|++.|++++|.++|++|.    .||..+||++|.+|++.|+.++|.++|++|.+
T Consensus        89 A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~  168 (501)
T 4g26_A           89 GFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVE  168 (501)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999996    68999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhc
Q 040365          237 DGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRA  292 (514)
Q Consensus       237 ~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~  292 (514)
                      .|+.||..||++||.+|++.|++++|.++|++|.+ .++.|+..+|+.+++.|...
T Consensus       169 ~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~-~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          169 SEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRD-LVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             TTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-HTSSBCHHHHHHHHHHHHSH
T ss_pred             cCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHH-hCCCcCHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999955 59999999999999998764

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.96  E-value=4.5e-26  Score=225.63  Aligned_cols=353  Identities=16%  Similarity=0.080  Sum_probs=310.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCC
Q 040365           12 VIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCAR   91 (514)
Q Consensus        12 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~   91 (514)
                      +...+.+.|++++|+..+..+.+.. +.+...+..+...+...|++++|...+..+++.. +.+..++..+...|.+.|+
T Consensus         5 ~a~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~   82 (388)
T 1w3b_A            5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCC
Confidence            3456788999999999999988753 3344566667777889999999999999998875 6788899999999999999


Q ss_pred             HHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHhccCChHHHHHHHHH
Q 040365           92 VEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR-HVSFSSIMPACAHLTTLHLGKQLHGC  167 (514)
Q Consensus        92 ~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~~~  167 (514)
                      +++|...|+++.   ..+..+|..+..++.+.|++++|++.|+++.+.  .|+ ...+..+...+...|++++|.+.+..
T Consensus        83 ~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  160 (388)
T 1w3b_A           83 LQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQY--NPDLYCVRSDLGNLLKALGRLEEAKACYLK  160 (388)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH--CTTCTHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            999999999875   335668999999999999999999999999885  354 44566777888999999999999999


Q ss_pred             HHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CH
Q 040365          168 IIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NS  243 (514)
Q Consensus       168 ~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~  243 (514)
                      +++.. +.+..+++.+...|.+.|++++|...|+++.   ..+...|..+...+...|++++|+..|++....  .| +.
T Consensus       161 al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~  237 (388)
T 1w3b_A          161 AIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHA  237 (388)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCH
T ss_pred             HHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCCH
Confidence            99875 5568899999999999999999999999985   446678999999999999999999999999885  45 46


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSA  320 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~  320 (514)
                      .++..+..++...|++++|...|+.+.+.   .| +...|..+...+.+.|++++|.+.++++.  .+++..+|..+...
T Consensus       238 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  314 (388)
T 1w3b_A          238 VVHGNLACVYYEQGLIDLAIDTYRRAIEL---QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANI  314 (388)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT---CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHH
Confidence            78899999999999999999999999753   45 57889999999999999999999999874  34678899999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +...|++++|...++++++..|+++.++..++.+|.+.|++++|.+.++++.+.
T Consensus       315 ~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  368 (388)
T 1w3b_A          315 KREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             HHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            999999999999999999999999999999999999999999999999999763

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.96  E-value=4.1e-25  Score=218.66  Aligned_cols=348  Identities=11%  Similarity=0.013  Sum_probs=306.8

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHH
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLIN   84 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (514)
                      +...+..+...+.+.|++++|...++...... +.+..+|..+..++...|++++|...++.+++.. +.+..++..+..
T Consensus        32 ~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  109 (388)
T 1w3b_A           32 NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLK-PDFIDGYINLAA  109 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-cchHHHHHHHHH
Confidence            45677788888999999999999999988753 5677899999999999999999999999999875 556778999999


Q ss_pred             HHHHCCCHHHHHHHHccCC--CC-ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHH
Q 040365           85 MYAKCARVEDSHRLFCLLP--VK-DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLG  161 (514)
Q Consensus        85 ~~~~~g~~~~A~~~f~~~~--~~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a  161 (514)
                      .|.+.|++++|.+.|+++.  .| +...+..+...+...|++++|++.|+++.+.. +-+..++..+...+...|++++|
T Consensus       110 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A  188 (388)
T 1w3b_A          110 ALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLA  188 (388)
T ss_dssp             HHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            9999999999999998875  34 45678888899999999999999999998863 34578889999999999999999


Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC
Q 040365          162 KQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG  238 (514)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  238 (514)
                      ...++++++.. +.+...+..+...|...|++++|...|++..   ..+..+|..+...|.+.|++++|++.|+++.+. 
T Consensus       189 ~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-  266 (388)
T 1w3b_A          189 IHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL-  266 (388)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-
T ss_pred             HHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-
Confidence            99999999876 5667889999999999999999999998764   446789999999999999999999999999985 


Q ss_pred             CCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-C-CCCHHHHH
Q 040365          239 VKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-A-GPTENVWL  315 (514)
Q Consensus       239 ~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~-~p~~~~~~  315 (514)
                       .| +..++..+..++.+.|++++|...|+.+.+.  .+.+...+..+...+.+.|++++|.+.++++. . +.+..+|.
T Consensus       267 -~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~  343 (388)
T 1w3b_A          267 -QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHS  343 (388)
T ss_dssp             -CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHH
T ss_pred             -CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHH
Confidence             44 4678999999999999999999999999764  24478899999999999999999999999874 2 34578999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      .+..++...|++++|...++++++.+|+++..|..+...+...|+
T Consensus       344 ~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~a~~~lg~~~~~~~~  388 (388)
T 1w3b_A          344 NLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHhHHHHHHHccC
Confidence            999999999999999999999999999999999999998877663

>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=99.93  E-value=2.4e-23  Score=210.02  Aligned_cols=305  Identities=11%  Similarity=-0.001  Sum_probs=225.3

Q ss_pred             hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHH
Q 040365           41 SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGC  117 (514)
Q Consensus        41 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~  117 (514)
                      ...+..+...+...|++++|..++..+++.. +.+..++..+...|.+.|++++|...|+.+.   ..+..+|..+...|
T Consensus        26 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~  104 (450)
T 2y4t_A           26 VEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLL  104 (450)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHH
Confidence            3445555555555566666666666555543 3445555556666666666666666655543   22445566666666


Q ss_pred             HHCCChhHHHHHHHHHHHCCCCCCH----HHHHHH------------HHHHhccCChHHHHHHHHHHHHcCCCCcHHHHH
Q 040365          118 VQNGLFDEGLKFFRQMLIAKIKPRH----VSFSSI------------MPACAHLTTLHLGKQLHGCIIRNGFDDNMFIAS  181 (514)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p~~----~t~~~l------------l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  181 (514)
                      .+.|++++|++.|+++.+.  .|+.    ..+..+            ...+...|++++|...+..+++.. +.+..++.
T Consensus       105 ~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  181 (450)
T 2y4t_A          105 LKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRE  181 (450)
T ss_dssp             HHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHH
Confidence            6666666666666666553  2322    233332            334677888888888888888764 56778888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH-HHHHH--------
Q 040365          182 SLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV-AFVAV--------  249 (514)
Q Consensus       182 ~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~l--------  249 (514)
                      .+..+|.+.|++++|.+.|+++.   ..+..+|..+...|...|++++|+..|+++...  .|+.. .+..+        
T Consensus       182 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~  259 (450)
T 2y4t_A          182 LRAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNK  259 (450)
T ss_dssp             HHHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHHHHHHHHHHHHHHH
Confidence            89999999999999999998875   457788999999999999999999999999874  45443 33333        


Q ss_pred             ----HHHHHccCCHHHHHHHHHHhHHhcCCCCC-----HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHH
Q 040365          250 ----LTACSHAGLIDKAWSYFNSMTKDYGIAPS-----FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLL  318 (514)
Q Consensus       250 ----l~a~~~~g~~~~a~~~~~~m~~~~~~~p~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll  318 (514)
                          ..+|.+.|++++|..+|+.+.+.   .|+     ..+|..+..++.+.|++++|.+.++++.  .+.+..+|..+.
T Consensus       260 ~~~~~~~~~~~g~~~~A~~~~~~~l~~---~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~  336 (450)
T 2y4t_A          260 LIESAEELIRDGRYTDATSKYESVMKT---EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQMEPDNVNALKDRA  336 (450)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc---CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHH
Confidence                78899999999999999999764   454     4588999999999999999999999863  334789999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 040365          319 SACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNT  354 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  354 (514)
                      .+|...|++++|...++++++++|+++..+..+..+
T Consensus       337 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~  372 (450)
T 2y4t_A          337 EAYLIEEMYDEAIQDYETAQEHNENDQQIREGLEKA  372 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHhCcchHHHHHHHHHH
Confidence            999999999999999999999999999999888854

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.92  E-value=6.1e-23  Score=210.41  Aligned_cols=362  Identities=12%  Similarity=-0.016  Sum_probs=307.2

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      +..|......+.+.|++++|+..|+++....  ||..++..+..++...|++++|.+.+..+++.+ +.+..++..+..+
T Consensus         6 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~   82 (514)
T 2gw1_A            6 ALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASA   82 (514)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHH
Confidence            4567778889999999999999999999865  799999999999999999999999999999986 6677899999999


Q ss_pred             HHHCCCHHHHHHHHccCCCC---C--------------------------------------------------------
Q 040365           86 YAKCARVEDSHRLFCLLPVK---D--------------------------------------------------------  106 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~~---d--------------------------------------------------------  106 (514)
                      |.+.|++++|...|+.+...   +                                                        
T Consensus        83 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (514)
T 2gw1_A           83 NEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVT  162 (514)
T ss_dssp             HHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHH
T ss_pred             HHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhH
Confidence            99999999999998765311   1                                                        


Q ss_pred             -----------------------hhHHHHHHHHHHH---CCChhHHHHHHHHHHH-----CCC--------CCCHHHHHH
Q 040365          107 -----------------------AISWNSIIAGCVQ---NGLFDEGLKFFRQMLI-----AKI--------KPRHVSFSS  147 (514)
Q Consensus       107 -----------------------~~~~~~li~~~~~---~g~~~~A~~l~~~m~~-----~g~--------~p~~~t~~~  147 (514)
                                             ...|......+..   .|++++|+.+|+++.+     ..-        +.+..++..
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (514)
T 2gw1_A          163 SMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEH  242 (514)
T ss_dssp             HHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHH
Confidence                                   2223333333443   8999999999999987     311        223456777


Q ss_pred             HHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCCh
Q 040365          148 IMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNA  224 (514)
Q Consensus       148 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~  224 (514)
                      +...+...|++++|...+..+++....  ..++..+...|...|++++|...|+++.   ..+...|..+...|...|++
T Consensus       243 ~~~~~~~~~~~~~A~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  320 (514)
T 2gw1_A          243 TGIFKFLKNDPLGAHEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNY  320 (514)
T ss_dssp             HHHHHHHSSCHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCH
Confidence            888899999999999999999987633  8888999999999999999999999875   34677899999999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          225 HDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       225 ~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  304 (514)
                      ++|+..|++..... +.+...+..+...+...|++++|..+++.+.+..  +.+...+..+...|.+.|++++|.+.+++
T Consensus       321 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~  397 (514)
T 2gw1_A          321 DQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKF--PEAPEVPNFFAEILTDKNDFDKALKQYDL  397 (514)
T ss_dssp             THHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS--TTCSHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc--ccCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            99999999998853 2356788889999999999999999999987642  22567888999999999999999999987


Q ss_pred             CC----CCCC----HHHHHHHHHHHHh---cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          305 MH----AGPT----ENVWLTLLSACRV---HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       305 m~----~~p~----~~~~~~ll~~~~~---~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      +.    ..++    ..+|..+...+..   .|++++|...++++++.+|+++.++..++.+|...|++++|...+++..+
T Consensus       398 a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  477 (514)
T 2gw1_A          398 AIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITLFEESAD  477 (514)
T ss_dssp             HHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            63    2233    4489999999999   99999999999999999999999999999999999999999999999877


Q ss_pred             CC
Q 040365          374 KG  375 (514)
Q Consensus       374 ~g  375 (514)
                      ..
T Consensus       478 ~~  479 (514)
T 2gw1_A          478 LA  479 (514)
T ss_dssp             HC
T ss_pred             hc
Confidence            53

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.90  E-value=4.6e-21  Score=193.18  Aligned_cols=305  Identities=14%  Similarity=0.049  Sum_probs=256.8

Q ss_pred             HHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCC
Q 040365           63 IHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIK  139 (514)
Q Consensus        63 ~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  139 (514)
                      .+..++... +.+..++..+...|.+.|++++|..+|+.+.   ..+..+|..+...|.+.|++++|+..|+++.+.+ +
T Consensus        14 ~~~~~~~~~-p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p   91 (450)
T 2y4t_A           14 GTENLYFQS-MADVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-M   91 (450)
T ss_dssp             ----------CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-T
T ss_pred             ccccccccc-HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-C
Confidence            333444333 5677889999999999999999999999875   3578899999999999999999999999998864 4


Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcH---HHHHHH------------HHHHHhcCCHHHHHHHHHhCC
Q 040365          140 PRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNM---FIASSL------------LDMYAKCGNIRLARCIFDKMD  204 (514)
Q Consensus       140 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l------------i~~y~k~g~~~~A~~~~~~m~  204 (514)
                      .+...+..+..++...|++++|.+.+..+.+.. +.+.   ..+..+            ...|.+.|++++|...|+++.
T Consensus        92 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~  170 (450)
T 2y4t_A           92 DFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN-PSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKIL  170 (450)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            467788899999999999999999999998865 3444   555555            444999999999999999875


Q ss_pred             ---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHh
Q 040365          205 ---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFE  280 (514)
Q Consensus       205 ---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~  280 (514)
                         ..+...|..+...|.+.|++++|+..|+++.+.. +.+..++..+...+...|++++|...|+.+.+.   .| +..
T Consensus       171 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~p~~~~  246 (450)
T 2y4t_A          171 EVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKL---DQDHKR  246 (450)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHH
T ss_pred             HhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCChHH
Confidence               4577899999999999999999999999998752 346788999999999999999999999999754   45 344


Q ss_pred             HHHHH------------HHHHHhcCCHHHHHHHHHhCC-CCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          281 HYAAV------------ADLLGRAGKLQEAYEFISNMH-AGPT-----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       281 ~~~~l------------i~~~~~~g~~~~A~~~~~~m~-~~p~-----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      .+..+            ...+.+.|++++|.+.|+++. ..|+     ...|..+...+...|++++|...++++++.+|
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p  326 (450)
T 2y4t_A          247 CFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQMEP  326 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc
Confidence            44444            788999999999999999873 2344     45788899999999999999999999999999


Q ss_pred             CCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          343 NNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       343 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +++.+|..++.+|...|++++|.+.+++..+.
T Consensus       327 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  358 (450)
T 2y4t_A          327 DNVNALKDRAEAYLIEEMYDEAIQDYETAQEH  358 (450)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999874

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.89  E-value=6.7e-21  Score=195.17  Aligned_cols=343  Identities=11%  Similarity=-0.040  Sum_probs=286.5

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCc--------
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDAN--------   75 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~--------   75 (514)
                      ||..+|..+...|.+.|++++|+..|+++.+.+ +.+..++..+..++...|++++|...+..+.+.+...+        
T Consensus        37 p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  115 (514)
T 2gw1_A           37 EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLE  115 (514)
T ss_dssp             CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHH
T ss_pred             ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHH
Confidence            688899999999999999999999999998864 44567899999999999999999999999987652111        


Q ss_pred             ----------------------------------------------------------------------hhHHHHHHHH
Q 040365           76 ----------------------------------------------------------------------VCIGSSLINM   85 (514)
Q Consensus        76 ----------------------------------------------------------------------~~~~~~li~~   85 (514)
                                                                                            ...+..+...
T Consensus       116 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  195 (514)
T 2gw1_A          116 RNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLS  195 (514)
T ss_dssp             HHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHH
Confidence                                                                                  2222223333


Q ss_pred             HHH---CCCHHHHHHHHccCCC----------------C-ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHH
Q 040365           86 YAK---CARVEDSHRLFCLLPV----------------K-DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSF  145 (514)
Q Consensus        86 ~~~---~g~~~~A~~~f~~~~~----------------~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~  145 (514)
                      +..   .|++++|...|+++..                | +..+|..+...+...|++++|+..|+++.+..  |+...+
T Consensus       196 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~  273 (514)
T 2gw1_A          196 NLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNSY  273 (514)
T ss_dssp             HHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHHH
T ss_pred             HHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHHH
Confidence            333   8999999999987643                1 35678889999999999999999999998864  447888


Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCC
Q 040365          146 SSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHG  222 (514)
Q Consensus       146 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g  222 (514)
                      ..+..++...|++++|...+..+++.. +.+..++..+...|.+.|++++|...|++..   ..+...|..+...|...|
T Consensus       274 ~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  352 (514)
T 2gw1_A          274 IYMALIMADRNDSTEYYNYFDKALKLD-SNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELDPENIFPYIQLACLAYREN  352 (514)
T ss_dssp             HHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHcC
Confidence            889999999999999999999998875 5567789999999999999999999999874   446788999999999999


Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC----HhHHHHHHHHHHh---cCCH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS----FEHYAAVADLLGR---AGKL  295 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~---~g~~  295 (514)
                      ++++|+..|+++.+.. +.+..++..+...+...|++++|...++.+.+...-.++    ...+..+...+.+   .|++
T Consensus       353 ~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  431 (514)
T 2gw1_A          353 KFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENF  431 (514)
T ss_dssp             CHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHH
T ss_pred             CHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCH
Confidence            9999999999998852 335678888999999999999999999998764322232    3488999999999   9999


Q ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          296 QEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       296 ~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      ++|.+.++++.  .+.+..+|..+...+...|++++|...++++++++|.++..+..+
T Consensus       432 ~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~  489 (514)
T 2gw1_A          432 IEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITLFEESADLARTMEEKLQAI  489 (514)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhccccHHHHHHH
Confidence            99999998863  234678899999999999999999999999999999987776655

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.89  E-value=3.5e-20  Score=191.06  Aligned_cols=360  Identities=12%  Similarity=-0.001  Sum_probs=293.4

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      ...|..+...+.+.|++++|+..|+++.... +.+..++..+..++...|++++|.+.+..+++.. +.+..++..+...
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~  102 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASA  102 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHH
Confidence            3567888889999999999999999998864 4567889999999999999999999999999986 6678899999999


Q ss_pred             HHHCCCHHHHHHHHccCC-CCChh--------------------------------------------------------
Q 040365           86 YAKCARVEDSHRLFCLLP-VKDAI--------------------------------------------------------  108 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~-~~d~~--------------------------------------------------------  108 (514)
                      |.+.|++++|...|+.+. .|+..                                                        
T Consensus       103 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  182 (537)
T 3fp2_A          103 NESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSS  182 (537)
T ss_dssp             HHHHTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHT
T ss_pred             HHHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHH
Confidence            999999999999886442 11100                                                        


Q ss_pred             -------------HHHHHHHHHH--------HCCChhHHHHHHHHHHHCCCCCC--------HHHHHHHHHHHhccCChH
Q 040365          109 -------------SWNSIIAGCV--------QNGLFDEGLKFFRQMLIAKIKPR--------HVSFSSIMPACAHLTTLH  159 (514)
Q Consensus       109 -------------~~~~li~~~~--------~~g~~~~A~~l~~~m~~~g~~p~--------~~t~~~ll~~~~~~~~~~  159 (514)
                                   .+..+...+.        ..|++++|+.+|+++.+.  .|+        ..++..+...+...|+++
T Consensus       183 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~  260 (537)
T 3fp2_A          183 VNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSA--NTVDDPLRENAALALCYTGIFHFLKNNLL  260 (537)
T ss_dssp             SCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH--CCCcchhhHHHHHHHHHHHHHHHhcccHH
Confidence                         1111111111        124788999999998875  344        234666667788899999


Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          160 LGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       160 ~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      +|...+..+++..  |+...+..+...|.+.|++++|.+.|+++.   ..+..+|..+...|...|++++|+..|++...
T Consensus       261 ~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  338 (537)
T 3fp2_A          261 DAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQS  338 (537)
T ss_dssp             HHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            9999999999875  457888899999999999999999999875   45678899999999999999999999999988


Q ss_pred             cCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC----CC---
Q 040365          237 DGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH----AG---  308 (514)
Q Consensus       237 ~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~~---  308 (514)
                      .. +.+...+..+...+...|++++|..+++.+.+.   .| +...+..+...+.+.|++++|.+.++++.    ..   
T Consensus       339 ~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~  414 (537)
T 3fp2_A          339 LN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLK---FPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKI  414 (537)
T ss_dssp             HC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSC
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhh
Confidence            53 224578888999999999999999999999765   34 57788999999999999999999998862    11   


Q ss_pred             -CCHHHHHHHHHHHHhc----------CCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          309 -PTENVWLTLLSACRVH----------KNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       309 -p~~~~~~~ll~~~~~~----------~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                       .....+..+...+...          |++++|...++++++.+|+++.++..++.+|...|++++|.+.+++..+..
T Consensus       415 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  492 (537)
T 3fp2_A          415 HVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILA  492 (537)
T ss_dssp             SSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence             1223345556677777          999999999999999999999999999999999999999999999987754

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.86  E-value=8.8e-19  Score=170.31  Aligned_cols=326  Identities=10%  Similarity=-0.016  Sum_probs=212.6

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHH
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLIN   84 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (514)
                      |+..|..+...+.+.|++++|+..|+++.... +.+..++..+...+...|++++|...+..+++.. +.+..++..+..
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHH
Confidence            34566777777777788888888877776643 3345566666777777777777777777777664 445566666666


Q ss_pred             HHHHCCCHHHHHHHHccCCCC------ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 040365           85 MYAKCARVEDSHRLFCLLPVK------DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTL  158 (514)
Q Consensus        85 ~~~~~g~~~~A~~~f~~~~~~------d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  158 (514)
                      .|.+.|++++|...|+.....      +...+..+...+.                       ...+..+...+...|++
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-----------------------~~~~~~~a~~~~~~~~~  136 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADE-----------------------MQRLRSQALDAFDGADY  136 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHTTCH
T ss_pred             HHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHccCH
Confidence            666666666666666655322      1222222211000                       00111223455566666


Q ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          159 HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      ++|.+.+..+.+.. +.+..++..+...|.+.|++++|...|++..   ..+..+|..+...|...|++++|...|++..
T Consensus       137 ~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~  215 (359)
T 3ieg_A          137 TAAITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECL  215 (359)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            66666666666554 4455666667777777777777777776653   3355677777777777777777777777776


Q ss_pred             HcCCCCCH-HHHH------------HHHHHHHccCCHHHHHHHHHHhHHhcCCCCCH--hHHHHHHHHHHhcCCHHHHHH
Q 040365          236 KDGVKPNS-VAFV------------AVLTACSHAGLIDKAWSYFNSMTKDYGIAPSF--EHYAAVADLLGRAGKLQEAYE  300 (514)
Q Consensus       236 ~~g~~p~~-~t~~------------~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~--~~~~~li~~~~~~g~~~~A~~  300 (514)
                      +.  .|+. ..+.            .+...+...|++++|...++.+.+...-.|..  ..+..+...+...|++++|.+
T Consensus       216 ~~--~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~  293 (359)
T 3ieg_A          216 KL--DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIR  293 (359)
T ss_dssp             HH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             hh--CccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHHH
Confidence            64  2332 2221            23556778888888888888886542111111  335567788888899999988


Q ss_pred             HHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 040365          301 FISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA  358 (514)
Q Consensus       301 ~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  358 (514)
                      .+++..  .+.+..+|..+...+...|++++|...++++++++|++...+..+..++...
T Consensus       294 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~  353 (359)
T 3ieg_A          294 ICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQIREGLEKAQRLL  353 (359)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Confidence            888763  2346788888889999999999999999999999998888877777766543

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.85  E-value=6.4e-18  Score=164.17  Aligned_cols=304  Identities=13%  Similarity=0.049  Sum_probs=224.4

Q ss_pred             hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHH
Q 040365           41 SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGC  117 (514)
Q Consensus        41 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~  117 (514)
                      ...+..+...+...|++++|...+..+++.. +.+..++..+...|...|++++|...|+...   ..+...|..+...+
T Consensus         3 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~   81 (359)
T 3ieg_A            3 VEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLL   81 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHH
Confidence            3445556666667777777777777776654 4455666666666777777777776666543   22455666666666


Q ss_pred             HHCCChhHHHHHHHHHHHCCCCC---CH-HHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCH
Q 040365          118 VQNGLFDEGLKFFRQMLIAKIKP---RH-VSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNI  193 (514)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p---~~-~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~  193 (514)
                      .+.|++++|+..|++..+.  .|   +. ..+..+...       ..                ...+..+...|...|++
T Consensus        82 ~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~-------~~----------------~~~~~~~a~~~~~~~~~  136 (359)
T 3ieg_A           82 LKQGKLDEAEDDFKKVLKS--NPSEQEEKEAESQLVKA-------DE----------------MQRLRSQALDAFDGADY  136 (359)
T ss_dssp             HHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHH-------HH----------------HHHHHHHHHHHHHTTCH
T ss_pred             HHcCChHHHHHHHHHHHhc--CCcccChHHHHHHHHHH-------HH----------------HHHHHHHHHHHHHccCH
Confidence            6677777777776666553  33   11 111111110       00                11223346789999999


Q ss_pred             HHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhH
Q 040365          194 RLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMT  270 (514)
Q Consensus       194 ~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  270 (514)
                      ++|.+.|+++.   +.+...|..+...+...|++++|+..|++..... +.+..++..+...+...|++++|...|+...
T Consensus       137 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~  215 (359)
T 3ieg_A          137 TAAITFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECL  215 (359)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999875   4577889999999999999999999999998853 3466788899999999999999999999987


Q ss_pred             HhcCCCCC-HhHHH------------HHHHHHHhcCCHHHHHHHHHhCC-CCCC-H----HHHHHHHHHHHhcCCHHHHH
Q 040365          271 KDYGIAPS-FEHYA------------AVADLLGRAGKLQEAYEFISNMH-AGPT-E----NVWLTLLSACRVHKNVELAG  331 (514)
Q Consensus       271 ~~~~~~p~-~~~~~------------~li~~~~~~g~~~~A~~~~~~m~-~~p~-~----~~~~~ll~~~~~~~~~~~a~  331 (514)
                      +.   .|+ ...+.            .+...+.+.|++++|.+.++++. ..|+ .    ..+..+...+...|++++|.
T Consensus       216 ~~---~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  292 (359)
T 3ieg_A          216 KL---DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAI  292 (359)
T ss_dssp             HH---CTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hh---CccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHH
Confidence            64   342 33322            23667899999999999998863 2333 3    23556788999999999999


Q ss_pred             HHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          332 KVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       332 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ..++++++.+|+++.++..++.+|...|++++|.+.+++..+.
T Consensus       293 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~  335 (359)
T 3ieg_A          293 RICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEH  335 (359)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999999999999865

>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=99.83  E-value=2.7e-18  Score=165.02  Aligned_cols=286  Identities=10%  Similarity=-0.036  Sum_probs=187.4

Q ss_pred             CCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040365           73 DANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIM  149 (514)
Q Consensus        73 ~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (514)
                      +.+..++..+...+...|++++|.++|+++.   ..+...+..++..+.+.|++++|+.+++++.+.. +.+...+..+.
T Consensus        19 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~   97 (330)
T 3hym_B           19 QENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVG   97 (330)
T ss_dssp             -CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHH
Confidence            3444555555556666666666666665543   2233445555566666666666666666665542 23445555556


Q ss_pred             HHHhccC-ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChH
Q 040365          150 PACAHLT-TLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAH  225 (514)
Q Consensus       150 ~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~  225 (514)
                      ..+...| ++++|.+.+..+++.. +.+...+..+...|...|++++|.+.|++..   ..+..+|..+...|...|+++
T Consensus        98 ~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~  176 (330)
T 3hym_B           98 CYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSK  176 (330)
T ss_dssp             HHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHH
Confidence            6666666 6666666666666543 3345556666677777777777777776654   234456666777777777777


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC-------CCCCHhHHHHHHHHHHhcCCHHHH
Q 040365          226 DAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG-------IAPSFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       226 ~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~-------~~p~~~~~~~li~~~~~~g~~~~A  298 (514)
                      +|+..|++..+.. +.+...+..+...+...|++++|..+++...+...       .......+..+...|.+.|++++|
T Consensus       177 ~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  255 (330)
T 3hym_B          177 LAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEA  255 (330)
T ss_dssp             HHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHH
Confidence            7777777776642 23456677777777777788877777777655321       122456777888888888888888


Q ss_pred             HHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH-HHccCh
Q 040365          299 YEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY-AAARRW  361 (514)
Q Consensus       299 ~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~-~~~g~~  361 (514)
                      .+.+++..  .+.+..+|..+...+...|++++|...++++++++|+++..+..+..++ ...|+.
T Consensus       256 ~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~g~~  321 (330)
T 3hym_B          256 LDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRRDDTFSVTMLGHCIEMYIGDS  321 (330)
T ss_dssp             HHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCSCCHHHHHHHHHHHHTTTTC-
T ss_pred             HHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCCCchHHHHHHHHHHHHHhCch
Confidence            88887753  2345677888888888888888888888888888888888888888877 344443

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.83  E-value=3.5e-18  Score=176.11  Aligned_cols=340  Identities=10%  Similarity=0.029  Sum_probs=269.6

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCC----------
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLD----------   73 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~----------   73 (514)
                      .++.+|..+...|.+.|++++|+..|+++...+ +.+..++..+..++...|++++|...+..+ .....          
T Consensus        57 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~  134 (537)
T 3fp2_A           57 NEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASANESLGNFTDAMFDLSVL-SLNGDFDGASIEPML  134 (537)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-C-----------CHH
T ss_pred             CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHHcCCHHHHHHHHHHH-hcCCCCChHHHHHHH
Confidence            477899999999999999999999999998864 445678888999999999999999988633 21100          


Q ss_pred             ---------------------------Cchh------------------------------HHHHHHHHHHHC-------
Q 040365           74 ---------------------------ANVC------------------------------IGSSLINMYAKC-------   89 (514)
Q Consensus        74 ---------------------------~~~~------------------------------~~~~li~~~~~~-------   89 (514)
                                                 |+..                              ....+...+...       
T Consensus       135 ~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a  214 (537)
T 3fp2_A          135 ERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVA  214 (537)
T ss_dssp             HHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHH
Confidence                                       0000                              222222222222       


Q ss_pred             -CCHHHHHHHHccCCC--CC--------hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 040365           90 -ARVEDSHRLFCLLPV--KD--------AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTL  158 (514)
Q Consensus        90 -g~~~~A~~~f~~~~~--~d--------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  158 (514)
                       |++++|..+|+.+.+  |+        ..+|..+...+...|++++|+..|++..+.  .|+...+..+...+...|++
T Consensus       215 ~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~  292 (537)
T 3fp2_A          215 NDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENS  292 (537)
T ss_dssp             HHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCC
T ss_pred             HHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCH
Confidence             478889999888754  22        235777778899999999999999999885  56688888899999999999


Q ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          159 HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      +.|...+..+++.. +.+..++..+...|.+.|++++|.+.|++..   ..+...|..+...|...|++++|+..|+++.
T Consensus       293 ~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  371 (537)
T 3fp2_A          293 QEFFKFFQKAVDLN-PEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETK  371 (537)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999999999876 5678889999999999999999999999875   4467889999999999999999999999998


Q ss_pred             HcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC----CHhHHHHHHHHHHhc----------CCHHHHHHH
Q 040365          236 KDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP----SFEHYAAVADLLGRA----------GKLQEAYEF  301 (514)
Q Consensus       236 ~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~----------g~~~~A~~~  301 (514)
                      +.. +.+...+..+...+...|++++|...|+.+.+...-.+    ....+..+...+.+.          |++++|...
T Consensus       372 ~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~  450 (537)
T 3fp2_A          372 LKF-PTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKL  450 (537)
T ss_dssp             HHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHH
T ss_pred             HhC-CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHH
Confidence            863 33467888899999999999999999999865421111    122344556677777          999999999


Q ss_pred             HHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHH
Q 040365          302 ISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYV  349 (514)
Q Consensus       302 ~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~  349 (514)
                      +++..  .+.+..+|..+...+...|++++|...+++++++.|.+.....
T Consensus       451 ~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  500 (537)
T 3fp2_A          451 LTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILARTMDEKLQ  500 (537)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CHHHHH
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHH
Confidence            99863  3356788999999999999999999999999999998765543

>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=99.81  E-value=2.1e-17  Score=158.72  Aligned_cols=264  Identities=13%  Similarity=0.037  Sum_probs=228.9

Q ss_pred             CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHH
Q 040365          105 KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL  184 (514)
Q Consensus       105 ~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li  184 (514)
                      .+...+..+...+...|++++|+++|+++.+.. +.+...+..++.++...|++++|..++..+++.. +.+..++..+.
T Consensus        20 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~   97 (330)
T 3hym_B           20 ENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVG   97 (330)
T ss_dssp             CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHH
Confidence            456677888899999999999999999998764 3455566677788899999999999999999875 55678888999


Q ss_pred             HHHHhcC-CHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHH
Q 040365          185 DMYAKCG-NIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLID  260 (514)
Q Consensus       185 ~~y~k~g-~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~  260 (514)
                      ..|...| ++++|.+.|++..   ..+...|..+...+...|++++|+..|+++.+.. +.+...+..+...+...|+++
T Consensus        98 ~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~  176 (330)
T 3hym_B           98 CYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSK  176 (330)
T ss_dssp             HHHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHH
Confidence            9999999 9999999999875   3467789999999999999999999999998863 224567777889999999999


Q ss_pred             HHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCCC-----------CCCHHHHHHHHHHHHhcCCHH
Q 040365          261 KAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMHA-----------GPTENVWLTLLSACRVHKNVE  328 (514)
Q Consensus       261 ~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-----------~p~~~~~~~ll~~~~~~~~~~  328 (514)
                      +|...++...+   ..| +...+..+...+.+.|++++|.+.+++...           +.+..+|..+...+...|+++
T Consensus       177 ~A~~~~~~al~---~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  253 (330)
T 3hym_B          177 LAERFFSQALS---IAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYA  253 (330)
T ss_dssp             HHHHHHHHHHT---TCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHH---hCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHH
Confidence            99999999864   345 678899999999999999999999987631           334678999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          329 LAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       329 ~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +|...++++++..|+++..+..++.+|...|++++|.+.+++..+.
T Consensus       254 ~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  299 (330)
T 3hym_B          254 EALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGL  299 (330)
T ss_dssp             HHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHcc
Confidence            9999999999999999999999999999999999999999976543

>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=99.80  E-value=1.6e-17  Score=162.36  Aligned_cols=278  Identities=10%  Similarity=-0.039  Sum_probs=217.7

Q ss_pred             HHCCCHHHHHH-HHccCCC-----C--ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 040365           87 AKCARVEDSHR-LFCLLPV-----K--DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTL  158 (514)
Q Consensus        87 ~~~g~~~~A~~-~f~~~~~-----~--d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  158 (514)
                      .-.|++++|.. .|++...     |  +...|..+...+.+.|++++|+..|+++.+.. +.+..++..+..++...|++
T Consensus        36 ~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~  114 (368)
T 1fch_A           36 PWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQE  114 (368)
T ss_dssp             ----------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCH
Confidence            33477777877 7664431     1  34567788888888999999999998888763 45667778888888888999


Q ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C-ChhHHHH---------------HHHHHHh
Q 040365          159 HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--H-DIVSWTA---------------VIMGNAL  220 (514)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~-d~~~~~~---------------li~~~~~  220 (514)
                      ++|...+..+++.. +.+..++..+...|.+.|++++|.+.|+++..  | +...+..               .+..+..
T Consensus       115 ~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (368)
T 1fch_A          115 LLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLS  193 (368)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHH
T ss_pred             HHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhh
Confidence            99999998888875 55777888888889999999999988887642  2 2222221               2333448


Q ss_pred             CCChHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHH
Q 040365          221 HGNAHDAISLFEQMEKDGVK-PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A  298 (514)
                      .|++++|+..|+++...... ++..++..+...+...|++++|...|+.+.+.   .| +...+..+...+.+.|++++|
T Consensus       194 ~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~~~~~~~~~~l~~~~~~~g~~~~A  270 (368)
T 1fch_A          194 DSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV---RPNDYLLWNKLGATLANGNQSEEA  270 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CcCCHHHHHHHHHHHHHcCCHHHH
Confidence            89999999999999885322 14788999999999999999999999998754   44 578899999999999999999


Q ss_pred             HHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-----------cchHHHHHHHHHHccChhHHH
Q 040365          299 YEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN-----------MGAYVILSNTYAAARRWKDAA  365 (514)
Q Consensus       299 ~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~-----------~~~~~~l~~~~~~~g~~~~a~  365 (514)
                      .+.++++.  .+.+..+|..+..++...|++++|...+++++++.|++           ..+|..++.+|...|++++|.
T Consensus       271 ~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  350 (368)
T 1fch_A          271 VAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYG  350 (368)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHH
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHH
Confidence            99999863  23567899999999999999999999999999988877           789999999999999999999


Q ss_pred             HHHH
Q 040365          366 SLRV  369 (514)
Q Consensus       366 ~~~~  369 (514)
                      .+++
T Consensus       351 ~~~~  354 (368)
T 1fch_A          351 AADA  354 (368)
T ss_dssp             HHHT
T ss_pred             HhHH
Confidence            9876

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.78  E-value=1.6e-17  Score=161.17  Aligned_cols=268  Identities=12%  Similarity=0.101  Sum_probs=123.7

Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHH
Q 040365            7 VSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMY   86 (514)
Q Consensus         7 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~   86 (514)
                      .+|+.|..++.+.|++++|++.|.+      .+|..+|..++.++...|++++|...+..+++.  .+++.+.+.|+.+|
T Consensus        33 ~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~Y  104 (449)
T 1b89_A           33 AVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFAL  104 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHHHH
Confidence            4888888888888888888888865      257778888888888888888888877777664  45577788888888


Q ss_pred             HHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHH
Q 040365           87 AKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHG  166 (514)
Q Consensus        87 ~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  166 (514)
                      .++|+++++.++|+.   |+..+|+.+...|...|++++|..+|..+         ..|..+..++.+.|++++|.+.+.
T Consensus       105 ~Klg~l~e~e~f~~~---pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~~  172 (449)
T 1b89_A          105 AKTNRLAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGAR  172 (449)
T ss_dssp             ----CHHHHTTTTTC---C----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHcC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHHH
Confidence            888888888887763   66778888888888888888888888876         367888888888888888888887


Q ss_pred             HHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHH
Q 040365          167 CIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAF  246 (514)
Q Consensus       167 ~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~  246 (514)
                      .+      .++.+|..++.+|...|+++.|......+. .++.-...++..|.+.|++++|+.+++...... +-....|
T Consensus       173 KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-~~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~f  244 (449)
T 1b89_A          173 KA------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV-VHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMF  244 (449)
T ss_dssp             HH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHH
T ss_pred             Hc------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH-hCHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHH
Confidence            77      367788888888888888888877766654 333334467788888888888888888876532 2223344


Q ss_pred             HHHHHHHH--ccCCHHHHHHHHHHhHHhcCCCC------CHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          247 VAVLTACS--HAGLIDKAWSYFNSMTKDYGIAP------SFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       247 ~~ll~a~~--~~g~~~~a~~~~~~m~~~~~~~p------~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      +.+.-+++  +.+++.+.++.|.   ++-+++|      +..+|.-++-.|..-++++.|...+-+-
T Consensus       245 tel~il~~ky~p~k~~ehl~~~~---~~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~tm~~h  308 (449)
T 1b89_A          245 TELAILYSKFKPQKMREHLELFW---SRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNH  308 (449)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHS---TTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHH---HHhcCcHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHHHhC
Confidence            44443443  4455555555554   3234444      4567888888888888888887765544

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.78  E-value=5.8e-15  Score=150.51  Aligned_cols=351  Identities=13%  Similarity=0.035  Sum_probs=294.0

Q ss_pred             CcchHHHHHHHHHh----cCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhC----CCChHHHHHHHHHHHHhCCCCch
Q 040365            5 DLVSWNTVIVGLAR----NGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFAD----YVDVIKGKEIHGYAIRHGLDANV   76 (514)
Q Consensus         5 ~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~g~~~~~   76 (514)
                      |+.++..+-..|..    .+++++|+..|++..+.|   +...+..+...+..    .++.++|.+.+....+.|   +.
T Consensus        38 ~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~  111 (490)
T 2xm6_A           38 EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LP  111 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            55667777777887    899999999999998865   55677777777877    899999999999999876   56


Q ss_pred             hHHHHHHHHHHH----CCCHHHHHHHHccCCC-CChhHHHHHHHHHHH----CCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040365           77 CIGSSLINMYAK----CARVEDSHRLFCLLPV-KDAISWNSIIAGCVQ----NGLFDEGLKFFRQMLIAKIKPRHVSFSS  147 (514)
Q Consensus        77 ~~~~~li~~~~~----~g~~~~A~~~f~~~~~-~d~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~  147 (514)
                      ..+..|..+|..    .++.++|.+.|+...+ .+..++..|...|..    .+++++|++.|++..+.|   +...+..
T Consensus       112 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~  188 (490)
T 2xm6_A          112 QAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQ  188 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHH
Confidence            777888899998    8899999999988654 467788888888887    789999999999998875   5667777


Q ss_pred             HHHHHhc----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh----cCCHHHHHHHHHhCC-CCChhHHHHHHHHH
Q 040365          148 IMPACAH----LTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK----CGNIRLARCIFDKMD-LHDIVSWTAVIMGN  218 (514)
Q Consensus       148 ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k----~g~~~~A~~~~~~m~-~~d~~~~~~li~~~  218 (514)
                      +...+..    .++.++|.+.+....+.|   +...+..|..+|..    .+++++|.+.|++.. ..+..++..+...|
T Consensus       189 Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y  265 (490)
T 2xm6_A          189 LGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGNSIAQFRLGYIL  265 (490)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            7777776    789999999999999876   45677788888886    899999999999875 45667788888888


Q ss_pred             Hh----CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcc-----CCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHH
Q 040365          219 AL----HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHA-----GLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLL  289 (514)
Q Consensus       219 ~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~-----g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~  289 (514)
                      ..    .++.++|+.+|++..+.|   +...+..+...+...     ++.++|...|+...+.    .+...+..|..+|
T Consensus       266 ~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~----~~~~a~~~lg~~y  338 (490)
T 2xm6_A          266 EQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQ----GDATAQANLGAIY  338 (490)
T ss_dssp             HHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHT----TCHHHHHHHHHHH
T ss_pred             HCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhc----CCHHHHHHHHHHH
Confidence            87    899999999999998764   445666677777776     8999999999988653    2456777888888


Q ss_pred             HhcC---CHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH----c
Q 040365          290 GRAG---KLQEAYEFISNMHAGPTENVWLTLLSACRV----HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA----A  358 (514)
Q Consensus       290 ~~~g---~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~  358 (514)
                      .+.|   ++++|.+.|++.....+...+..|...+..    .+++++|...++++.+.+  ++..+..|..+|..    .
T Consensus       339 ~~~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~--~~~a~~~Lg~~y~~g~g~~  416 (490)
T 2xm6_A          339 FRLGSEEEHKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG--LSAAQVQLGEIYYYGLGVE  416 (490)
T ss_dssp             HHSCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSC
T ss_pred             HhCCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC--CHHHHHHHHHHHHcCCCCC
Confidence            7766   789999999987655788899999999988    899999999999998865  56789999999998    8


Q ss_pred             cChhHHHHHHHHHHhCCC
Q 040365          359 RRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       359 g~~~~a~~~~~~m~~~g~  376 (514)
                      +++++|...+++..+.+.
T Consensus       417 ~d~~~A~~~~~~A~~~~~  434 (490)
T 2xm6_A          417 RDYVQAWAWFDTASTNDM  434 (490)
T ss_dssp             CCHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHHCCC
Confidence            999999999999988764

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.78  E-value=2.5e-17  Score=161.07  Aligned_cols=276  Identities=9%  Similarity=-0.029  Sum_probs=215.4

Q ss_pred             CCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHH
Q 040365           90 ARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHG  166 (514)
Q Consensus        90 g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~  166 (514)
                      +....+...+...+   ..+...|..+...+.+.|++++|+.+|+++.+.. +.+..++..+..++...|++++|...+.
T Consensus        45 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~  123 (365)
T 4eqf_A           45 VTVSASEKGYYFHTENPFKDWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQ  123 (365)
T ss_dssp             --------CCCCCSSCTTTTCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hhhHHHHHhhhcccCCcccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            33344444444333   2355668888999999999999999999998763 4567788888999999999999999999


Q ss_pred             HHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C-C----------hhHHHHHHHHHHhCCChHHHHHHHHH
Q 040365          167 CIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--H-D----------IVSWTAVIMGNALHGNAHDAISLFEQ  233 (514)
Q Consensus       167 ~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~-d----------~~~~~~li~~~~~~g~~~~A~~l~~~  233 (514)
                      ++++.. +.+..++..+...|.+.|++++|.+.|+++..  | +          ...+..+...+...|++++|+.+|++
T Consensus       124 ~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  202 (365)
T 4eqf_A          124 RCLELQ-PNNLKALMALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLE  202 (365)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHH
T ss_pred             HHHhcC-CCCHHHHHHHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            998875 55688889999999999999999999988752  2 1          22334457889999999999999999


Q ss_pred             HHHcCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-C-CC
Q 040365          234 MEKDGVK-PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-A-GP  309 (514)
Q Consensus       234 m~~~g~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~-~p  309 (514)
                      +.+.... ++..++..+...+...|++++|...|+.+.+.   .| +...|..+..+|.+.|++++|.+.++++. . +.
T Consensus       203 al~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~  279 (365)
T 4eqf_A          203 AAHQNGDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTV---RPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPG  279 (365)
T ss_dssp             HHHHSCSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHhCcCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence            9986322 25788999999999999999999999998764   34 68899999999999999999999999863 2 34


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC------------CcchHHHHHHHHHHccChhHHHHHHHH
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN------------NMGAYVILSNTYAAARRWKDAASLRVF  370 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~------------~~~~~~~l~~~~~~~g~~~~a~~~~~~  370 (514)
                      +..+|..+..++...|++++|...+++++++.|.            +...|..|..++...|+.+.+.++.+.
T Consensus       280 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          280 FIRSRYNLGISCINLGAYREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             CHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            5889999999999999999999999999998765            367889999999999999998887653

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.78  E-value=5.2e-19  Score=171.60  Aligned_cols=250  Identities=11%  Similarity=0.071  Sum_probs=99.9

Q ss_pred             HCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHH
Q 040365           88 KCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGC  167 (514)
Q Consensus        88 ~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~  167 (514)
                      +.|++++|.+.++++..|+  +|..|+.++.+.|++++|++.|.+      .+|..+|..++.++...|++++|..++..
T Consensus        15 ~~~~ld~A~~fae~~~~~~--vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~   86 (449)
T 1b89_A           15 HIGNLDRAYEFAERCNEPA--VWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQM   86 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCCChH--HHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            5677888888888875553  788888888888888888888754      25666778888888888888888887776


Q ss_pred             HHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHH
Q 040365          168 IIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFV  247 (514)
Q Consensus       168 ~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~  247 (514)
                      ..+.  .+++.+.+.|+.+|.|+|+++++.++++   .|+..+|+.+...|...|++++|..+|..+         ..|.
T Consensus        87 ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~---~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~  152 (449)
T 1b89_A           87 ARKK--ARESYVETELIFALAKTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFG  152 (449)
T ss_dssp             ------------------------CHHHHTTTTT---CC----------------CTTTHHHHHHHT---------TCHH
T ss_pred             HHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc---CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHH
Confidence            6663  4456777778888888888888777765   356668888888888888888888888865         2577


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 040365          248 AVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNV  327 (514)
Q Consensus       248 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~  327 (514)
                      .+..++.+.|++++|.+.+..+       .++.+|..++.+|...|+++.|......+...|+.  ...++..|.+.|.+
T Consensus       153 ~LA~~L~~Lg~yq~AVea~~KA-------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~~~ad~--l~~lv~~Yek~G~~  223 (449)
T 1b89_A          153 RLASTLVHLGEYQAAVDGARKA-------NSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADE--LEELINYYQDRGYF  223 (449)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHH-------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTTTCHHH--HHHHHHHHHHTTCH
T ss_pred             HHHHHHHHhccHHHHHHHHHHc-------CCchhHHHHHHHHHHcCcHHHHHHHHHHHHhCHhh--HHHHHHHHHHCCCH
Confidence            7888888888888888887765       25677888888888888888886655554433433  34577778888888


Q ss_pred             HHHHHHHHHHHhcCCCCcchHHHHHHHHHHc--cChhHHHHHH
Q 040365          328 ELAGKVAEKIFMIDPNNMGAYVILSNTYAAA--RRWKDAASLR  368 (514)
Q Consensus       328 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~--g~~~~a~~~~  368 (514)
                      ++|..+++..+.+++...+.|.-|..+|++-  ++..+..+.|
T Consensus       224 eEai~lLe~aL~le~ah~~~ftel~il~~ky~p~k~~ehl~~~  266 (449)
T 1b89_A          224 EELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELF  266 (449)
T ss_dssp             HHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            8888888888888877777777777777654  3444444444

>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=99.76  E-value=9.5e-17  Score=156.89  Aligned_cols=269  Identities=11%  Similarity=-0.027  Sum_probs=146.3

Q ss_pred             hHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHH
Q 040365           43 TLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQ  119 (514)
Q Consensus        43 t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~  119 (514)
                      .+..+...+...|++++|...+..+++.. +.+..++..+...|.+.|++++|...|+...   ..+..+|..+...|..
T Consensus        66 ~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~  144 (368)
T 1fch_A           66 QPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTN  144 (368)
T ss_dssp             SHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            34445555555555555555555555543 3444555555555555555555555555432   2244455555555555


Q ss_pred             CCChhHHHHHHHHHHHCCCCCCHH-HHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHH
Q 040365          120 NGLFDEGLKFFRQMLIAKIKPRHV-SFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARC  198 (514)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~  198 (514)
                      .|++++|+..|+++....  |+.. .+..+..       ...           ...+ ...+..+...+ +.|++++|..
T Consensus       145 ~g~~~~A~~~~~~~~~~~--~~~~~~~~~~~~-------~~~-----------~~~~-~~~~~~~~~~~-~~~~~~~A~~  202 (368)
T 1fch_A          145 ESLQRQACEILRDWLRYT--PAYAHLVTPAEE-------GAG-----------GAGL-GPSKRILGSLL-SDSLFLEVKE  202 (368)
T ss_dssp             TTCHHHHHHHHHHHHHTS--TTTGGGCC----------------------------------CTTHHHH-HHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhC--cCcHHHHHHHHH-------Hhh-----------hhcc-cHHHHHHHHHh-hcccHHHHHH
Confidence            555555555555555432  2111 1100000       000           0000 00000122222 6666666666


Q ss_pred             HHHhCC--CC---ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhc
Q 040365          199 IFDKMD--LH---DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDY  273 (514)
Q Consensus       199 ~~~~m~--~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~  273 (514)
                      .|+++.  .|   +..+|..+...|...|++++|+..|+++.... +.+..++..+...+...|++++|...|+.+.+. 
T Consensus       203 ~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-  280 (368)
T 1fch_A          203 LFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL-  280 (368)
T ss_dssp             HHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-
Confidence            666653  22   35566666667777777777777777766542 223456666667777777777777777766543 


Q ss_pred             CCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC------------CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040365          274 GIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP------------TENVWLTLLSACRVHKNVELAGKVAEKIF  338 (514)
Q Consensus       274 ~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p------------~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  338 (514)
                        .| +...+..+..+|.+.|++++|.+.++++. ..|            ...+|..+..++...|+.++|..++++.+
T Consensus       281 --~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  357 (368)
T 1fch_A          281 --QPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARDL  357 (368)
T ss_dssp             --CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTCH
T ss_pred             --CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHHHH
Confidence              33 45666677777777777777777766542 011            15677777777777888777777766543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.76  E-value=2.1e-15  Score=142.46  Aligned_cols=269  Identities=7%  Similarity=-0.044  Sum_probs=210.3

Q ss_pred             HHHCCCHHHHHHHHccCCCCCh----hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHH
Q 040365           86 YAKCARVEDSHRLFCLLPVKDA----ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLG  161 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~~d~----~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a  161 (514)
                      ....|++..|...++.....++    ...-.+..+|...|++++|+..++.   . -+|+..++..+...+...++.+.|
T Consensus         9 ~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~-~~~~~~a~~~la~~~~~~~~~~~A   84 (291)
T 3mkr_A            9 AFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP---S-SAPELQAVRMFAEYLASHSRRDAI   84 (291)
T ss_dssp             HHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---T-SCHHHHHHHHHHHHHHCSTTHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc---c-CChhHHHHHHHHHHHcCCCcHHHH
Confidence            4457888888888877654332    2445577888888888888876654   2 356777788888888888888999


Q ss_pred             HHHHHHHHHcCC-CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCC
Q 040365          162 KQLHGCIIRNGF-DDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK  240 (514)
Q Consensus       162 ~~~~~~~~~~~~-~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  240 (514)
                      .+.++.++..+. +.+..++..+...|.+.|++++|.+.|++  ..+...+..++..|.+.|++++|.+.|+++.+.  .
T Consensus        85 ~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~  160 (291)
T 3mkr_A           85 VAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQ--D  160 (291)
T ss_dssp             HHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--C
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh--C
Confidence            998888887764 44566777788999999999999999998  567889999999999999999999999999986  4


Q ss_pred             CCHHHH---HHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-C-CCCHHHHH
Q 040365          241 PNSVAF---VAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-A-GPTENVWL  315 (514)
Q Consensus       241 p~~~t~---~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~-~p~~~~~~  315 (514)
                      |+....   ...+..+...|++++|..+|+++.+.  .+.+...++.+..++.+.|++++|.+.+++.. . +.+..+|.
T Consensus       161 p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~  238 (291)
T 3mkr_A          161 EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK--CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLI  238 (291)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence            664321   22334445669999999999999875  24478899999999999999999999999863 2 34788899


Q ss_pred             HHHHHHHhcCCHHH-HHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHH
Q 040365          316 TLLSACRVHKNVEL-AGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLR  368 (514)
Q Consensus       316 ~ll~~~~~~~~~~~-a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~  368 (514)
                      .++..+...|+.++ +.++++++.+++|+++.+    .+...+.+.++++..-|
T Consensus       239 ~l~~~~~~~g~~~eaa~~~~~~~~~~~P~~~~~----~d~~~~~~~fd~~~~~~  288 (291)
T 3mkr_A          239 NLVVLSQHLGKPPEVTNRYLSQLKDAHRSHPFI----KEYRAKENDFDRLVLQY  288 (291)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHH----HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHhCCCChHH----HHHHHHHHHHHHHHHHc
Confidence            99999999999875 678999999999998744    34455666666655433

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.75  E-value=8.8e-17  Score=157.21  Aligned_cols=261  Identities=11%  Similarity=-0.053  Sum_probs=201.3

Q ss_pred             ChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHH
Q 040365           40 DSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAG  116 (514)
Q Consensus        40 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~  116 (514)
                      +...+..+...+...|++++|...++.+++.. +.+..++..+...|.+.|++++|...|++..   ..+..+|..+...
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  142 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAVS  142 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            44557777778888888888888888888875 5677788888888888888888888888764   3457788888888


Q ss_pred             HHHCCChhHHHHHHHHHHHCCCCCC-----------HHHHHHHHHHHhccCChHHHHHHHHHHHHcCCC-CcHHHHHHHH
Q 040365          117 CVQNGLFDEGLKFFRQMLIAKIKPR-----------HVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFD-DNMFIASSLL  184 (514)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~-----------~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~li  184 (514)
                      |.+.|++++|+..|+++.+..  |+           ...+..+...+...|++++|.+.+..+++.... .+..++..+.
T Consensus       143 ~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~  220 (365)
T 4eqf_A          143 YTNTSHQQDACEALKNWIKQN--PKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLG  220 (365)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC--HHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHH
T ss_pred             HHccccHHHHHHHHHHHHHhC--ccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHH
Confidence            889999999999988887642  32           122334567888899999999999999887522 1678888899


Q ss_pred             HHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHH
Q 040365          185 DMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLID  260 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~  260 (514)
                      ..|.+.|++++|.+.|++..   ..+..+|+.+...|...|++++|+..|+++.+.  .| +..++..+..++...|+++
T Consensus       221 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~  298 (365)
T 4eqf_A          221 VLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEI--QPGFIRSRYNLGISCINLGAYR  298 (365)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHCCCHH
Confidence            99999999999999998865   456788999999999999999999999998885  34 4678888999999999999


Q ss_pred             HHHHHHHHhHHhcCCC----------CCHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          261 KAWSYFNSMTKDYGIA----------PSFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       261 ~a~~~~~~m~~~~~~~----------p~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      +|...|+.+.+...-.          .+...|..+...+...|+.+.+.+..++-
T Consensus       299 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  353 (365)
T 4eqf_A          299 EAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLGD  353 (365)
T ss_dssp             HHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHhh
Confidence            9999999886542110          13678899999999999999999888764

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.75  E-value=2.2e-15  Score=152.59  Aligned_cols=364  Identities=10%  Similarity=-0.043  Sum_probs=243.1

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhC-----C--CCC-ChhhHHHHHHHHhCCCChHHHHHHHHHHHHhC------
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNV-----N--LKP-DSFTLSSVLPIFADYVDVIKGKEIHGYAIRHG------   71 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g--~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g------   71 (514)
                      +..||.|...+...|++++|++.|++..+.     +  ..| ...+|..+..++...|++++|...++.+++..      
T Consensus        51 a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~  130 (472)
T 4g1t_A           51 ATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSP  130 (472)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccc
Confidence            457899999999999999999999887541     1  123 34678899999999999999999999887641      


Q ss_pred             C-CCchhHHHHHHHHHHHC--CCHHHHHHHHccCC--CC-ChhHHHHHHHH---HHHCCChhHHHHHHHHHHHCCCCCCH
Q 040365           72 L-DANVCIGSSLINMYAKC--ARVEDSHRLFCLLP--VK-DAISWNSIIAG---CVQNGLFDEGLKFFRQMLIAKIKPRH  142 (514)
Q Consensus        72 ~-~~~~~~~~~li~~~~~~--g~~~~A~~~f~~~~--~~-d~~~~~~li~~---~~~~g~~~~A~~l~~~m~~~g~~p~~  142 (514)
                      . .....++..+..++.+.  +++++|...|++..  .| +...+..+...   +...++.++|++.|++..+.. +.+.
T Consensus       131 ~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~~  209 (472)
T 4g1t_A          131 YRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDNQ  209 (472)
T ss_dssp             SCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSCH
T ss_pred             cchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-Ccch
Confidence            1 12234565555555554  46899999998764  23 55556555544   345678899999999887753 3345


Q ss_pred             HHHHHHHHHHhc----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHH
Q 040365          143 VSFSSIMPACAH----LTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVI  215 (514)
Q Consensus       143 ~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li  215 (514)
                      ..+..+...+..    .++.++|.+.++...+.. +.+..++..+...|.+.|++++|...|++..   +.+..+|..+.
T Consensus       210 ~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg  288 (472)
T 4g1t_A          210 YLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPNNAYLHCQIG  288 (472)
T ss_dssp             HHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCChHHHHHHHH
Confidence            555555544443    467889999999988875 6677888899999999999999999998875   33556676666


Q ss_pred             HHHHhC-------------------CChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCC
Q 040365          216 MGNALH-------------------GNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA  276 (514)
Q Consensus       216 ~~~~~~-------------------g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~  276 (514)
                      ..|...                   +..++|...|++..+.. +.+..++..+...+...|++++|...|+...+.   .
T Consensus       289 ~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~---~  364 (472)
T 4g1t_A          289 CCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSK---E  364 (472)
T ss_dssp             HHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHS---C
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhc---C
Confidence            555322                   23567888888877642 223456778888999999999999999988653   3


Q ss_pred             CCHh----HHHHHHH-HHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHH
Q 040365          277 PSFE----HYAAVAD-LLGRAGKLQEAYEFISNM-HAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVI  350 (514)
Q Consensus       277 p~~~----~~~~li~-~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~  350 (514)
                      |+..    .+..+.. .+...|+.++|++.+++. ...|+...+..         ....+..++++.++.+|+++.+|..
T Consensus       365 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~---------~~~~l~~~~~~~l~~~p~~~~~~~~  435 (472)
T 4g1t_A          365 LTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEK---------MKDKLQKIAKMRLSKNGADSEALHV  435 (472)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHH---------HHHHHHHHHHHHHHHCC-CTTHHHH
T ss_pred             CCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHH---------HHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            3322    2233332 235678999999998875 34565443332         2345567788888899999999999


Q ss_pred             HHHHHHHccChhHHHHHHHHHHhCCCccCCcccE
Q 040365          351 LSNTYAAARRWKDAASLRVFMRNKGMKKTPACSW  384 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~  384 (514)
                      |+.+|...|++++|.+.+++..+.|-..+...+|
T Consensus       436 LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          436 LAFLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             HHHHHHHHHHCC----------------------
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence            9999999999999999999988776443334455

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.75  E-value=8e-15  Score=151.01  Aligned_cols=362  Identities=9%  Similarity=0.024  Sum_probs=215.5

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHH
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLIN   84 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (514)
                      |+.+|..++. +.+.|++++|..+|+++.... +-+...|...+..+.+.|+++.|..+|+.+++..  |+...|..++.
T Consensus        12 ~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--p~~~lw~~~~~   87 (530)
T 2ooe_A           12 DLDAWSILIR-EAQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--LHIDLWKCYLS   87 (530)
T ss_dssp             CHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--CCHHHHHHHHH
T ss_pred             CHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CChHHHHHHHH
Confidence            6778999998 578999999999999998752 4456678889999999999999999999998764  57777777775


Q ss_pred             -HHHHCCCHHHHHH----HHccCC------CCChhHHHHHHHHHHH---------CCChhHHHHHHHHHHHCCCCCCHHH
Q 040365           85 -MYAKCARVEDSHR----LFCLLP------VKDAISWNSIIAGCVQ---------NGLFDEGLKFFRQMLIAKIKPRHVS  144 (514)
Q Consensus        85 -~~~~~g~~~~A~~----~f~~~~------~~d~~~~~~li~~~~~---------~g~~~~A~~l~~~m~~~g~~p~~~t  144 (514)
                       .....|+.++|.+    +|+...      .++...|...+....+         .|++++|..+|++..+....+....
T Consensus        88 ~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~  167 (530)
T 2ooe_A           88 YVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQL  167 (530)
T ss_dssp             HHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHH
T ss_pred             HHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHH
Confidence             3345677766654    665431      2356678887776654         6788999999998877311111223


Q ss_pred             HHHHHHHH-------------hccCChHHHHHHHHHHH------HcC---CCCc--------HHHHHHHHHHHHhc----
Q 040365          145 FSSIMPAC-------------AHLTTLHLGKQLHGCII------RNG---FDDN--------MFIASSLLDMYAKC----  190 (514)
Q Consensus       145 ~~~ll~~~-------------~~~~~~~~a~~~~~~~~------~~~---~~~~--------~~~~~~li~~y~k~----  190 (514)
                      |.......             ...+.+..|..++....      +..   ++|+        ...|...+......    
T Consensus       168 ~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~  247 (530)
T 2ooe_A          168 WRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRT  247 (530)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCC
T ss_pred             HHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccC
Confidence            32221110             12234455555544421      111   1222        23444433322211    


Q ss_pred             CCH----HHHHHHHHhCC---CCChhHHHHHHHHHHh-------CCChH-------HHHHHHHHHHHcCCCCC-HHHHHH
Q 040365          191 GNI----RLARCIFDKMD---LHDIVSWTAVIMGNAL-------HGNAH-------DAISLFEQMEKDGVKPN-SVAFVA  248 (514)
Q Consensus       191 g~~----~~A~~~~~~m~---~~d~~~~~~li~~~~~-------~g~~~-------~A~~l~~~m~~~g~~p~-~~t~~~  248 (514)
                      ++.    +.|..+|++..   ..+...|..+...+.+       .|+.+       +|..+|++..+. +.|+ ...+..
T Consensus       248 ~~~~~~~~~a~~~y~~al~~~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~-~~p~~~~l~~~  326 (530)
T 2ooe_A          248 EDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST-LLKKNMLLYFA  326 (530)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTT-TCSSCHHHHHH
T ss_pred             CcchhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHH-hCcccHHHHHH
Confidence            122    24555555543   2345566666665554       56655       666666666542 2333 455566


Q ss_pred             HHHHHHccCCHHHHHHHHHHhHHhcCCCCC-H-hHHHHHHHHHHhcCCHHHHHHHHHhCCC-CCC-HHHHHHHHHH-HHh
Q 040365          249 VLTACSHAGLIDKAWSYFNSMTKDYGIAPS-F-EHYAAVADLLGRAGKLQEAYEFISNMHA-GPT-ENVWLTLLSA-CRV  323 (514)
Q Consensus       249 ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~-~-~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~-~~~~~~ll~~-~~~  323 (514)
                      ++..+...|++++|..+|+.+.+   +.|+ . ..|..++..+.+.|++++|.++|++... .|+ ...|...... +..
T Consensus       327 ~~~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~  403 (530)
T 2ooe_A          327 YADYEESRMKYEKVHSIYNRLLA---IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYC  403 (530)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH---SSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCHHHHHHHHHHHhC---ccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHH
Confidence            66666666667777666666653   2442 2 3566666666666666666666666432 121 2222221111 234


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .|+.+.|..+|+++++..|+++..|..++..+.+.|+.++|..++++....
T Consensus       404 ~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~  454 (530)
T 2ooe_A          404 SKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTS  454 (530)
T ss_dssp             TCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHS
T ss_pred             cCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhc
Confidence            666666776676666666666666666666666666666676666666654

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.74  E-value=2.4e-16  Score=151.02  Aligned_cols=258  Identities=9%  Similarity=-0.056  Sum_probs=190.8

Q ss_pred             hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 040365          108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMY  187 (514)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y  187 (514)
                      ..|..+...+...|++++|+.+|+++.+.. +.+...+..+..++...|++++|.+.+..+++.. +.+..++..+...|
T Consensus        22 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~   99 (327)
T 3cv0_A           22 ENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSH   99 (327)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHH
Confidence            345555666666666666666666665542 2345555566666666666666666666666653 44556666666677


Q ss_pred             HhcCCHHHHHHHHHhCC---CCChhHHHHH--------------HH-HHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHH
Q 040365          188 AKCGNIRLARCIFDKMD---LHDIVSWTAV--------------IM-GNALHGNAHDAISLFEQMEKDGVKPNSVAFVAV  249 (514)
Q Consensus       188 ~k~g~~~~A~~~~~~m~---~~d~~~~~~l--------------i~-~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l  249 (514)
                      .+.|++++|.+.|+++.   ..+...+..+              .. .+...|++++|+..++++.+.. +.+...+..+
T Consensus       100 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l  178 (327)
T 3cv0_A          100 TNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLHASL  178 (327)
T ss_dssp             HHTTCHHHHHHHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHH
Confidence            77777777777666653   1122222222              22 3677888999999999998763 3367788889


Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCC
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKN  326 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~  326 (514)
                      ...+...|++++|..+++.+.+.   .| +...+..+...+.+.|++++|.+.++++.  .+.+..+|..+...+...|+
T Consensus       179 a~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~  255 (327)
T 3cv0_A          179 GVLYNLSNNYDSAAANLRRAVEL---RPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQ  255 (327)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhccHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcc
Confidence            99999999999999999988654   34 57888999999999999999999998863  23467889999999999999


Q ss_pred             HHHHHHHHHHHHhcCCC------------CcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          327 VELAGKVAEKIFMIDPN------------NMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       327 ~~~a~~~~~~~~~~~p~------------~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                      +++|...++++++..|.            ++..+..++.+|...|++++|..++++.
T Consensus       256 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  312 (327)
T 3cv0_A          256 YDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQN  312 (327)
T ss_dssp             HHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            99999999999999988            6889999999999999999999998643

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.73  E-value=2.1e-18  Score=180.10  Aligned_cols=148  Identities=11%  Similarity=0.100  Sum_probs=127.2

Q ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHccCC-------CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040365           75 NVCIGSSLINMYAKCARVEDSHRLFCLLP-------VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSS  147 (514)
Q Consensus        75 ~~~~~~~li~~~~~~g~~~~A~~~f~~~~-------~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~  147 (514)
                      -..+||+||++|+++|++++|.++|++|.       .||++|||+||.+|++.|++++|+++|++|.+.|+.||.+||++
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            34689999999999999999999997753       68999999999999999999999999999999999999999999


Q ss_pred             HHHHHhccCCh-HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC-----ChhHHHHHHHHHHhC
Q 040365          148 IMPACAHLTTL-HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH-----DIVSWTAVIMGNALH  221 (514)
Q Consensus       148 ll~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~-----d~~~~~~li~~~~~~  221 (514)
                      +|.++++.|.. +.|.+++++|.+.|+.||..+|+++++.+.+.+-++...+++..+..+     .+.+.+.|.+.|.+.
T Consensus       206 LI~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f~p~~~~~~~~~t~~LL~dl~s~d  285 (1134)
T 3spa_A          206 ALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKD  285 (1134)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCCCCCCCCCCCCCTTTHHHHCCC
T ss_pred             HHHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHhCcccCCCCCCcccccchHHHHHHHccC
Confidence            99999999985 789999999999999999999999999888876666666665544321     244555566666665


Q ss_pred             C
Q 040365          222 G  222 (514)
Q Consensus       222 g  222 (514)
                      +
T Consensus       286 ~  286 (1134)
T 3spa_A          286 G  286 (1134)
T ss_dssp             S
T ss_pred             C
Confidence            5

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.73  E-value=3e-14  Score=145.24  Aligned_cols=334  Identities=10%  Similarity=-0.011  Sum_probs=276.1

Q ss_pred             CcchHHHHHHHHHh----cCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhC----CCChHHHHHHHHHHHHhCCCCch
Q 040365            5 DLVSWNTVIVGLAR----NGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFAD----YVDVIKGKEIHGYAIRHGLDANV   76 (514)
Q Consensus         5 ~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~g~~~~~   76 (514)
                      ++.++..|-..|..    .+++++|+..|++..+.|   +...+..+...+..    .++.++|...++...+.|   +.
T Consensus        74 ~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~  147 (490)
T 2xm6_A           74 YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RD  147 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            55677888888888    899999999999998865   55667777777776    789999999999999876   56


Q ss_pred             hHHHHHHHHHHH----CCCHHHHHHHHccCC-CCChhHHHHHHHHHHH----CCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040365           77 CIGSSLINMYAK----CARVEDSHRLFCLLP-VKDAISWNSIIAGCVQ----NGLFDEGLKFFRQMLIAKIKPRHVSFSS  147 (514)
Q Consensus        77 ~~~~~li~~~~~----~g~~~~A~~~f~~~~-~~d~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~  147 (514)
                      ..+..|..+|..    .++.++|.+.|++.. ..+..++..+...|.+    .+++++|++.|++..+.|   +...+..
T Consensus       148 ~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~  224 (490)
T 2xm6_A          148 SGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQGNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLH  224 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHH
Confidence            778888899988    889999999998765 3577889999999988    899999999999998865   4556666


Q ss_pred             HHHHHhc----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh----cCCHHHHHHHHHhCCC-CChhHHHHHHHHH
Q 040365          148 IMPACAH----LTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK----CGNIRLARCIFDKMDL-HDIVSWTAVIMGN  218 (514)
Q Consensus       148 ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k----~g~~~~A~~~~~~m~~-~d~~~~~~li~~~  218 (514)
                      +...+..    .+++++|.+.+....+.|   +...+..|..+|..    .++.++|.+.|++..+ .+..++..+...|
T Consensus       225 lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y  301 (490)
T 2xm6_A          225 LADMYYFGIGVTQDYTQSRVLFSQSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLY  301 (490)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            6666664    789999999999998865   45566778888888    8999999999998764 4677888888888


Q ss_pred             HhC-----CChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccC---CHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHH
Q 040365          219 ALH-----GNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAG---LIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLG  290 (514)
Q Consensus       219 ~~~-----g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g---~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~  290 (514)
                      ...     +++++|+..|++..+.|   +...+..+...+...|   +.++|..+|+...+.    .++..+..|..+|.
T Consensus       302 ~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~----~~~~a~~~Lg~~y~  374 (490)
T 2xm6_A          302 DKGAEGVAKNREQAISWYTKSAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK----GEKAAQFNLGNALL  374 (490)
T ss_dssp             HHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT----TCHHHHHHHHHHHH
T ss_pred             HcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC----CCHHHHHHHHHHHH
Confidence            887     89999999999999875   4456666777777656   889999999998653    46778888999998


Q ss_pred             h----cCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCC---CcchHHHHHHHHHH
Q 040365          291 R----AGKLQEAYEFISNMHAGPTENVWLTLLSACRV----HKNVELAGKVAEKIFMIDPN---NMGAYVILSNTYAA  357 (514)
Q Consensus       291 ~----~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~p~---~~~~~~~l~~~~~~  357 (514)
                      .    .+++++|.+.|++.....+...+..|...+..    .++.++|...++++.+.+|+   ++.....|..++..
T Consensus       375 ~g~g~~~~~~~A~~~~~~A~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~~a~~~l~~~~~~  452 (490)
T 2xm6_A          375 QGKGVKKDEQQAAIWMRKAAEQGLSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDMNLFGTENRNITEKKLTAK  452 (490)
T ss_dssp             HTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHTTSCHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCCCcCCHHHHHHHHhcCHh
Confidence            8    89999999999987655678889999999988    89999999999999999854   66666666655543

>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=99.73  E-value=4e-16  Score=149.49  Aligned_cols=263  Identities=10%  Similarity=-0.054  Sum_probs=166.5

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      ...|..+...+.+.|++++|+.+|+++.... +.+...+..+...+...|++++|.+.+..+++.. +.+          
T Consensus        21 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~----------   88 (327)
T 3cv0_A           21 HENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKD----------   88 (327)
T ss_dssp             SSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTC----------
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCC----------
Confidence            3344455555555555555555555554432 2233444444455555555555555555555442 233          


Q ss_pred             HHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHH-HHHHH--------------HH
Q 040365           86 YAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHV-SFSSI--------------MP  150 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~l--------------l~  150 (514)
                                           ..+|..+...|...|++++|++.|+++....  |+.. .+..+              ..
T Consensus        89 ---------------------~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  145 (327)
T 3cv0_A           89 ---------------------IAVHAALAVSHTNEHNANAALASLRAWLLSQ--PQYEQLGSVNLQADVDIDDLNVQSED  145 (327)
T ss_dssp             ---------------------HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS--TTTTTC--------------------
T ss_pred             ---------------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CccHHHHHHHhHHHHHHHHHHHHHHh
Confidence                                 3444555555555555555555555554431  2111 11111              11


Q ss_pred             -HHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHH
Q 040365          151 -ACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHD  226 (514)
Q Consensus       151 -~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~  226 (514)
                       .+...|++++|...+..+++.. +.+..++..+...|.+.|++++|.+.|+++.   ..+..+|..+...+...|++++
T Consensus       146 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  224 (327)
T 3cv0_A          146 FFFAAPNEYRECRTLLHAALEMN-PNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQE  224 (327)
T ss_dssp             CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHH
Confidence             2667778888888888877765 4467777888888888888888888887764   3456778888888888888888


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCC----------CCHhHHHHHHHHHHhcCCHH
Q 040365          227 AISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA----------PSFEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       227 A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~----------p~~~~~~~li~~~~~~g~~~  296 (514)
                      |+..|+++.+.. +.+..++..+...+...|++++|...|+.+.+...-.          .+...+..+..++.+.|+.+
T Consensus       225 A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  303 (327)
T 3cv0_A          225 ALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPD  303 (327)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHH
Confidence            888888887752 2346778888888888888988888888876542110          03677888888899999999


Q ss_pred             HHHHHHHhC
Q 040365          297 EAYEFISNM  305 (514)
Q Consensus       297 ~A~~~~~~m  305 (514)
                      +|..++++.
T Consensus       304 ~A~~~~~~~  312 (327)
T 3cv0_A          304 LVELTYAQN  312 (327)
T ss_dssp             HHHHHTTCC
T ss_pred             HHHHHHHHH
Confidence            998888764

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.73  E-value=4.5e-18  Score=177.57  Aligned_cols=132  Identities=14%  Similarity=0.193  Sum_probs=111.4

Q ss_pred             CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC-------CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHH
Q 040365          173 FDDNMFIASSLLDMYAKCGNIRLARCIFDKMD-------LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVA  245 (514)
Q Consensus       173 ~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~-------~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  245 (514)
                      ...-..+||+||++|+++|++++|.++|++|.       .||++|||+||.+|++.|+.++|.++|++|.+.|+.||.+|
T Consensus       123 ~~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvT  202 (1134)
T 3spa_A          123 LSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLS  202 (1134)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHH
T ss_pred             HHhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHH
Confidence            44456789999999999999999999997753       67999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHccCC-HHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          246 FVAVLTACSHAGL-IDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       246 ~~~ll~a~~~~g~-~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      |+++|.++++.|+ .++|.++|++|.++ |+.||..+|++++....+.+-++...++..++
T Consensus       203 YntLI~glcK~G~~~e~A~~Ll~EM~~k-G~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f  262 (1134)
T 3spa_A          203 YAAALQCMGRQDQDAGTIERCLEQMSQE-GLKLQALFTAVLLSEEDRATVLKAVHKVKPTF  262 (1134)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHH-TCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCC
T ss_pred             HHHHHHHHHhCCCcHHHHHHHHHHHHHc-CCCCChhhcccccChhhHHHHHHHHHHhCccc
Confidence            9999999999887 57889999999665 99999999999998887776555555443333

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.72  E-value=1.1e-15  Score=144.39  Aligned_cols=247  Identities=11%  Similarity=0.007  Sum_probs=203.1

Q ss_pred             HHHHHHCCChhHHHHHHHHHHHCCCCCCH--HHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC
Q 040365          114 IAGCVQNGLFDEGLKFFRQMLIAKIKPRH--VSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG  191 (514)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~--~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g  191 (514)
                      |.-....|++..|+..+++...  ..|+.  .....+.+++...|+++.|...++.    .-+|+...+..+...|...|
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~--~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~   79 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKP--SSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHS   79 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCC--CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCST
T ss_pred             HHHHHHHHHHHHHHHHHHhccc--CCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCC
Confidence            3445678999999999887644  34544  3456678899999999999876543    24678888899999999999


Q ss_pred             CHHHHHHHHHhCC----CC-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040365          192 NIRLARCIFDKMD----LH-DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYF  266 (514)
Q Consensus       192 ~~~~A~~~~~~m~----~~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  266 (514)
                      +.++|.+.++++.    .| +...+..+...|.+.|++++|++.+++      ..+...+..+...+.+.|++++|...|
T Consensus        80 ~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l  153 (291)
T 3mkr_A           80 RRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKEL  153 (291)
T ss_dssp             THHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            9999999999863    24 566777788999999999999999997      456788889999999999999999999


Q ss_pred             HHhHHhcCCCCCHh---HHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 040365          267 NSMTKDYGIAPSFE---HYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMID  341 (514)
Q Consensus       267 ~~m~~~~~~~p~~~---~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  341 (514)
                      +.+.+.   .|+..   ....++..+...|++++|..+|+++.  .+.+...|+.+..++...|++++|+..++++++.+
T Consensus       154 ~~~~~~---~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~  230 (291)
T 3mkr_A          154 KKMQDQ---DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD  230 (291)
T ss_dssp             HHHHHH---CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhh---CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            999765   46532   12234455556699999999999874  34678899999999999999999999999999999


Q ss_pred             CCCcchHHHHHHHHHHccChhH-HHHHHHHHHhCC
Q 040365          342 PNNMGAYVILSNTYAAARRWKD-AASLRVFMRNKG  375 (514)
Q Consensus       342 p~~~~~~~~l~~~~~~~g~~~~-a~~~~~~m~~~g  375 (514)
                      |+++.++..++..+...|++++ +.++++++.+..
T Consensus       231 p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~  265 (291)
T 3mkr_A          231 SGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAH  265 (291)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence            9999999999999999999976 578888887643

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.65  E-value=1.6e-13  Score=141.22  Aligned_cols=331  Identities=11%  Similarity=0.019  Sum_probs=241.4

Q ss_pred             CChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC--CCChhHHHHHHHH
Q 040365           39 PDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP--VKDAISWNSIIAG  116 (514)
Q Consensus        39 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~--~~d~~~~~~li~~  116 (514)
                      -|...|..++.. .+.|++++|..+++.+++.. |.+...|..++..+.+.|++++|.++|++..  .|++..|...+..
T Consensus        11 ~~~~~w~~l~~~-~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~~~~~   88 (530)
T 2ooe_A           11 YDLDAWSILIRE-AQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSY   88 (530)
T ss_dssp             TCHHHHHHHHHH-HHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHHHHHH
Confidence            356688888884 67899999999999999863 7778899999999999999999999999976  3677788877753


Q ss_pred             -HHHCCChhHHHH----HHHHHHH-CCCCCC-HHHHHHHHHHHhc---------cCChHHHHHHHHHHHHcCCCCcHHHH
Q 040365          117 -CVQNGLFDEGLK----FFRQMLI-AKIKPR-HVSFSSIMPACAH---------LTTLHLGKQLHGCIIRNGFDDNMFIA  180 (514)
Q Consensus       117 -~~~~g~~~~A~~----l~~~m~~-~g~~p~-~~t~~~ll~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~  180 (514)
                       ....|+.++|.+    +|++... .|..|+ ...|...+.....         .|+++.|..+++..++........+|
T Consensus        89 ~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~~  168 (530)
T 2ooe_A           89 VRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLW  168 (530)
T ss_dssp             HHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHHH
T ss_pred             HHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHHH
Confidence             345688877765    6766654 355543 4555555555433         68899999999999884222222344


Q ss_pred             HHHHHHH-------------HhcCCHHHHHHHHHh-------CC------CCC--------hhHHHHHHHHHHhC----C
Q 040365          181 SSLLDMY-------------AKCGNIRLARCIFDK-------MD------LHD--------IVSWTAVIMGNALH----G  222 (514)
Q Consensus       181 ~~li~~y-------------~k~g~~~~A~~~~~~-------m~------~~d--------~~~~~~li~~~~~~----g  222 (514)
                      .......             .+.++++.|..++..       +.      .|+        ...|...+.-....    +
T Consensus       169 ~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~  248 (530)
T 2ooe_A          169 RDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTE  248 (530)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCS
T ss_pred             HHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCC
Confidence            3332211             134567778776664       11      122        34676666443332    2


Q ss_pred             Ch----HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc-------cCCHH-------HHHHHHHHhHHhcCCCC-CHhHHH
Q 040365          223 NA----HDAISLFEQMEKDGVKPNSVAFVAVLTACSH-------AGLID-------KAWSYFNSMTKDYGIAP-SFEHYA  283 (514)
Q Consensus       223 ~~----~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~-------~g~~~-------~a~~~~~~m~~~~~~~p-~~~~~~  283 (514)
                      +.    .+|..+|++..... +-+...|..+...+.+       .|+++       +|..+|++..+  .+.| +...|.
T Consensus       249 ~~~~~~~~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~--~~~p~~~~l~~  325 (530)
T 2ooe_A          249 DQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIS--TLLKKNMLLYF  325 (530)
T ss_dssp             CSHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTT--TTCSSCHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHH--HhCcccHHHHH
Confidence            32    47888999988752 2345677777777664       78877       99999998864  2456 588999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC-CCCC-H-HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHH-HHHcc
Q 040365          284 AVADLLGRAGKLQEAYEFISNMH-AGPT-E-NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNT-YAAAR  359 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m~-~~p~-~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~-~~~~g  359 (514)
                      .++..+.+.|++++|.++|+++. ..|+ . .+|..++..+.+.|+.+.|..+|+++++..|.+...|...+.. +...|
T Consensus       326 ~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~  405 (530)
T 2ooe_A          326 AYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSK  405 (530)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcC
Confidence            99999999999999999999863 3454 3 5899999999999999999999999999888777666655544 34689


Q ss_pred             ChhHHHHHHHHHHhC
Q 040365          360 RWKDAASLRVFMRNK  374 (514)
Q Consensus       360 ~~~~a~~~~~~m~~~  374 (514)
                      ++++|.++|+...+.
T Consensus       406 ~~~~A~~~~e~al~~  420 (530)
T 2ooe_A          406 DKSVAFKIFELGLKK  420 (530)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             ChhHHHHHHHHHHHH
Confidence            999999999988764

>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=99.64  E-value=7.1e-13  Score=143.01  Aligned_cols=321  Identities=11%  Similarity=0.055  Sum_probs=234.5

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHhhCCC--CCChhhHHHHH---------------------------HHHhCCCChHHH
Q 040365           10 NTVIVGLARNGLYEEALNIVRQMGNVNL--KPDSFTLSSVL---------------------------PIFADYVDVIKG   60 (514)
Q Consensus        10 ~~li~~~~~~g~~~~A~~l~~~m~~~g~--~p~~~t~~~ll---------------------------~~~~~~~~~~~a   60 (514)
                      ...+.+|...|.+.+|++++++....+-  .-+...-+.++                           ..|...|.+++|
T Consensus       989 s~~vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIkaD~~Rv~eyI~kLd~~d~~eIA~Iai~lglyEEA 1068 (1630)
T 1xi4_A          989 SVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISNELFEEA 1068 (1630)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHhChhhHHHHHHHhhhccHHHHHHHHHhCCCHHHH
Confidence            4568899999999999999999985421  01112222232                           234455666666


Q ss_pred             HHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCC
Q 040365           61 KEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKP  140 (514)
Q Consensus        61 ~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  140 (514)
                      .++|++..     ......+.++   -..|++++|.++.++..  +..+|..+..++.+.|++++|++.|.+.      -
T Consensus      1069 f~IYkKa~-----~~~~A~~VLi---e~i~nldrAiE~Aervn--~p~vWsqLAKAql~~G~~kEAIdsYiKA------d 1132 (1630)
T 1xi4_A         1069 FAIFRKFD-----VNTSAVQVLI---EHIGNLDRAYEFAERCN--EPAVWSQLAKAQLQKGMVKEAIDSYIKA------D 1132 (1630)
T ss_pred             HHHHHHcC-----CHHHHHHHHH---HHHhhHHHHHHHHHhcC--CHHHHHHHHHHHHhCCCHHHHHHHHHhc------C
Confidence            66665531     1111122222   25667777777777653  4667888899999999999999988653      4


Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHh
Q 040365          141 RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNAL  220 (514)
Q Consensus       141 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~  220 (514)
                      |...|..++.+|.+.|+++++.+.+....+..  ++..+.+.++.+|+|.+++++.....   ..++...|..+...|..
T Consensus      1133 D~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI---~~~n~ad~~~iGd~le~ 1207 (1630)
T 1xi4_A         1133 DPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI---NGPNNAHIQQVGDRCYD 1207 (1630)
T ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH---hCCCHHHHHHHHHHHHh
Confidence            67778888999999999999999998877754  44444456888899998888644443   45566777788888889


Q ss_pred             CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHH
Q 040365          221 HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYE  300 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~  300 (514)
                      .|++++|..+|...         ..|..+...+.+.|++++|.+.++..       .+..+|..+..++...|++..|..
T Consensus      1208 eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA-------~n~~aWkev~~acve~~Ef~LA~~ 1271 (1630)
T 1xi4_A         1208 EKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA-------NSTRTWKEVCFACVDGKEFRLAQM 1271 (1630)
T ss_pred             cCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh-------CCHHHHHHHHHHHhhhhHHHHHHH
Confidence            99999999999874         37888889999999999999988865       245788888888888889988888


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc--cChhHHHHHHH
Q 040365          301 FISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA--RRWKDAASLRV  369 (514)
Q Consensus       301 ~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~--g~~~~a~~~~~  369 (514)
                      ....+.  .++..+..++..|...|.+++|+.+++..+.++|.+...|.-|..+|++.  ++..++.+.|.
T Consensus      1272 cgl~Ii--v~~deLeeli~yYe~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~ 1340 (1630)
T 1xi4_A         1272 CGLHIV--VHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFW 1340 (1630)
T ss_pred             HHHhhh--cCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            776543  34555668888999999999999999999999988888898888887764  34555555554

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.63  E-value=4.9e-14  Score=129.89  Aligned_cols=224  Identities=13%  Similarity=0.050  Sum_probs=154.4

Q ss_pred             hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 040365          108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMY  187 (514)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y  187 (514)
                      ..|..+...+...|++++|+..|++..+..  ++...+..+..++...|++++|...+..+++..  |+.          
T Consensus         6 ~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~--~~~----------   71 (258)
T 3uq3_A            6 DKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQG--REM----------   71 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--HHT----------
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC--ccc----------
Confidence            345555566666666666666666655544  444555555555555555555555555544321  000          


Q ss_pred             HhcCCHHHHHHHHHhCCCCC----hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040365          188 AKCGNIRLARCIFDKMDLHD----IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAW  263 (514)
Q Consensus       188 ~k~g~~~~A~~~~~~m~~~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  263 (514)
                                       .++    ..+|..+...|...|++++|+..|++....  .|+.       ..+...|++++|.
T Consensus        72 -----------------~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~  125 (258)
T 3uq3_A           72 -----------------RADYKVISKSFARIGNAYHKLGDLKKTIEYYQKSLTE--HRTA-------DILTKLRNAEKEL  125 (258)
T ss_dssp             -----------------TCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHH
T ss_pred             -----------------ccchHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHH
Confidence                             001    355666777777777777777777777763  3443       2345567788888


Q ss_pred             HHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040365          264 SYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMI  340 (514)
Q Consensus       264 ~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  340 (514)
                      ..++.+..   ..| +...+..+...+...|++++|.+.+++..  .+.+..+|..+...+...|++++|...++++++.
T Consensus       126 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  202 (258)
T 3uq3_A          126 KKAEAEAY---VNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEK  202 (258)
T ss_dssp             HHHHHHHH---CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH---cCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            88887754   244 46677788888888888888888888763  2346778888888999999999999999999999


Q ss_pred             CCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          341 DPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       341 ~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +|+++.+|..++.+|...|++++|.+.+++..+.
T Consensus       203 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  236 (258)
T 3uq3_A          203 DPNFVRAYIRKATAQIAVKEYASALETLDAARTK  236 (258)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence            9998889999999999999999999998887654

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.62  E-value=6.1e-14  Score=130.75  Aligned_cols=241  Identities=10%  Similarity=-0.075  Sum_probs=188.1

Q ss_pred             HCCChhHHHHHHHHHHHCCC---CCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHH
Q 040365          119 QNGLFDEGLKFFRQMLIAKI---KPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRL  195 (514)
Q Consensus       119 ~~g~~~~A~~l~~~m~~~g~---~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~  195 (514)
                      ..|++++|+..|+++.+...   +.+..++..+...+...|++++|...+..+++.. +.+..++..+...|...|++++
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~   95 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDA   95 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHH
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHH
Confidence            35778888888888877532   1245567777888888899999999998888875 5567888889999999999999


Q ss_pred             HHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHh
Q 040365          196 ARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKD  272 (514)
Q Consensus       196 A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~  272 (514)
                      |.+.|++..   +.+..+|..+...|...|++++|+..|+++.+.  .|+.......+..+...|++++|...++.....
T Consensus        96 A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  173 (275)
T 1xnf_A           96 AYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  173 (275)
T ss_dssp             HHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            999998875   346788999999999999999999999999884  466555555556667789999999999877654


Q ss_pred             cCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCC-CC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc
Q 040365          273 YGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAG-PT-----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG  346 (514)
Q Consensus       273 ~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-p~-----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~  346 (514)
                      .  +++...+ .++..+...++.++|.+.+++.... |+     ..+|..+...+...|++++|...++++++.+|++..
T Consensus       174 ~--~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~  250 (275)
T 1xnf_A          174 S--DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFV  250 (275)
T ss_dssp             S--CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTCH
T ss_pred             C--CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCchhHH
Confidence            2  3343444 4777788888899999999886432 32     578899999999999999999999999999997754


Q ss_pred             hHHHHHHHHHHccChhHHHHHH
Q 040365          347 AYVILSNTYAAARRWKDAASLR  368 (514)
Q Consensus       347 ~~~~l~~~~~~~g~~~~a~~~~  368 (514)
                      .+   ..++...|++++|.+.+
T Consensus       251 ~~---~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          251 EH---RYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HH---HHHHHHHHHHHHC----
T ss_pred             HH---HHHHHHHHHHHhhHHHH
Confidence            44   66778889999988766

>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=99.61  E-value=1.2e-12  Score=141.37  Aligned_cols=316  Identities=11%  Similarity=0.085  Sum_probs=249.3

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHC
Q 040365           10 NTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKC   89 (514)
Q Consensus        10 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~   89 (514)
                      ..+...+...|.+++|..+|++...     .....+.++.   ..+++++|.++..++      .++.+|..+..++.+.
T Consensus      1053 ~eIA~Iai~lglyEEAf~IYkKa~~-----~~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~ 1118 (1630)
T 1xi4_A         1053 PDIANIAISNELFEEAFAIFRKFDV-----NTSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQK 1118 (1630)
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHcCC-----HHHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhC
Confidence            3456678889999999999998531     1122233332   567889998888754      4578899999999999


Q ss_pred             CCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040365           90 ARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCII  169 (514)
Q Consensus        90 g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~  169 (514)
                      |++++|...|.+.  .|...|.-++..+.+.|++++|++.|...++..  ++....+.++.+|++.++++....+.    
T Consensus      1119 G~~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI---- 1190 (1630)
T 1xi4_A         1119 GMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI---- 1190 (1630)
T ss_pred             CCHHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----
Confidence            9999999999764  678889999999999999999999999877754  34333445888999999988655443    


Q ss_pred             HcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHH
Q 040365          170 RNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAV  249 (514)
Q Consensus       170 ~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l  249 (514)
                      +   .++...+..+.+.|...|++++|..+|...     ..|..+...|.+.|++++|++.+++.      -+..+|..+
T Consensus      1191 ~---~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA-----~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev 1256 (1630)
T 1xi4_A         1191 N---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEV 1256 (1630)
T ss_pred             h---CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh-----hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHH
Confidence            2   445666777999999999999999999996     58999999999999999999999986      366899999


Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhc--C
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRVH--K  325 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~--~  325 (514)
                      -.+|...|++..|......      +..++..+..++..|.+.|.+++|..+++... .. .....|+-|...+.+.  +
T Consensus      1257 ~~acve~~Ef~LA~~cgl~------Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~pe 1330 (1630)
T 1xi4_A         1257 CFACVDGKEFRLAQMCGLH------IVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQ 1330 (1630)
T ss_pred             HHHHhhhhHHHHHHHHHHh------hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHH
Confidence            9999999999999887653      34467778899999999999999999998753 22 3445676666666554  4


Q ss_pred             CHHHHHHHHHHHHhcCC-----CCcchHHHHHHHHHHccChhHHHHH
Q 040365          326 NVELAGKVAEKIFMIDP-----NNMGAYVILSNTYAAARRWKDAASL  367 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p-----~~~~~~~~l~~~~~~~g~~~~a~~~  367 (514)
                      +..++.+.|..-....|     .+...|.-+...|.+.|+|+.|...
T Consensus      1331 klmEhlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~t 1377 (1630)
T 1xi4_A         1331 KMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIIT 1377 (1630)
T ss_pred             HHHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHH
Confidence            56666667766555444     5677899999999999999999853

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.61  E-value=4.8e-14  Score=129.97  Aligned_cols=233  Identities=13%  Similarity=0.021  Sum_probs=149.0

Q ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHccCCC--CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCC--CCCC----HHHHHH
Q 040365           76 VCIGSSLINMYAKCARVEDSHRLFCLLPV--KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAK--IKPR----HVSFSS  147 (514)
Q Consensus        76 ~~~~~~li~~~~~~g~~~~A~~~f~~~~~--~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--~~p~----~~t~~~  147 (514)
                      ...+..+...|.+.|++++|...|+...+  .+..+|..+...|...|++++|+..|++..+..  ..|+    ..++..
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            45788899999999999999999987532  678899999999999999999999999987642  1112    456666


Q ss_pred             HHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHH
Q 040365          148 IMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDA  227 (514)
Q Consensus       148 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A  227 (514)
                      +...+...|++++|...+..+.+..  |+.       ..+.+.|++++|...+                           
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~~--~~~-------~~~~~~~~~~~a~~~~---------------------------  128 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTEH--RTA-------DILTKLRNAEKELKKA---------------------------  128 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--CCH-------HHHHHHHHHHHHHHHH---------------------------
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcC--chh-------HHHHHHhHHHHHHHHH---------------------------
Confidence            7777777777777777777777653  221       2333444445554444                           


Q ss_pred             HHHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          228 ISLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH  306 (514)
Q Consensus       228 ~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~  306 (514)
                          +++...  .|+ ...+..+...+...|++++|...|+...+..  +.+...+..+...|.+.|++++|.+.+++..
T Consensus       129 ----~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al  200 (258)
T 3uq3_A          129 ----EAEAYV--NPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRA--PEDARGYSNRAAALAKLMSFPEAIADCNKAI  200 (258)
T ss_dssp             ----HHHHHC--CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ----HHHHHc--CcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC--cccHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence                444432  222 2334444455555555555555555554321  1134555555666666666666666665542


Q ss_pred             --CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC------CCCcchHHHHH
Q 040365          307 --AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMID------PNNMGAYVILS  352 (514)
Q Consensus       307 --~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~------p~~~~~~~~l~  352 (514)
                        .+.+..+|..+...+...|++++|...+++++++.      |.+...+..+.
T Consensus       201 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~p~~~~~~~~l~  254 (258)
T 3uq3_A          201 EKDPNFVRAYIRKATAQIAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYY  254 (258)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHH
T ss_pred             HhCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhChhhcCCCchHHHHHHHH
Confidence              22346667777777777777777777777777766      65555444443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.60  E-value=5.1e-14  Score=126.88  Aligned_cols=192  Identities=12%  Similarity=0.037  Sum_probs=151.0

Q ss_pred             CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHH
Q 040365          174 DDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAV  249 (514)
Q Consensus       174 ~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~l  249 (514)
                      +++...+..+...|.+.|++++|...|++..   +.+...|..+...+.+.|++++|+..|++..+.  .| +...+..+
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~l   79 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVAR--TPRYLGGYMVL   79 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHH
Confidence            4566677778888888888888888888764   346678888888888899999999999988875  34 45677788


Q ss_pred             HHHHHcc-----------CCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHH
Q 040365          250 LTACSHA-----------GLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWL  315 (514)
Q Consensus       250 l~a~~~~-----------g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~  315 (514)
                      ..++...           |++++|...|+...+.   .| +...+..+..+|...|++++|.+.|++..  . .+...|.
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~---~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~  155 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAERV---NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE-DTPEIRS  155 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCHHHHH
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh---CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc-cchHHHH
Confidence            8888888           9999999999988754   56 57888899999999999999999998762  3 7888999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                      .+..++...|++++|...++++++.+|+++..+..++.++...|++++|.+.+++.
T Consensus       156 ~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          156 ALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC--------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999988754

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.56  E-value=2.6e-13  Score=126.40  Aligned_cols=241  Identities=13%  Similarity=0.046  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC--HHHHHHHHHHHh
Q 040365           79 GSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR--HVSFSSIMPACA  153 (514)
Q Consensus        79 ~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~t~~~ll~~~~  153 (514)
                      .......+.+.|++++|...|+...   ..+...|..+...|.+.|++++|+..|++..+.+..|+  ...|..+...+.
T Consensus         6 ~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~~   85 (272)
T 3u4t_A            6 EFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKILM   85 (272)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHH
Confidence            3344555666666666666666543   22344566666666666666666666666655321111  122455555555


Q ss_pred             ccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC---CChhHHHHHHHHHHhCCChHHHHHH
Q 040365          154 HLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL---HDIVSWTAVIMGNALHGNAHDAISL  230 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~---~d~~~~~~li~~~~~~g~~~~A~~l  230 (514)
                      ..|++++|...+..+++.. +.+..++..+...|.+.|++++|.+.|++...   .+...|..+...+...+++++|++.
T Consensus        86 ~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  164 (272)
T 3u4t_A           86 KKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYNKEYVKADSS  164 (272)
T ss_dssp             HTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666666666655543 33344555555555555555555555555442   2333444444122222355555555


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCC---HHHHHHHHHhCC-
Q 040365          231 FEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGK---LQEAYEFISNMH-  306 (514)
Q Consensus       231 ~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~---~~~A~~~~~~m~-  306 (514)
                      |++..+.  .|+                                   +...+..+...+...|+   +++|...+++.. 
T Consensus       165 ~~~a~~~--~p~-----------------------------------~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~  207 (272)
T 3u4t_A          165 FVKVLEL--KPN-----------------------------------IYIGYLWRARANAAQDPDTKQGLAKPYYEKLIE  207 (272)
T ss_dssp             HHHHHHH--STT-----------------------------------CHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHH
T ss_pred             HHHHHHh--Ccc-----------------------------------chHHHHHHHHHHHHcCcchhhHHHHHHHHHHHH
Confidence            5544442  222                                   23333344444444444   333444333321 


Q ss_pred             ---CCCC------HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH
Q 040365          307 ---AGPT------ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA  357 (514)
Q Consensus       307 ---~~p~------~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  357 (514)
                         ..|+      ..+|..+...+...|++++|...++++++++|+++.+...+......
T Consensus       208 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~~  267 (272)
T 3u4t_A          208 VCAPGGAKYKDELIEANEYIAYYYTINRDKVKADAAWKNILALDPTNKKAIDGLKMKLEH  267 (272)
T ss_dssp             HHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHC-----
T ss_pred             HHhcccccchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCccHHHHHHHhhhhhcc
Confidence               1122      24677788888999999999999999999999988777666555443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.55  E-value=2.9e-13  Score=121.95  Aligned_cols=195  Identities=12%  Similarity=-0.069  Sum_probs=127.5

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLI   83 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (514)
                      ++...|..+...+.+.|++++|+..|++..+.. +.+...+..+...+...|++++|...++.+++.. |.+...+..+.
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg   80 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLS   80 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            467788888889999999999999999988754 4456678888888889999999999999998876 56677788888


Q ss_pred             HHHHHC-----------CCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040365           84 NMYAKC-----------ARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIM  149 (514)
Q Consensus        84 ~~~~~~-----------g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (514)
                      ..|.+.           |++++|...|++..   ..+...|..+...|.+.|++++|+..|++..+..  .+...+..+.
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la  158 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALA  158 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHH
T ss_pred             HHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHH
Confidence            888877           66666666666543   2245556666666666666666666666666554  4555556666


Q ss_pred             HHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          150 PACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKM  203 (514)
Q Consensus       150 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m  203 (514)
                      .++...|++++|...++.+++.. +.+...+..+...|.+.|++++|.+.|++.
T Consensus       159 ~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          159 ELYLSMGRLDEALAQYAKALEQA-PKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHTC--------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            66666666666666666666553 344555555666666666666666555543

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.55  E-value=1.8e-12  Score=131.09  Aligned_cols=332  Identities=12%  Similarity=-0.026  Sum_probs=214.7

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhC-----C-CCC-ChhhHHHHHHHHh--CCCChHHHHHHHHHHHHhCCCCc
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNV-----N-LKP-DSFTLSSVLPIFA--DYVDVIKGKEIHGYAIRHGLDAN   75 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g-~~p-~~~t~~~ll~~~~--~~~~~~~a~~~~~~~~~~g~~~~   75 (514)
                      ..++|+.+...|...|++++|+..|++....     + ..+ ...++.....++.  ..+++++|...|+.+++.. |.+
T Consensus        93 ~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~-p~~  171 (472)
T 4g1t_A           93 SLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK-PKN  171 (472)
T ss_dssp             THHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-TTC
T ss_pred             HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC-CCC
Confidence            4578999999999999999999999887542     1 112 2345555444443  3467899999999999885 455


Q ss_pred             hhHHHHHHHHH---HHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHH----CCChhHHHHHHHHHHHCCCCCCHHHH
Q 040365           76 VCIGSSLINMY---AKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQ----NGLFDEGLKFFRQMLIAKIKPRHVSF  145 (514)
Q Consensus        76 ~~~~~~li~~~---~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~  145 (514)
                      +..+..+...+   ...++.++|.+.|++..   ..+..++..+...+..    .|++++|.+++++..... +.+...+
T Consensus       172 ~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~  250 (472)
T 4g1t_A          172 PEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVL  250 (472)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHH
T ss_pred             HHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHH
Confidence            66666665553   45677777777776543   3456667666655544    467889999999987753 4566778


Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc-------------------CCHHHHHHHHHhCC--
Q 040365          146 SSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKC-------------------GNIRLARCIFDKMD--  204 (514)
Q Consensus       146 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~-------------------g~~~~A~~~~~~m~--  204 (514)
                      ..+...+...|++++|...+..+++.. +.+..++..+...|...                   +..+.|...|++..  
T Consensus       251 ~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~  329 (472)
T 4g1t_A          251 RSAAKFYRRKDEPDKAIELLKKALEYI-PNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEA  329 (472)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCchHHHHHHHHHHHHhC-CChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhc
Confidence            889999999999999999999999875 55667777777666432                   23566777776653  


Q ss_pred             -CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHH--HHHHHHH-HHHccCCHHHHHHHHHHhHHhcCCCCCHh
Q 040365          205 -LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSV--AFVAVLT-ACSHAGLIDKAWSYFNSMTKDYGIAPSFE  280 (514)
Q Consensus       205 -~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~--t~~~ll~-a~~~~g~~~~a~~~~~~m~~~~~~~p~~~  280 (514)
                       ..+..+|..+...|...|++++|++.|++.......|...  .+..+.. ...+.|+.++|+..|....+   +.|+..
T Consensus       330 ~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~---i~~~~~  406 (472)
T 4g1t_A          330 NDNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK---INQKSR  406 (472)
T ss_dssp             CTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH---SCCCCH
T ss_pred             CCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCcccH
Confidence             4466789999999999999999999999998864443321  2222222 34578999999999998764   456543


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNM-H-AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m-~-~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      .....         ...+.++++.. . .+.+..+|..|...+...|++++|+..|+++++++|.++.++.-+
T Consensus       407 ~~~~~---------~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~~  470 (472)
T 4g1t_A          407 EKEKM---------KDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASSWN  470 (472)
T ss_dssp             HHHHH---------HHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC-----------------------
T ss_pred             HHHHH---------HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhcC
Confidence            22222         22333344332 1 234677899999999999999999999999999998777655443

>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=99.54  E-value=4.3e-12  Score=118.41  Aligned_cols=226  Identities=10%  Similarity=-0.023  Sum_probs=142.0

Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhc----cCChHHHHHHHHHHHHcCCCCcHHHHH
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH----LTTLHLGKQLHGCIIRNGFDDNMFIAS  181 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  181 (514)
                      +..++..+...|...|++++|++.|++..+.   -+...+..+...+..    .+++++|...+.+..+.+   +...+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            4556666677777777777777777777662   234455556666666    677777777777776654   455566


Q ss_pred             HHHHHHHh----cCCHHHHHHHHHhCC-CCChhHHHHHHHHHHh----CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040365          182 SLLDMYAK----CGNIRLARCIFDKMD-LHDIVSWTAVIMGNAL----HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTA  252 (514)
Q Consensus       182 ~li~~y~k----~g~~~~A~~~~~~m~-~~d~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a  252 (514)
                      .|..+|..    .|++++|.+.|++.. ..+..++..+...|..    .+++++|+..|++..+.+   +...+..+...
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~  155 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSL  155 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHH
Confidence            66666666    677777776666654 2355566666666666    677777777777766654   34455555555


Q ss_pred             HHc----cCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHh----cCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh-
Q 040365          253 CSH----AGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGR----AGKLQEAYEFISNMHAGPTENVWLTLLSACRV-  323 (514)
Q Consensus       253 ~~~----~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~-  323 (514)
                      +..    .+++++|...|+...+.    .+...+..+..+|..    .+++++|.+.+++.....+...+..|...+.. 
T Consensus       156 ~~~~~~~~~~~~~A~~~~~~a~~~----~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~l~~~~~~g  231 (273)
T 1ouv_A          156 YDAGRGTPKDLKKALASYDKACDL----KDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGCFNLGAMQYNG  231 (273)
T ss_dssp             HHHTSSSCCCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHcCCCCCCCHHHHHHHHHHHHHC----CCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHcC
Confidence            555    66777777777666432    234555566666666    66666666666654323335556666666666 


Q ss_pred             ---cCCHHHHHHHHHHHHhcCCCC
Q 040365          324 ---HKNVELAGKVAEKIFMIDPNN  344 (514)
Q Consensus       324 ---~~~~~~a~~~~~~~~~~~p~~  344 (514)
                         .+++++|...++++.+.+|++
T Consensus       232 ~~~~~~~~~A~~~~~~a~~~~~~~  255 (273)
T 1ouv_A          232 EGVTRNEKQAIENFKKGCKLGAKG  255 (273)
T ss_dssp             SSSSCCSTTHHHHHHHHHHHTCHH
T ss_pred             CCcccCHHHHHHHHHHHHHcCCHH
Confidence               666666666666666666543

>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=99.54  E-value=2.1e-12  Score=118.80  Aligned_cols=205  Identities=12%  Similarity=0.058  Sum_probs=104.8

Q ss_pred             hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 040365          107 AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDM  186 (514)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  186 (514)
                      ...|..+...+...|++++|++.|+++.+.. +.+...+..+...+...|++++|.+.+..+.+.. +.           
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~-----------  103 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SR-----------  103 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TT-----------
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cC-----------
Confidence            3455566666666666666666666655432 2233344444444444444444444444444332 12           


Q ss_pred             HHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHH
Q 040365          187 YAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSY  265 (514)
Q Consensus       187 y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~  265 (514)
                                          +...|..+...|...|++++|+++|+++...+..|+ ...+..+...+...|++++|..+
T Consensus       104 --------------------~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  163 (252)
T 2ho1_A          104 --------------------NARVLNNYGGFLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEY  163 (252)
T ss_dssp             --------------------CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             --------------------cHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHH
Confidence                                233344444444444444444444444444222332 23444455555555555555555


Q ss_pred             HHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          266 FNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       266 ~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      |+.+.+.   .| +...+..+...|.+.|++++|.+.++++.  .+.+...+..+...+...|+.++|...++++.+..|
T Consensus       164 ~~~~~~~---~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p  240 (252)
T 2ho1_A          164 FEKSLRL---NRNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYP  240 (252)
T ss_dssp             HHHHHHH---CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHhc---CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCC
Confidence            5555432   22 34455555555666666666666655542  123445556666666666666666666666666666


Q ss_pred             CCcch
Q 040365          343 NNMGA  347 (514)
Q Consensus       343 ~~~~~  347 (514)
                      +++..
T Consensus       241 ~~~~~  245 (252)
T 2ho1_A          241 GSLEY  245 (252)
T ss_dssp             TSHHH
T ss_pred             CCHHH
Confidence            65443

>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=99.54  E-value=1.1e-12  Score=120.66  Aligned_cols=197  Identities=11%  Similarity=-0.035  Sum_probs=170.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTAC  253 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~  253 (514)
                      ...+..+...|...|++++|.+.|+++.   ..+...|..+...|...|++++|++.|+++.+.. +.+...+..+...+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~  115 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHH
Confidence            5667778888888999999999888764   4467788899999999999999999999998863 33667888899999


Q ss_pred             HccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHH
Q 040365          254 SHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELA  330 (514)
Q Consensus       254 ~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a  330 (514)
                      ...|++++|..+|+.+.+ .+..| +...+..+...+.+.|++++|.+.+++..  .+.+..+|..+...+...|++++|
T Consensus       116 ~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  194 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQ-DTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPA  194 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTT-CTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhHHHHHHHHHHHHHh-CccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHH
Confidence            999999999999999865 23456 56788889999999999999999998863  234688899999999999999999


Q ss_pred             HHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          331 GKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       331 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ...++++.+..|++...+..++..|...|++++|.+.++.+.+..
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          195 RQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             HHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC
Confidence            999999999999999999999999999999999999999997754

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.54  E-value=5.7e-13  Score=124.09  Aligned_cols=241  Identities=9%  Similarity=-0.077  Sum_probs=167.7

Q ss_pred             HhcCChhHHHHHHHHHhhCCCC---CChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHH
Q 040365           17 ARNGLYEEALNIVRQMGNVNLK---PDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVE   93 (514)
Q Consensus        17 ~~~g~~~~A~~l~~~m~~~g~~---p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~   93 (514)
                      ...|++++|+..|+++.+....   .+..++..+...+...|++++|...+..+++.. +.+..++..+...|...|+++
T Consensus        16 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~   94 (275)
T 1xnf_A           16 QPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFD   94 (275)
T ss_dssp             CCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHH
T ss_pred             CccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHH
Confidence            3457889999999998875321   134567788888889999999999999998875 557788888999999999999


Q ss_pred             HHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHH
Q 040365           94 DSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIR  170 (514)
Q Consensus        94 ~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~  170 (514)
                      +|.+.|+...   ..+..+|..+...|.+.|++++|+..|+++.+.  .|+.......+..+...|++++|...+.....
T Consensus        95 ~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  172 (275)
T 1xnf_A           95 AAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFE  172 (275)
T ss_dssp             HHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            9999888765   346778888888899999999999999888874  45555555555556667888888888877776


Q ss_pred             cCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCC-------hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCH
Q 040365          171 NGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHD-------IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNS  243 (514)
Q Consensus       171 ~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d-------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~  243 (514)
                      .. +++...+. ++..+...++.++|.+.+++....+       ..+|..+...|...|++++|...|++....  .|+.
T Consensus       173 ~~-~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~  248 (275)
T 1xnf_A          173 KS-DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVAN--NVHN  248 (275)
T ss_dssp             HS-CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--CCTT
T ss_pred             cC-CcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--Cchh
Confidence            54 33333333 6666777777777777777765332       355666666777777777777777776653  3422


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYF  266 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~  266 (514)
                        +.....++...|++++|++.+
T Consensus       249 --~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          249 --FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             --CHHHHHHHHHHHHHHHC----
T ss_pred             --HHHHHHHHHHHHHHHhhHHHH
Confidence              111233444555555555443

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.54  E-value=1.1e-12  Score=128.18  Aligned_cols=246  Identities=12%  Similarity=0.057  Sum_probs=202.5

Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC-hHHHHHHHHHHHHcCCCCcHHHHHHHH
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTT-LHLGKQLHGCIIRNGFDDNMFIASSLL  184 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~li  184 (514)
                      +...|+.+...+.+.|++++|+..|++..+.. +-+...|..+..++...|+ +++|...++++++.. +.+..+|+.+.
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g  173 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHH
Confidence            34578888999999999999999999998853 3356677888888999996 999999999999876 56788999999


Q ss_pred             HHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc-cCCHH
Q 040365          185 DMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSH-AGLID  260 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~-~g~~~  260 (514)
                      .+|.+.|++++|...|+++.   ..+...|..+..++.+.|++++|+..|+++++... -+...|..+..++.. .|..+
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~~l~~~~~  252 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGYND  252 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCcch
Confidence            99999999999999999875   55788999999999999999999999999998532 256788888888888 66657


Q ss_pred             HH-----HHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcC--CHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcC------
Q 040365          261 KA-----WSYFNSMTKDYGIAP-SFEHYAAVADLLGRAG--KLQEAYEFISNMHAGP-TENVWLTLLSACRVHK------  325 (514)
Q Consensus       261 ~a-----~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g--~~~~A~~~~~~m~~~p-~~~~~~~ll~~~~~~~------  325 (514)
                      +|     +..|+...+.   .| +...|..+..+|...|  ++++|.+++.++...| +...+..|...+...|      
T Consensus       253 eA~~~~el~~~~~Al~l---~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~~~~p~~~~al~~La~~~~~~~~~~~~~  329 (382)
T 2h6f_A          253 RAVLEREVQYTLEMIKL---VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDN  329 (382)
T ss_dssp             HHHHHHHHHHHHHHHHH---STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHccCccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhcccccc
Confidence            77     4778777643   56 5778888888898888  6899999998874334 5678888888888764      


Q ss_pred             ---CHHHHHHHHHHH-HhcCCCCcchHHHHHHHHHH
Q 040365          326 ---NVELAGKVAEKI-FMIDPNNMGAYVILSNTYAA  357 (514)
Q Consensus       326 ---~~~~a~~~~~~~-~~~~p~~~~~~~~l~~~~~~  357 (514)
                         ..++|+.+++++ .+++|.....|..++..+..
T Consensus       330 ~~~~~~~A~~~~~~l~~~~DP~r~~~w~~~~~~l~~  365 (382)
T 2h6f_A          330 KEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQS  365 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHH
Confidence               358999999999 89999988888877776654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.54  E-value=1.8e-12  Score=116.63  Aligned_cols=197  Identities=10%  Similarity=-0.036  Sum_probs=126.1

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 040365          176 NMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTA  252 (514)
Q Consensus       176 ~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a  252 (514)
                      +..++..+...|...|++++|.+.|+++.   ..+...|..+...|...|++++|.+.|+++.... +.+..++..+...
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~   85 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGWF   85 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHHH
Confidence            34455556666666666666666666543   2345566666666666677777777776666542 2244566666666


Q ss_pred             HHcc-CCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHH
Q 040365          253 CSHA-GLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVE  328 (514)
Q Consensus       253 ~~~~-g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~  328 (514)
                      +... |++++|..+++.+.+ .+..| +...+..+...+...|++++|.+.++++.  .+.+...|..+...+...|+++
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~  164 (225)
T 2vq2_A           86 LCGRLNRPAESMAYFDKALA-DPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQLG  164 (225)
T ss_dssp             HHTTTCCHHHHHHHHHHHHT-STTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHhcCcHHHHHHHHHHHHc-CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHH
Confidence            6677 777777777776654 22333 24566666667777777777777766542  1234666777777777777777


Q ss_pred             HHHHHHHHHHhcCC-CCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          329 LAGKVAEKIFMIDP-NNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       329 ~a~~~~~~~~~~~p-~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +|...++++++..| ++...+..+...+...|+.+.|...++.+.+.
T Consensus       165 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          165 DADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHh
Confidence            77777777777777 66677777777777777777777777766543

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.53  E-value=3.7e-12  Score=114.52  Aligned_cols=172  Identities=12%  Similarity=0.031  Sum_probs=115.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhC-CChHHHHHHHHHHHHcCCCCC-HHHHHHHHH
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALH-GNAHDAISLFEQMEKDGVKPN-SVAFVAVLT  251 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~-g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~  251 (514)
                      ...+..+...|...|++++|.+.|++..   ..+..+|..+...|... |++++|+..|+++.+.+..|+ ...+..+..
T Consensus        42 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~  121 (225)
T 2vq2_A           42 ELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGI  121 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHH
Confidence            3344444555555555555555555442   23445666666667777 777777777777766333343 456667777


Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CC-CCHHHHHHHHHHHHhcCCH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AG-PTENVWLTLLSACRVHKNV  327 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~-p~~~~~~~ll~~~~~~~~~  327 (514)
                      ++...|++++|...|+.+.+.   .| +...+..+...+.+.|++++|.+.++++.  .+ .+...+..+...+...|+.
T Consensus       122 ~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  198 (225)
T 2vq2_A          122 CSAKQGQFGLAEAYLKRSLAA---QPQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNA  198 (225)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh---CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcH
Confidence            777788888888888777543   33 46677778888888888888888887753  22 4666777777788888999


Q ss_pred             HHHHHHHHHHHhcCCCCcchHHHH
Q 040365          328 ELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       328 ~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      +.+...++.+.+..|+++.....+
T Consensus       199 ~~a~~~~~~~~~~~p~~~~~~~~l  222 (225)
T 2vq2_A          199 QAAYEYEAQLQANFPYSEELQTVL  222 (225)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHh
Confidence            999999998888888877655443

>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=99.52  E-value=9.5e-12  Score=116.06  Aligned_cols=224  Identities=12%  Similarity=-0.024  Sum_probs=195.1

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh----cCCHHHHHHHHHhCC-CCChhHHHHHH
Q 040365          141 RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK----CGNIRLARCIFDKMD-LHDIVSWTAVI  215 (514)
Q Consensus       141 ~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k----~g~~~~A~~~~~~m~-~~d~~~~~~li  215 (514)
                      +..++..+...+...+++++|.+.+....+.   .+...+..|...|..    .|++++|.+.|++.. ..+..++..+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg   81 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLG   81 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4566777788888999999999999999983   355678889999999    999999999999875 34778899999


Q ss_pred             HHHHh----CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc----cCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHH
Q 040365          216 MGNAL----HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSH----AGLIDKAWSYFNSMTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       216 ~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  287 (514)
                      ..|..    .+++++|+..|++..+.+   +...+..+...+..    .+++++|..+|+...+. +   +...+..+..
T Consensus        82 ~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg~  154 (273)
T 1ouv_A           82 NLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL-N---DGDGCTILGS  154 (273)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT-T---CHHHHHHHHH
T ss_pred             HHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhc-C---cHHHHHHHHH
Confidence            99999    999999999999999875   67788888888988    99999999999998653 3   5667788888


Q ss_pred             HHHh----cCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH--
Q 040365          288 LLGR----AGKLQEAYEFISNMHAGPTENVWLTLLSACRV----HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA--  357 (514)
Q Consensus       288 ~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~--  357 (514)
                      .|..    .+++++|.+.+++.....+...+..+...+..    .+++++|...++++.+.+|  +..+..|..+|..  
T Consensus       155 ~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~--~~a~~~l~~~~~~g~  232 (273)
T 1ouv_A          155 LYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN--GGGCFNLGAMQYNGE  232 (273)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHTTS
T ss_pred             HHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC--HHHHHHHHHHHHcCC
Confidence            8888    99999999999987545677888999999999    9999999999999999876  6788899999999  


Q ss_pred             --ccChhHHHHHHHHHHhCCC
Q 040365          358 --ARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       358 --~g~~~~a~~~~~~m~~~g~  376 (514)
                        .+++++|.+.+++..+.|.
T Consensus       233 ~~~~~~~~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          233 GVTRNEKQAIENFKKGCKLGA  253 (273)
T ss_dssp             SSSCCSTTHHHHHHHHHHHTC
T ss_pred             CcccCHHHHHHHHHHHHHcCC
Confidence              9999999999999987763

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.52  E-value=4.8e-13  Score=122.15  Aligned_cols=143  Identities=16%  Similarity=0.098  Sum_probs=80.5

Q ss_pred             hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHH
Q 040365          208 IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       208 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  287 (514)
                      ...|..+...|...|++++|++.|+++.+.. +.+...+..+...+...|++++|..+++.+.+..  +.+...+..+..
T Consensus        91 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~  167 (243)
T 2q7f_A           91 ATAYYGAGNVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN--ENDTEARFQFGM  167 (243)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC--CccHHHHHHHHH
Confidence            3444445555555555555555555555432 2234445555555556666666666666554321  123455555666


Q ss_pred             HHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHH
Q 040365          288 LLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSN  353 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~  353 (514)
                      .+.+.|++++|.+.++++.  .+.+..+|..+...+...|++++|...++++++.+|+++..+..+..
T Consensus       168 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~  235 (243)
T 2q7f_A          168 CLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKL  235 (243)
T ss_dssp             HHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTTCHHHHHHHTC
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCcchHHHHHHHHH
Confidence            6666666666666665542  12345566666667777777777777777777777766655554443

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.50  E-value=4.8e-12  Score=117.70  Aligned_cols=228  Identities=10%  Similarity=-0.062  Sum_probs=182.0

Q ss_pred             hhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCC--CC----hhHHHHHH
Q 040365           41 SFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPV--KD----AISWNSII  114 (514)
Q Consensus        41 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~--~d----~~~~~~li  114 (514)
                      ...+......+...|++++|...+..+++.. +.+..++..+...|.+.|++++|...|+...+  ++    ..+|..+.
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg   81 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYG   81 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHH
Confidence            3445566778889999999999999999875 55667889999999999999999999987653  22    23488999


Q ss_pred             HHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHH-HHHHhcCCH
Q 040365          115 AGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLL-DMYAKCGNI  193 (514)
Q Consensus       115 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li-~~y~k~g~~  193 (514)
                      ..|...|++++|+..|++..+.. +.+...+..+...+...|++++|...+...++.. +.+..++..+. ..|. .+++
T Consensus        82 ~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~-~~~~  158 (272)
T 3u4t_A           82 KILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPT-TTDPKVFYELGQAYYY-NKEY  158 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSS-CCCHHHHHHHHHHHHH-TTCH
T ss_pred             HHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHH-HHHH
Confidence            99999999999999999998853 4466788899999999999999999999998773 55677777787 5555 5699


Q ss_pred             HHHHHHHHhCC---CCChhHHHHHHHHHHhCCC---hHHHHHHHHHHHHcC-CCCCH------HHHHHHHHHHHccCCHH
Q 040365          194 RLARCIFDKMD---LHDIVSWTAVIMGNALHGN---AHDAISLFEQMEKDG-VKPNS------VAFVAVLTACSHAGLID  260 (514)
Q Consensus       194 ~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~---~~~A~~l~~~m~~~g-~~p~~------~t~~~ll~a~~~~g~~~  260 (514)
                      ++|.+.|++..   +.+...|..+...+...|+   +++|...|++..+.. -.|+.      ..|..+...+...|+++
T Consensus       159 ~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  238 (272)
T 3u4t_A          159 VKADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKV  238 (272)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHH
Confidence            99999999875   3456778888888888888   888999999887631 22331      45666777778888888


Q ss_pred             HHHHHHHHhHHh
Q 040365          261 KAWSYFNSMTKD  272 (514)
Q Consensus       261 ~a~~~~~~m~~~  272 (514)
                      +|..+|+...+.
T Consensus       239 ~A~~~~~~al~~  250 (272)
T 3u4t_A          239 KADAAWKNILAL  250 (272)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc
Confidence            888888877643

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.49  E-value=1e-12  Score=119.99  Aligned_cols=198  Identities=10%  Similarity=0.045  Sum_probs=155.1

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLT  251 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  251 (514)
                      .....+..+...|.+.|++++|...|+++.   ..+...|..+...|...|++++|+..|++..+.. +.+...+..+..
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~   99 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGN   99 (243)
T ss_dssp             ---------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHH
Confidence            345566777788888999999988888874   3467788889999999999999999999998863 335678888999


Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~  329 (514)
                      .+...|++++|..+++.+.+..  +.+...+..+...+.+.|++++|.+.++++.  .+.+...|..+...+...|++++
T Consensus       100 ~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  177 (243)
T 2q7f_A          100 VYVVKEMYKEAKDMFEKALRAG--MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDE  177 (243)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHT--CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHH
Confidence            9999999999999999987642  3367888899999999999999999998863  23568889999999999999999


Q ss_pred             HHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          330 AGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      |...++++.+..|+++.++..++.+|...|++++|.+.+++..+..
T Consensus       178 A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  223 (243)
T 2q7f_A          178 ALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQ  223 (243)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccC
Confidence            9999999999999999999999999999999999999999987643

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.49  E-value=1.6e-12  Score=130.68  Aligned_cols=343  Identities=10%  Similarity=-0.029  Sum_probs=207.0

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCCh---HHHHHHHHHHHHhCCCCchhHHHHHHHHHHH
Q 040365           12 VIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDV---IKGKEIHGYAIRHGLDANVCIGSSLINMYAK   88 (514)
Q Consensus        12 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~---~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~   88 (514)
                      +...+.+.|++++|+.+|++..+.|   +...+..+...+...|+.   ++|...+....+.    ++..+..|..++..
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~~   81 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLAA   81 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC--------------------------------CHHHHHHHHHT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHHh
Confidence            4566777888888888888887765   233334444455556666   7888888877754    44555666664555


Q ss_pred             CC-----CHHHHHHHHccCCCC-ChhHHHHHHHHHHHCCChh---HHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChH
Q 040365           89 CA-----RVEDSHRLFCLLPVK-DAISWNSIIAGCVQNGLFD---EGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLH  159 (514)
Q Consensus        89 ~g-----~~~~A~~~f~~~~~~-d~~~~~~li~~~~~~g~~~---~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~  159 (514)
                      .|     +.++|.+.|+...++ +..++..|...|...+..+   ++++.+.+....|.   ......+...+...+.++
T Consensus        82 ~~~~~~~~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~Lg~~y~~~~~~~  158 (452)
T 3e4b_A           82 KPGATEAEHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGY---PEAGLAQVLLYRTQGTYD  158 (452)
T ss_dssp             C--CCHHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTC---TTHHHHHHHHHHHHTCGG
T ss_pred             CCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHcCCCcc
Confidence            54     677888888775533 4557777777777766543   34445555444442   334445555666666444


Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC---CHHHHHHHHHhCC---CCChhHHHHHHHHHHhC----CChHHHHH
Q 040365          160 LGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG---NIRLARCIFDKMD---LHDIVSWTAVIMGNALH----GNAHDAIS  229 (514)
Q Consensus       160 ~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g---~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~----g~~~~A~~  229 (514)
                      .+......+.+.-...+...+..|..+|.+.|   +.++|.+.|++..   .++...+..+...|...    +++++|+.
T Consensus       159 ~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~  238 (452)
T 3e4b_A          159 QHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQA  238 (452)
T ss_dssp             GGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHH
Confidence            44433333322222233337777888888888   8888888887764   33444446666666544    67888888


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHH-H--HccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcC-----CHHHHHHH
Q 040365          230 LFEQMEKDGVKPNSVAFVAVLTA-C--SHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAG-----KLQEAYEF  301 (514)
Q Consensus       230 l~~~m~~~g~~p~~~t~~~ll~a-~--~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g-----~~~~A~~~  301 (514)
                      +|++.. .|   +...+..+... +  ...++.++|..+|+...+. |   +...+..|..+|. .|     ++++|.+.
T Consensus       239 ~~~~aa-~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~-g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~  309 (452)
T 3e4b_A          239 LLEKIA-PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAA-D---QPRAELLLGKLYY-EGKWVPADAKAAEAH  309 (452)
T ss_dssp             HHHHHG-GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHH-HCSSSCCCHHHHHHH
T ss_pred             HHHHHc-CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHH-cCCCCCCCHHHHHHH
Confidence            888876 33   33444445444 3  4578888888888887543 3   5666667777776 44     88888888


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH----ccChhHHHHHHHHHHh
Q 040365          302 ISNMHAGPTENVWLTLLSACRV----HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA----ARRWKDAASLRVFMRN  373 (514)
Q Consensus       302 ~~~m~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~  373 (514)
                      |++.. ..+...+..|...|..    ..+.++|...+++..+.+  ++.....|..+|..    ..+.++|...++...+
T Consensus       310 ~~~Aa-~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g--~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~  386 (452)
T 3e4b_A          310 FEKAV-GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNG--QNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKA  386 (452)
T ss_dssp             HHTTT-TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTT--CTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHT
T ss_pred             HHHHh-CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhC--hHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Confidence            88877 6677777777777765    348888888888877654  45677788888875    4578888888888877


Q ss_pred             CCC
Q 040365          374 KGM  376 (514)
Q Consensus       374 ~g~  376 (514)
                      .|.
T Consensus       387 ~g~  389 (452)
T 3e4b_A          387 QDT  389 (452)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            764

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.48  E-value=3.7e-12  Score=128.05  Aligned_cols=311  Identities=9%  Similarity=0.016  Sum_probs=209.4

Q ss_pred             HHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCH---HHHHHHHccCCCCChhHHHHHHHHHHHCC--
Q 040365           47 VLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARV---EDSHRLFCLLPVKDAISWNSIIAGCVQNG--  121 (514)
Q Consensus        47 ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~---~~A~~~f~~~~~~d~~~~~~li~~~~~~g--  121 (514)
                      +...+.+.|++++|.+++..+.+.|   +...+..|..+|...|+.   ++|...|+...+.++.++..|...+...+  
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~   85 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGA   85 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC----------------------------CHHHHHHHHHTC--C
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCC
Confidence            4455567789999999999998887   334445566777777887   89999998887667777777777566655  


Q ss_pred             ---ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh---HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC----
Q 040365          122 ---LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTL---HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG----  191 (514)
Q Consensus       122 ---~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g----  191 (514)
                         ++++|+..|++..+.|.. +  .+..+...|...+..   ..+.+.+....+.|.   ......|...|...+    
T Consensus        86 ~~~~~~~A~~~~~~Aa~~g~~-~--A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~Lg~~y~~~~~~~~  159 (452)
T 3e4b_A           86 TEAEHHEAESLLKKAFANGEG-N--TLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGY---PEAGLAQVLLYRTQGTYDQ  159 (452)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCS-S--CHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTC---TTHHHHHHHHHHHHTCGGG
T ss_pred             CCcCHHHHHHHHHHHHHCCCH-H--HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHcCCCccc
Confidence               678999999998887643 3  444455555544433   334555555555553   445666778888877    


Q ss_pred             CHHHHHHHHHhCCCCChhHHHHHHHHHHhCC---ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHcc----CCHHHHHH
Q 040365          192 NIRLARCIFDKMDLHDIVSWTAVIMGNALHG---NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHA----GLIDKAWS  264 (514)
Q Consensus       192 ~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g---~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~----g~~~~a~~  264 (514)
                      +.+.|..+++.....+..++..+...|...|   +.++|++.|++..+.| .++...+..+...|...    ++.++|..
T Consensus       160 ~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~  238 (452)
T 3e4b_A          160 HLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLGTPDEKTAQA  238 (452)
T ss_dssp             GHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGSSCCHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCCCCCHHHHHH
Confidence            4566667777777777778889999999999   8999999999998876 44555555666666655    78999999


Q ss_pred             HHHHhHHhcCCCCCHhHHHHHHHH-H--HhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-----CHHHHHHHHHH
Q 040365          265 YFNSMTKDYGIAPSFEHYAAVADL-L--GRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHK-----NVELAGKVAEK  336 (514)
Q Consensus       265 ~~~~m~~~~~~~p~~~~~~~li~~-~--~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~-----~~~~a~~~~~~  336 (514)
                      +|+...     .-++..+..|..+ |  ...|++++|.++|++.-...+...+..|...|. .|     ++++|...|++
T Consensus       239 ~~~~aa-----~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~  312 (452)
T 3e4b_A          239 LLEKIA-----PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY-EGKWVPADAKAAEAHFEK  312 (452)
T ss_dssp             HHHHHG-----GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHT
T ss_pred             HHHHHc-----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHH
Confidence            998774     2356666677776 4  568899999999988755567888888888777 55     99999999998


Q ss_pred             HHhcCCCCcchHHHHHHHHHH----ccChhHHHHHHHHHHhCCC
Q 040365          337 IFMIDPNNMGAYVILSNTYAA----ARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       337 ~~~~~p~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~g~  376 (514)
                      ..   |.++..+..|..+|..    ..++++|.+.+++..+.|.
T Consensus       313 Aa---~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  353 (452)
T 3e4b_A          313 AV---GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQ  353 (452)
T ss_dssp             TT---TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTC
T ss_pred             Hh---CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhCh
Confidence            87   7788889999988887    3489999999998877653

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.48  E-value=2.9e-12  Score=126.47  Aligned_cols=265  Identities=14%  Similarity=0.034  Sum_probs=159.4

Q ss_pred             hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC----HHHHHHHHHHHhccCChHHHHHHHHHHHHc----CCCC-cHH
Q 040365          108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR----HVSFSSIMPACAHLTTLHLGKQLHGCIIRN----GFDD-NMF  178 (514)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~  178 (514)
                      ..+......+...|++++|+..|++..+.+ +.+    ...+..+...+...|+++.|...+.++++.    +..| ...
T Consensus        10 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~   88 (406)
T 3sf4_A           10 LELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAK   88 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHHH
Confidence            334444555555555555555555555432 111    123444455555555555555555554332    1111 234


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCCC-----CC----hhHHHHHHHHHHhCCC--------------------hHHHHH
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMDL-----HD----IVSWTAVIMGNALHGN--------------------AHDAIS  229 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~~-----~d----~~~~~~li~~~~~~g~--------------------~~~A~~  229 (514)
                      ++..+...|...|++++|...|++...     ++    ..++..+...|...|+                    +++|+.
T Consensus        89 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~  168 (406)
T 3sf4_A           89 ASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVD  168 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHH
Confidence            455566666666666666666655431     11    2356666666666777                    777777


Q ss_pred             HHHHHHHc----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC----HhHHHHHHHHHHhcCCHHHHHH
Q 040365          230 LFEQMEKD----GVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS----FEHYAAVADLLGRAGKLQEAYE  300 (514)
Q Consensus       230 l~~~m~~~----g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~  300 (514)
                      .+++....    +..|. ..++..+...+...|++++|...++...+...-.++    ...+..+...|...|++++|.+
T Consensus       169 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  248 (406)
T 3sf4_A          169 FYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASE  248 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            77665431    11121 235666777777788888888877776543211122    2366777777888888888888


Q ss_pred             HHHhCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------cchHHHHHHHHHHccChhHHHH
Q 040365          301 FISNMH----AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN------MGAYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       301 ~~~~m~----~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~------~~~~~~l~~~~~~~g~~~~a~~  366 (514)
                      .+++..    ..++    ..++..+...+...|++++|...++++++..+..      ..++..++.+|...|++++|.+
T Consensus       249 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  328 (406)
T 3sf4_A          249 YYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMH  328 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            777642    1122    4567777888888888888888888887764322      4577788888888888888888


Q ss_pred             HHHHHHh
Q 040365          367 LRVFMRN  373 (514)
Q Consensus       367 ~~~~m~~  373 (514)
                      .+++..+
T Consensus       329 ~~~~al~  335 (406)
T 3sf4_A          329 FAEKHLE  335 (406)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8887654

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.48  E-value=7.9e-13  Score=131.10  Aligned_cols=260  Identities=12%  Similarity=-0.006  Sum_probs=153.4

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCCCC-H----HHHHHHHHHHhccCChHHHHHHHHHHHHc----C-CCCcHHHHHH
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIAKIKPR-H----VSFSSIMPACAHLTTLHLGKQLHGCIIRN----G-FDDNMFIASS  182 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~----~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~-~~~~~~~~~~  182 (514)
                      +...+...|++++|+..|++..+..  |+ .    ..+..+...+...|++++|...+.+.++.    + .+....++..
T Consensus        54 ~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  131 (411)
T 4a1s_A           54 EGERLCNAGDCRAGVAFFQAAIQAG--TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGN  131 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHhCcHHHHHHHHHHHHHhc--ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHH
Confidence            3444455555555555555554431  22 1    23444444455555555555555544332    1 1122344555


Q ss_pred             HHHHHHhcCCHHHHHHHHHhCCC---------CChhHHHHHHHHHHhCCC-----------------hHHHHHHHHHHHH
Q 040365          183 LLDMYAKCGNIRLARCIFDKMDL---------HDIVSWTAVIMGNALHGN-----------------AHDAISLFEQMEK  236 (514)
Q Consensus       183 li~~y~k~g~~~~A~~~~~~m~~---------~d~~~~~~li~~~~~~g~-----------------~~~A~~l~~~m~~  236 (514)
                      +...|...|++++|...|++...         ....+|..+...|...|+                 +++|++.+++..+
T Consensus       132 l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~  211 (411)
T 4a1s_A          132 LGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLK  211 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHH
Confidence            55566666666666665555431         122355566666666666                 6666666666543


Q ss_pred             c----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC----HhHHHHHHHHHHhcCCHHHHHHHHHhCC-
Q 040365          237 D----GVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS----FEHYAAVADLLGRAGKLQEAYEFISNMH-  306 (514)
Q Consensus       237 ~----g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~m~-  306 (514)
                      .    +-.|. ..++..+...+...|++++|..+++...+...-.++    ...+..+...|...|++++|.+.+++.. 
T Consensus       212 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  291 (411)
T 4a1s_A          212 LMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLA  291 (411)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            1    11111 235666667777777877777777766543111111    2366777777888888888888776642 


Q ss_pred             ---CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC------CcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          307 ---AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN------NMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       307 ---~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~------~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                         ...+    ..++..+...+...|++++|...++++++..+.      ...++..++.+|...|++++|.+.+++..+
T Consensus       292 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          292 LAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence               1111    456777888888888888888888888776422      234777888899999999999998887765


Q ss_pred             C
Q 040365          374 K  374 (514)
Q Consensus       374 ~  374 (514)
                      .
T Consensus       372 ~  372 (411)
T 4a1s_A          372 L  372 (411)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.47  E-value=3.2e-12  Score=122.28  Aligned_cols=263  Identities=15%  Similarity=0.052  Sum_probs=174.9

Q ss_pred             HHHHHHHHHHCCChhHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHhccCChHHHHHHHHHHHHc----CCC-CcHHH
Q 040365          110 WNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPR-----HVSFSSIMPACAHLTTLHLGKQLHGCIIRN----GFD-DNMFI  179 (514)
Q Consensus       110 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~----~~~-~~~~~  179 (514)
                      +......+...|++++|+..|++..+..  |+     ...+..+...+...|+++.|.+.+...++.    +.. ....+
T Consensus         8 l~~~g~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   85 (338)
T 3ro2_A            8 LALEGERLCKSGDCRAGVSFFEAAVQVG--TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKA   85 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhhC--cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHH
Confidence            3344455666666666666666665542  22     234555556666666666666666655432    111 12445


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhCC-----CCC----hhHHHHHHHHHHhCCC--------------------hHHHHHH
Q 040365          180 ASSLLDMYAKCGNIRLARCIFDKMD-----LHD----IVSWTAVIMGNALHGN--------------------AHDAISL  230 (514)
Q Consensus       180 ~~~li~~y~k~g~~~~A~~~~~~m~-----~~d----~~~~~~li~~~~~~g~--------------------~~~A~~l  230 (514)
                      +..+...|...|++++|...|++..     .++    ..++..+...|...|+                    +++|+..
T Consensus        86 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~  165 (338)
T 3ro2_A           86 SGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDL  165 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHH
Confidence            6666777777777777777776653     112    2366677777777777                    7777777


Q ss_pred             HHHHHHc----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC----HhHHHHHHHHHHhcCCHHHHHHH
Q 040365          231 FEQMEKD----GVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS----FEHYAAVADLLGRAGKLQEAYEF  301 (514)
Q Consensus       231 ~~~m~~~----g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~  301 (514)
                      +++....    +..|. ..++..+...+...|++++|...++...+...-.++    ...+..+...+...|++++|.+.
T Consensus       166 ~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  245 (338)
T 3ro2_A          166 YEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEY  245 (338)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            7765432    11121 245667777888888888888888877543211111    34677788888899999999888


Q ss_pred             HHhCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC------CcchHHHHHHHHHHccChhHHHHH
Q 040365          302 ISNMH----AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN------NMGAYVILSNTYAAARRWKDAASL  367 (514)
Q Consensus       302 ~~~m~----~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~------~~~~~~~l~~~~~~~g~~~~a~~~  367 (514)
                      +++..    ..++    ..++..+...+...|++++|...++++++..|.      ...++..++.+|...|++++|.+.
T Consensus       246 ~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~  325 (338)
T 3ro2_A          246 YKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHF  325 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHH
Confidence            87652    1122    456778888899999999999999998876432      144778899999999999999999


Q ss_pred             HHHHHhC
Q 040365          368 RVFMRNK  374 (514)
Q Consensus       368 ~~~m~~~  374 (514)
                      +++..+.
T Consensus       326 ~~~a~~~  332 (338)
T 3ro2_A          326 AEKHLEI  332 (338)
T ss_dssp             HHHHHHC
T ss_pred             HHHHHHH
Confidence            9988754

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.47  E-value=5.2e-12  Score=123.42  Aligned_cols=225  Identities=9%  Similarity=0.025  Sum_probs=192.3

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCC-HHHHHHHHHhCC---CCChhHHHHHHHHH
Q 040365          143 VSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGN-IRLARCIFDKMD---LHDIVSWTAVIMGN  218 (514)
Q Consensus       143 ~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~-~~~A~~~~~~m~---~~d~~~~~~li~~~  218 (514)
                      ..|..+..++...|++++|.+.++++++.. +.+..+|+.+...|.+.|+ +++|...|++..   ..+...|+.+...+
T Consensus        98 ~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P~~~~a~~~~g~~~  176 (382)
T 2h6f_A           98 DVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLV  176 (382)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            456667777888999999999999999986 6678899999999999997 999999999885   45778999999999


Q ss_pred             HhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHh-cCCH
Q 040365          219 ALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGR-AGKL  295 (514)
Q Consensus       219 ~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~-~g~~  295 (514)
                      ...|++++|+..|+++.+.  .| +...|..+..++...|++++|+..|+.+.+.   .| +...|+.+..+|.+ .|..
T Consensus       177 ~~~g~~~eAl~~~~kal~l--dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l---~P~~~~a~~~lg~~l~~l~~~~  251 (382)
T 2h6f_A          177 EWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE---DVRNNSVWNQRYFVISNTTGYN  251 (382)
T ss_dssp             HHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCSC
T ss_pred             HHccCHHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHhcCcc
Confidence            9999999999999999985  44 5678999999999999999999999999764   56 67889999999999 6665


Q ss_pred             HHH-----HHHHHhCC-CC-CCHHHHHHHHHHHHhcC--CHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHcc-------
Q 040365          296 QEA-----YEFISNMH-AG-PTENVWLTLLSACRVHK--NVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR-------  359 (514)
Q Consensus       296 ~~A-----~~~~~~m~-~~-p~~~~~~~ll~~~~~~~--~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g-------  359 (514)
                      ++|     ++.+++.. .. .+...|..+...+...|  ++++|...++++ +.+|+++..+..|+.+|.+.|       
T Consensus       252 ~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~p~~~~al~~La~~~~~~~~~~~~~~  330 (382)
T 2h6f_A          252 DRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPSHSSPYLIAFLVDIYEDMLENQCDNK  330 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTTCCCHHHHHHHHHHHHHHHHTTCSSH
T ss_pred             hHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccCCCCHHHHHHHHHHHHHHhcccccch
Confidence            777     46676652 23 46789999999999888  689999999998 888999999999999999875       


Q ss_pred             --ChhHHHHHHHHH-HhC
Q 040365          360 --RWKDAASLRVFM-RNK  374 (514)
Q Consensus       360 --~~~~a~~~~~~m-~~~  374 (514)
                        .+++|.++++++ .+.
T Consensus       331 ~~~~~~A~~~~~~l~~~~  348 (382)
T 2h6f_A          331 EDILNKALELCEILAKEK  348 (382)
T ss_dssp             HHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHh
Confidence              358999999988 443

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.45  E-value=2.5e-12  Score=126.92  Aligned_cols=295  Identities=14%  Similarity=0.019  Sum_probs=178.0

Q ss_pred             CChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCc----hhHHHHHHHHHHHCCCHHHHHHHHccCCC-----C----
Q 040365           39 PDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDAN----VCIGSSLINMYAKCARVEDSHRLFCLLPV-----K----  105 (514)
Q Consensus        39 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~----~~~~~~li~~~~~~g~~~~A~~~f~~~~~-----~----  105 (514)
                      +....+......+...|++++|...++.+++.+ +.+    ..++..+...|...|++++|...|++...     .    
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~   85 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLG   85 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHH
Confidence            344455566667777888888888888887774 223    24566677777777777777777665421     1    


Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCC-CCC----HHHHHHHHHHHhccCC--------------------hHH
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKI-KPR----HVSFSSIMPACAHLTT--------------------LHL  160 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~----~~t~~~ll~~~~~~~~--------------------~~~  160 (514)
                      ...+|..+...|...|++++|+..|.+..+... .++    ..++..+...+...|+                    +++
T Consensus        86 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~  165 (406)
T 3sf4_A           86 EAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQA  165 (406)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHH
Confidence            133566666667777777777777666544210 011    1233344444444444                    333


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC--ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH--DIVSWTAVIMGNALHGNAHDAISLFEQMEKDG  238 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~--d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  238 (514)
                      |...+...++.                            +.....+  ...+|..+...|...|++++|+..|++..+..
T Consensus       166 A~~~~~~al~~----------------------------~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~  217 (406)
T 3sf4_A          166 AVDFYEENLSL----------------------------VTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIA  217 (406)
T ss_dssp             HHHHHHHHHHH----------------------------HHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH----------------------------HHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHH
Confidence            33333332221                            1111101  12355666666666777777777776665421


Q ss_pred             -CCCC----HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC----HhHHHHHHHHHHhcCCHHHHHHHHHhCC---
Q 040365          239 -VKPN----SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS----FEHYAAVADLLGRAGKLQEAYEFISNMH---  306 (514)
Q Consensus       239 -~~p~----~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~m~---  306 (514)
                       -.++    ..++..+...+...|++++|..+++.......-.++    ...+..+...|...|++++|.+.+++..   
T Consensus       218 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  297 (406)
T 3sf4_A          218 KEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIA  297 (406)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHH
Confidence             0111    235666677777778888887777766432111111    4566777888888888888888877652   


Q ss_pred             -CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC------CCCcchHHHHHHHHHHccChh
Q 040365          307 -AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMID------PNNMGAYVILSNTYAAARRWK  362 (514)
Q Consensus       307 -~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~------p~~~~~~~~l~~~~~~~g~~~  362 (514)
                       ..++    ..++..+...+...|++++|...+++++++.      +....++..+..+|...|+..
T Consensus       298 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  364 (406)
T 3sf4_A          298 QELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLSY  364 (406)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHhH
Confidence             1122    4577888888999999999999999988763      223456777888888888764

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.43  E-value=2.2e-12  Score=130.49  Aligned_cols=192  Identities=8%  Similarity=-0.064  Sum_probs=154.4

Q ss_pred             CcHHHHHHHHHHHHhcCCH-HHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 040365          175 DNMFIASSLLDMYAKCGNI-RLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVL  250 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~-~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  250 (514)
                      .+...+..+...|...|++ ++|.+.|++..   ..+...|..+...|...|++++|+..|++..+.  .|+...+..+.
T Consensus       100 ~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~lg  177 (474)
T 4abn_A          100 VEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSGALTH--CKNKVSLQNLS  177 (474)
T ss_dssp             CCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--CCCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCHHHHHHHH
Confidence            4555666666666667777 77777666653   334667777888888888888888888888774  57777788888


Q ss_pred             HHHHcc---------CCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhc--------CCHHHHHHHHHhCC-CCC--
Q 040365          251 TACSHA---------GLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRA--------GKLQEAYEFISNMH-AGP--  309 (514)
Q Consensus       251 ~a~~~~---------g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~--------g~~~~A~~~~~~m~-~~p--  309 (514)
                      ..+...         |++++|...|+...+.   .| +...|..+..+|...        |++++|.+.|++.. ..|  
T Consensus       178 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~  254 (474)
T 4abn_A          178 MVLRQLQTDSGDEHSRHVMDSVRQAKLAVQM---DVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKVDRKA  254 (474)
T ss_dssp             HHHTTCCCSCHHHHHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGG
T ss_pred             HHHHHhccCChhhhhhhHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhCCCc
Confidence            888888         8899999999888654   45 577888888888888        88999999998763 234  


Q ss_pred             --CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          310 --TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       310 --~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                        +...|..+..++...|++++|...++++++++|+++.++..+..++...|++++|.+.+.++
T Consensus       255 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~~~~  318 (474)
T 4abn_A          255 SSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESKGKT  318 (474)
T ss_dssp             GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             ccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence              78899999999999999999999999999999999999999999999999999999765443

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.41  E-value=4.6e-11  Score=104.09  Aligned_cols=163  Identities=15%  Similarity=0.112  Sum_probs=118.9

Q ss_pred             ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHH
Q 040365          207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAA  284 (514)
Q Consensus       207 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~  284 (514)
                      +...|..+...|.+.|++++|++.|++..+.  .| +...+..+..++.+.|++++|...+......   .| +...+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~~~   78 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKA--DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVL---DTTSAEAYYI   78 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CchhHHHHHH
Confidence            3455666667777777777777777776664  33 3456666777777777777777777766543   33 4556666


Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChh
Q 040365          285 VADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWK  362 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  362 (514)
                      +...+...+++++|.+.+++..  .+.+...|..+...+...|++++|+..++++++.+|.++.+|..++.+|.+.|+++
T Consensus        79 ~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~  158 (184)
T 3vtx_A           79 LGSANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRD  158 (184)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHH
Confidence            6677777777777777776652  23456778888888888888888888888888888888888888888888888888


Q ss_pred             HHHHHHHHHHhC
Q 040365          363 DAASLRVFMRNK  374 (514)
Q Consensus       363 ~a~~~~~~m~~~  374 (514)
                      +|.+.+++..+.
T Consensus       159 ~A~~~~~~al~~  170 (184)
T 3vtx_A          159 EAVKYFKKALEK  170 (184)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhC
Confidence            888888877654

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.40  E-value=6.9e-12  Score=124.27  Aligned_cols=266  Identities=15%  Similarity=0.006  Sum_probs=154.8

Q ss_pred             HHHHHHHhCCCChHHHHHHHHHHHHhCCCCch----hHHHHHHHHHHHCCCHHHHHHHHccCCC---------CChhHHH
Q 040365           45 SSVLPIFADYVDVIKGKEIHGYAIRHGLDANV----CIGSSLINMYAKCARVEDSHRLFCLLPV---------KDAISWN  111 (514)
Q Consensus        45 ~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~----~~~~~li~~~~~~g~~~~A~~~f~~~~~---------~d~~~~~  111 (514)
                      ..+...+...|++++|...++.+++.+ +.+.    .++..+...|...|++++|...|++..+         ....+|.
T Consensus        52 ~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  130 (411)
T 4a1s_A           52 ALEGERLCNAGDCRAGVAFFQAAIQAG-TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSG  130 (411)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHhCcHHHHHHHHHHHHHhc-ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHH
Confidence            334445566667777777776666653 2222    3455566666666666666665554321         1223455


Q ss_pred             HHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcC-CCCcHHHHHHHHHHHHhc
Q 040365          112 SIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNG-FDDNMFIASSLLDMYAKC  190 (514)
Q Consensus       112 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~li~~y~k~  190 (514)
                      .+...|...|++++|+..|++......                               +.+ .+....++..+...|...
T Consensus       131 ~l~~~~~~~g~~~~A~~~~~~al~~~~-------------------------------~~~~~~~~~~~~~~l~~~~~~~  179 (411)
T 4a1s_A          131 NLGNTLKVMGRFDEAAICCERHLTLAR-------------------------------QLGDRLSEGRALYNLGNVYHAK  179 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHH-------------------------------HHTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHH-------------------------------HhhchHHHHHHHHHHHHHHHHc
Confidence            555555556666666555555433100                               000 011223444445555555


Q ss_pred             CC-----------------HHHHHHHHHhCC-------CC--ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCC-CCC-
Q 040365          191 GN-----------------IRLARCIFDKMD-------LH--DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV-KPN-  242 (514)
Q Consensus       191 g~-----------------~~~A~~~~~~m~-------~~--d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~-  242 (514)
                      |+                 +++|.+.|++..       .+  ...+|..+...|...|++++|+..|++..+... .++ 
T Consensus       180 g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  259 (411)
T 4a1s_A          180 GKHLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDR  259 (411)
T ss_dssp             HHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCH
T ss_pred             CcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCc
Confidence            55                 555555544432       11  123566666677777777777777776654210 011 


Q ss_pred             ---HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCCC----CCC-
Q 040365          243 ---SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP----SFEHYAAVADLLGRAGKLQEAYEFISNMHA----GPT-  310 (514)
Q Consensus       243 ---~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~p~-  310 (514)
                         ..++..+...+...|++++|...++.......-..    ....+..+...|...|++++|.+.+++...    .++ 
T Consensus       260 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  339 (411)
T 4a1s_A          260 AAERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDR  339 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCh
Confidence               13566777777788888888887776654321111    246677788888888888888888876521    122 


Q ss_pred             ---HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          311 ---ENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       311 ---~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                         ..++..+...+...|++++|...+++++++.+
T Consensus       340 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~  374 (411)
T 4a1s_A          340 IGEARACWSLGNAHSAIGGHERALKYAEQHLQLAX  374 (411)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHh
Confidence               34677888889999999999999999988764

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.39  E-value=1.5e-10  Score=110.00  Aligned_cols=218  Identities=11%  Similarity=0.091  Sum_probs=141.4

Q ss_pred             hHHHHHHHHHHHCCCCCCHHHHHHHHHHHh-------ccCCh-------HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh
Q 040365          124 DEGLKFFRQMLIAKIKPRHVSFSSIMPACA-------HLTTL-------HLGKQLHGCIIRNGFDDNMFIASSLLDMYAK  189 (514)
Q Consensus       124 ~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~-------~~~~~-------~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k  189 (514)
                      ++|+.+|++..... +-+...|......+.       +.|++       ++|..++++.++.-.+.+...|..++..+.+
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~  111 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHh
Confidence            56667777766642 334445555554443       24664       6777777777763124455677777777777


Q ss_pred             cCCHHHHHHHHHhCC--CC-Chh-HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-ccCCHHHHHH
Q 040365          190 CGNIRLARCIFDKMD--LH-DIV-SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACS-HAGLIDKAWS  264 (514)
Q Consensus       190 ~g~~~~A~~~~~~m~--~~-d~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~-~~g~~~~a~~  264 (514)
                      .|++++|.++|++..  .| +.. .|..+...+.+.|++++|..+|++..+.. +++...|........ ..|+.++|..
T Consensus       112 ~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~  190 (308)
T 2ond_A          112 RMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFK  190 (308)
T ss_dssp             TTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHHHH
Confidence            777777777777764  22 333 67777777777788888888888777643 223334433332222 3578888888


Q ss_pred             HHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCC----CC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040365          265 YFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHA----GP--TENVWLTLLSACRVHKNVELAGKVAEKIF  338 (514)
Q Consensus       265 ~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  338 (514)
                      +|+...+..  +-+...|..++..+.+.|++++|..+|++...    .|  ....|..++......|+.+.|..+++++.
T Consensus       191 ~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~  268 (308)
T 2ond_A          191 IFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRF  268 (308)
T ss_dssp             HHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHhC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            887776542  12566777777777777888888887776532    33  35677777777777888888888888887


Q ss_pred             hcCCCCc
Q 040365          339 MIDPNNM  345 (514)
Q Consensus       339 ~~~p~~~  345 (514)
                      +..|++.
T Consensus       269 ~~~p~~~  275 (308)
T 2ond_A          269 TAFREEY  275 (308)
T ss_dssp             HHTTTTT
T ss_pred             HHccccc
Confidence            7777654

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.39  E-value=9.5e-12  Score=118.92  Aligned_cols=98  Identities=14%  Similarity=0.061  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC----CCCC----HH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP----SFEHYAAVADLLGRAGKLQEAYEFISNMH----AGPT----EN  312 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~~p~----~~  312 (514)
                      ++..+...+...|++++|..+++...+...-.+    ....+..+...|...|++++|.+.+++..    ..++    ..
T Consensus       225 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  304 (338)
T 3ro2_A          225 AYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGR  304 (338)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHH
Confidence            444445555555555555555554432211011    13455556666666666666666665542    0111    34


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      ++..+...+...|++++|...+++++++.+
T Consensus       305 ~~~~la~~~~~~g~~~~A~~~~~~a~~~~~  334 (338)
T 3ro2_A          305 ACWSLGNAYTALGNHDQAMHFAEKHLEISR  334 (338)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHHHH
Confidence            566777777788888888888888777654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.37  E-value=2.6e-12  Score=121.82  Aligned_cols=243  Identities=8%  Similarity=0.020  Sum_probs=127.0

Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHC-------CCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHc------C
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIA-------KIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN------G  172 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-------g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~------~  172 (514)
                      +..+|..+...+...|++++|+.+|+++.+.       ..+.....+..+...+...|++++|...+..+++.      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            3456888888888999999999999888762       22333455666777777778888888777777654      2


Q ss_pred             C-CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC----------C-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHc---
Q 040365          173 F-DDNMFIASSLLDMYAKCGNIRLARCIFDKMDL----------H-DIVSWTAVIMGNALHGNAHDAISLFEQMEKD---  237 (514)
Q Consensus       173 ~-~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~----------~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~---  237 (514)
                      . +....++..+...|...|++++|.+.|++...          + ...+|..+...|...|++++|+++|+++...   
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~  185 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQT  185 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            1 22345556666666666666666666655431          1 1234555555555555555555555555442   


Q ss_pred             ---CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhc------CCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCC
Q 040365          238 ---GVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDY------GIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHA  307 (514)
Q Consensus       238 ---g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~------~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  307 (514)
                         +..|+ ..++..+...+...|++++|..+++.+.+..      ...+.......                       
T Consensus       186 ~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~-----------------------  242 (311)
T 3nf1_A          186 KLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWM-----------------------  242 (311)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHH-----------------------
T ss_pred             HhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHH-----------------------
Confidence               11222 1234444555555555555555555543210      00000000000                       


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          308 GPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       308 ~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                        ....+..+...+...+.+.++...++......|.++.++..++.+|.+.|++++|.+.+++..+
T Consensus       243 --~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          243 --HAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             --HHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             --HHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence              0111222223334444555555566666655666666777777777777777777777776543

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.36  E-value=5e-11  Score=103.84  Aligned_cols=167  Identities=12%  Similarity=-0.000  Sum_probs=137.9

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLT  251 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  251 (514)
                      .+..+|..|...|.+.|++++|.+.|++..   +.+..+|..+...|.+.|++++|+..+.+..... +-+...+..+..
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~   81 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGS   81 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHH
Confidence            356778888888999999999999988864   4467788889999999999999999999888753 224566777777


Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVE  328 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~  328 (514)
                      .+...++++.+...+....+.   .| +...+..+...|.+.|++++|.+.|++..  .+.+..+|..+..++...|+++
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~~---~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~  158 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIAL---NTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRD  158 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh---CccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHH
Confidence            888899999999999988653   44 57788889999999999999999998763  2346788999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCc
Q 040365          329 LAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       329 ~a~~~~~~~~~~~p~~~  345 (514)
                      +|+..++++++++|+++
T Consensus       159 ~A~~~~~~al~~~p~~a  175 (184)
T 3vtx_A          159 EAVKYFKKALEKEEKKA  175 (184)
T ss_dssp             HHHHHHHHHHHTTHHHH
T ss_pred             HHHHHHHHHHhCCccCH
Confidence            99999999999998753

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.34  E-value=6e-12  Score=119.26  Aligned_cols=242  Identities=11%  Similarity=0.022  Sum_probs=168.4

Q ss_pred             CCchhHHHHHHHHHHHCCCHHHHHHHHccCCC--------C---ChhHHHHHHHHHHHCCChhHHHHHHHHHHHC-----
Q 040365           73 DANVCIGSSLINMYAKCARVEDSHRLFCLLPV--------K---DAISWNSIIAGCVQNGLFDEGLKFFRQMLIA-----  136 (514)
Q Consensus        73 ~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~--------~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----  136 (514)
                      +.+..++..+...|...|++++|..+|++..+        .   ...++..+...|...|++++|+..|++....     
T Consensus        24 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  103 (311)
T 3nf1_A           24 PARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTL  103 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            33456788899999999999999999988653        1   3456888999999999999999999998764     


Q ss_pred             -CC-CCCHHHHHHHHHHHhccCChHHHHHHHHHHHHc------CC-CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--
Q 040365          137 -KI-KPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRN------GF-DDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--  205 (514)
Q Consensus       137 -g~-~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--  205 (514)
                       +- +....++..+...+...|++++|...+..+++.      +. +....++..+...|.+.|++++|.+.|++...  
T Consensus       104 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~  183 (311)
T 3nf1_A          104 GKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIY  183 (311)
T ss_dssp             CTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence             22 234567788888999999999999999998875      22 23456788899999999999999999988742  


Q ss_pred             -----C----ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC-------CCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          206 -----H----DIVSWTAVIMGNALHGNAHDAISLFEQMEKDG-------VKPNSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       206 -----~----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-------~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                           +    ...++..+...|...|++++|+..|+++.+..       ..|.......                     
T Consensus       184 ~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~---------------------  242 (311)
T 3nf1_A          184 QTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWM---------------------  242 (311)
T ss_dssp             HHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHH---------------------
T ss_pred             HHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHH---------------------
Confidence                 1    23578889999999999999999999988641       1111100000                     


Q ss_pred             HHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCC-C-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          270 TKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHA-G-PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       270 ~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                              ....+..+...+...+.+.+|...++.... . .+..+|..+..++...|++++|...+++++++.|.
T Consensus       243 --------~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~~~  310 (311)
T 3nf1_A          243 --------HAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRSRKQ  310 (311)
T ss_dssp             --------HHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-
T ss_pred             --------HHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhc
Confidence                    111222233334445555566666655532 2 23466788888888888888888888888877653

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.33  E-value=4.1e-11  Score=117.74  Aligned_cols=195  Identities=12%  Similarity=0.060  Sum_probs=100.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhCC-----CC-----ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCC-CCC----
Q 040365          178 FIASSLLDMYAKCGNIRLARCIFDKMD-----LH-----DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV-KPN----  242 (514)
Q Consensus       178 ~~~~~li~~y~k~g~~~~A~~~~~~m~-----~~-----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~----  242 (514)
                      .++..+...|...|++++|...+++..     .+     ...+++.+...|...|++++|++.|++..+... .++    
T Consensus       144 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  223 (383)
T 3ulq_A          144 EFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLM  223 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHH
Confidence            344444555555555555544444432     01     123455555556666666666666655543200 011    


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHhHHhc---CCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC----CCCCH---
Q 040365          243 SVAFVAVLTACSHAGLIDKAWSYFNSMTKDY---GIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH----AGPTE---  311 (514)
Q Consensus       243 ~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~---~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~~p~~---  311 (514)
                      ..++..+...+...|++++|...|+...+-.   +..| ....+..+...|.+.|++++|.+.+++..    ..++.   
T Consensus       224 ~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  303 (383)
T 3ulq_A          224 GRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYL  303 (383)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHH
Confidence            1345555666666666666666666554310   1112 24455566666666666666666665532    00111   


Q ss_pred             HHHHHHHHHHHhcCC---HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          312 NVWLTLLSACRVHKN---VELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..+..+...+...|+   .+.|...+++. ...|.....+..++..|...|++++|...+++..+
T Consensus       304 ~~~~~l~~~~~~~~~~~~~~~al~~~~~~-~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          304 SEFEFLKSLYLSGPDEEAIQGFFDFLESK-MLYADLEDFAIDVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHHHHTSSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHC-cCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            223445555666666   55555555544 11233344666777777777777777777776643

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.33  E-value=3e-10  Score=107.95  Aligned_cols=162  Identities=10%  Similarity=0.018  Sum_probs=88.9

Q ss_pred             hHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHH--HHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHH
Q 040365          108 ISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHV--SFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLD  185 (514)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~--t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  185 (514)
                      ..|..++..+.+.|++++|..+|++..+.  .|+..  .|..+...+.+.|++++|..+++..++.. +.+..+|.....
T Consensus       100 ~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~  176 (308)
T 2ond_A          100 LLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAAL  176 (308)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            34555555555555555555555555442  33221  44555555555555555555555555443 222333333322


Q ss_pred             HHH-hcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC-CCCC--HHHHHHHHHHHHccCC
Q 040365          186 MYA-KCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG-VKPN--SVAFVAVLTACSHAGL  258 (514)
Q Consensus       186 ~y~-k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~--~~t~~~ll~a~~~~g~  258 (514)
                      ... ..|+.++|.++|++..   ..+...|..++..+.+.|+.++|..+|++..... +.|+  ...|..++......|+
T Consensus       177 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~  256 (308)
T 2ond_A          177 MEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGD  256 (308)
T ss_dssp             HHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCC
Confidence            221 2466666666666553   2355666666666667777777777777776642 3443  3456666666666777


Q ss_pred             HHHHHHHHHHhHHh
Q 040365          259 IDKAWSYFNSMTKD  272 (514)
Q Consensus       259 ~~~a~~~~~~m~~~  272 (514)
                      .++|..+++++.+.
T Consensus       257 ~~~a~~~~~~a~~~  270 (308)
T 2ond_A          257 LASILKVEKRRFTA  270 (308)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            77777777776544

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.32  E-value=1.3e-10  Score=114.13  Aligned_cols=229  Identities=13%  Similarity=0.063  Sum_probs=168.3

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHhccCChHHHHHHHHHHHHcC--C----CCcHHHHH
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIA----KIKP-RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNG--F----DDNMFIAS  181 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~----~~~~~~~~  181 (514)
                      ....+...|++++|+..|++..+.    +-.+ ...++..+...+...|+++.|...+.+.++.-  .    +....+++
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            445667778888888888887653    1111 23456677777788888888888887776531  1    11245677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC-----CCC----hhHHHHHHHHHHhCCChHHHHHHHHHHHHc----CCCCC-HHHHH
Q 040365          182 SLLDMYAKCGNIRLARCIFDKMD-----LHD----IVSWTAVIMGNALHGNAHDAISLFEQMEKD----GVKPN-SVAFV  247 (514)
Q Consensus       182 ~li~~y~k~g~~~~A~~~~~~m~-----~~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~-~~t~~  247 (514)
                      .+...|...|++++|.+.|++..     .++    ..+++.+...|...|++++|+..|++..+.    +..|+ ..++.
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  268 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYF  268 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHH
Confidence            78888999999999988887764     112    247888889999999999999999988762    33243 46788


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhHHhcCC--CC-CHhHHHHHHHHHHhcCC---HHHHHHHHHhCCCCCC-HHHHHHHHHH
Q 040365          248 AVLTACSHAGLIDKAWSYFNSMTKDYGI--AP-SFEHYAAVADLLGRAGK---LQEAYEFISNMHAGPT-ENVWLTLLSA  320 (514)
Q Consensus       248 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~--~p-~~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~p~-~~~~~~ll~~  320 (514)
                      .+...+...|++++|..+++...+...-  .| ....+..+...|...|+   +++|..++++....|+ ..++..|...
T Consensus       269 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~  348 (383)
T 3ulq_A          269 LITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKY  348 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            8889999999999999999887543211  12 23345678888889999   9999999999864443 3467788899


Q ss_pred             HHhcCCHHHHHHHHHHHHhcC
Q 040365          321 CRVHKNVELAGKVAEKIFMID  341 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~  341 (514)
                      +...|++++|...+++++++.
T Consensus       349 y~~~g~~~~A~~~~~~al~~~  369 (383)
T 3ulq_A          349 YHERKNFQKASAYFLKVEQVR  369 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHH
Confidence            999999999999999988754

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.29  E-value=1.5e-10  Score=122.14  Aligned_cols=162  Identities=15%  Similarity=0.175  Sum_probs=130.8

Q ss_pred             ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHH
Q 040365          207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAA  284 (514)
Q Consensus       207 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~  284 (514)
                      +..+|+.+...|.+.|++++|++.|++..+.  .|+ ...+..+..++.+.|++++|+..|++..+.   .| +...|..
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l---~P~~~~a~~n   82 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI---SPTFADAYSN   82 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHH
Confidence            3456777777778888888888888887774  454 567777888888888888888888877643   55 4677888


Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChh
Q 040365          285 VADLLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWK  362 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  362 (514)
                      +..+|.+.|++++|.+.|++.. .. .+...|..|..++...|++++|+..++++++++|+++..|..|+.+|...|+|+
T Consensus        83 Lg~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~  162 (723)
T 4gyw_A           83 MGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWT  162 (723)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHH
Confidence            8888888888888888887753 23 357889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHh
Q 040365          363 DAASLRVFMRN  373 (514)
Q Consensus       363 ~a~~~~~~m~~  373 (514)
                      +|.+.+++..+
T Consensus       163 ~A~~~~~kal~  173 (723)
T 4gyw_A          163 DYDERMKKLVS  173 (723)
T ss_dssp             THHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99988887653

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.29  E-value=6.4e-09  Score=108.47  Aligned_cols=369  Identities=6%  Similarity=-0.060  Sum_probs=226.5

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCC---hHHHHHHHHHHHHhC-CCCchhHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVD---VIKGKEIHGYAIRHG-LDANVCIG   79 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~---~~~a~~~~~~~~~~g-~~~~~~~~   79 (514)
                      .|..+|..+|..+.+.+.++.+..+|+.+... .+.....|..-+..-.+.++   ++.+.++|+..+... .+|++..|
T Consensus        64 ~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW  142 (679)
T 4e6h_A           64 TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLW  142 (679)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHH
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            47889999999999999999999999999875 34555667777777777788   899999999888764 13777788


Q ss_pred             HHHHHHHHHCCCH--------HHHHHHHccCC------CC-ChhHHHHHHHHHH---------HCCChhHHHHHHHHHHH
Q 040365           80 SSLINMYAKCARV--------EDSHRLFCLLP------VK-DAISWNSIIAGCV---------QNGLFDEGLKFFRQMLI  135 (514)
Q Consensus        80 ~~li~~~~~~g~~--------~~A~~~f~~~~------~~-d~~~~~~li~~~~---------~~g~~~~A~~l~~~m~~  135 (514)
                      ...+....+.+++        +...++|+...      .+ +...|...+.-..         .+++.+.+..+|.+...
T Consensus       143 ~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~  222 (679)
T 4e6h_A          143 LSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLC  222 (679)
T ss_dssp             HHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHHHh
Confidence            8777766555543        23446676521      22 3456777765433         23345667777777764


Q ss_pred             CCCCCCHHHHH---HHHHHHhc----------cCChH-------------------------------------------
Q 040365          136 AKIKPRHVSFS---SIMPACAH----------LTTLH-------------------------------------------  159 (514)
Q Consensus       136 ~g~~p~~~t~~---~ll~~~~~----------~~~~~-------------------------------------------  159 (514)
                      .....-..+|.   ........          ...++                                           
T Consensus       223 iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~ql  302 (679)
T 4e6h_A          223 QPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYDVQQL  302 (679)
T ss_dssp             SCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCCHHHH
T ss_pred             CccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhHHHHH
Confidence            21111111211   11100000          00011                                           


Q ss_pred             ------------------------HHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHH-HHHHhCC---CCChhHH
Q 040365          160 ------------------------LGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLAR-CIFDKMD---LHDIVSW  211 (514)
Q Consensus       160 ------------------------~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~-~~~~~m~---~~d~~~~  211 (514)
                                              .+..++++.+.. ++.+..+|-..+..+...|+.++|. ++|++..   ..+...|
T Consensus       303 ~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~~P~s~~Lw  381 (679)
T 4e6h_A          303 LIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQCIPNSAVLA  381 (679)
T ss_dssp             HHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhCCCCHHHH
Confidence                                    122233333332 1333444444555556667777775 7777654   3355567


Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHcC---------CCCC------------HHHHHHHHHHHHccCCHHHHHHHHHHhH
Q 040365          212 TAVIMGNALHGNAHDAISLFEQMEKDG---------VKPN------------SVAFVAVLTACSHAGLIDKAWSYFNSMT  270 (514)
Q Consensus       212 ~~li~~~~~~g~~~~A~~l~~~m~~~g---------~~p~------------~~t~~~ll~a~~~~g~~~~a~~~~~~m~  270 (514)
                      -..+...-+.|++++|.++|+++....         -.|+            ...|...+....+.|..+.|..+|....
T Consensus       382 l~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~  461 (679)
T 4e6h_A          382 FSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCR  461 (679)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            777777777888888888888876531         0132            2346666666667778888888888776


Q ss_pred             HhcCCCCCHhHHHHHHHHHHhcC-CHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC---C
Q 040365          271 KDYGIAPSFEHYAAVADLLGRAG-KLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN---N  344 (514)
Q Consensus       271 ~~~~~~p~~~~~~~li~~~~~~g-~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~---~  344 (514)
                      +.. -.+....|...+.+-.+.| +.+.|.++|+...  .+.+...|...+......|+.+.|..+|++++...|+   .
T Consensus       462 ~~~-~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~  540 (679)
T 4e6h_A          462 RLK-KLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLL  540 (679)
T ss_dssp             HTG-GGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHH
T ss_pred             Hhc-CCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHH
Confidence            531 1112334444444444444 4788888877653  2235666777777777778888888888888877663   3


Q ss_pred             cchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          345 MGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       345 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ...|...+..-.+.|+.+.+.++.+++.+.-
T Consensus       541 ~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~  571 (679)
T 4e6h_A          541 KMIFQKVIFFESKVGSLNSVRTLEKRFFEKF  571 (679)
T ss_dssp             HHHHHHHHHHHHHTCCSHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            4566677777777888888888888887654

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.27  E-value=4.6e-09  Score=102.50  Aligned_cols=260  Identities=13%  Similarity=0.010  Sum_probs=163.5

Q ss_pred             HHHHHHCCChhHHHHHHHHHHHCCCCCCHH----HHHHHHHHHhccCChHHHHHHHHHHHHcC--C-CC--cHHHHHHHH
Q 040365          114 IAGCVQNGLFDEGLKFFRQMLIAKIKPRHV----SFSSIMPACAHLTTLHLGKQLHGCIIRNG--F-DD--NMFIASSLL  184 (514)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~-~~--~~~~~~~li  184 (514)
                      ...+...|++++|...+++........+..    .+..+...+...|+++.|.+.+.+..+..  . .+  .......+.
T Consensus        21 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la  100 (373)
T 1hz4_A           21 AQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQS  100 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            344556667777777766665543111211    33344455566677777777666655421  0 11  122345566


Q ss_pred             HHHHhcCCHHHHHHHHHhCC-------C---C-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCC--C--CHHHHHHH
Q 040365          185 DMYAKCGNIRLARCIFDKMD-------L---H-DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVK--P--NSVAFVAV  249 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~-------~---~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~--p--~~~t~~~l  249 (514)
                      ..|...|++++|...+++..       .   + ....+..+...+...|++++|...+++.......  |  ...++..+
T Consensus       101 ~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  180 (373)
T 1hz4_A          101 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAML  180 (373)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHHH
Confidence            67777788877777776653       1   1 1234556667778888888888888887653221  1  13456677


Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHH-----HHHHHHHhcCCHHHHHHHHHhCCCC-CC-----HHHHHHHH
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYA-----AVADLLGRAGKLQEAYEFISNMHAG-PT-----ENVWLTLL  318 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~-----~li~~~~~~g~~~~A~~~~~~m~~~-p~-----~~~~~~ll  318 (514)
                      ...+...|++++|...++.......-......+.     ..+..+...|++++|...+++.... |.     ...+..+.
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            7778888888888888887754321111111111     2334477889999999988876421 21     23566777


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCC-----C-cchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          319 SACRVHKNVELAGKVAEKIFMIDPN-----N-MGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~p~-----~-~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..+...|++++|...++++....+.     + ...+..+..+|...|++++|...+++...
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            8888899999999999888765321     1 23667788889999999999999887764

>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=99.27  E-value=2.6e-10  Score=98.74  Aligned_cols=161  Identities=14%  Similarity=0.013  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhCCC---CChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040365          178 FIASSLLDMYAKCGNIRLARCIFDKMDL---HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACS  254 (514)
Q Consensus       178 ~~~~~li~~y~k~g~~~~A~~~~~~m~~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~  254 (514)
                      ..+..+...|...|++++|.+.|+++..   .+...|..+...+...|++++|...++++.+.. +.+...+..+...+.
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~   87 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTYV   87 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHH
Confidence            3445556666666666666666666542   234455555555555566666655555555431 122334444444444


Q ss_pred             ccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHH
Q 040365          255 HAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVA  334 (514)
Q Consensus       255 ~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~  334 (514)
                      ..|++++|..+++.+.+.                                  .+.+...|..+...+...|++++|...+
T Consensus        88 ~~~~~~~A~~~~~~~~~~----------------------------------~~~~~~~~~~~a~~~~~~~~~~~A~~~~  133 (186)
T 3as5_A           88 QVQKYDLAVPLLIKVAEA----------------------------------NPINFNVRFRLGVALDNLGRFDEAIDSF  133 (186)
T ss_dssp             HHTCHHHHHHHHHHHHHH----------------------------------CTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhc----------------------------------CcHhHHHHHHHHHHHHHcCcHHHHHHHH
Confidence            444444444444444321                                  1234556666666666777777777777


Q ss_pred             HHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          335 EKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       335 ~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      +++.+..|.++..+..++.+|...|++++|.+.++...+
T Consensus       134 ~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  172 (186)
T 3as5_A          134 KIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHFKKANE  172 (186)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            777777777777777777777777777777777776654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.25  E-value=4e-10  Score=110.46  Aligned_cols=220  Identities=10%  Similarity=0.014  Sum_probs=122.0

Q ss_pred             HhccCChHHHHHHHHHHHHcC--CC---CcHHHHHHHHHHHHhcCCHHHHHHHHHhCC-----CC-----ChhHHHHHHH
Q 040365          152 CAHLTTLHLGKQLHGCIIRNG--FD---DNMFIASSLLDMYAKCGNIRLARCIFDKMD-----LH-----DIVSWTAVIM  216 (514)
Q Consensus       152 ~~~~~~~~~a~~~~~~~~~~~--~~---~~~~~~~~li~~y~k~g~~~~A~~~~~~m~-----~~-----d~~~~~~li~  216 (514)
                      +...|++++|...+.+..+..  ..   ....++..+...|...|+++.|...+++..     .+     ...+++.+..
T Consensus       111 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~  190 (378)
T 3q15_A          111 EFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAG  190 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHH
T ss_pred             HHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHH
Confidence            345566666666665555431  01   123345556666666666666655555432     11     1235566666


Q ss_pred             HHHhCCChHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC--CCC-CHhHHHHHHHH
Q 040365          217 GNALHGNAHDAISLFEQMEKD----GVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG--IAP-SFEHYAAVADL  288 (514)
Q Consensus       217 ~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~--~~p-~~~~~~~li~~  288 (514)
                      .|...|++++|++.|++..+.    +-.+ ...++..+...+...|++++|...|+....-..  ..| ....+..+...
T Consensus       191 ~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~  270 (378)
T 3q15_A          191 NYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLSWT  270 (378)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHHHH
Confidence            666777777777766665542    1111 123455666667777777777777766654110  122 24556666677


Q ss_pred             HHhcCCHHHHHHHHHhCC----C--CCC-HHHHHHHHHHHHhcCC---HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 040365          289 LGRAGKLQEAYEFISNMH----A--GPT-ENVWLTLLSACRVHKN---VELAGKVAEKIFMIDPNNMGAYVILSNTYAAA  358 (514)
Q Consensus       289 ~~~~g~~~~A~~~~~~m~----~--~p~-~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  358 (514)
                      |.+.|++++|.+.+++..    .  .|. ...+..+...+...++   +++|...+++. ...|.....+..++..|...
T Consensus       271 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~-~~~~~~~~~~~~la~~y~~~  349 (378)
T 3q15_A          271 LCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK-NLHAYIEACARSAAAVFESS  349 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC-CChhHHHHHHHHHHHHHHHC
Confidence            777777777777776541    1  122 2334444455555666   55555555541 11133344566777778888


Q ss_pred             cChhHHHHHHHHHH
Q 040365          359 RRWKDAASLRVFMR  372 (514)
Q Consensus       359 g~~~~a~~~~~~m~  372 (514)
                      |++++|.+.+++..
T Consensus       350 g~~~~A~~~~~~al  363 (378)
T 3q15_A          350 CHFEQAAAFYRKVL  363 (378)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            88888877777664

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.24  E-value=6.2e-10  Score=96.31  Aligned_cols=157  Identities=14%  Similarity=0.038  Sum_probs=117.6

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHH
Q 040365          142 HVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGN  218 (514)
Q Consensus       142 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~  218 (514)
                      ...+..+...+...|++++|...+..+.+.. +.+..++..+...|...|++++|...|+++.   ..+...|..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~   86 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            3456677788899999999999999887654 5578888999999999999999999999875   44678899999999


Q ss_pred             HhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040365          219 ALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       219 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  298 (514)
                      ...|++++|.+.|+++.... +.+...+..+...+...|++++|..+++.+.+..  +.+...+..+...+...|++++|
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR--PNEGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC--ccchHHHHHHHHHHHHcCCHHHH
Confidence            99999999999999998863 3456677777778888888888888888775431  11233344444444444444444


Q ss_pred             HHHH
Q 040365          299 YEFI  302 (514)
Q Consensus       299 ~~~~  302 (514)
                      .+.+
T Consensus       164 ~~~~  167 (186)
T 3as5_A          164 LPHF  167 (186)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4433

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.24  E-value=1.7e-10  Score=116.60  Aligned_cols=209  Identities=8%  Similarity=-0.066  Sum_probs=176.0

Q ss_pred             hHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCH-HHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHH
Q 040365           57 VIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARV-EDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQ  132 (514)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~-~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~  132 (514)
                      ++++.+.+....+.. +.+...+..+...|...|++ ++|.+.|++..   ..+..+|..+...|.+.|++++|++.|++
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~  162 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSG  162 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            566777777655443 45777888888899999999 99999988764   34577899999999999999999999999


Q ss_pred             HHHCCCCCCHHHHHHHHHHHhcc---------CChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc--------CCHHH
Q 040365          133 MLIAKIKPRHVSFSSIMPACAHL---------TTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKC--------GNIRL  195 (514)
Q Consensus       133 m~~~g~~p~~~t~~~ll~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~--------g~~~~  195 (514)
                      ..+.  .|+...+..+..++...         |++++|.+.+.++++.. +.+...+..+..+|...        |++++
T Consensus       163 al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~  239 (474)
T 4abn_A          163 ALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQQ  239 (474)
T ss_dssp             HHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHHH
Confidence            8875  57778888888899998         99999999999999875 56788889999999998        99999


Q ss_pred             HHHHHHhCC---C---CChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040365          196 ARCIFDKMD---L---HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNS  268 (514)
Q Consensus       196 A~~~~~~m~---~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~  268 (514)
                      |.+.|++..   .   .+...|..+...|...|++++|++.|++..+.  .| +...+..+..++...|++++|...+..
T Consensus       240 A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~a~~~l~~~~~~lg~~~eAi~~~~~  317 (474)
T 4abn_A          240 ALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL--DPAWPEPQQREQQLLEFLSRLTSLLESKGK  317 (474)
T ss_dssp             HHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            999999875   3   47788999999999999999999999999885  34 456788888899999999999998887


Q ss_pred             hHH
Q 040365          269 MTK  271 (514)
Q Consensus       269 m~~  271 (514)
                      +..
T Consensus       318 ~~~  320 (474)
T 4abn_A          318 TKP  320 (474)
T ss_dssp             CCH
T ss_pred             ccC
Confidence            743

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.18  E-value=7.7e-09  Score=101.19  Aligned_cols=228  Identities=9%  Similarity=0.010  Sum_probs=161.0

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCC-CCC----HHHHHHHHHHHhccCChHHHHHHHHHHHHcC--C---C-CcHHHHH
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIAKI-KPR----HVSFSSIMPACAHLTTLHLGKQLHGCIIRNG--F---D-DNMFIAS  181 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~g~-~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~---~-~~~~~~~  181 (514)
                      ....+...|++++|+..|++...... .++    ..++..+..++...|+++.|...+.+.++..  .   . ....+++
T Consensus       107 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  186 (378)
T 3q15_A          107 RGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLF  186 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHH
Confidence            34455677888888888877754311 122    3355666777777888888887777766531  1   1 1245667


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCCC-----CC----hhHHHHHHHHHHhCCChHHHHHHHHHHHHc----CCCCCHHHHHH
Q 040365          182 SLLDMYAKCGNIRLARCIFDKMDL-----HD----IVSWTAVIMGNALHGNAHDAISLFEQMEKD----GVKPNSVAFVA  248 (514)
Q Consensus       182 ~li~~y~k~g~~~~A~~~~~~m~~-----~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~~~t~~~  248 (514)
                      .+...|...|++++|.+.|++...     ++    ..+++.+...|...|++++|+..|++....    +.+....++..
T Consensus       187 ~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  266 (378)
T 3q15_A          187 VIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFG  266 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHH
Confidence            788888888888888888876541     12    246777888888999999999999888761    22223567788


Q ss_pred             HHHHHHccCCHHHHHHHHHHhHHhcCCC--C-CHhHHHHHHHHHHhcCC---HHHHHHHHHhCCCCCCH-HHHHHHHHHH
Q 040365          249 VLTACSHAGLIDKAWSYFNSMTKDYGIA--P-SFEHYAAVADLLGRAGK---LQEAYEFISNMHAGPTE-NVWLTLLSAC  321 (514)
Q Consensus       249 ll~a~~~~g~~~~a~~~~~~m~~~~~~~--p-~~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~p~~-~~~~~ll~~~  321 (514)
                      +...+.+.|++++|..+++...+...-.  | ....+..+...+...|+   +.+|..++++....|+. ..+..+...|
T Consensus       267 la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y  346 (378)
T 3q15_A          267 LSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVF  346 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence            8889999999999999999886643321  2 23456666777778888   88999999886544433 4567788899


Q ss_pred             HhcCCHHHHHHHHHHHHhc
Q 040365          322 RVHKNVELAGKVAEKIFMI  340 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~  340 (514)
                      ...|+++.|...++++.+.
T Consensus       347 ~~~g~~~~A~~~~~~al~~  365 (378)
T 3q15_A          347 ESSCHFEQAAAFYRKVLKA  365 (378)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHH
Confidence            9999999999999987654

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.18  E-value=1.3e-08  Score=99.22  Aligned_cols=258  Identities=7%  Similarity=-0.058  Sum_probs=142.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCChh----hHHHHHHHHhCCCChHHHHHHHHHHHHhCC-CCc----hhHHHHH
Q 040365           12 VIVGLARNGLYEEALNIVRQMGNVNLKPDSF----TLSSVLPIFADYVDVIKGKEIHGYAIRHGL-DAN----VCIGSSL   82 (514)
Q Consensus        12 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-~~~----~~~~~~l   82 (514)
                      ....+...|++++|+..+++........+..    .+..+...+...|++++|.+.+...++..- ..+    ..++..+
T Consensus        20 ~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l   99 (373)
T 1hz4_A           20 RAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQ   99 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            3445667888888888888877653222222    344455566677888888888887765421 111    1234556


Q ss_pred             HHHHHHCCCHHHHHHHHccCC-------C---C-ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCC--C--CHHHHHH
Q 040365           83 INMYAKCARVEDSHRLFCLLP-------V---K-DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIK--P--RHVSFSS  147 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~-------~---~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~--p--~~~t~~~  147 (514)
                      ...|...|++++|...+++..       .   + ...++..+...+...|++++|...+++.......  +  ...++..
T Consensus       100 a~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  179 (373)
T 1hz4_A          100 SEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAM  179 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHHH
Confidence            667777788777777766542       1   1 1234555666777777777777777776543211  1  1234555


Q ss_pred             HHHHHhccCChHHHHHHHHHHHHcCCCCc--HHHH-H---HHHHHHHhcCCHHHHHHHHHhCCCCC-------hhHHHHH
Q 040365          148 IMPACAHLTTLHLGKQLHGCIIRNGFDDN--MFIA-S---SLLDMYAKCGNIRLARCIFDKMDLHD-------IVSWTAV  214 (514)
Q Consensus       148 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~-~---~li~~y~k~g~~~~A~~~~~~m~~~d-------~~~~~~l  214 (514)
                      +...+...|++++|...++...+..-.++  .... .   .++..+...|++++|...+++...++       ...+..+
T Consensus       180 la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~l  259 (373)
T 1hz4_A          180 LIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNI  259 (373)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHHH
Confidence            66666677777777777776654311111  1111 1   23334566777777777776665321       1134455


Q ss_pred             HHHHHhCCChHHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          215 IMGNALHGNAHDAISLFEQMEKD----GVKPNS-VAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       215 i~~~~~~g~~~~A~~l~~~m~~~----g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      ...+...|++++|...+++....    |..++. ..+..+..++...|+.++|...++..
T Consensus       260 a~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a  319 (373)
T 1hz4_A          260 ARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDA  319 (373)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            55566666666666666655431    111111 13333344444555555555555444

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.18  E-value=1.3e-09  Score=98.38  Aligned_cols=188  Identities=13%  Similarity=0.014  Sum_probs=124.5

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---C-CChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-HHHHHHH
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMD---L-HDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-SVAFVAV  249 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~-~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~l  249 (514)
                      .|+..+..+...|.+.|++++|...|++..   + ++...|..+..++...|++++|+..|++..+.  .|+ ...+..+
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l   82 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGK   82 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHH
Confidence            345666677777778888888888777654   2 56666666777777788888888888877764  444 3566777


Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCC-CH-------hHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC---HHHHHHH
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAP-SF-------EHYAAVADLLGRAGKLQEAYEFISNMH-AGPT---ENVWLTL  317 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~-------~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~---~~~~~~l  317 (514)
                      ...+...|++++|...|+...+.   .| +.       ..|..+...+...|++++|.+.+++.. ..|+   ...|..+
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l  159 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKA---VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSL  159 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHH
Confidence            77777788888888888777654   33 23       446666677777777777777777653 3454   3456666


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          318 LSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       318 l~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ..++..     .+...++++..+.+.+...|..+.  ....+.+++|...+++..+.
T Consensus       160 ~~~~~~-----~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l  209 (228)
T 4i17_A          160 GVLFYN-----NGADVLRKATPLASSNKEKYASEK--AKADAAFKKAVDYLGEAVTL  209 (228)
T ss_dssp             HHHHHH-----HHHHHHHHHGGGTTTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHH-----HHHHHHHHHHhcccCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhc
Confidence            666543     344455666666655544443332  34456679999999988764

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.18  E-value=2e-09  Score=97.18  Aligned_cols=203  Identities=10%  Similarity=0.043  Sum_probs=158.9

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHH
Q 040365          140 PRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIM  216 (514)
Q Consensus       140 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~  216 (514)
                      .|+..+......+...|++++|...+...++...+++...+..+...|.+.|++++|.+.|++..   +.+...|..+..
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   84 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKSA   84 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHH
Confidence            45678888888999999999999999999998743777777779999999999999999999875   345678999999


Q ss_pred             HHHhCCChHHHHHHHHHHHHcCCCCC-H-------HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC---HhHHHHH
Q 040365          217 GNALHGNAHDAISLFEQMEKDGVKPN-S-------VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS---FEHYAAV  285 (514)
Q Consensus       217 ~~~~~g~~~~A~~l~~~m~~~g~~p~-~-------~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~---~~~~~~l  285 (514)
                      .|...|++++|+..|++..+.  .|+ .       ..|..+...+...|++++|...|+...   .+.|+   ...+..+
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al---~~~p~~~~~~~~~~l  159 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHAT---DVTSKKWKTDALYSL  159 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHT---TSSCHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHH---hcCCCcccHHHHHHH
Confidence            999999999999999999885  344 3       457777888899999999999999886   44665   5677777


Q ss_pred             HHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 040365          286 ADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNT  354 (514)
Q Consensus       286 i~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  354 (514)
                      ...|...|+.     +++++.  ...+...+..+.  ....+.+++|...++++++++|+++.+...+..+
T Consensus       160 ~~~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~p~~~~~~~~l~~i  223 (228)
T 4i17_A          160 GVLFYNNGAD-----VLRKATPLASSNKEKYASEK--AKADAAFKKAVDYLGEAVTLSPNRTEIKQMQDQV  223 (228)
T ss_dssp             HHHHHHHHHH-----HHHHHGGGTTTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHH-----HHHHHHhcccCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Confidence            7777665543     233321  123444444433  3455678999999999999999998777666554

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.10  E-value=5.5e-10  Score=103.82  Aligned_cols=32  Identities=16%  Similarity=0.145  Sum_probs=22.3

Q ss_pred             CCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          342 PNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       342 p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      |..+.++..++.+|...|++++|.+.+++..+
T Consensus       249 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          249 PTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34455677777777777777777777776654

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.08  E-value=2.6e-07  Score=96.44  Aligned_cols=352  Identities=10%  Similarity=0.008  Sum_probs=235.4

Q ss_pred             hhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCC---HHHHHHH
Q 040365           22 YEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCAR---VEDSHRL   98 (514)
Q Consensus        22 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~---~~~A~~~   98 (514)
                      ..+.+..|+..+..+ +-|..+|..++..+.+.+.++.+..+++.++.. ++.....|...+..-.+.|+   ++.+..+
T Consensus        48 ~~d~i~~lE~~l~~n-p~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~l  125 (679)
T 4e6h_A           48 ESDVIGKLNDMIEEQ-PTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPV  125 (679)
T ss_dssp             CSCHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHH
Confidence            344555566665554 468889999999999999999999999999988 57788899999999999999   9999999


Q ss_pred             HccCC--C---CChhHHHHHHHHHHHCCCh--------hHHHHHHHHHHH-CCC-CCCH-HHHHHHHHHHh---------
Q 040365           99 FCLLP--V---KDAISWNSIIAGCVQNGLF--------DEGLKFFRQMLI-AKI-KPRH-VSFSSIMPACA---------  153 (514)
Q Consensus        99 f~~~~--~---~d~~~~~~li~~~~~~g~~--------~~A~~l~~~m~~-~g~-~p~~-~t~~~ll~~~~---------  153 (514)
                      |++..  .   |++..|..-+.-..+.++.        +...++|+.... .|. .|+. ..|...+....         
T Consensus       126 feRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~e  205 (679)
T 4e6h_A          126 LARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFE  205 (679)
T ss_dssp             HHHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHH
Confidence            99865  3   7888898877765555543        234467776554 466 5653 45555554432         


Q ss_pred             ccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHH-------------hcCCHHHHHHHHH-------------------
Q 040365          154 HLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYA-------------KCGNIRLARCIFD-------------------  201 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~-------------k~g~~~~A~~~~~-------------------  201 (514)
                      ..++++.++.+|..++......-..+|......--             ...+++.|+..+.                   
T Consensus       206 eq~~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~  285 (679)
T 4e6h_A          206 EQQRVQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQ  285 (679)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTT
T ss_pred             HHhHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhcccccccc
Confidence            23346778888888775322211222211111000             0011222333322                   


Q ss_pred             ------------------------------------------------hCC---CCChhHHHHHHHHHHhCCChHHHH-H
Q 040365          202 ------------------------------------------------KMD---LHDIVSWTAVIMGNALHGNAHDAI-S  229 (514)
Q Consensus       202 ------------------------------------------------~m~---~~d~~~~~~li~~~~~~g~~~~A~-~  229 (514)
                                                                      +..   ..+...|-..+.-+.+.|+.++|. +
T Consensus       286 ~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p~~~~lW~~ya~~~~~~~~~~~a~r~  365 (679)
T 4e6h_A          286 ATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVCFAPEIWFNMANYQGEKNTDSTVITK  365 (679)
T ss_dssp             CCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSCCTTHHHH
T ss_pred             chhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCcHHHHHHH
Confidence                                                            211   112234545555556678888886 9


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC--------CCCC------------HhHHHHHHHHH
Q 040365          230 LFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG--------IAPS------------FEHYAAVADLL  289 (514)
Q Consensus       230 l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~--------~~p~------------~~~~~~li~~~  289 (514)
                      +|++.... .+.+...+...+...-..|++++|..+|+.+.....        -.|+            ...|...+...
T Consensus       366 il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~e  444 (679)
T 4e6h_A          366 YLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTM  444 (679)
T ss_dssp             HHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHH
Confidence            99888764 333444566677778888999999999998875310        0132            34688888888


Q ss_pred             HhcCCHHHHHHHHHhCCCC---CCHHHHHHHHHHHHh-cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHH
Q 040365          290 GRAGKLQEAYEFISNMHAG---PTENVWLTLLSACRV-HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAA  365 (514)
Q Consensus       290 ~~~g~~~~A~~~~~~m~~~---p~~~~~~~ll~~~~~-~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~  365 (514)
                      .+.|.++.|..+|.+....   +...+|......-.. .++.+.|..+|+.+++..|+++..+...+......|+.+.|+
T Consensus       445 rR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR  524 (679)
T 4e6h_A          445 KRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVK  524 (679)
T ss_dssp             HHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHH
Confidence            8999999999999987422   223344333222233 355899999999999999999888888899889999999999


Q ss_pred             HHHHHHHhCCC
Q 040365          366 SLRVFMRNKGM  376 (514)
Q Consensus       366 ~~~~~m~~~g~  376 (514)
                      .+|++......
T Consensus       525 ~lferal~~~~  535 (679)
T 4e6h_A          525 SLFESSIDKIS  535 (679)
T ss_dssp             HHHHHHTTTSS
T ss_pred             HHHHHHHHhcC
Confidence            99998877654

>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=99.04  E-value=8.9e-09  Score=95.51  Aligned_cols=199  Identities=9%  Similarity=0.022  Sum_probs=116.6

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHHc------CC-CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC---------
Q 040365          142 HVSFSSIMPACAHLTTLHLGKQLHGCIIRN------GF-DDNMFIASSLLDMYAKCGNIRLARCIFDKMDL---------  205 (514)
Q Consensus       142 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~------~~-~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~---------  205 (514)
                      ..++..+...+...|++++|...+..+++.      +- +....++..+...|...|++++|.+.|++...         
T Consensus        43 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  122 (283)
T 3edt_B           43 ATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKF  122 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCC
Confidence            344555555566666666666666655543      11 22344566666667777777777666665531         


Q ss_pred             -C-ChhHHHHHHHHHHhCCChHHHHHHHHHHHHc------CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhc---
Q 040365          206 -H-DIVSWTAVIMGNALHGNAHDAISLFEQMEKD------GVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDY---  273 (514)
Q Consensus       206 -~-d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~---  273 (514)
                       | ...+|..+...|...|++++|+..|++....      +-.|+ ..++..+...+...|++++|..+++...+..   
T Consensus       123 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~  202 (283)
T 3edt_B          123 HPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEK  202 (283)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence             1 2346677777777788888888888777653      11332 3567777788888888888888888775431   


Q ss_pred             ---CCCC-CHhHHHHHHHHHHhc------CCHHHHHHHHHhCCCC-C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040365          274 ---GIAP-SFEHYAAVADLLGRA------GKLQEAYEFISNMHAG-P-TENVWLTLLSACRVHKNVELAGKVAEKIFMI  340 (514)
Q Consensus       274 ---~~~p-~~~~~~~li~~~~~~------g~~~~A~~~~~~m~~~-p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  340 (514)
                         ...+ ....+..+...+...      ..+.++...++..... | ...++..+...+...|++++|...++++++.
T Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          203 EFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             cCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence               1122 223333333333332      2344455555544322 2 3457888899999999999999999988764

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.03  E-value=2e-08  Score=92.65  Aligned_cols=205  Identities=16%  Similarity=0.043  Sum_probs=134.8

Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C-C---hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCC-CCC-HHHH
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKMDL--H-D---IVSWTAVIMGNALHGNAHDAISLFEQMEKDGV-KPN-SVAF  246 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~-d---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~-~~t~  246 (514)
                      .+...+-.+...+.+.|++++|...|+++..  | +   ...+..+..+|.+.|++++|+..|++...... .|+ ...+
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            3455556667777778888888888877652  2 3   45667777777778888888888887776421 122 2445


Q ss_pred             HHHHHHHHc--------cCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHH
Q 040365          247 VAVLTACSH--------AGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTL  317 (514)
Q Consensus       247 ~~ll~a~~~--------~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~l  317 (514)
                      ..+..++..        .|++++|...|+.+.+.+   |+ ......+....       .....+        ...+..+
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~---p~~~~~~~a~~~~~-------~~~~~~--------~~~~~~l  154 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRY---PNHELVDDATQKIR-------ELRAKL--------ARKQYEA  154 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHC---TTCTTHHHHHHHHH-------HHHHHH--------HHHHHHH
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHC---cCchhHHHHHHHHH-------HHHHHH--------HHHHHHH
Confidence            556666666        777778887777776542   32 22221111111       000000        1124667


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCc---chHHHHHHHHHHc----------cChhHHHHHHHHHHhCCCccCCcccE
Q 040365          318 LSACRVHKNVELAGKVAEKIFMIDPNNM---GAYVILSNTYAAA----------RRWKDAASLRVFMRNKGMKKTPACSW  384 (514)
Q Consensus       318 l~~~~~~~~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~~~~~----------g~~~~a~~~~~~m~~~g~~~~~~~s~  384 (514)
                      ...+...|+++.|+..++++++..|+++   ..+..++.+|...          |++++|...+++..+..    |    
T Consensus       155 a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~----p----  226 (261)
T 3qky_A          155 ARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIF----P----  226 (261)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHC----T----
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHC----C----
Confidence            8889999999999999999999998854   4788889999877          89999999999987643    1    


Q ss_pred             EEECCEEEEEEeCCCCCCChHHHHHHHHHHHHHHHh
Q 040365          385 IEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQ  420 (514)
Q Consensus       385 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~  420 (514)
                                     .++...++...+.++...+.+
T Consensus       227 ---------------~~~~~~~a~~~l~~~~~~~~~  247 (261)
T 3qky_A          227 ---------------DSPLLRTAEELYTRARQRLTE  247 (261)
T ss_dssp             ---------------TCTHHHHHHHHHHHHHHHHHH
T ss_pred             ---------------CChHHHHHHHHHHHHHHHHHH
Confidence                           134455666666666665543

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.03  E-value=7.7e-09  Score=97.33  Aligned_cols=216  Identities=10%  Similarity=-0.067  Sum_probs=113.1

Q ss_pred             CHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHhccCChHHHHHHH
Q 040365           91 RVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIA----KIKPR-HVSFSSIMPACAHLTTLHLGKQLH  165 (514)
Q Consensus        91 ~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~-~~t~~~ll~~~~~~~~~~~a~~~~  165 (514)
                      ++++|...|+.           ....|...|++++|+..|.+..+.    |-+++ ..+|..+..++...|++++|...+
T Consensus        32 ~~~~A~~~~~~-----------a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~  100 (292)
T 1qqe_A           32 KFEEAADLCVQ-----------AATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSL  100 (292)
T ss_dssp             HHHHHHHHHHH-----------HHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cHHHHHHHHHH-----------HHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            36777666554           366677778888887777766442    21111 345555556666666666666665


Q ss_pred             HHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhC-CChHHHHHHHHHHHHcCC---CC
Q 040365          166 GCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALH-GNAHDAISLFEQMEKDGV---KP  241 (514)
Q Consensus       166 ~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~-g~~~~A~~l~~~m~~~g~---~p  241 (514)
                      ++.++..               .+.|+...+           ..+|+.+...|... |++++|+..|++..+...   .+
T Consensus       101 ~~Al~l~---------------~~~g~~~~~-----------a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~  154 (292)
T 1qqe_A          101 ENAIQIF---------------THRGQFRRG-----------ANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSV  154 (292)
T ss_dssp             HHHHHHH---------------HHTTCHHHH-----------HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHH---------------HHcCCHHHH-----------HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCCh
Confidence            5554321               111111111           22455555666664 666666666666554210   00


Q ss_pred             -C-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCH-----hHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCH--
Q 040365          242 -N-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSF-----EHYAAVADLLGRAGKLQEAYEFISNMH-AGPTE--  311 (514)
Q Consensus       242 -~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~-----~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~--  311 (514)
                       . ..++..+...+...|++++|+.+|+...+...-.+..     ..|..+..++...|++++|...+++.. ..|+.  
T Consensus       155 ~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~  234 (292)
T 1qqe_A          155 ALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFAD  234 (292)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC------
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCC
Confidence             0 2345566666666677777777776665431111111     134555666666777777777766653 22321  


Q ss_pred             ----HHHHHHHHHHH--hcCCHHHHHHHHHHHHhcCCC
Q 040365          312 ----NVWLTLLSACR--VHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       312 ----~~~~~ll~~~~--~~~~~~~a~~~~~~~~~~~p~  343 (514)
                          ..+..++.++.  ..+++++|...|+++..++|.
T Consensus       235 ~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l~~~  272 (292)
T 1qqe_A          235 SRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKW  272 (292)
T ss_dssp             ---HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCccHHH
Confidence                12334444443  345566666666666666554

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.03  E-value=5.8e-09  Score=110.04  Aligned_cols=159  Identities=13%  Similarity=0.051  Sum_probs=88.5

Q ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040365           76 VCIGSSLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPAC  152 (514)
Q Consensus        76 ~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~  152 (514)
                      ..+++.|...|.+.|++++|.+.|++..   ..+..+|+.+...|.+.|++++|++.|++..+.. +-+...|..+..++
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~~l   87 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGNTL   87 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            3445555555555555555555555432   2234455555555555566666666555555432 12344555555555


Q ss_pred             hccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHH
Q 040365          153 AHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAIS  229 (514)
Q Consensus       153 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~  229 (514)
                      ...|++++|.+.+++.++.. +.+...++.|...|.+.|++++|.+.|++..   ..+...|..+...|...|++++|.+
T Consensus        88 ~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~A~~  166 (723)
T 4gyw_A           88 KEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDE  166 (723)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTTHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHHHHH
Confidence            55666666666665555543 3345556666666666666666666666543   2345566666666666666666666


Q ss_pred             HHHHHHH
Q 040365          230 LFEQMEK  236 (514)
Q Consensus       230 l~~~m~~  236 (514)
                      .+++..+
T Consensus       167 ~~~kal~  173 (723)
T 4gyw_A          167 RMKKLVS  173 (723)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6665543

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.97  E-value=1.3e-07  Score=87.91  Aligned_cols=137  Identities=9%  Similarity=0.103  Sum_probs=60.9

Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC-----CChhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          161 GKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL-----HDIVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       161 a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~-----~d~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      +...++..++.+ +++......+..+|...|++++|.+++.+...     .+...+..++..+.+.|+.+.|.+.+++|.
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~  163 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYT  163 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334444444333 23333333455555555555555555555421     133444455555555555555555555555


Q ss_pred             HcCCCC-----CHHHHHHHHHHHH--c--cCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHH
Q 040365          236 KDGVKP-----NSVAFVAVLTACS--H--AGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFIS  303 (514)
Q Consensus       236 ~~g~~p-----~~~t~~~ll~a~~--~--~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~  303 (514)
                      +.  .|     +..+...+..++.  .  .++.++|..+|+++...   .|+...-..+..++.+.|++++|.+.++
T Consensus       164 ~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~---~p~~~~~~lLln~~~~~g~~~eAe~~L~  235 (310)
T 3mv2_B          164 NA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT---FPTWKTQLGLLNLHLQQRNIAEAQGIVE  235 (310)
T ss_dssp             HH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT---SCSHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             hc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh---CCCcccHHHHHHHHHHcCCHHHHHHHHH
Confidence            42  34     2334444443321  1  22555555555555322   2221222222224445555555555544

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.97  E-value=3.3e-08  Score=91.18  Aligned_cols=203  Identities=12%  Similarity=0.042  Sum_probs=143.2

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCc---HHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C----ChhH
Q 040365          140 PRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDN---MFIASSLLDMYAKCGNIRLARCIFDKMDL--H----DIVS  210 (514)
Q Consensus       140 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~----d~~~  210 (514)
                      .+...+-.....+.+.|++++|...+..+++.. +.+   ...+..+...|.+.|++++|...|++...  |    ...+
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a   91 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQA   91 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHH
Confidence            455666677788899999999999999998864 333   67788899999999999999999998752  2    2346


Q ss_pred             HHHHHHHHHh--------CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHH
Q 040365          211 WTAVIMGNAL--------HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHY  282 (514)
Q Consensus       211 ~~~li~~~~~--------~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~  282 (514)
                      +..+..++..        .|++++|+..|++....  .|+....             ..+...+......     ....+
T Consensus        92 ~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~-------------~~a~~~~~~~~~~-----~~~~~  151 (261)
T 3qky_A           92 EYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR--YPNHELV-------------DDATQKIRELRAK-----LARKQ  151 (261)
T ss_dssp             HHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH--CTTCTTH-------------HHHHHHHHHHHHH-----HHHHH
T ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH--CcCchhH-------------HHHHHHHHHHHHH-----HHHHH
Confidence            7778888888        99999999999999885  3443111             1111111111110     11235


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhc----------CCHHHHHHHHHHHHhcCCCCcc-
Q 040365          283 AAVADLLGRAGKLQEAYEFISNMH-AGPT----ENVWLTLLSACRVH----------KNVELAGKVAEKIFMIDPNNMG-  346 (514)
Q Consensus       283 ~~li~~~~~~g~~~~A~~~~~~m~-~~p~----~~~~~~ll~~~~~~----------~~~~~a~~~~~~~~~~~p~~~~-  346 (514)
                      ..+...|.+.|++++|...|+++. ..|+    ...+..+..++...          |++++|...++++++..|+++. 
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~  231 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDSPLL  231 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTCTHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCChHH
Confidence            567778888999999998888763 2233    45677777777765          8899999999999999998864 


Q ss_pred             --hHHHHHHHHHHccChhH
Q 040365          347 --AYVILSNTYAAARRWKD  363 (514)
Q Consensus       347 --~~~~l~~~~~~~g~~~~  363 (514)
                        +...+...+...+++++
T Consensus       232 ~~a~~~l~~~~~~~~~~~~  250 (261)
T 3qky_A          232 RTAEELYTRARQRLTELEG  250 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHhhh
Confidence              33344445544444433

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.95  E-value=7.1e-08  Score=89.72  Aligned_cols=142  Identities=14%  Similarity=0.090  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCC-CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          126 GLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGF-DDNMFIASSLLDMYAKCGNIRLARCIFDKMD  204 (514)
Q Consensus       126 A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~  204 (514)
                      |+..|++....+ .++..++..+..++...|++++|.+++...+..+- .-+...+..++..|.+.|+.+.|.+.+++|.
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~  163 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYT  163 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            555555555443 34444445555666666666666666666554442 1345555556666666666666666666654


Q ss_pred             --CC-----ChhHHHHHHHHH--HhCC--ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhH
Q 040365          205 --LH-----DIVSWTAVIMGN--ALHG--NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMT  270 (514)
Q Consensus       205 --~~-----d~~~~~~li~~~--~~~g--~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  270 (514)
                        .|     +-.+...+..++  ...|  ++.+|..+|+++.+.  .|+..+-..++.++.+.|++++|...++.+.
T Consensus       164 ~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~  238 (310)
T 3mv2_B          164 NAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence              22     123334444442  2222  566666666665443  3443333344445666666666666666543

>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=98.95  E-value=2.8e-08  Score=80.51  Aligned_cols=129  Identities=17%  Similarity=0.225  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHH
Q 040365          210 SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLL  289 (514)
Q Consensus       210 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~  289 (514)
                      +|..+...+...|++++|+.+|+++.... +.+...+..+...+...|++++|..+++.+.+.                 
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-----------------   64 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL-----------------   64 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----------------
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHH-----------------
Confidence            34455555555555555655555555432 123344444444455555555555555544322                 


Q ss_pred             HhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHH
Q 040365          290 GRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRV  369 (514)
Q Consensus       290 ~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~  369 (514)
                                       .+.+...|..+...+...|++++|...++++.+..|.+...+..++.+|...|++++|.+.++
T Consensus        65 -----------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~  127 (136)
T 2fo7_A           65 -----------------DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQ  127 (136)
T ss_dssp             -----------------CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             -----------------CCCchHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHH
Confidence                             122344555555566666666666666666666666666666666666666666666666666


Q ss_pred             HHHh
Q 040365          370 FMRN  373 (514)
Q Consensus       370 ~m~~  373 (514)
                      ++.+
T Consensus       128 ~~~~  131 (136)
T 2fo7_A          128 KALE  131 (136)
T ss_dssp             HHHH
T ss_pred             HHHc
Confidence            6544

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=98.94  E-value=9.2e-08  Score=89.89  Aligned_cols=197  Identities=11%  Similarity=0.045  Sum_probs=130.7

Q ss_pred             hHHHHHHHHHHHCCCHHHHHHHHccCCC-------C--ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHH
Q 040365           77 CIGSSLINMYAKCARVEDSHRLFCLLPV-------K--DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSS  147 (514)
Q Consensus        77 ~~~~~li~~~~~~g~~~~A~~~f~~~~~-------~--d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~  147 (514)
                      ..|+.....|...|++++|...|++..+       +  ...+|+.+...|.+.|++++|+..|++..+.           
T Consensus        38 ~~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l-----------  106 (292)
T 1qqe_A           38 DLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQI-----------  106 (292)
T ss_dssp             HHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----------
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-----------
Confidence            3577788899999999999988876531       1  1457899999999999999999999987652           


Q ss_pred             HHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc-CCHHHHHHHHHhCCC-----CC----hhHHHHHHHH
Q 040365          148 IMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKC-GNIRLARCIFDKMDL-----HD----IVSWTAVIMG  217 (514)
Q Consensus       148 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~-g~~~~A~~~~~~m~~-----~d----~~~~~~li~~  217 (514)
                          +...|+...+               ..+++.+...|... |++++|...|++...     .+    ..+|+.+...
T Consensus       107 ----~~~~g~~~~~---------------a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~  167 (292)
T 1qqe_A          107 ----FTHRGQFRRG---------------ANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADL  167 (292)
T ss_dssp             ----HHHTTCHHHH---------------HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ----HHHcCCHHHH---------------HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHH
Confidence                1112222211               12344455566664 666666666665431     11    2457777888


Q ss_pred             HHhCCChHHHHHHHHHHHHcCCCCCH------HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCH------hHHHHH
Q 040365          218 NALHGNAHDAISLFEQMEKDGVKPNS------VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSF------EHYAAV  285 (514)
Q Consensus       218 ~~~~g~~~~A~~l~~~m~~~g~~p~~------~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~------~~~~~l  285 (514)
                      |.+.|++++|+..|++..........      ..|..+..++...|++++|...|+...   .+.|+.      ..+..+
T Consensus       168 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al---~l~p~~~~~~~~~~l~~l  244 (292)
T 1qqe_A          168 KALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQ---SEDPNFADSRESNFLKSL  244 (292)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGG---CC---------HHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH---hhCCCCCCcHHHHHHHHH
Confidence            88888888888888888774322221      156667777888889999988888775   344532      123445


Q ss_pred             HHHHH--hcCCHHHHHHHHHhCC
Q 040365          286 ADLLG--RAGKLQEAYEFISNMH  306 (514)
Q Consensus       286 i~~~~--~~g~~~~A~~~~~~m~  306 (514)
                      +..+.  ..+++++|++.|+.+.
T Consensus       245 ~~~~~~~~~~~~~~A~~~~~~~~  267 (292)
T 1qqe_A          245 IDAVNEGDSEQLSEHCKEFDNFM  267 (292)
T ss_dssp             HHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             HHHHHcCCHHHHHHHHHHhccCC
Confidence            55554  4577889999887764

>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=98.93  E-value=5.1e-08  Score=78.99  Aligned_cols=123  Identities=18%  Similarity=0.193  Sum_probs=93.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHc
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSH  255 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  255 (514)
                      .+..+...|...|++++|.++|+++.   ..+...|..+...+...|++++|..+|+++...+ +.+...+..+...+..
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHH
Confidence            56778899999999999999999875   4567889999999999999999999999998863 3355677778888888


Q ss_pred             cCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          256 AGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       256 ~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~  304 (514)
                      .|++++|..+++.+.+..  +.+...+..+...+.+.|++++|.+.+++
T Consensus        82 ~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~  128 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALELD--PRSAEAWYNLGNAYYKQGDYDEAIEYYQK  128 (136)
T ss_dssp             TTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHccHHHHHHHHHH
Confidence            888888888888876431  12344555555555555555555555544

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.91  E-value=1.4e-07  Score=84.96  Aligned_cols=179  Identities=12%  Similarity=0.031  Sum_probs=117.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhCCC--CC----hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCH----HHHH
Q 040365          178 FIASSLLDMYAKCGNIRLARCIFDKMDL--HD----IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNS----VAFV  247 (514)
Q Consensus       178 ~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~t~~  247 (514)
                      ..+..+...+.+.|++++|...|+++..  |+    ...+..+..+|.+.|++++|+..|++..+.  .|+.    ..+.
T Consensus         5 ~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~--~P~~~~~~~a~~   82 (225)
T 2yhc_A            5 NEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL--NPTHPNIDYVMY   82 (225)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCcHHHHHH
Confidence            3445566778888888888888887752  22    246777778888888888888888888774  2332    1333


Q ss_pred             HHHHHHHc------------------cCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhCCCC
Q 040365          248 AVLTACSH------------------AGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRAGKLQEAYEFISNMHAG  308 (514)
Q Consensus       248 ~ll~a~~~------------------~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  308 (514)
                      .+..++..                  .|+.++|...|+.+.+.   .|+ ...+.....+    +.+....         
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~---~P~~~~a~~a~~~l----~~~~~~~---------  146 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG---YPNSQYTTDATKRL----VFLKDRL---------  146 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT---CTTCTTHHHHHHHH----HHHHHHH---------
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH---CcCChhHHHHHHHH----HHHHHHH---------
Confidence            33344432                  35666666666666533   232 1111111100    0000000         


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc---chHHHHHHHHHHccChhHHHHHHHHHHhCCC
Q 040365          309 PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM---GAYVILSNTYAAARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  376 (514)
                        ......+...+...|+++.|+..++++++..|+++   .++..++.+|.+.|++++|.+.++.+...+.
T Consensus       147 --~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~  215 (225)
T 2yhc_A          147 --AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS  215 (225)
T ss_dssp             --HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCS
T ss_pred             --HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCC
Confidence              01123456678899999999999999999999876   5688999999999999999999999987654

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.90  E-value=6.8e-08  Score=90.57  Aligned_cols=173  Identities=11%  Similarity=-0.077  Sum_probs=131.7

Q ss_pred             HHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhc
Q 040365          195 LARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDY  273 (514)
Q Consensus       195 ~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~  273 (514)
                      ...+.+......+...+..+...+.+.|++++|+..|++....  .| +...+..+...+...|++++|...++.+... 
T Consensus       104 ~l~~~l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~-  180 (287)
T 3qou_A          104 AIRALLDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ-  180 (287)
T ss_dssp             HHHHHHHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG-
T ss_pred             HHHHHHHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh-
Confidence            3444444444445566677777788888999999999888875  44 4567778888888999999999999887543 


Q ss_pred             CCCCCHhHHHHH-HHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--cchH
Q 040365          274 GIAPSFEHYAAV-ADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN--MGAY  348 (514)
Q Consensus       274 ~~~p~~~~~~~l-i~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~--~~~~  348 (514)
                        .|+....... ...+.+.++.++|.+.+++..  .+.+...+..|...+...|++++|...++++++.+|++  ...+
T Consensus       181 --~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~  258 (287)
T 3qou_A          181 --DQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTR  258 (287)
T ss_dssp             --GCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHH
T ss_pred             --hcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHH
Confidence              4554333222 233666777788888777653  23467889999999999999999999999999999987  7889


Q ss_pred             HHHHHHHHHccChhHHHHHHHHHH
Q 040365          349 VILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       349 ~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      ..|+.+|...|+.++|...+++-.
T Consensus       259 ~~l~~~~~~~g~~~~a~~~~r~al  282 (287)
T 3qou_A          259 XTFQEILAALGTGDALASXYRRQL  282 (287)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHH
Confidence            999999999999999988887643

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.88  E-value=4.1e-09  Score=88.45  Aligned_cols=137  Identities=11%  Similarity=0.031  Sum_probs=90.5

Q ss_pred             HhCCChHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHH
Q 040365          219 ALHGNAHDAISLFEQMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       219 ~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~  296 (514)
                      ...|++++|+..+++....  .|+ ...+..+...|.+.|++++|+..|+...+.   .| +...|..+..+|.+.|+++
T Consensus         8 ~~~~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~---~p~~~~a~~~lg~~~~~~~~~~   82 (150)
T 4ga2_A            8 RSKADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV---QERDPKAHRFLGLLYELEENTD   82 (150)
T ss_dssp             CCHHHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHcChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCchH
Confidence            3445556666666554431  222 233445566666667777777766666543   44 4666777777777777777


Q ss_pred             HHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHH-HHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          297 EAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKV-AEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       297 ~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~-~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      +|...|++.. ..| +..+|..+...+...|+.++|... ++++++++|+++.+|......+...|+
T Consensus        83 ~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           83 KAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            7777776642 233 567788888888888888765554 588889999998888888887777664

>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=98.86  E-value=9.2e-09  Score=108.71  Aligned_cols=167  Identities=12%  Similarity=-0.015  Sum_probs=129.7

Q ss_pred             HhcCCHHHHHHHHHhCC-----------CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHc
Q 040365          188 AKCGNIRLARCIFDKMD-----------LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSH  255 (514)
Q Consensus       188 ~k~g~~~~A~~~~~~m~-----------~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~  255 (514)
                      ...|++++|.+.|++..           ..+...|..+...|.+.|++++|+..|++..+.  .| +...+..+..++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAER--VGWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhcc--CcchHHHHHHHHHHHHH
Confidence            66788888888887764           345677888888888888888888888888874  34 45677778888888


Q ss_pred             cCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHH
Q 040365          256 AGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGK  332 (514)
Q Consensus       256 ~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~  332 (514)
                      .|++++|...|++..+.   .| +...|..+..+|.+.|++++ .+.|++..  .+.+...|..+..++...|++++|..
T Consensus       480 ~g~~~~A~~~~~~al~l---~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~  555 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDT---FPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVR  555 (681)
T ss_dssp             HTCHHHHHHHHHHHHHH---STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHH
Confidence            88899998888887653   45 56777888888888888888 88887753  23466788888888888899999999


Q ss_pred             HHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          333 VAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       333 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      .++++++++|++..++..++.+|...|+
T Consensus       556 ~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          556 TLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            9998888888888888888888866555

>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=98.80  E-value=4.6e-07  Score=80.68  Aligned_cols=161  Identities=10%  Similarity=-0.033  Sum_probs=108.5

Q ss_pred             ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccC----CHHHHHHHHHHhHHhcCCCCCHhHH
Q 040365          207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAG----LIDKAWSYFNSMTKDYGIAPSFEHY  282 (514)
Q Consensus       207 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g----~~~~a~~~~~~m~~~~~~~p~~~~~  282 (514)
                      +..++..+...|...+++++|+..|++..+.|   +...+..+...|.. +    +.++|..+|+...+.    -++..+
T Consensus        17 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~----g~~~a~   88 (212)
T 3rjv_A           17 DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEA----GSKSGE   88 (212)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHT----TCHHHH
T ss_pred             CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHC----CCHHHH
Confidence            45555555566666666666666666666554   34445555555555 4    677777777766432    245556


Q ss_pred             HHHHHHHHh----cCCHHHHHHHHHhCCCCCC----HHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCcchHHH
Q 040365          283 AAVADLLGR----AGKLQEAYEFISNMHAGPT----ENVWLTLLSACRV----HKNVELAGKVAEKIFMIDPNNMGAYVI  350 (514)
Q Consensus       283 ~~li~~~~~----~g~~~~A~~~~~~m~~~p~----~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~p~~~~~~~~  350 (514)
                      ..|..+|..    .+++++|.++|++.....+    +..+..|...|..    .++.++|...+++..+. |.++..+..
T Consensus        89 ~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~-~~~~~a~~~  167 (212)
T 3rjv_A           89 IVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL-SRTGYAEYW  167 (212)
T ss_dssp             HHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT-SCTTHHHHH
T ss_pred             HHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc-CCCHHHHHH
Confidence            666666665    6777888887777643333    6777777777777    77888888888888877 556667888


Q ss_pred             HHHHHHHc-c-----ChhHHHHHHHHHHhCCC
Q 040365          351 LSNTYAAA-R-----RWKDAASLRVFMRNKGM  376 (514)
Q Consensus       351 l~~~~~~~-g-----~~~~a~~~~~~m~~~g~  376 (514)
                      |..+|... |     ++++|...+++..+.|.
T Consensus       168 Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          168 AGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            88888764 3     78888888888877664

>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=98.79  E-value=9.1e-08  Score=99.04  Aligned_cols=158  Identities=12%  Similarity=0.051  Sum_probs=124.6

Q ss_pred             cCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHH
Q 040365          190 CGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSY  265 (514)
Q Consensus       190 ~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~  265 (514)
                      .|++++|.+.|++..   ..+...|..+...|.+.|++++|++.|++..+.  .| +...+..+..++...|++++|...
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLAL--HPGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--STTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            478999999999876   335788999999999999999999999999885  44 467888899999999999999999


Q ss_pred             HHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhc---CCHHHHHHHHHHHHh
Q 040365          266 FNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVH---KNVELAGKVAEKIFM  339 (514)
Q Consensus       266 ~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~---~~~~~a~~~~~~~~~  339 (514)
                      +++..+.   .| +...+..+..+|.+.|++++|.+.+++..  .+.+...+..+...+...   |+.++|...++++++
T Consensus        80 ~~~al~~---~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           80 LQQASDA---APEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHHHhc---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            9998764   45 57889999999999999999999998863  234678899999999999   999999999999999


Q ss_pred             cCCCCcchHHHHH
Q 040365          340 IDPNNMGAYVILS  352 (514)
Q Consensus       340 ~~p~~~~~~~~l~  352 (514)
                      .+|.+...|..+.
T Consensus       157 ~~p~~~~~~~~l~  169 (568)
T 2vsy_A          157 QGVGAVEPFAFLS  169 (568)
T ss_dssp             HTCCCSCHHHHTT
T ss_pred             cCCcccChHHHhC
Confidence            9999988887776

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.79  E-value=5.6e-06  Score=77.59  Aligned_cols=226  Identities=12%  Similarity=0.028  Sum_probs=142.7

Q ss_pred             HCCChhHHHHHHHHHHHCCCCCCHHH-HHHHHHHHhccC--ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHH----Hhc-
Q 040365          119 QNGLFDEGLKFFRQMLIAKIKPRHVS-FSSIMPACAHLT--TLHLGKQLHGCIIRNGFDDNMFIASSLLDMY----AKC-  190 (514)
Q Consensus       119 ~~g~~~~A~~l~~~m~~~g~~p~~~t-~~~ll~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y----~k~-  190 (514)
                      +....++|++++.++...  .|+..| |+.--.++...+  +++++.++++.++... +-+..+|+.--..+    .+. 
T Consensus        45 ~~e~s~~aL~~t~~~L~~--nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y~aW~~R~~iL~~~~~~l~  121 (306)
T 3dra_A           45 AEEYSERALHITELGINE--LASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNYQIWNYRQLIIGQIMELNN  121 (306)
T ss_dssp             TTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCCHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHHHH--CcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccHHHHHHHHHHHHHHHHhcc
Confidence            344456788888888774  454443 455555556666  7888888888887765 44445555433333    444 


Q ss_pred             --CCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChH--HHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCC-----
Q 040365          191 --GNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAH--DAISLFEQMEKDGVKPNSVAFVAVLTACSHAGL-----  258 (514)
Q Consensus       191 --g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~--~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~-----  258 (514)
                        ++++++.++++.+.   .++..+|+.-.-.+.+.|.++  ++++.+.++.+.... |...|..-.....+.+.     
T Consensus       122 ~~~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll~~l~~~~~~~  200 (306)
T 3dra_A          122 NDFDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK-NNSAWSHRFFLLFSKKHLATDN  200 (306)
T ss_dssp             TCCCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHSSGGGCCHH
T ss_pred             ccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccchhh
Confidence              67788888887775   456677777777777777777  888888888875432 55566655555555555     


Q ss_pred             -HHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHH-HHHHHHhCCC-----CCCHHHHHHHHHHHHhcCCHHHH
Q 040365          259 -IDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQE-AYEFISNMHA-----GPTENVWLTLLSACRVHKNVELA  330 (514)
Q Consensus       259 -~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~-A~~~~~~m~~-----~p~~~~~~~ll~~~~~~~~~~~a  330 (514)
                       +++++++++.+...   .| |...|+-+-..+.+.|+..+ +.++.+++..     ..+...+..+...+.+.|+.++|
T Consensus       201 ~~~eEl~~~~~aI~~---~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A  277 (306)
T 3dra_A          201 TIDEELNYVKDKIVK---CPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNES  277 (306)
T ss_dssp             HHHHHHHHHHHHHHH---CSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hHHHHHHHHHHHHHh---CCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHH
Confidence             67777777766543   44 56666666666666666333 4445554421     23566667777777777777777


Q ss_pred             HHHHHHHHh-cCCCCcchHHHH
Q 040365          331 GKVAEKIFM-IDPNNMGAYVIL  351 (514)
Q Consensus       331 ~~~~~~~~~-~~p~~~~~~~~l  351 (514)
                      .++++.+.+ .+|.....|...
T Consensus       278 ~~~~~~l~~~~Dpir~~yW~~~  299 (306)
T 3dra_A          278 RTVYDLLKSKYNPIRSNFWDYQ  299 (306)
T ss_dssp             HHHHHHHHHTTCGGGHHHHHHH
T ss_pred             HHHHHHHHhccChHHHHHHHHH
Confidence            777777765 566655555433

>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=98.78  E-value=2.1e-07  Score=98.29  Aligned_cols=188  Identities=11%  Similarity=0.061  Sum_probs=145.1

Q ss_pred             hccCChHHHHHHHHHHH--------HcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhC
Q 040365          153 AHLTTLHLGKQLHGCII--------RNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALH  221 (514)
Q Consensus       153 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~  221 (514)
                      ...+++++|.+.+++.+        +.. +.+...+..+...|.+.|++++|.+.|++..   ..+...|..+...|.+.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHc
Confidence            67889999999999888        432 5566788888999999999999999998876   44778899999999999


Q ss_pred             CChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHH
Q 040365          222 GNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAY  299 (514)
Q Consensus       222 g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~  299 (514)
                      |++++|++.|++..+.  .| +...+..+..++...|++++ ...|+...+.   .| +...|..+..+|.+.|++++|.
T Consensus       481 g~~~~A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~---~P~~~~a~~~lg~~~~~~g~~~~A~  554 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDT--FPGELAPKLALAATAELAGNTDE-HKFYQTVWST---NDGVISAAFGLARARSAEGDRVGAV  554 (681)
T ss_dssp             TCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             CCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHh---CCchHHHHHHHHHHHHHcCCHHHHH
Confidence            9999999999999885  44 45778888889999999999 9999988754   55 5788899999999999999999


Q ss_pred             HHHHhCC-CCCC-HHHHHHHHHHHHhcCC-----HHHHHHHHHHHHhcCCCCcch
Q 040365          300 EFISNMH-AGPT-ENVWLTLLSACRVHKN-----VELAGKVAEKIFMIDPNNMGA  347 (514)
Q Consensus       300 ~~~~~m~-~~p~-~~~~~~ll~~~~~~~~-----~~~a~~~~~~~~~~~p~~~~~  347 (514)
                      +.|++.. ..|+ ...|..+..++...++     .+...++.+.+..+.+.++..
T Consensus       555 ~~~~~al~l~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~~~~~~~  609 (681)
T 2pzi_A          555 RTLDEVPPTSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALPPTEPRV  609 (681)
T ss_dssp             HHHHTSCTTSTTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSCTTSTTH
T ss_pred             HHHHhhcccCcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCCCCcHHH
Confidence            9999875 4465 5677777777766554     344444444444554444443

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.77  E-value=2.7e-07  Score=81.85  Aligned_cols=184  Identities=12%  Similarity=0.069  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHH-HHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHH
Q 040365          110 WNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVS-FSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYA  188 (514)
Q Consensus       110 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t-~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~  188 (514)
                      +-.....+.+.|++++|+..|++..+.  .|+... +.. . .   ....              ........+.+...|.
T Consensus         7 ~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~-~-~---~~~~--------------~~~~~~~~~~lg~~~~   65 (208)
T 3urz_A            7 MLQKVSAAIEAGQNGQAVSYFRQTIAL--NIDRTEMYYW-T-N---VDKN--------------SEISSKLATELALAYK   65 (208)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CHHHHHHHHH-H-H---SCTT--------------SHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHH-h-h---hcch--------------hhhhHHHHHHHHHHHH
Confidence            333445566777888888887777664  343222 211 0 0   0000              0011222334666677


Q ss_pred             hcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCC--HHHH
Q 040365          189 KCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGL--IDKA  262 (514)
Q Consensus       189 k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~--~~~a  262 (514)
                      +.|++++|...|++..   +.+...|..+...|...|++++|+..|++..+.  .| +..++..+..++...|.  .+.+
T Consensus        66 ~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~  143 (208)
T 3urz_A           66 KNRNYDKAYLFYKELLQKAPNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKL  143 (208)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHH
Confidence            7777777777776654   335667777777777777777777777777764  34 34556666666554443  2334


Q ss_pred             HHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCHHHHHHHHH
Q 040365          263 WSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPTENVWLTLLS  319 (514)
Q Consensus       263 ~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~~~~~~ll~  319 (514)
                      ...++...   ...|....+..+..++...|++++|...|++.. ..|+......|..
T Consensus       144 ~~~~~~~~---~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l~~  198 (208)
T 3urz_A          144 ETDYKKLS---SPTKMQYARYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTLDK  198 (208)
T ss_dssp             HHHHC------CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHHHH
T ss_pred             HHHHHHHh---CCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            44444332   112222223334445556677777777777653 4566655554443

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.76  E-value=7.7e-08  Score=80.46  Aligned_cols=102  Identities=11%  Similarity=0.067  Sum_probs=89.3

Q ss_pred             CCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHH
Q 040365          274 GIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVI  350 (514)
Q Consensus       274 ~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~  350 (514)
                      .+.| +...+..+...+.+.|++++|.+.|++..  .+.+...|..+..++...|++++|+..|+++++++|+++..|..
T Consensus        30 ~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~  109 (151)
T 3gyz_A           30 AIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFH  109 (151)
T ss_dssp             CSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHH
Confidence            4566 46677788888899999999999998863  33478899999999999999999999999999999999999999


Q ss_pred             HHHHHHHccChhHHHHHHHHHHhCC
Q 040365          351 LSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ++.+|...|++++|.+.+++..+..
T Consensus       110 lg~~~~~lg~~~eA~~~~~~al~l~  134 (151)
T 3gyz_A          110 TGQCQLRLKAPLKAKECFELVIQHS  134 (151)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            9999999999999999999987754

>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=98.76  E-value=2.1e-07  Score=96.24  Aligned_cols=146  Identities=10%  Similarity=-0.046  Sum_probs=104.0

Q ss_pred             cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHH
Q 040365          155 LTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLF  231 (514)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~  231 (514)
                      .|++++|.+.++++++.. +.+...+..+...|.+.|++++|.+.|++..   ..+...|..+...|...|++++|++.|
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            467888888888887764 4567788888899999999999999998764   345678888888999999999999999


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhc---CCHHHHHHHHHhC
Q 040365          232 EQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRA---GKLQEAYEFISNM  305 (514)
Q Consensus       232 ~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~---g~~~~A~~~~~~m  305 (514)
                      ++..+.. +.+...+..+..++...|++++|.+.|+...+.   .| +...+..+...+...   |+.++|.+.+++.
T Consensus        81 ~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~a  154 (568)
T 2vsy_A           81 QQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL---LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAA  154 (568)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHH
T ss_pred             HHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence            9988752 224567888888899999999999999988654   44 567788888888888   9999999888875

>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=98.75  E-value=5e-07  Score=85.50  Aligned_cols=220  Identities=10%  Similarity=0.009  Sum_probs=152.7

Q ss_pred             CCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHH
Q 040365          120 NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCI  199 (514)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~  199 (514)
                      .|++++|.+++++..+.. +..      +   +.-.++++.|...+..+               ...|...|++++|...
T Consensus         4 ~~~~~eA~~~~~~a~k~~-~~~------~---~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~   58 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYL-KTS------F---MKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAKDA   58 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHH-CCC------S---SSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHc-ccc------c---cCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHHHH
Confidence            567889999998876531 111      0   11146677777766654               4567778888888888


Q ss_pred             HHhCCC-----CC----hhHHHHHHHHHHhCCChHHHHHHHHHHHHcC---CCCC--HHHHHHHHHHHHccCCHHHHHHH
Q 040365          200 FDKMDL-----HD----IVSWTAVIMGNALHGNAHDAISLFEQMEKDG---VKPN--SVAFVAVLTACSHAGLIDKAWSY  265 (514)
Q Consensus       200 ~~~m~~-----~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g---~~p~--~~t~~~ll~a~~~~g~~~~a~~~  265 (514)
                      |.+...     .+    ..+|+.+...|...|++++|+..|++....-   -.|.  ..++..+...|.. |++++|+..
T Consensus        59 ~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~  137 (307)
T 2ifu_A           59 YLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHL  137 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHH
Confidence            776531     11    3478888888999999999999999876521   1222  3567788888888 999999999


Q ss_pred             HHHhHHhcCCCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHH
Q 040365          266 FNSMTKDYGIAP----SFEHYAAVADLLGRAGKLQEAYEFISNMH----AGPT----ENVWLTLLSACRVHKNVELAGKV  333 (514)
Q Consensus       266 ~~~m~~~~~~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~~p~----~~~~~~ll~~~~~~~~~~~a~~~  333 (514)
                      |+.....+.-..    ....+..+...|.+.|++++|.+.|++..    ..++    ...+..+...+...|+++.|...
T Consensus       138 ~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~  217 (307)
T 2ifu_A          138 YQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKC  217 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            998765321111    14678888999999999999999998763    1122    23566777788888999999999


Q ss_pred             HHHHHhcCCCCcch-----HHHHHHHHHHccChhHHHHH
Q 040365          334 AEKIFMIDPNNMGA-----YVILSNTYAAARRWKDAASL  367 (514)
Q Consensus       334 ~~~~~~~~p~~~~~-----~~~l~~~~~~~g~~~~a~~~  367 (514)
                      +++.+ +.|....+     ...++.+| ..|+.+.+.++
T Consensus       218 ~~~al-~~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          218 VRESY-SIPGFSGSEDCAALEDLLQAY-DEQDEEQLLRV  254 (307)
T ss_dssp             HHHHT-TSTTSTTSHHHHHHHHHHHHH-HTTCHHHHHHH
T ss_pred             HHHHh-CCCCCCCCHHHHHHHHHHHHH-HhcCHHHHHHH
Confidence            99999 88865432     33455555 56776665553

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.74  E-value=3.6e-08  Score=82.59  Aligned_cols=121  Identities=9%  Similarity=-0.028  Sum_probs=100.9

Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCC
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-A-GPTENVWLTLLSACRVHKN  326 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~-~p~~~~~~~ll~~~~~~~~  326 (514)
                      ...+...|++++|+..++...   ...| +...+-.+...|.+.|++++|.+.|++.. . +.+..+|..+..++...|+
T Consensus         4 G~~~~~~~~~e~ai~~~~~a~---~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            4 GSMRRSKADVERYIASVQGST---PSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ---CCCHHHHHHHHHHHHHHS---CSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcChHHHHHHHHHHhc---ccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCc
Confidence            344566789999999998764   3445 45666788999999999999999999863 3 3478899999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHH-HHHHHh
Q 040365          327 VELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASL-RVFMRN  373 (514)
Q Consensus       327 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~-~~~m~~  373 (514)
                      +++|+..++++++++|+++.+|..++.+|.+.|++++|.+. +++..+
T Consensus        81 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~  128 (150)
T 4ga2_A           81 TDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAK  128 (150)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999887765 466654

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.72  E-value=9.2e-08  Score=79.86  Aligned_cols=101  Identities=12%  Similarity=0.027  Sum_probs=87.3

Q ss_pred             CCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHH
Q 040365          274 GIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVI  350 (514)
Q Consensus       274 ~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~  350 (514)
                      .+.| +...+..+...+.+.|++++|...|++..  .+.+...|..+..++...|++++|+..++++++++|+++.++..
T Consensus        15 ~~~p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~   94 (148)
T 2vgx_A           15 EISSDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFH   94 (148)
T ss_dssp             TCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHH
T ss_pred             cCCHhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHH
Confidence            4455 45667778888899999999999998763  33478889999999999999999999999999999999999999


Q ss_pred             HHHHHHHccChhHHHHHHHHHHhC
Q 040365          351 LSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++.+|...|++++|.+.++...+.
T Consensus        95 lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           95 AAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH
Confidence            999999999999999999988664

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.72  E-value=6.8e-07  Score=83.67  Aligned_cols=164  Identities=9%  Similarity=-0.009  Sum_probs=104.1

Q ss_pred             CCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--CChhHHH-HHH
Q 040365          139 KPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--HDIVSWT-AVI  215 (514)
Q Consensus       139 ~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~d~~~~~-~li  215 (514)
                      +.+...+..+...+.+.|++++|.+.++.+++.. +.+...+..|...|.+.|++++|...|++...  |+..... ...
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~  192 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQ  192 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHH
Confidence            3344455566667777788888888888877764 45566777778888888888888888887763  3333222 222


Q ss_pred             HHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCH
Q 040365          216 MGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKL  295 (514)
Q Consensus       216 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~  295 (514)
                      ..+.+.++.++|+..|++..... +.+...+..+..++...|++++|...|..+.+...-..+...+..++..|...|+.
T Consensus       193 ~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~  271 (287)
T 3qou_A          193 IELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTG  271 (287)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTT
T ss_pred             HHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCC
Confidence            23556667777777777776642 22445666677777777777777777777765411111245566666666666666


Q ss_pred             HHHHHHHHh
Q 040365          296 QEAYEFISN  304 (514)
Q Consensus       296 ~~A~~~~~~  304 (514)
                      ++|...+++
T Consensus       272 ~~a~~~~r~  280 (287)
T 3qou_A          272 DALASXYRR  280 (287)
T ss_dssp             CHHHHHHHH
T ss_pred             CcHHHHHHH
Confidence            666655543

>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=98.72  E-value=2.3e-07  Score=79.84  Aligned_cols=75  Identities=12%  Similarity=-0.061  Sum_probs=57.1

Q ss_pred             HHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--cchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          298 AYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN--MGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       298 A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~--~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      |.+.+++.. ..| +...+..+...+...|++++|...++++++.+|+.  +..+..++.+|...|+.++|...+++..
T Consensus        93 a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~~al  171 (176)
T 2r5s_A           93 ELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQL  171 (176)
T ss_dssp             HHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHHHHH
Confidence            444444431 223 57788888888888899999999999988888764  5588888899999999999888887654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.70  E-value=3.5e-07  Score=81.14  Aligned_cols=126  Identities=10%  Similarity=0.079  Sum_probs=94.0

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHH
Q 040365          213 AVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLG  290 (514)
Q Consensus       213 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~  290 (514)
                      .+...|.+.|++++|+..|++..+.  .| +...+..+...+...|++++|...|+...+.   .| +...+..+...|.
T Consensus        59 ~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~---~P~~~~a~~~lg~~~~  133 (208)
T 3urz_A           59 ELALAYKKNRNYDKAYLFYKELLQK--APNNVDCLEACAEMQVCRGQEKDALRMYEKILQL---EADNLAANIFLGNYYY  133 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHH
Confidence            3788888999999999999998885  44 4577888888899999999999999988754   56 5778888888776


Q ss_pred             hcCC--HHHHHHHHHhCCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040365          291 RAGK--LQEAYEFISNMHAGPTE--NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN  344 (514)
Q Consensus       291 ~~g~--~~~A~~~~~~m~~~p~~--~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~  344 (514)
                      ..|.  .+.+...++... .|+.  ..|..+..++...|++++|+..+++++++.|++
T Consensus       134 ~~~~~~~~~~~~~~~~~~-~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~  190 (208)
T 3urz_A          134 LTAEQEKKKLETDYKKLS-SPTKMQYARYRDGLSKLFTTRYEKARNSLQKVILRFPST  190 (208)
T ss_dssp             HHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCH
T ss_pred             HHhHHHHHHHHHHHHHHh-CCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCH
Confidence            6553  445566666654 3433  344555666777889999999999999998863

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.70  E-value=5.8e-06  Score=77.46  Aligned_cols=212  Identities=9%  Similarity=0.084  Sum_probs=168.4

Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC--CHHHHHHHHHhCC---CCChhHHHHHHHHH----HhC---CCh
Q 040365          157 TLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG--NIRLARCIFDKMD---LHDIVSWTAVIMGN----ALH---GNA  224 (514)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g--~~~~A~~~~~~m~---~~d~~~~~~li~~~----~~~---g~~  224 (514)
                      ..++|.+..+.++..+ +.+..+|+.--..+...|  +++++.+.++.+.   ..+..+|+.--..+    ...   +++
T Consensus        48 ~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~  126 (306)
T 3dra_A           48 YSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDP  126 (306)
T ss_dssp             CSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCT
T ss_pred             CCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCH
Confidence            3468889999998876 566778888888888888  9999999999886   44667788765555    555   789


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHH--HHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCC------H
Q 040365          225 HDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLID--KAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGK------L  295 (514)
Q Consensus       225 ~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~--~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~------~  295 (514)
                      +++++++.++.+.. +-|...|..-...+.+.|.++  +++++++.+.+.   .| +...|+.-...+.+.|.      +
T Consensus       127 ~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~---d~~N~sAW~~R~~ll~~l~~~~~~~~~  202 (306)
T 3dra_A          127 YREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDT---DLKNNSAWSHRFFLLFSKKHLATDNTI  202 (306)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHSSGGGCCHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHhccccchhhhH
Confidence            99999999999863 336677777777777888888  999999999765   44 56666666666666666      8


Q ss_pred             HHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHH-HHHHHHHHHHhcC---CCCcchHHHHHHHHHHccChhHHHHHHH
Q 040365          296 QEAYEFISNMH--AGPTENVWLTLLSACRVHKNVE-LAGKVAEKIFMID---PNNMGAYVILSNTYAAARRWKDAASLRV  369 (514)
Q Consensus       296 ~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~-~a~~~~~~~~~~~---p~~~~~~~~l~~~~~~~g~~~~a~~~~~  369 (514)
                      +++++.++++.  .+-|...|+.+-..+...|+.. ....+++++.+++   |.++.++..++.+|.+.|+.++|.++++
T Consensus       203 ~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~  282 (306)
T 3dra_A          203 DEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYD  282 (306)
T ss_dssp             HHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Confidence            89999888763  3458889999999998888744 4566778777776   7888899999999999999999999999


Q ss_pred             HHHh
Q 040365          370 FMRN  373 (514)
Q Consensus       370 ~m~~  373 (514)
                      .+.+
T Consensus       283 ~l~~  286 (306)
T 3dra_A          283 LLKS  286 (306)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            9875

>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=98.70  E-value=2.3e-06  Score=80.27  Aligned_cols=159  Identities=8%  Similarity=-0.067  Sum_probs=114.4

Q ss_pred             HHHHHHhCCChHHHHHHHHHHHHcC-CCCCHH----HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC----HhHHHH
Q 040365          214 VIMGNALHGNAHDAISLFEQMEKDG-VKPNSV----AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS----FEHYAA  284 (514)
Q Consensus       214 li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~----t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~----~~~~~~  284 (514)
                      .+..+...|++++|..++++..... ..|+..    .+..+...+...+++++|...|+...+...-.++    ...++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            3566777888888888888877632 223321    2334566667777888888888887653221222    236788


Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC-------CC-CC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC------CcchHH
Q 040365          285 VADLLGRAGKLQEAYEFISNMH-------AG-PT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN------NMGAYV  349 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~-------~~-p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~------~~~~~~  349 (514)
                      +...|...|++++|.+.++++.       .. +. ..++..+...|...|++++|...+++++++.+.      -+.+|.
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~  240 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            8888888888888888887653       11 11 247888999999999999999999999876522      256888


Q ss_pred             HHHHHHHHccC-hhHHHHHHHHHH
Q 040365          350 ILSNTYAAARR-WKDAASLRVFMR  372 (514)
Q Consensus       350 ~l~~~~~~~g~-~~~a~~~~~~m~  372 (514)
                      .++.+|.+.|+ +++|.+.+++..
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHH
Confidence            99999999995 699999888765

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.69  E-value=3.8e-07  Score=78.44  Aligned_cols=155  Identities=9%  Similarity=-0.056  Sum_probs=96.3

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHccCCC---CChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHH-Hh
Q 040365           78 IGSSLINMYAKCARVEDSHRLFCLLPV---KDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPA-CA  153 (514)
Q Consensus        78 ~~~~li~~~~~~g~~~~A~~~f~~~~~---~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~-~~  153 (514)
                      ....+...+.+.|++++|...|++..+   .+...|..+...+.+.|++++|+..|++....  .|+...+...... +.
T Consensus         8 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~~~~~~~   85 (176)
T 2r5s_A            8 QLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLE--YQDNSYKSLIAKLELH   85 (176)
T ss_dssp             THHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG--GCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc--cCChHHHHHHHHHHHH
Confidence            344556667777888888888877663   35667777778888888888888888776553  2333322211111 11


Q ss_pred             ccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC--C---ChhHHHHHHHHHHhCCChHHHH
Q 040365          154 HLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL--H---DIVSWTAVIMGNALHGNAHDAI  228 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~--~---d~~~~~~li~~~~~~g~~~~A~  228 (514)
                      ..+....+...++..++.. +.+...+..+...|.+.|++++|...|+++..  |   +...|..+...+...|+.++|.
T Consensus        86 ~~~~~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~  164 (176)
T 2r5s_A           86 QQAAESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIA  164 (176)
T ss_dssp             HHHTSCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHH
T ss_pred             hhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHH
Confidence            2222233566666666653 44566666777777777777777777776542  2   2346677777777777777777


Q ss_pred             HHHHHHH
Q 040365          229 SLFEQME  235 (514)
Q Consensus       229 ~l~~~m~  235 (514)
                      ..|++..
T Consensus       165 ~~y~~al  171 (176)
T 2r5s_A          165 SKYRRQL  171 (176)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776654

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.68  E-value=3.4e-07  Score=73.96  Aligned_cols=112  Identities=16%  Similarity=0.102  Sum_probs=75.6

Q ss_pred             CCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHH
Q 040365          239 VKPNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVW  314 (514)
Q Consensus       239 ~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~  314 (514)
                      +.|+. ..+......+.+.|++++|+..|+...+.   .| +...|..+..+|.+.|++++|++.+++..  .+.+...|
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~   84 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKR---DPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGY   84 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHH
Confidence            34443 34556666677777777777777766543   34 56666677777777777777777776642  23456677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHH
Q 040365          315 LTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSN  353 (514)
Q Consensus       315 ~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~  353 (514)
                      ..+..++...|++++|+..|+++++++|++..++..|.+
T Consensus        85 ~~lg~~~~~~~~~~~A~~~~~~al~l~P~~~~a~~~l~~  123 (126)
T 4gco_A           85 IRKAACLVAMREWSKAQRAYEDALQVDPSNEEAREGVRN  123 (126)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHCcCCHHHHHHHHH
Confidence            777777888888888888888888888877766665544

>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=98.68  E-value=6.5e-07  Score=79.35  Aligned_cols=125  Identities=11%  Similarity=0.035  Sum_probs=99.0

Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHh
Q 040365          246 FVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRV  323 (514)
Q Consensus       246 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~  323 (514)
                      +..+...+...|++++|...|+..     +.|+...+..+...|.+.|++++|.+.+++..  .+.+...|..+..++..
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a-----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~   83 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQ   83 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHH-----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHH
Confidence            344555666777777777777755     24566777777777888888888888777652  23467788888889999


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCc----------------chHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          324 HKNVELAGKVAEKIFMIDPNNM----------------GAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~----------------~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      .|++++|...++++++..|.+.                ..+..++.+|...|++++|.+.++...+..
T Consensus        84 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           84 TEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             TTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             cccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            9999999999999999888776                889999999999999999999999987654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.65  E-value=3.1e-05  Score=78.12  Aligned_cols=385  Identities=7%  Similarity=-0.072  Sum_probs=228.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCC-hHHHHHHHHHHHHh-CC-CCchhHHHHHHH
Q 040365            8 SWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVD-VIKGKEIHGYAIRH-GL-DANVCIGSSLIN   84 (514)
Q Consensus         8 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~-~~~a~~~~~~~~~~-g~-~~~~~~~~~li~   84 (514)
                      .|...+..+-. |+++.+..+|++....  .|+...|..-++...+.++ .+...++|+.++.. |. +.+..+|...+.
T Consensus        17 vyer~l~~~P~-~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~~vg~d~~s~~iW~~Yi~   93 (493)
T 2uy1_A           17 IMEHARRLYMS-KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLGQFENYWDSYGLYKEYIE   93 (493)
T ss_dssp             HHHHHHHHHHT-TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHHHSTTCTTCHHHHHHHHH
T ss_pred             HHHHHHHHCCC-CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHcCCCcccHHHHHHHHH
Confidence            45566666654 7899999999999874  5788888887776655543 35567788888775 53 346677777777


Q ss_pred             HHH----HCCCHHHHHHHHccCCC-C--Ch-hHHHHHHHHHH-------------HCCChhHHHHHHHHHHHCCCCCCHH
Q 040365           85 MYA----KCARVEDSHRLFCLLPV-K--DA-ISWNSIIAGCV-------------QNGLFDEGLKFFRQMLIAKIKPRHV  143 (514)
Q Consensus        85 ~~~----~~g~~~~A~~~f~~~~~-~--d~-~~~~~li~~~~-------------~~g~~~~A~~l~~~m~~~g~~p~~~  143 (514)
                      .+.    ..|+++.++++|++... |  +. ..|......-.             ..+.+..|..++.++...--..+..
T Consensus        94 f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~~~~~y~~ar~~y~~~~~~~~~~s~~  173 (493)
T 2uy1_A           94 EEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENFELELNKITGKKIVGDTLPIFQSSFQRYQQIQPLIRGWSVK  173 (493)
T ss_dssp             HTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSHH
T ss_pred             HHHhchhhhHHHHHHHHHHHHHHhChhhhHHHHHHHHHHHHHHhccccHHHHHHHHhHHHHHHHHHHHHHHHHHhhccHH
Confidence            654    34678889999987642 2  11 12222211100             0112333444444443210001333


Q ss_pred             HHHHHHHHHhcc--CC-----hHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CCChhHHHHH
Q 040365          144 SFSSIMPACAHL--TT-----LHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD--LHDIVSWTAV  214 (514)
Q Consensus       144 t~~~ll~~~~~~--~~-----~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~d~~~~~~l  214 (514)
                      .|...+.--...  +.     .+.+..++++++... +.+..+|-..+..+.+.|+++.|..+|++..  +.+...|.  
T Consensus       174 ~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~-p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~P~~~~l~~--  250 (493)
T 2uy1_A          174 NAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSF-YYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEMSDGMFLSL--  250 (493)
T ss_dssp             HHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHT-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHH--
T ss_pred             HHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCcHHHHH--
Confidence            454444433221  11     345677888888764 5567788888888888999999999998653  22333333  


Q ss_pred             HHHHHhCCChHHHHHHHHHHHHcC---------CCC---CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHH
Q 040365          215 IMGNALHGNAHDAISLFEQMEKDG---------VKP---NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHY  282 (514)
Q Consensus       215 i~~~~~~g~~~~A~~l~~~m~~~g---------~~p---~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~  282 (514)
                        .|+...+.++.   ++.+.+.-         ..+   ....|...+....+.+..+.|..+|+.. +..+  ++...|
T Consensus       251 --~y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~~--~~~~v~  322 (493)
T 2uy1_A          251 --YYGLVMDEEAV---YGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNEG--VGPHVF  322 (493)
T ss_dssp             --HHHHHTTCTHH---HHHHHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTSC--CCHHHH
T ss_pred             --HHHhhcchhHH---HHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCCC--CChHHH
Confidence              23322222222   23322210         011   1244666666666778899999999988 3211  244555


Q ss_pred             HHHHHHHHhcC-CHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHcc
Q 040365          283 AAVADLLGRAG-KLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR  359 (514)
Q Consensus       283 ~~li~~~~~~g-~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  359 (514)
                      .....+-.+.+ +.+.|..+|+...  .+.+...|...+.-....|+.+.|..+|+++    +.....|...+..-...|
T Consensus       323 i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~~~~~aR~l~er~----~k~~~lw~~~~~fE~~~G  398 (493)
T 2uy1_A          323 IYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDEENARALFKRL----EKTSRMWDSMIEYEFMVG  398 (493)
T ss_dssp             HHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHS----CCBHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH----HHHHHHHHHHHHHHHHCC
Confidence            44343333334 6999999998752  2223556777777778899999999999997    234566777777777889


Q ss_pred             ChhHHHHHHHHHHh----CC-CccCCc-ccEEEECCEEEEEEeCCCCCCChHHHHHHHHHHHHHHHhCCcccCC
Q 040365          360 RWKDAASLRVFMRN----KG-MKKTPA-CSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERMEQEGYVPDT  427 (514)
Q Consensus       360 ~~~~a~~~~~~m~~----~g-~~~~~~-~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~  427 (514)
                      +.+.+.++++++.+    .+ -.|.+- .+|.                 ..++....++.++..-.-..+.|-.
T Consensus       399 ~~~~~r~v~~~~~~~~~~~~~~~~~~~~~~~~-----------------~fe~~~g~l~~~~~~~~~~~~~~~~  455 (493)
T 2uy1_A          399 SMELFRELVDQKMDAIKADAILPPLPPREHNV-----------------QMEGILGRYHCFLDSFNFLDLKIRD  455 (493)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCBCCCCCC--CC-----------------CCCHHHHHHHHHHHHHCBTTBCCCC
T ss_pred             CHHHHHHHHHHHHHHhcccccCCcccccccHH-----------------HHHHHhhhHHHHHHHhhhhccccCC
Confidence            99999998887764    11 111111 2443                 2245555666777776666666654

>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=98.65  E-value=1.7e-06  Score=76.90  Aligned_cols=171  Identities=12%  Similarity=-0.016  Sum_probs=108.5

Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC-CCChhHHHHHHHHHHhCC----ChHHHHHHHHHHHH
Q 040365          162 KQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD-LHDIVSWTAVIMGNALHG----NAHDAISLFEQMEK  236 (514)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~-~~d~~~~~~li~~~~~~g----~~~~A~~l~~~m~~  236 (514)
                      .+.+....+.|   +...+..|..+|...|++++|.+.|++.. ..+..++..+...|.. +    ++++|+.+|++..+
T Consensus         6 ~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~   81 (212)
T 3rjv_A            6 GSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQQADYPQARQLAEKAVE   81 (212)
T ss_dssp             THHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHH
Confidence            34444444433   34445555556666666666666666554 2345555556555555 4    67777777777766


Q ss_pred             cCCCCCHHHHHHHHHHHHc----cCCHHHHHHHHHHhHHhcCCCCC---HhHHHHHHHHHHh----cCCHHHHHHHHHhC
Q 040365          237 DGVKPNSVAFVAVLTACSH----AGLIDKAWSYFNSMTKDYGIAPS---FEHYAAVADLLGR----AGKLQEAYEFISNM  305 (514)
Q Consensus       237 ~g~~p~~~t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~p~---~~~~~~li~~~~~----~g~~~~A~~~~~~m  305 (514)
                      .|   +...+..+...+..    .+++++|..+|+...+   ..|.   +..+..|..+|..    .+++++|.++|++.
T Consensus        82 ~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~---~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A  155 (212)
T 3rjv_A           82 AG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAAR---DSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGS  155 (212)
T ss_dssp             TT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTS---STTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHH
T ss_pred             CC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHH---cCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            54   44556666666665    6778888888877643   2332   5667777777777    67788888888776


Q ss_pred             CCC-CCHHHHHHHHHHHHhc-C-----CHHHHHHHHHHHHhcCC
Q 040365          306 HAG-PTENVWLTLLSACRVH-K-----NVELAGKVAEKIFMIDP  342 (514)
Q Consensus       306 ~~~-p~~~~~~~ll~~~~~~-~-----~~~~a~~~~~~~~~~~p  342 (514)
                      ... ++...+..|...|... |     +.++|...+++..+.+.
T Consensus       156 ~~~~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          156 SSLSRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHTSCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            322 4556677777776543 2     78888888888877764

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.64  E-value=3e-07  Score=74.28  Aligned_cols=101  Identities=11%  Similarity=0.069  Sum_probs=90.6

Q ss_pred             CCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHH
Q 040365          274 GIAPS-FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVI  350 (514)
Q Consensus       274 ~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~  350 (514)
                      -+.|+ ...+......|.+.|++++|.+.|++..  .+.+..+|..+..++...|++++|+..++++++++|+++.+|..
T Consensus         7 ~inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~   86 (126)
T 4gco_A            7 YINPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIR   86 (126)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHH
Confidence            35663 5677888999999999999999999863  34578899999999999999999999999999999999999999


Q ss_pred             HHHHHHHccChhHHHHHHHHHHhC
Q 040365          351 LSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++.+|...|++++|.+.+++..+.
T Consensus        87 lg~~~~~~~~~~~A~~~~~~al~l  110 (126)
T 4gco_A           87 KAACLVAMREWSKAQRAYEDALQV  110 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHH
Confidence            999999999999999999988764

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.62  E-value=1.7e-07  Score=87.55  Aligned_cols=190  Identities=9%  Similarity=-0.102  Sum_probs=109.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHH
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTA  252 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a  252 (514)
                      ...+..+...|.+.|++++|...|++..   ..+...|..+...|.+.|++++|+..+++..+.  .| +...+..+..+
T Consensus         4 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~   81 (281)
T 2c2l_A            4 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQC   81 (281)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            3444555556666666666666666543   235556666666666667777777766666553  33 34556666666


Q ss_pred             HHccCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHH
Q 040365          253 CSHAGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAG  331 (514)
Q Consensus       253 ~~~~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~  331 (514)
                      +...|++++|...|+...+.   .|+ ...+...+....+........ ........++..+...+. .+ ..|+.++|.
T Consensus        82 ~~~~g~~~~A~~~~~~al~l---~p~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~i~~~l~-~l-~~~~~~~A~  155 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYSL---AKEQRLNFGDDIPSALRIAKKKRWN-SIEERRIHQESELHSYLT-RL-IAAEREREL  155 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---HHHTTCCCCSHHHHHHHHHHHHHHH-HHHHTCCCCCCHHHHHHH-HH-HHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh---CccchhhHHHHHHHHHHHHHHHHHH-HHHHHHHhhhHHHHHHHH-HH-HHHHHHHHH
Confidence            77777777777777665432   121 001111111111111111111 122223333444433332 22 268889999


Q ss_pred             HHHHHHHhcCCCCcchHHHHHHHHHHc-cChhHHHHHHHHHHhC
Q 040365          332 KVAEKIFMIDPNNMGAYVILSNTYAAA-RRWKDAASLRVFMRNK  374 (514)
Q Consensus       332 ~~~~~~~~~~p~~~~~~~~l~~~~~~~-g~~~~a~~~~~~m~~~  374 (514)
                      ..++++.+++|++......+...+.+. +++++|.++|....+.
T Consensus       156 ~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          156 EECQRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             TTTSGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HHHHhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            999999999998777777777777766 7799999999888653

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.62  E-value=1.3e-06  Score=81.88  Aligned_cols=163  Identities=8%  Similarity=-0.094  Sum_probs=112.5

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCC-H----HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCC--CCC--Hh
Q 040365          210 SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPN-S----VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGI--APS--FE  280 (514)
Q Consensus       210 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~----~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~--~p~--~~  280 (514)
                      .+...+..+...|++++|++.+.+..+.....+ .    ..+..+...+...|++++|...++...+...-  .+.  ..
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            444556667777888888888877766422211 1    12334455567778888888888776532111  111  34


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC----CCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC------Cc
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNMH----AGPT-----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN------NM  345 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m~----~~p~-----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~------~~  345 (514)
                      .|+.+...|...|++++|.+.+++..    ..|+     ..++..+...|...|++++|...++++++..+.      -.
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~  236 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            77788888888888888888887652    1122     257888889999999999999999998876421      15


Q ss_pred             chHHHHHHHHHHccChhHH-HHHHHHHH
Q 040365          346 GAYVILSNTYAAARRWKDA-ASLRVFMR  372 (514)
Q Consensus       346 ~~~~~l~~~~~~~g~~~~a-~~~~~~m~  372 (514)
                      .+|..++.+|.+.|++++| ...+++..
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al  264 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            6788999999999999999 77676654

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.62  E-value=6.7e-07  Score=73.85  Aligned_cols=101  Identities=16%  Similarity=0.011  Sum_probs=85.3

Q ss_pred             CCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHH
Q 040365          274 GIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVI  350 (514)
Q Consensus       274 ~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~  350 (514)
                      .+.| +...+..+...+.+.|++++|...|++..  .+.+...|..+..++...|++++|+..++++++++|+++..+..
T Consensus        12 ~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~   91 (142)
T 2xcb_A           12 GLSEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFH   91 (142)
T ss_dssp             TCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHH
Confidence            3445 34556667778888999999999988763  23477889999999999999999999999999999999999999


Q ss_pred             HHHHHHHccChhHHHHHHHHHHhC
Q 040365          351 LSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++.+|...|++++|.+.++...+.
T Consensus        92 lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           92 AAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh
Confidence            999999999999999999988654

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.62  E-value=3.6e-06  Score=75.46  Aligned_cols=183  Identities=15%  Similarity=0.040  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHHcCCC-C-cHHHHHHHHHHHHhcCCHHHHHHHHHhCC--CCC-h---hHHHH
Q 040365          142 HVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFD-D-NMFIASSLLDMYAKCGNIRLARCIFDKMD--LHD-I---VSWTA  213 (514)
Q Consensus       142 ~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~d-~---~~~~~  213 (514)
                      ...+-.+...+.+.|++++|...++.+++.... + ....+..+..+|.+.|++++|...|++..  .|+ .   .++..
T Consensus         4 ~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~~   83 (225)
T 2yhc_A            4 PNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYM   83 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHHH
Confidence            345556677788999999999999999986421 1 24567788999999999999999999975  232 2   24555


Q ss_pred             HHHHHHh------------------CCChHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHHccCCHHHHHHHHHHhHHhcC
Q 040365          214 VIMGNAL------------------HGNAHDAISLFEQMEKDGVKPNSV-AFVAVLTACSHAGLIDKAWSYFNSMTKDYG  274 (514)
Q Consensus       214 li~~~~~------------------~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~  274 (514)
                      +..++..                  .|+.++|+..|+++.+.  .|+.. ......    ..      ..+...+     
T Consensus        84 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~----~l------~~~~~~~-----  146 (225)
T 2yhc_A           84 RGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATK----RL------VFLKDRL-----  146 (225)
T ss_dssp             HHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHH----HH------HHHHHHH-----
T ss_pred             HHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHH----HH------HHHHHHH-----
Confidence            5555543                  57899999999999874  45542 111110    00      0111111     


Q ss_pred             CCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          275 IAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       275 ~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                          ......+...|.+.|++++|...|+++. ..|+    ...+..+..++.+.|+.++|...++.+....|++.
T Consensus       147 ----~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~~  218 (225)
T 2yhc_A          147 ----AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTL  218 (225)
T ss_dssp             ----HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCCC
T ss_pred             ----HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCch
Confidence                1122356777889999999999998763 2243    25688889999999999999999999988888764

>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=98.61  E-value=1.4e-06  Score=73.54  Aligned_cols=126  Identities=10%  Similarity=0.011  Sum_probs=93.3

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSAC  321 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~  321 (514)
                      .+..+...+...|++++|...|+...+.   .| +...+..+...+...|++++|.+.+++..  .+.+...|..+..++
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~   91 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            3455555666677777777777766543   23 46666777777777777777777776642  234577888888899


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHH--HHHccChhHHHHHHHHHHh
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNT--YAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~--~~~~g~~~~a~~~~~~m~~  373 (514)
                      ...|++++|...++++++..|.+...+..+..+  +...|++++|.+.+.....
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            999999999999999999999888877544444  8888999999999887653

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.60  E-value=6.7e-06  Score=83.00  Aligned_cols=324  Identities=8%  Similarity=-0.080  Sum_probs=197.8

Q ss_pred             cC-ChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCC-HHHHH
Q 040365           19 NG-LYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCAR-VEDSH   96 (514)
Q Consensus        19 ~g-~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~-~~~A~   96 (514)
                      .| +++.|..+|+.+...  -|.              ++.+.+.++|+..+..  .|++.+|...+..-.+.++ .+...
T Consensus         7 ~~~~i~~aR~vyer~l~~--~P~--------------~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~   68 (493)
T 2uy1_A            7 MGVELSSPSAIMEHARRL--YMS--------------KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLY   68 (493)
T ss_dssp             -----CCHHHHHHHHHHH--HHT--------------TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTH
T ss_pred             cCcchHHHHHHHHHHHHH--CCC--------------CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHH
Confidence            45 367777777777652  232              7899999999999885  4799999998888877764 34455


Q ss_pred             HHHccCC------CCChhHHHHHHHHHH----HCCChhHHHHHHHHHHHCCCCCCH--HHHHHHHHHHh-----------
Q 040365           97 RLFCLLP------VKDAISWNSIIAGCV----QNGLFDEGLKFFRQMLIAKIKPRH--VSFSSIMPACA-----------  153 (514)
Q Consensus        97 ~~f~~~~------~~d~~~~~~li~~~~----~~g~~~~A~~l~~~m~~~g~~p~~--~t~~~ll~~~~-----------  153 (514)
                      .+|+...      ..+...|...+.-+.    .+++.+.+..+|++....  ++..  ..|......-.           
T Consensus        69 ~~fe~al~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~--P~~~~~~lw~~Y~~fE~~~~~~~~~~~~  146 (493)
T 2uy1_A           69 EVYEFTLGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQT--PMGSLSELWKDFENFELELNKITGKKIV  146 (493)
T ss_dssp             HHHHHHHHHSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTS--CCTTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhC--hhhhHHHHHHHHHHHHHHhccccHHHHH
Confidence            5665532      235677888776543    346788899999999873  2221  12211111000           


Q ss_pred             --ccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhc--CC-----HHHHHHHHHhCC---CCChhHHHHHHHHHHhC
Q 040365          154 --HLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKC--GN-----IRLARCIFDKMD---LHDIVSWTAVIMGNALH  221 (514)
Q Consensus       154 --~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~--g~-----~~~A~~~~~~m~---~~d~~~~~~li~~~~~~  221 (514)
                        ..+.+..|+.++..+.+.--..+...|...++.--..  |-     .+.+..+|+++.   ..+...|-..+.-+.+.
T Consensus       147 ~~~~~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~p~~~~lW~~ya~~~~~~  226 (493)
T 2uy1_A          147 GDTLPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFYYAEEVYFFYSEYLIGI  226 (493)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHT
T ss_pred             HHHhHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHc
Confidence              0122333455554443321011334555555543221  11     244566777765   34567888888888899


Q ss_pred             CChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC--------CCC---CHhHHHHHHHHHH
Q 040365          222 GNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG--------IAP---SFEHYAAVADLLG  290 (514)
Q Consensus       222 g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~--------~~p---~~~~~~~li~~~~  290 (514)
                      |+.++|..+|++....   |+...+..   ++......++.   ++.+.+.+-        ..+   ....|...++.+.
T Consensus       227 ~~~~~ar~i~erAi~~---P~~~~l~~---~y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~  297 (493)
T 2uy1_A          227 GQKEKAKKVVERGIEM---SDGMFLSL---YYGLVMDEEAV---YGDLKRKYSMGEAESAEKVFSKELDLLRINHLNYVL  297 (493)
T ss_dssp             TCHHHHHHHHHHHHHH---CCSSHHHH---HHHHHTTCTHH---HHHHHHHTC----------CHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhC---CCcHHHHH---HHHhhcchhHH---HHHHHHHHHhhccchhhhhcccccHHHHHHHHHHHH
Confidence            9999999999999987   55433222   12221111111   222222110        011   2355777777777


Q ss_pred             hcCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHH-hcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHH
Q 040365          291 RAGKLQEAYEFISNMHAG-PTENVWLTLLSACR-VHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLR  368 (514)
Q Consensus       291 ~~g~~~~A~~~~~~m~~~-p~~~~~~~ll~~~~-~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~  368 (514)
                      +.+.++.|..+|++...+ .+..+|......-. ..++.+.|..+|+.+++..|+++..+...+....+.|+.+.|+.++
T Consensus       298 r~~~~~~AR~i~~~A~~~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~~~~~aR~l~  377 (493)
T 2uy1_A          298 KKRGLELFRKLFIELGNEGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIGDEENARALF  377 (493)
T ss_dssp             HHHCHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHhhCCCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            888999999999988322 23445543222222 2346999999999999988888877777888888999999999999


Q ss_pred             HHH
Q 040365          369 VFM  371 (514)
Q Consensus       369 ~~m  371 (514)
                      +..
T Consensus       378 er~  380 (493)
T 2uy1_A          378 KRL  380 (493)
T ss_dssp             HHS
T ss_pred             HHH
Confidence            986

>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=98.58  E-value=2.6e-06  Score=75.40  Aligned_cols=146  Identities=10%  Similarity=-0.077  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCC
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGL  258 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~  258 (514)
                      .+..+...|.+.|++++|.+.|++...++...|..+...|...|++++|+..|++..... +.+...+..+..++...|+
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~   86 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   86 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHccc
Confidence            344556667777777777777777766666777777777777777777777777766642 2244556666666667777


Q ss_pred             HHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040365          259 IDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGP-TENVWLTLLSACRVHKNVELAGKVAEKI  337 (514)
Q Consensus       259 ~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~  337 (514)
                      +++|...|+...+...-.+...        +...|           +...| +...|..+..++...|+++.|...++++
T Consensus        87 ~~~A~~~~~~al~~~~~~~~~~--------~~~~~-----------~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  147 (213)
T 1hh8_A           87 YDLAIKDLKEALIQLRGNQLID--------YKILG-----------LQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALA  147 (213)
T ss_dssp             HHHHHHHHHHHHHTTTTCSEEE--------CGGGT-----------BCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCccHHH--------HHHhc-----------cccCccchHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            7777777766654211111000        00000           01122 2467888888899999999999999999


Q ss_pred             HhcCCCC
Q 040365          338 FMIDPNN  344 (514)
Q Consensus       338 ~~~~p~~  344 (514)
                      ++..|.+
T Consensus       148 l~~~p~~  154 (213)
T 1hh8_A          148 TSMKSEP  154 (213)
T ss_dssp             HTTCCSG
T ss_pred             HHcCccc
Confidence            9998875

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.56  E-value=1.5e-06  Score=69.02  Aligned_cols=114  Identities=20%  Similarity=0.221  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSAC  321 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~  321 (514)
                      ..+..+...+...|++++|..+|+.+.+..  +.+...+..+...+.+.|++++|..+++++.  .+.+..+|..+...+
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~   87 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHH
Confidence            445555666666666666666666665431  1245566666777777777777777776652  234667788888888


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHcc
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAAR  359 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  359 (514)
                      ...|+++.|...++++.+..|.++..+..+..++...|
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  125 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQKQG  125 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHC
T ss_pred             HHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcc
Confidence            88899999999999998888888888888777776543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.54  E-value=1.5e-06  Score=69.71  Aligned_cols=116  Identities=11%  Similarity=-0.002  Sum_probs=86.7

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHH
Q 040365          243 SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLS  319 (514)
Q Consensus       243 ~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~  319 (514)
                      ...+..+...+...|++++|...|+.....   .| +...+..+...+...|++++|.+.+++..  .+.+...|..+..
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~   88 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIEL---NPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGL   88 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHH
Confidence            345556666666777777777777766543   23 45666777777777777777777776642  2345677888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccCh
Q 040365          320 ACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRW  361 (514)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  361 (514)
                      .+...|+++.|...++++++..|.++..+..+..++...|++
T Consensus        89 ~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~  130 (131)
T 2vyi_A           89 ALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREA  130 (131)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhcC
Confidence            899999999999999999999999888888898888888775

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.53  E-value=1.5e-06  Score=70.13  Aligned_cols=114  Identities=15%  Similarity=0.038  Sum_probs=75.1

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSA  320 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~  320 (514)
                      ..+..+...+...|++++|...|+...+   ..| +...+..+...|...|++++|.+.+++..  .+.+...|..+..+
T Consensus        17 ~~~~~~~~~~~~~~~~~~A~~~~~~al~---~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   93 (133)
T 2lni_A           17 LMVKNKGNECFQKGDYPQAMKHYTEAIK---RNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAA   93 (133)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHHHHHHT---TCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH---cCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            4455555555555555555555555532   233 44555556666666666666666665542  22356677778888


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      +...|++++|...++++++.+|.+...+..+..++...|+
T Consensus        94 ~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  133 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYN  133 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHTC
T ss_pred             HHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhcC
Confidence            8888888888888888888888888888888888776653

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.53  E-value=1.1e-06  Score=84.37  Aligned_cols=94  Identities=19%  Similarity=0.051  Sum_probs=81.1

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          279 FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                      ...|..+..+|.+.|++++|.+.+++..  .+.+...|..+..++...|++++|+..|+++++++|++..++..+..++.
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~  275 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQ  275 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            4677788888888999999988888763  23467889999999999999999999999999999999999999999999


Q ss_pred             HccChhHH-HHHHHHHH
Q 040365          357 AARRWKDA-ASLRVFMR  372 (514)
Q Consensus       357 ~~g~~~~a-~~~~~~m~  372 (514)
                      ..|++++| .+.++.|.
T Consensus       276 ~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          276 RIRRQLAREKKLYANMF  292 (336)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999999 44666664

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.51  E-value=1.1e-05  Score=75.62  Aligned_cols=158  Identities=6%  Similarity=0.006  Sum_probs=95.7

Q ss_pred             HHHHHHCCChhHHHHHHHHHHHCC-CCCCHH----HHHHHHHHHhccCChHHHHHHHHHHHHcCCC-Cc----HHHHHHH
Q 040365          114 IAGCVQNGLFDEGLKFFRQMLIAK-IKPRHV----SFSSIMPACAHLTTLHLGKQLHGCIIRNGFD-DN----MFIASSL  183 (514)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~----t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l  183 (514)
                      +..+...|++++|..++++..+.. ..|+..    .+..+...+...+++++|...+..+++.... ++    ..+++.+
T Consensus        82 i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~l  161 (293)
T 3u3w_A           82 VIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAI  161 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHH
Confidence            455666666777776666665532 122211    2223455555666677777777766663221 12    2356777


Q ss_pred             HHHHHhcCCHHHHHHHHHhCCC------CC----hhHHHHHHHHHHhCCChHHHHHHHHHHHHc----CCCCC-HHHHHH
Q 040365          184 LDMYAKCGNIRLARCIFDKMDL------HD----IVSWTAVIMGNALHGNAHDAISLFEQMEKD----GVKPN-SVAFVA  248 (514)
Q Consensus       184 i~~y~k~g~~~~A~~~~~~m~~------~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~-~~t~~~  248 (514)
                      ...|...|++++|...|++...      .+    ..+|+.+...|.+.|++++|+..+++..+.    +..+. ..+|..
T Consensus       162 g~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~  241 (293)
T 3u3w_A          162 ANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQ  241 (293)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            7777777777777777766541      11    236677777788888888888877776542    22222 456777


Q ss_pred             HHHHHHccC-CHHHHHHHHHHhHH
Q 040365          249 VLTACSHAG-LIDKAWSYFNSMTK  271 (514)
Q Consensus       249 ll~a~~~~g-~~~~a~~~~~~m~~  271 (514)
                      +..++...| ..++|...++....
T Consensus       242 lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          242 RGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHH
Confidence            777788888 45788777776643

>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=98.49  E-value=1.2e-06  Score=82.85  Aligned_cols=197  Identities=8%  Similarity=-0.069  Sum_probs=148.4

Q ss_pred             ccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHH
Q 040365          154 HLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQ  233 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~  233 (514)
                      ..|++++|.+++.+..+..- ..         .+...|+++.|...|.+.           ...|...|++++|...|.+
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~-~~---------~~~~~~~~~~A~~~~~~a-----------~~~~~~~g~~~~A~~~~~~   61 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLK-TS---------FMKWKPDYDSAASEYAKA-----------AVAFKNAKQLEQAKDAYLQ   61 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHC-CC---------SSSCSCCHHHHHHHHHHH-----------HHHHHHTTCHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHcc-cc---------ccCCCCCHHHHHHHHHHH-----------HHHHHHcCCHHHHHHHHHH
Confidence            35678889998888776421 11         111158889988887654           5678889999999999998


Q ss_pred             HHHc----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCC--CC--CHhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040365          234 MEKD----GVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGI--AP--SFEHYAAVADLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       234 m~~~----g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~--~p--~~~~~~~li~~~~~~g~~~~A~~~~~~  304 (514)
                      ..+.    |-.+. ..+|..+...|...|++++|...|+...+-+.-  .|  ....+..+...|.+ |++++|++.+++
T Consensus        62 al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~  140 (307)
T 2ifu_A           62 EAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQ  140 (307)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHH
Confidence            7653    21111 357888889999999999999999987553211  12  24677888889988 999999999987


Q ss_pred             CC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc------chHHHHHHHHHHccChhHHHHHHHH
Q 040365          305 MH----AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM------GAYVILSNTYAAARRWKDAASLRVF  370 (514)
Q Consensus       305 m~----~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~------~~~~~l~~~~~~~g~~~~a~~~~~~  370 (514)
                      ..    ...+    ..++..+...+...|++++|+..+++++++.|.+.      ..+..++.++...|++++|...+++
T Consensus       141 Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~  220 (307)
T 2ifu_A          141 AAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRE  220 (307)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            53    1111    46788899999999999999999999998765432      3666778888899999999999998


Q ss_pred             HH
Q 040365          371 MR  372 (514)
Q Consensus       371 m~  372 (514)
                      ..
T Consensus       221 al  222 (307)
T 2ifu_A          221 SY  222 (307)
T ss_dssp             HT
T ss_pred             Hh
Confidence            87

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.48  E-value=6.3e-07  Score=82.22  Aligned_cols=134  Identities=15%  Similarity=0.005  Sum_probs=87.9

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC--HhHHHHHHHHHH
Q 040365          213 AVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS--FEHYAAVADLLG  290 (514)
Q Consensus       213 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~--~~~~~~li~~~~  290 (514)
                      .....+...|++++|.++|..+...  .|+......+...+.+.+++++|+..|+...+. . .|.  ...+..+..++.
T Consensus       107 ayA~~L~~~g~y~eA~~~l~~~~~~--~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~-~-d~~~~~~a~~~LG~al~  182 (282)
T 4f3v_A          107 GFAACEAAQGNYADAMEALEAAPVA--GSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKW-P-DKFLAGAAGVAHGVAAA  182 (282)
T ss_dssp             HHHHHHHHHTCHHHHHHHHTSSCCT--TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGC-S-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHcCCHHHHHHHHHHhhcc-C-CcccHHHHHHHHHHHHH
Confidence            3455566677777777777766553  354444444445677778888888887754221 1 121  235666777788


Q ss_pred             hcCCHHHHHHHHHhCCCC---CC--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          291 RAGKLQEAYEFISNMHAG---PT--ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       291 ~~g~~~~A~~~~~~m~~~---p~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      +.|++++|++.|++....   |.  ...+..+..++...|+.++|...|+++...+|+ ...+..|
T Consensus       183 ~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~-~~~~~aL  247 (282)
T 4f3v_A          183 NLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE-PKVAAAL  247 (282)
T ss_dssp             HTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC-HHHHHHH
T ss_pred             HCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-HHHHHHH
Confidence            888888888888876322   32  346677777888888888888888888888887 5444443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.45  E-value=7.8e-06  Score=76.56  Aligned_cols=162  Identities=9%  Similarity=-0.071  Sum_probs=112.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC---CCCh------hHHHHHHHHHHhCCChHHHHHHHHHHHHcCC---CCC--HH
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMD---LHDI------VSWTAVIMGNALHGNAHDAISLFEQMEKDGV---KPN--SV  244 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~---~p~--~~  244 (514)
                      .+...+..|...|++++|.+.+++..   ....      ..+..+...+...|++++|+..|++......   .+.  ..
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~  156 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLY  156 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHH
Confidence            34456677788888888888876543   1111      2234455566778889999998888875321   122  34


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC-----HhHHHHHHHHHHhcCCHHHHHHHHHhCC-C------CC-CH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS-----FEHYAAVADLLGRAGKLQEAYEFISNMH-A------GP-TE  311 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~-----~~~~~~li~~~~~~g~~~~A~~~~~~m~-~------~p-~~  311 (514)
                      ++..+...|...|++++|..+|+...+.....|+     ...+..+...|.+.|++++|.+.+++.. .      .. -.
T Consensus       157 ~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~  236 (293)
T 2qfc_A          157 IENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIG  236 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHH
Confidence            7788888888899999999998887632111222     2577888888999999999998887652 0      11 15


Q ss_pred             HHHHHHHHHHHhcCCHHHH-HHHHHHHHhc
Q 040365          312 NVWLTLLSACRVHKNVELA-GKVAEKIFMI  340 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a-~~~~~~~~~~  340 (514)
                      .+|..+...+...|++++| ...+++++.+
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~~  266 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKASFF  266 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence            6788888899999999999 7778776653

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.42  E-value=2.5e-06  Score=68.50  Aligned_cols=96  Identities=17%  Similarity=0.041  Sum_probs=75.7

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          279 FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                      ...+..+...+.+.|++++|.+.|++..  .+.+...|..+..++...|++++|+..++++++++|+++..|..++.+|.
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   83 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            3455566667777888888888777652  23467788888888888888888888888888888888888888888888


Q ss_pred             HccChhHHHHHHHHHHhC
Q 040365          357 AARRWKDAASLRVFMRNK  374 (514)
Q Consensus       357 ~~g~~~~a~~~~~~m~~~  374 (514)
                      ..|++++|...+++..+.
T Consensus        84 ~~~~~~~A~~~~~~al~~  101 (126)
T 3upv_A           84 AVKEYASALETLDAARTK  101 (126)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHHh
Confidence            888888888888877654

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.42  E-value=1.4e-06  Score=74.87  Aligned_cols=116  Identities=10%  Similarity=0.135  Sum_probs=70.9

Q ss_pred             cCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHH-HHhcCCH--HH
Q 040365          256 AGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSA-CRVHKNV--EL  329 (514)
Q Consensus       256 ~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~-~~~~~~~--~~  329 (514)
                      .|++++|...++...+.   .| +...+..+...|...|++++|.+.+++..  .+.+...|..+..+ +...|++  ++
T Consensus        23 ~~~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~   99 (177)
T 2e2e_A           23 QQNPEAQLQALQDKIRA---NPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQ   99 (177)
T ss_dssp             ----CCCCHHHHHHHHH---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHH
T ss_pred             ccCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHH
Confidence            45555555555554432   22 44555556666666666666666665542  12345566666666 5666776  77


Q ss_pred             HHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          330 AGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      |...++++++.+|.++..+..++.+|...|++++|...+++..+.
T Consensus       100 A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A          100 TRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            777777777777777777777777777777777777777776654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.42  E-value=2.2e-06  Score=74.99  Aligned_cols=82  Identities=9%  Similarity=-0.065  Sum_probs=38.8

Q ss_pred             HCCCHHHHHH---HHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHhccCChH
Q 040365           88 KCARVEDSHR---LFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIA----KIKP-RHVSFSSIMPACAHLTTLH  159 (514)
Q Consensus        88 ~~g~~~~A~~---~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~  159 (514)
                      ..|++++|.+   ++..-+.....+++.+...+...|++++|+..|++....    +..| ....+..+...+...|+++
T Consensus         4 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~   83 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWD   83 (203)
T ss_dssp             ---CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             ccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            3455555555   443333233445556666666666666666666655431    1111 1223344444455555555


Q ss_pred             HHHHHHHHHH
Q 040365          160 LGKQLHGCII  169 (514)
Q Consensus       160 ~a~~~~~~~~  169 (514)
                      +|.+.+.+.+
T Consensus        84 ~A~~~~~~al   93 (203)
T 3gw4_A           84 AARRCFLEER   93 (203)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555554443

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.41  E-value=3.2e-06  Score=85.13  Aligned_cols=116  Identities=9%  Similarity=0.001  Sum_probs=89.8

Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-A-GPTENVWLTLLSACRVHKNVE  328 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~-~p~~~~~~~ll~~~~~~~~~~  328 (514)
                      .+...|++++|...|++..+.   .| +...|..+..+|.+.|++++|.+.+++.. . +.+..+|..+..++...|+++
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHh---CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHH
Confidence            445667777887777777543   44 46777788888888888888888887752 2 346788999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCcchHHHHHHH--HHHccChhHHHHHHHH
Q 040365          329 LAGKVAEKIFMIDPNNMGAYVILSNT--YAAARRWKDAASLRVF  370 (514)
Q Consensus       329 ~a~~~~~~~~~~~p~~~~~~~~l~~~--~~~~g~~~~a~~~~~~  370 (514)
                      +|+..++++++++|++...+..+..+  +.+.|++++|.+.+++
T Consensus        92 eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~~  135 (477)
T 1wao_1           92 AALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEH  135 (477)
T ss_dssp             HHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC------
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            99999999999999999999888888  8899999999999874

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.41  E-value=0.00024  Score=67.33  Aligned_cols=178  Identities=9%  Similarity=0.014  Sum_probs=115.6

Q ss_pred             HHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHH-HHHHHHHHHhccC-ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHH
Q 040365          110 WNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHV-SFSSIMPACAHLT-TLHLGKQLHGCIIRNGFDDNMFIASSLLDMY  187 (514)
Q Consensus       110 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y  187 (514)
                      ++.+-....+.+..++|++++.++...  .|+.. .|+.--.++...+ .++++.++++.+++.. +-+..+|+.-...+
T Consensus        57 ~~~~r~~~~~~e~se~AL~lt~~~L~~--nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL  133 (349)
T 3q7a_A           57 MDYFRAIAAKEEKSERALELTEIIVRM--NPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLL  133 (349)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHh--CchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            444444445556667899999988875  34444 4455445555666 5888888888888765 56677777766666


Q ss_pred             Hhc-C-CHHHHHHHHHhCCC---CChhHHHHHHHHHHhCCChH--------HHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040365          188 AKC-G-NIRLARCIFDKMDL---HDIVSWTAVIMGNALHGNAH--------DAISLFEQMEKDGVKPNSVAFVAVLTACS  254 (514)
Q Consensus       188 ~k~-g-~~~~A~~~~~~m~~---~d~~~~~~li~~~~~~g~~~--------~A~~l~~~m~~~g~~p~~~t~~~ll~a~~  254 (514)
                      .+. + +++++.++++.+..   +|..+|+.-.-.+.+.|.++        ++++.+.++.+... -|...|+.....+.
T Consensus       134 ~~l~~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~~lL~  212 (349)
T 3q7a_A          134 DRISPQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRWYLRV  212 (349)
T ss_dssp             HHHCCSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHT
T ss_pred             HHhcCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHH
Confidence            666 6 78888888888864   35567776555555555555        78888888877542 25566666666666


Q ss_pred             ccCC-------HHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCC
Q 040365          255 HAGL-------IDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGK  294 (514)
Q Consensus       255 ~~g~-------~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~  294 (514)
                      +.+.       +++++++++.+...   .| |...|+-+-..+.+.|+
T Consensus       213 ~l~~~~~~~~~~~eELe~~~~aI~~---~P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          213 SRPGAETSSRSLQDELIYILKSIHL---IPHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             TSTTCCCCHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTC
T ss_pred             hccccccchHHHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHhcCC
Confidence            6654       56677777666543   44 45555555555555544

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.41  E-value=2.3e-06  Score=66.58  Aligned_cols=98  Identities=13%  Similarity=0.067  Sum_probs=76.7

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC--CcchHHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN--NMGAYVILSN  353 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~--~~~~~~~l~~  353 (514)
                      +...+..+...+.+.|++++|...+++..  .+.+..+|..+...+...|++++|...++++++..|.  +...+..++.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~   84 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKAD   84 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHH
Confidence            34556667777777888888887777652  2345677888888888888888888888888888888  8888888888


Q ss_pred             HHHHc-cChhHHHHHHHHHHhCC
Q 040365          354 TYAAA-RRWKDAASLRVFMRNKG  375 (514)
Q Consensus       354 ~~~~~-g~~~~a~~~~~~m~~~g  375 (514)
                      +|... |++++|.+.++...+..
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~  107 (112)
T 2kck_A           85 ALRYIEGKEVEAEIAEARAKLEH  107 (112)
T ss_dssp             HHTTCSSCSHHHHHHHHHHGGGC
T ss_pred             HHHHHhCCHHHHHHHHHHHhhcc
Confidence            88888 88888888888887654

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.39  E-value=4.4e-06  Score=69.65  Aligned_cols=104  Identities=10%  Similarity=0.001  Sum_probs=87.0

Q ss_pred             CCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHH
Q 040365          239 VKPNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVW  314 (514)
Q Consensus       239 ~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~  314 (514)
                      +.|+. ..+..+...+.+.|++++|...|+.....   .| +...|..+..+|.+.|++++|.+.|++..  .+.+...|
T Consensus        31 l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~---~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~  107 (151)
T 3gyz_A           31 IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIY---DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPV  107 (151)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHH
Confidence            45544 46777788889999999999999988754   56 67888999999999999999999998863  23457789


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc
Q 040365          315 LTLLSACRVHKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       315 ~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      ..+..++...|++++|...|++++++.|+++
T Consensus       108 ~~lg~~~~~lg~~~eA~~~~~~al~l~~~~~  138 (151)
T 3gyz_A          108 FHTGQCQLRLKAPLKAKECFELVIQHSNDEK  138 (151)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCCHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCHH
Confidence            9999999999999999999999999998753

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.38  E-value=2.5e-06  Score=68.23  Aligned_cols=94  Identities=14%  Similarity=0.038  Sum_probs=82.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA  358 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  358 (514)
                      .+..+...+.+.|++++|...+++..  .+.+...|..+..++...|++++|+..++++++++|+++..+..++.+|...
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNE   98 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            45566777889999999999998863  2347888999999999999999999999999999999999999999999999


Q ss_pred             cChhHHHHHHHHHHhC
Q 040365          359 RRWKDAASLRVFMRNK  374 (514)
Q Consensus       359 g~~~~a~~~~~~m~~~  374 (514)
                      |++++|...+++..+.
T Consensus        99 g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           99 HNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHC-
T ss_pred             CCHHHHHHHHHHHHHh
Confidence            9999999999988754

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.37  E-value=9.9e-06  Score=70.78  Aligned_cols=151  Identities=15%  Similarity=0.019  Sum_probs=69.6

Q ss_pred             hcCCHHHHHH---HHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHHccCCHH
Q 040365          189 KCGNIRLARC---IFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKD----GVKP-NSVAFVAVLTACSHAGLID  260 (514)
Q Consensus       189 k~g~~~~A~~---~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~  260 (514)
                      ..|++++|.+   .+..-+.....+++.+...+...|++++|+..|++....    +..| ...++..+...+...|+++
T Consensus         4 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~   83 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWD   83 (203)
T ss_dssp             ---CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             ccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            3456666666   443322233455566666666666666666666665441    1111 1234455555566666666


Q ss_pred             HHHHHHHHhHHhcCCCC-----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC----CCCCH----HHHHHHHHHHHhcCCH
Q 040365          261 KAWSYFNSMTKDYGIAP-----SFEHYAAVADLLGRAGKLQEAYEFISNMH----AGPTE----NVWLTLLSACRVHKNV  327 (514)
Q Consensus       261 ~a~~~~~~m~~~~~~~p-----~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~~p~~----~~~~~ll~~~~~~~~~  327 (514)
                      +|...++.......-.+     ....+..+...+...|++++|.+.+++..    ..++.    .++..+...+...|++
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            66666655433211111     12234444455555555555555544431    01111    1233444444455555


Q ss_pred             HHHHHHHHHHHh
Q 040365          328 ELAGKVAEKIFM  339 (514)
Q Consensus       328 ~~a~~~~~~~~~  339 (514)
                      ++|...++++++
T Consensus       164 ~~A~~~~~~al~  175 (203)
T 3gw4_A          164 LEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            555554444433

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.36  E-value=5.9e-06  Score=67.21  Aligned_cols=97  Identities=11%  Similarity=-0.025  Sum_probs=79.4

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY  355 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  355 (514)
                      +...+..+...+...|++++|...|++..  .+.+...|..+..++...|+++.|...++++++++|+++..+..++.+|
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~   87 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQ   87 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHHH
Confidence            56677777777888888888888777652  2345778888888888899999999999999999998888999999999


Q ss_pred             HHccChhHHHHHHHHHHhC
Q 040365          356 AAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       356 ~~~g~~~~a~~~~~~m~~~  374 (514)
                      ...|++++|...+++..+.
T Consensus        88 ~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           88 LEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHH
Confidence            9999999999988887654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.36  E-value=5.5e-06  Score=65.70  Aligned_cols=93  Identities=14%  Similarity=0.121  Sum_probs=43.6

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      ...|..+...+.+.|++++|+..|+++.... +.+..++..+...+...|++++|...+..+.+.. +.+..++..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            3445555555555555555555555555432 2233344444444555555555555555554432 2233333344444


Q ss_pred             HHHCCCHHHHHHHHc
Q 040365           86 YAKCARVEDSHRLFC  100 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~  100 (514)
                      |.+.|++++|...|+
T Consensus        87 ~~~~~~~~~A~~~~~  101 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQ  101 (125)
T ss_dssp             HHHTTCHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHH
Confidence            444444444444333

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.35  E-value=6.6e-06  Score=72.01  Aligned_cols=171  Identities=11%  Similarity=-0.028  Sum_probs=100.8

Q ss_pred             HHHHHhcCCHHHHHHHHHhCCCC---ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHH
Q 040365          184 LDMYAKCGNIRLARCIFDKMDLH---DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLID  260 (514)
Q Consensus       184 i~~y~k~g~~~~A~~~~~~m~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~  260 (514)
                      +......|++++|.+.++.-...   ....|..+...+...|++++|+..|++....  .|+...+...        ..+
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~--------~~~   80 (198)
T 2fbn_A           11 SSGRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDF--FIHTEEWDDQ--------ILL   80 (198)
T ss_dssp             -----------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TTTCTTCCCH--------HHH
T ss_pred             hhhhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--Hhcccccchh--------hHH
Confidence            34444556666666666543211   3445666677777778888888877777663  1211100000        000


Q ss_pred             HHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 040365          261 KAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIF  338 (514)
Q Consensus       261 ~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~  338 (514)
                      .-.   ..        .....|..+..+|.+.|++++|...+++..  .+.+...|..+..++...|+++.|...+++++
T Consensus        81 ~~~---~~--------~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al  149 (198)
T 2fbn_A           81 DKK---KN--------IEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAA  149 (198)
T ss_dssp             HHH---HH--------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHH---HH--------HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            000   00        013566677777888888888888887653  23467888899999999999999999999999


Q ss_pred             hcCCCCcchHHHHHHHHHHccChhHHH-HHHHHHHhCC
Q 040365          339 MIDPNNMGAYVILSNTYAAARRWKDAA-SLRVFMRNKG  375 (514)
Q Consensus       339 ~~~p~~~~~~~~l~~~~~~~g~~~~a~-~~~~~m~~~g  375 (514)
                      +++|.+...+..+..++...++.+++. ..+..|..++
T Consensus       150 ~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          150 SLNPNNLDIRNSYELCVNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             HHSTTCHHHHHHHHHHHHHHHHHHC-------------
T ss_pred             HHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            999999999999999999988888777 5566555443

>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=98.33  E-value=1.1e-05  Score=67.79  Aligned_cols=126  Identities=12%  Similarity=-0.039  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHH
Q 040365          210 SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADL  288 (514)
Q Consensus       210 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~  288 (514)
                      .|..+...+...|++++|+..|++..... +.+...+..+...+...|++++|...++...+.   .| +...+..+...
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~---~~~~~~~~~~~a~~   90 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL---DKKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CcccHHHHHHHHHH
Confidence            34444444555555555555555554431 113344444555555555555555555554432   22 34455555555


Q ss_pred             HHhcCCHHHHHHHHHhCC--CCCCHHHHHH--HHHHHHhcCCHHHHHHHHHHHHh
Q 040365          289 LGRAGKLQEAYEFISNMH--AGPTENVWLT--LLSACRVHKNVELAGKVAEKIFM  339 (514)
Q Consensus       289 ~~~~g~~~~A~~~~~~m~--~~p~~~~~~~--ll~~~~~~~~~~~a~~~~~~~~~  339 (514)
                      +.+.|++++|.+.+++..  .+.+...+..  +...+...|++++|...+++...
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            555555555555555432  1123333322  22224555666666666655443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.33  E-value=4.6e-06  Score=70.57  Aligned_cols=92  Identities=14%  Similarity=0.023  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA  358 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  358 (514)
                      .+..+...+.+.|++++|.+.|++..  .+.+...|..+..++...|++++|+..++++++++|.++..|..++.+|...
T Consensus        13 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~   92 (164)
T 3sz7_A           13 KLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLARFDM   92 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            33344444444444444444444331  1123444444445555555555555555555555555555555555555555


Q ss_pred             cChhHHHHHHHHHH
Q 040365          359 RRWKDAASLRVFMR  372 (514)
Q Consensus       359 g~~~~a~~~~~~m~  372 (514)
                      |++++|.+.+++..
T Consensus        93 g~~~~A~~~~~~al  106 (164)
T 3sz7_A           93 ADYKGAKEAYEKGI  106 (164)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHH
Confidence            55555555555444

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.32  E-value=8e-06  Score=69.94  Aligned_cols=126  Identities=13%  Similarity=0.094  Sum_probs=96.5

Q ss_pred             HhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHH-HHhcCCH-
Q 040365          219 ALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADL-LGRAGKL-  295 (514)
Q Consensus       219 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~-~~~~g~~-  295 (514)
                      ...|++++|+..|++..... +.+...+..+...+...|++++|...|+...+.   .| +...+..+..+ +...|++ 
T Consensus        21 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~la~~l~~~~~~~~   96 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQL---RGENAELYAALATVLYYQASQHM   96 (177)
T ss_dssp             C-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---HCSCHHHHHHHHHHHHHHTTTCC
T ss_pred             hhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHHHhcCCcc
Confidence            34678888888888877752 335677888888888999999999999888654   33 56777778888 7788998 


Q ss_pred             -HHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchH
Q 040365          296 -QEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAY  348 (514)
Q Consensus       296 -~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~  348 (514)
                       ++|...+++..  .+.+...|..+...+...|+++.|...++++++..|+++...
T Consensus        97 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  152 (177)
T 2e2e_A           97 TAQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPRINRT  152 (177)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTSCHH
T ss_pred             hHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCCccHH
Confidence             99999888763  234577888899999999999999999999999999876543

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.32  E-value=1.5e-05  Score=62.31  Aligned_cols=107  Identities=19%  Similarity=0.112  Sum_probs=60.8

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSAC  321 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~  321 (514)
                      .+..+...+...|++++|...|+.....   .| +...+..+...+.+.|++++|...+++..  .+.+...|..+..++
T Consensus         6 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~   82 (118)
T 1elw_A            6 ELKEKGNKALSVGNIDDALQCYSEAIKL---DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            3444444555555555555555555432   22 34455555555555666666665555432  123455666666677


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNT  354 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  354 (514)
                      ...|++++|...++++.+.+|+++..+..+..+
T Consensus        83 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  115 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNM  115 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHh
Confidence            777777777777777777777666555554443

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.31  E-value=7.9e-06  Score=64.05  Aligned_cols=98  Identities=10%  Similarity=0.028  Sum_probs=87.3

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY  355 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  355 (514)
                      ....+..+...+...|++++|.+.+++..  .+.+...|..+...+...|++++|...++++++.+|.++..+..++.+|
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~   82 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            34567778888999999999999999863  2347888999999999999999999999999999999999999999999


Q ss_pred             HHccChhHHHHHHHHHHhCC
Q 040365          356 AAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       356 ~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ...|++++|.+.++...+..
T Consensus        83 ~~~~~~~~A~~~~~~~~~~~  102 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKHE  102 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHhhHHHHHHHHHHHHHcC
Confidence            99999999999999887653

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.31  E-value=2e-05  Score=72.32  Aligned_cols=182  Identities=7%  Similarity=-0.050  Sum_probs=132.4

Q ss_pred             hcCCHHHHHHHHHhCC---CCChhHHHHH-------HHHHHhCCChHHHHHHHHHHHHcCCCCCH---------------
Q 040365          189 KCGNIRLARCIFDKMD---LHDIVSWTAV-------IMGNALHGNAHDAISLFEQMEKDGVKPNS---------------  243 (514)
Q Consensus       189 k~g~~~~A~~~~~~m~---~~d~~~~~~l-------i~~~~~~g~~~~A~~l~~~m~~~g~~p~~---------------  243 (514)
                      ..++.+.|.+.|.+..   ......|+.+       ...+...++..+++..++.-..  +.|+.               
T Consensus        18 ~~~d~~~A~~~F~~a~~~dP~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y~~~~   95 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNYDESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLYGDIT   95 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTTCCCE
T ss_pred             cCCCHHHHHHHHHHHHHhChhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCcccccc
Confidence            4678888888887775   3345677766       3455555555555555554333  33321               


Q ss_pred             -------HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCH----H
Q 040365          244 -------VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTE----N  312 (514)
Q Consensus       244 -------~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~----~  312 (514)
                             .....+...+...|++++|.+.|..+..   ..|+......+...+.+.|++++|+..|+.....|+.    .
T Consensus        96 ~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~---~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~  172 (282)
T 4f3v_A           96 YPVTSPLAITMGFAACEAAQGNYADAMEALEAAPV---AGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGA  172 (282)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCC---TTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHH
T ss_pred             cccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHH
Confidence                   1233456677889999999999998853   3464335566667899999999999999877544433    4


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CC-CcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFMID--PN-NMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--p~-~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      .+..|..++...|++++|+..|++.....  |. .+.....+..++.+.|+.++|..+|+++....
T Consensus       173 a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          173 AGVAHGVAAANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            68888999999999999999999998543  43 44577888999999999999999999998753

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.31  E-value=2.8e-06  Score=70.65  Aligned_cols=102  Identities=8%  Similarity=-0.074  Sum_probs=77.4

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSA  320 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~  320 (514)
                      ..+..+...+...|++++|...|+.....   .| +...|..+..+|.+.|++++|.+.|++..  .+.+...|..+..+
T Consensus        22 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~   98 (148)
T 2vgx_A           22 EQLYSLAFNQYQSGXYEDAHXVFQALCVL---DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAEC   98 (148)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHHc---CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHH
Confidence            45556666777778888888888777543   44 56677777788888888888888887753  23356778888889


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCcchH
Q 040365          321 CRVHKNVELAGKVAEKIFMIDPNNMGAY  348 (514)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~p~~~~~~  348 (514)
                      +...|++++|...+++++++.|+++...
T Consensus        99 ~~~~g~~~~A~~~~~~al~~~p~~~~~~  126 (148)
T 2vgx_A           99 LLQXGELAEAESGLFLAQELIANXPEFX  126 (148)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHTTCGGGH
T ss_pred             HHHcCCHHHHHHHHHHHHHHCcCCCcch
Confidence            9999999999999999999988876553

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.30  E-value=8.4e-06  Score=67.10  Aligned_cols=105  Identities=10%  Similarity=-0.051  Sum_probs=76.2

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSAC  321 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~  321 (514)
                      .+..+...+...|++++|...|+.....   .| +...|..+..+|.+.|++++|...|++..  .+.+...|..+..++
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   96 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCML---DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECH   96 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHh---CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHH
Confidence            4455556667777777777777777543   44 56667777777788888888888777652  233566778888888


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      ...|++++|...+++++++.|+++.......
T Consensus        97 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~  127 (142)
T 2xcb_A           97 LQLGDLDGAESGFYSARALAAAQPAHEALAA  127 (142)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHTCGGGHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCcchHHHHH
Confidence            8999999999999999888887776554433

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.27  E-value=1.2e-05  Score=64.75  Aligned_cols=114  Identities=6%  Similarity=-0.099  Sum_probs=76.3

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLI   83 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (514)
                      .++..|..+...+.+.|++++|+..|++..... +.+...+..+...+...|++++|...+..+++.. +.+..++..+.
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la   91 (133)
T 2lni_A           14 DLALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKA   91 (133)
T ss_dssp             CHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHH
Confidence            355677888888888888888888888887653 3355667777777778888888888888877764 44556666666


Q ss_pred             HHHHHCCCHHHHHHHHccCCC---CChhHHHHHHHHHHH
Q 040365           84 NMYAKCARVEDSHRLFCLLPV---KDAISWNSIIAGCVQ  119 (514)
Q Consensus        84 ~~~~~~g~~~~A~~~f~~~~~---~d~~~~~~li~~~~~  119 (514)
                      ..|.+.|++++|.+.|++..+   .+...+..+...+.+
T Consensus        92 ~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~  130 (133)
T 2lni_A           92 AALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMA  130 (133)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHH
Confidence            666677777776666665431   123344444444443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.27  E-value=1.5e-05  Score=63.87  Aligned_cols=108  Identities=13%  Similarity=-0.017  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSAC  321 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~  321 (514)
                      .+......+...|++++|...|+...+.   .| +...|..+..+|.+.|++++|.+.+++..  .+.+...|..+..++
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   82 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKR---APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHH
Confidence            4445555666666666666666666543   33 45666666777777777777777766542  223566777788888


Q ss_pred             HhcCCHHHHHHHHHHHHhcC------CCCcchHHHHHHHH
Q 040365          322 RVHKNVELAGKVAEKIFMID------PNNMGAYVILSNTY  355 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~------p~~~~~~~~l~~~~  355 (514)
                      ...|++++|...++++++++      |.+......+..+.
T Consensus        83 ~~~~~~~~A~~~~~~al~~~p~~~~~p~~~~~~~~l~~~~  122 (126)
T 3upv_A           83 IAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYYKAS  122 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHhCcccCCchhHHHHHHHHHHHH
Confidence            88888888888888888887      76665555555443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.27  E-value=1.6e-05  Score=67.14  Aligned_cols=107  Identities=16%  Similarity=-0.009  Sum_probs=82.5

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHH
Q 040365          243 SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLS  319 (514)
Q Consensus       243 ~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~  319 (514)
                      ...+..+...+...|++++|+..|+...+.   .| +...|..+..+|.+.|++++|.+.+++..  .+.+...|..+..
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~   87 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSI---APANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            345666667777777777777777777543   34 56777778888888888888888887753  2345788999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          320 ACRVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      ++...|++++|...++++++++|++...+....
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~  120 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEAEGNGGSDAMKRG  120 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHSSSCCHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhCCCchHHHHHHH
Confidence            999999999999999999999999887665443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.27  E-value=2e-05  Score=64.75  Aligned_cols=108  Identities=12%  Similarity=-0.020  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC----HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS----FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTL  317 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~----~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~l  317 (514)
                      ..+..+...+...|++++|...|+...   ...|+    ...+..+...|...|++++|.+.+++..  .+.+...|..+
T Consensus        29 ~~~~~~a~~~~~~~~~~~A~~~~~~a~---~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~  105 (148)
T 2dba_A           29 EQLRKEGNELFKCGDYGGALAAYTQAL---GLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYRR  105 (148)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHH---TSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHH---HHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHHH
Confidence            344444455555555555555555443   22343    3455555556666666666666665532  12355667777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 040365          318 LSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNT  354 (514)
Q Consensus       318 l~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  354 (514)
                      ..++...|++++|...++++++.+|++...+..+..+
T Consensus       106 a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~  142 (148)
T 2dba_A          106 SQALEKLGRLDQAVLDLQRCVSLEPKNKVFQEALRNI  142 (148)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHH
Confidence            7777777888888888888877777776655555443

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.24  E-value=4.1e-06  Score=78.06  Aligned_cols=182  Identities=8%  Similarity=-0.061  Sum_probs=79.9

Q ss_pred             HHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHH
Q 040365          109 SWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYA  188 (514)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~  188 (514)
                      .+..+...+.+.|++++|+..|++..... +.+...|..+..++...|++++|...+..+++.. +.+...+..+..+|.
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~   83 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQCQL   83 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            34444444445555555555555444431 1233444444444455555555555555444432 333444455555555


Q ss_pred             hcCCHHHHHHHHHhCCC--C-C-----hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHH
Q 040365          189 KCGNIRLARCIFDKMDL--H-D-----IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLID  260 (514)
Q Consensus       189 k~g~~~~A~~~~~~m~~--~-d-----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~  260 (514)
                      +.|++++|...|++...  | +     ...|..+  ...+      +. -+.........++... ...+..+. .|+.+
T Consensus        84 ~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~--~~~~------~~-~~~~~~~~~~~~~~~i-~~~l~~l~-~~~~~  152 (281)
T 2c2l_A           84 EMESYDEAIANLQRAYSLAKEQRLNFGDDIPSAL--RIAK------KK-RWNSIEERRIHQESEL-HSYLTRLI-AAERE  152 (281)
T ss_dssp             HTTCHHHHHHHHHHHHHHHHHTTCCCCSHHHHHH--HHHH------HH-HHHHHHHTCCCCCCHH-HHHHHHHH-HHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCccchhhHHHHHHHHH--HHHH------HH-HHHHHHHHHHhhhHHH-HHHHHHHH-HHHHH
Confidence            55555555555544321  1 0     1111111  1111      11 1111222222222222 22222222 46777


Q ss_pred             HHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhc-CCHHHHHHHHHhCC
Q 040365          261 KAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRA-GKLQEAYEFISNMH  306 (514)
Q Consensus       261 ~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~-g~~~~A~~~~~~m~  306 (514)
                      +|.+.++...   ...|+ ......+...+.+. +.+++|.++|....
T Consensus       153 ~A~~~~~~al---~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~  197 (281)
T 2c2l_A          153 RELEECQRNH---EGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVD  197 (281)
T ss_dssp             HHHTTTSGGG---TTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHhhh---ccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            7777776554   33553 23333344444444 56777888887765

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.23  E-value=0.00037  Score=65.69  Aligned_cols=188  Identities=10%  Similarity=0.027  Sum_probs=96.5

Q ss_pred             hHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC--CHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCC-hHHHHHHH
Q 040365          158 LHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG--NIRLARCIFDKMD---LHDIVSWTAVIMGNALHGN-AHDAISLF  231 (514)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g--~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~-~~~A~~l~  231 (514)
                      ++++..+++.++... +-+..+|+.-...+.+.|  +++++..+++.+.   .+|..+|+.-.-.+...|. ++++++.+
T Consensus        90 l~~EL~~~~~~L~~~-PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~  168 (331)
T 3dss_A           90 VKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFT  168 (331)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHH
Confidence            455566666666543 445566665555555555  3667777666664   4455666666666666666 46777777


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHHcc--------------CCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhc----
Q 040365          232 EQMEKDGVKPNSVAFVAVLTACSHA--------------GLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRA----  292 (514)
Q Consensus       232 ~~m~~~g~~p~~~t~~~ll~a~~~~--------------g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~----  292 (514)
                      .++.+..+ -|...|+.....+.+.              +.++++++++......   .| |...|+-+--.+.+.    
T Consensus       169 ~~~I~~~p-~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~---~P~d~SaW~Y~r~ll~~~~~~~  244 (331)
T 3dss_A          169 DSLITRNF-SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFT---DPNDQSAWFYHRWLLGAGSGRC  244 (331)
T ss_dssp             HHHHHHCS-CCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHSSSCGG
T ss_pred             HHHHHHCC-CCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHhccCcc
Confidence            77766532 2444444443333332              3355555555555432   34 344444333333333    


Q ss_pred             -------CCHHHHHHHHHhCC-CCCCHHHHHHHHHH-----HHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          293 -------GKLQEAYEFISNMH-AGPTENVWLTLLSA-----CRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       293 -------g~~~~A~~~~~~m~-~~p~~~~~~~ll~~-----~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                             +.++++++.++++. ..||. .|..+..+     ....+..++....+.++.+++|...+-|.-|
T Consensus       245 ~~~~~~~~~l~~el~~~~elle~~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~Dp~r~~~y~d~  315 (331)
T 3dss_A          245 ELSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDL  315 (331)
T ss_dssp             GCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHhhCccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCcchhhHHHHH
Confidence                   33555555555442 23332 23221111     1124455566666666666666555444443

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=98.22  E-value=0.00046  Score=65.01  Aligned_cols=178  Identities=8%  Similarity=0.048  Sum_probs=130.1

Q ss_pred             HHHHHHHHHhCC---CCChhHHHHHHHHHHhCCC--hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCC-HHHHHHHH
Q 040365          193 IRLARCIFDKMD---LHDIVSWTAVIMGNALHGN--AHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGL-IDKAWSYF  266 (514)
Q Consensus       193 ~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~--~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~-~~~a~~~~  266 (514)
                      ++++..+++.+.   .++..+|+.-.-.+...|+  +++++.++.++.+... -|...|+.-...+.+.|. ++++++++
T Consensus        90 l~~EL~~~~~~L~~~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dp-rNy~AW~~R~~vl~~l~~~~~eel~~~  168 (331)
T 3dss_A           90 VKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELAFT  168 (331)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhCcCHHHHHHHH
Confidence            567777777765   5577889988888888884  8999999999998642 366777776667777787 69999999


Q ss_pred             HHhHHhcCCCC-CHhHHHHHHHHHHhc--------------CCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhc-----
Q 040365          267 NSMTKDYGIAP-SFEHYAAVADLLGRA--------------GKLQEAYEFISNMH--AGPTENVWLTLLSACRVH-----  324 (514)
Q Consensus       267 ~~m~~~~~~~p-~~~~~~~li~~~~~~--------------g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~-----  324 (514)
                      ..+.+.   .| |...|+....++.+.              +.++++++++.+..  .+-|...|+-+-..+...     
T Consensus       169 ~~~I~~---~p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~  245 (331)
T 3dss_A          169 DSLITR---NFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCE  245 (331)
T ss_dssp             HHHHHH---CSCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGG
T ss_pred             HHHHHH---CCCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccc
Confidence            999765   44 566666655555544              45888999888763  345788888766666555     


Q ss_pred             ------CCHHHHHHHHHHHHhcCCCCcchHHHHHHHH---HHccChhHHHHHHHHHHhC
Q 040365          325 ------KNVELAGKVAEKIFMIDPNNMGAYVILSNTY---AAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       325 ------~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~---~~~g~~~~a~~~~~~m~~~  374 (514)
                            +.++++++.++++++++|++...+..++...   ...|..+++...+.++.+-
T Consensus       246 ~~~~~~~~l~~el~~~~elle~~pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          246 LSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHhhCcccchHHHHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence                  4688999999999999999865554443322   2356777888888888754

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.22  E-value=0.00063  Score=64.44  Aligned_cols=179  Identities=8%  Similarity=-0.032  Sum_probs=108.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChh-hHHHHHHHHhCCC-ChHHHHHHHHHHHHhCCCCchhHHHHHHHHH
Q 040365            9 WNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSF-TLSSVLPIFADYV-DVIKGKEIHGYAIRHGLDANVCIGSSLINMY   86 (514)
Q Consensus         9 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~-~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~   86 (514)
                      |+.+-....+.+..++|++++..++..+  |+.. .|+.--..+...+ .+++++++++.+++.. +.+..+|+.--..+
T Consensus        57 ~~~~r~~~~~~e~se~AL~lt~~~L~~n--P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL  133 (349)
T 3q7a_A           57 MDYFRAIAAKEEKSERALELTEIIVRMN--PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLL  133 (349)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHhC--chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            3433334444556678888888887753  4443 4555555555666 4888888888888765 56666777766666


Q ss_pred             HHC-C-CHHHHHHHHccCCCC---ChhHHHHHHHHHHHCCChh--------HHHHHHHHHHHCCCCCCHHHHHHHHHHHh
Q 040365           87 AKC-A-RVEDSHRLFCLLPVK---DAISWNSIIAGCVQNGLFD--------EGLKFFRQMLIAKIKPRHVSFSSIMPACA  153 (514)
Q Consensus        87 ~~~-g-~~~~A~~~f~~~~~~---d~~~~~~li~~~~~~g~~~--------~A~~l~~~m~~~g~~p~~~t~~~ll~~~~  153 (514)
                      .+. + +.++++++++.+.+.   |-.+|+--.-.+.+.|.++        ++++.+.++.+.. +-|...|+.....+.
T Consensus       134 ~~l~~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~  212 (349)
T 3q7a_A          134 DRISPQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRV  212 (349)
T ss_dssp             HHHCCSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHT
T ss_pred             HHhcCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            665 6 777888877777643   4556665554444444555        7777777777654 345556665555555


Q ss_pred             ccCC-------hHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCC
Q 040365          154 HLTT-------LHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGN  192 (514)
Q Consensus       154 ~~~~-------~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~  192 (514)
                      +.+.       ++++.+.....+... +.|...|+-+-..+.+.|.
T Consensus       213 ~l~~~~~~~~~~~eELe~~~~aI~~~-P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          213 SRPGAETSSRSLQDELIYILKSIHLI-PHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             TSTTCCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             hccccccchHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCC
Confidence            5554       455555555555543 4455555555444444443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.21  E-value=2.3e-05  Score=64.34  Aligned_cols=97  Identities=14%  Similarity=0.001  Sum_probs=88.1

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      +...+..+...+.+.|++++|.+.|++.. ..|+    ...|..+...+...|++++|+..++++++..|+++..+..++
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a  106 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYRRS  106 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHHHH
Confidence            56778888999999999999999999863 4576    678899999999999999999999999999999999999999


Q ss_pred             HHHHHccChhHHHHHHHHHHhC
Q 040365          353 NTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       353 ~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .+|...|++++|.+.+++..+.
T Consensus       107 ~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A          107 QALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHc
Confidence            9999999999999999988764

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.21  E-value=1.6e-05  Score=63.44  Aligned_cols=97  Identities=13%  Similarity=0.062  Sum_probs=87.5

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY  355 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  355 (514)
                      +...+..+...+...|++++|.+.+++..  .+.+...|..+...+...|++++|...++++++..|+++..+..++.+|
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   90 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLAL   90 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHHH
Confidence            45677788889999999999999998863  3347888999999999999999999999999999999999999999999


Q ss_pred             HHccChhHHHHHHHHHHhC
Q 040365          356 AAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       356 ~~~g~~~~a~~~~~~m~~~  374 (514)
                      ...|++++|.+.+++..+.
T Consensus        91 ~~~~~~~~A~~~~~~~~~~  109 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKALEL  109 (131)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHhc
Confidence            9999999999999988765

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.19  E-value=1.2e-05  Score=64.83  Aligned_cols=94  Identities=7%  Similarity=-0.049  Sum_probs=74.4

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc-------hHHH
Q 040365          280 EHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG-------AYVI  350 (514)
Q Consensus       280 ~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~-------~~~~  350 (514)
                      ..+..+...+.+.|++++|++.|++..  .+.+..+|..+..++...|++++|+..++++++++|++..       +|..
T Consensus         9 ~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A            9 IAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            345567777788888888888887652  2345778888899999999999999999999988776543       5677


Q ss_pred             HHHHHHHccChhHHHHHHHHHHh
Q 040365          351 LSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ++.+|...|++++|.+.+++..+
T Consensus        89 lg~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           89 AGNAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHh
Confidence            88888899999999999987765

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.18  E-value=2.7e-05  Score=63.21  Aligned_cols=99  Identities=8%  Similarity=-0.036  Sum_probs=68.8

Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHH
Q 040365          242 NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLL  318 (514)
Q Consensus       242 ~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll  318 (514)
                      +...+..+...+...|++++|...|+.....   .| +...+..+..++...|++++|...+++..  .+.+...|..+.
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~---~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~   84 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITR---NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLG   84 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhh---CcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHH
Confidence            4455666666666777777777777666543   23 45666677777777777777777776642  233567788888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCC
Q 040365          319 SACRVHKNVELAGKVAEKIFMIDPN  343 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~p~  343 (514)
                      .++...|+++.|...+++++++.|+
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~~p~  109 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSLAKE  109 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHChh
Confidence            8888888888888888888887766

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.16  E-value=3e-05  Score=77.56  Aligned_cols=129  Identities=14%  Similarity=0.053  Sum_probs=92.2

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-------------CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCC
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-------------SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGP  309 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-------------~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p  309 (514)
                      .+..+...+.+.|++++|...|+...+...-.+             ....|..+..+|.+.|++++|+..+++..  .+.
T Consensus       270 ~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~  349 (457)
T 1kt0_A          270 IVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSA  349 (457)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc
Confidence            344444455555555555555555443211111             14678888889999999999999988763  234


Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHH-HHHHHHh
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAAS-LRVFMRN  373 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~-~~~~m~~  373 (514)
                      +...|..+..++...|++++|+..|+++++++|++..++..+..++...|+++++.+ .++.|..
T Consensus       350 ~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~f~  414 (457)
T 1kt0_A          350 NEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERDRRIYANMFK  414 (457)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            688899999999999999999999999999999999999999999999999998875 4555543

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.12  E-value=3.2e-05  Score=73.94  Aligned_cols=143  Identities=10%  Similarity=-0.029  Sum_probs=82.8

Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHH
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLD  185 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~  185 (514)
                      +...|..+...|.+.|++++|+..|++..+..  |+...+           ..+.+.++-        +....++..+..
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~--p~~~~~-----------~~~~~~~~~--------~~~~~~~~nla~  204 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWL--EYESSF-----------SNEEAQKAQ--------ALRLASHLNLAM  204 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTCCCC-----------CSHHHHHHH--------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh--hccccC-----------ChHHHHHHH--------HHHHHHHHHHHH
Confidence            34567777788888888888888888877642  322000           001111000        011345555666


Q ss_pred             HHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHH
Q 040365          186 MYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDK  261 (514)
Q Consensus       186 ~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~  261 (514)
                      +|.+.|++++|...|++..   ..+...|..+..+|...|++++|+..|++..+.  .| +...+..+..++...|+.++
T Consensus       205 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~  282 (336)
T 1p5q_A          205 CHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRRQLA  282 (336)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHH
Confidence            6666666666666666553   335566666666777777777777777776664  33 34556666666666677666


Q ss_pred             H-HHHHHHhHH
Q 040365          262 A-WSYFNSMTK  271 (514)
Q Consensus       262 a-~~~~~~m~~  271 (514)
                      + ...++.|..
T Consensus       283 a~~~~~~~~~~  293 (336)
T 1p5q_A          283 REKKLYANMFE  293 (336)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            6 345555543

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.07  E-value=7.5e-06  Score=71.68  Aligned_cols=160  Identities=10%  Similarity=-0.046  Sum_probs=75.0

Q ss_pred             HHHHHHHCCCHHHHHHHHccCCCC---ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 040365           82 LINMYAKCARVEDSHRLFCLLPVK---DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTL  158 (514)
Q Consensus        82 li~~~~~~g~~~~A~~~f~~~~~~---d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  158 (514)
                      .+......|+++.|.+.++.-.+.   ....|..+...+.+.|++++|+..|++.....  |+...+...        ..
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~--~~~~~~~~~--------~~   79 (198)
T 2fbn_A           10 HSSGRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFF--IHTEEWDDQ--------IL   79 (198)
T ss_dssp             ------------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--TTCTTCCCH--------HH
T ss_pred             hhhhhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH--hcccccchh--------hH
Confidence            344445556677777666643321   34467777888888999999999998887642  211100000        00


Q ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          159 HLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       159 ~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      ..-.   .       .....++..+..+|.+.|++++|...|++..   ..+...|..+..+|...|++++|+..|++..
T Consensus        80 ~~~~---~-------~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al  149 (198)
T 2fbn_A           80 LDKK---K-------NIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAA  149 (198)
T ss_dssp             HHHH---H-------HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHH---H-------HHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            0000   0       0012344445555555555555555555443   2344555555555666666666666666655


Q ss_pred             HcCCCC-CHHHHHHHHHHHHccCCHHHHH
Q 040365          236 KDGVKP-NSVAFVAVLTACSHAGLIDKAW  263 (514)
Q Consensus       236 ~~g~~p-~~~t~~~ll~a~~~~g~~~~a~  263 (514)
                      +.  .| +...+..+..++...++.+++.
T Consensus       150 ~~--~p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          150 SL--NPNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             HH--STTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             HH--CCCcHHHHHHHHHHHHHHHHHHHHH
Confidence            53  23 2334444444444444444444

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.07  E-value=2.2e-05  Score=62.74  Aligned_cols=95  Identities=12%  Similarity=0.098  Sum_probs=76.3

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-------cchHHH
Q 040365          280 EHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN-------MGAYVI  350 (514)
Q Consensus       280 ~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~-------~~~~~~  350 (514)
                      ..+..+...+...|++++|...+++..  .+.+...|..+...+...|+++.|...++++++..|.+       +.++..
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYAR   84 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHH
Confidence            456666777777888888888777652  23467778888888888999999999999988887665       778889


Q ss_pred             HHHHHHHccChhHHHHHHHHHHhC
Q 040365          351 LSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       351 l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++.+|...|++++|.+.++...+.
T Consensus        85 la~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           85 IGNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHh
Confidence            999999999999999999988764

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.06  E-value=4.6e-05  Score=76.64  Aligned_cols=114  Identities=8%  Similarity=-0.011  Sum_probs=58.1

Q ss_pred             HHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHH
Q 040365          185 DMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLID  260 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~  260 (514)
                      ..|.+.|++++|.+.|++..   ..+..+|..+..+|.+.|++++|++.|++..+.  .| +...+..+..++...|+++
T Consensus        14 ~~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           14 NDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--DKKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             SSTTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHH
Confidence            34555666666666665543   234555666666666666666666666666553  23 3345555555666666666


Q ss_pred             HHHHHHHHhHHhcCCCC-CHhHHHHHHHH--HHhcCCHHHHHHHHH
Q 040365          261 KAWSYFNSMTKDYGIAP-SFEHYAAVADL--LGRAGKLQEAYEFIS  303 (514)
Q Consensus       261 ~a~~~~~~m~~~~~~~p-~~~~~~~li~~--~~~~g~~~~A~~~~~  303 (514)
                      +|...|++..+.   .| +...+..+..+  +.+.|++++|.+.++
T Consensus        92 eA~~~~~~al~~---~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           92 AALRDYETVVKV---KPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHH---STTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHh---CCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            666666655443   22 22233333333  455555555555555

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.05  E-value=5e-05  Score=63.84  Aligned_cols=64  Identities=9%  Similarity=0.060  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ..+|..+..++...|+++.|+..++++++++|.++.+|..++.+|...|++++|...+++..+.
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  126 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRN  126 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhc
Confidence            4577888888888899999999999999989988888889999999999999999888877654

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.04  E-value=5.8e-05  Score=74.66  Aligned_cols=162  Identities=8%  Similarity=-0.090  Sum_probs=84.4

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHc-CCCCCHH----HHHHHHHHHHccCCHHHHHHHHHHhHHh---cCCCC-CHhH
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKD-GVKPNSV----AFVAVLTACSHAGLIDKAWSYFNSMTKD---YGIAP-SFEH  281 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~----t~~~ll~a~~~~g~~~~a~~~~~~m~~~---~~~~p-~~~~  281 (514)
                      +..+...|...|++++|.+++.++... +..++..    ..+.+-..+...|+.+++..++......   .+..+ ....
T Consensus        58 l~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  137 (434)
T 4b4t_Q           58 ILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSL  137 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHH
Confidence            444555555566666666655554431 1111111    1112222233455666666665554321   11222 2345


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhCC-------CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC---CCC----cc
Q 040365          282 YAAVADLLGRAGKLQEAYEFISNMH-------AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMID---PNN----MG  346 (514)
Q Consensus       282 ~~~li~~~~~~g~~~~A~~~~~~m~-------~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~---p~~----~~  346 (514)
                      +..+...|...|++++|..++++..       .+| ...++..++..|...|+++.|..+++++....   +.+    ..
T Consensus       138 ~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  217 (434)
T 4b4t_Q          138 SIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAE  217 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHH
Confidence            5666666777777777766665531       112 13456666677777777777777777666542   211    23


Q ss_pred             hHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          347 AYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       347 ~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      .+..++..+...|++++|.+.+....
T Consensus       218 ~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          218 LDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            44555666666777777776665553

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.04  E-value=5.3e-05  Score=60.90  Aligned_cols=90  Identities=13%  Similarity=0.093  Sum_probs=40.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC--CCCC----HHHHHHHHH
Q 040365          181 SSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG--VKPN----SVAFVAVLT  251 (514)
Q Consensus       181 ~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--~~p~----~~t~~~ll~  251 (514)
                      ..|...|.+.|++++|++.|++..   +.+...|+.+..+|.+.|++++|++.|++..+..  ..++    ..+|..+..
T Consensus        12 ~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~   91 (127)
T 4gcn_A           12 KDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGN   91 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHH
Confidence            334445555555555555554432   2234445555555555555555555555544311  0111    123334444


Q ss_pred             HHHccCCHHHHHHHHHHhH
Q 040365          252 ACSHAGLIDKAWSYFNSMT  270 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~  270 (514)
                      ++...|++++|++.|+...
T Consensus        92 ~~~~~~~~~~A~~~~~kal  110 (127)
T 4gcn_A           92 AFQKQNDLSLAVQWFHRSL  110 (127)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            4444555555555554443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.03  E-value=6.5e-06  Score=65.20  Aligned_cols=83  Identities=17%  Similarity=0.115  Sum_probs=53.6

Q ss_pred             cCCHHHHHHHHHhCCCC----C-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHH
Q 040365          292 AGKLQEAYEFISNMHAG----P-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAAS  366 (514)
Q Consensus       292 ~g~~~~A~~~~~~m~~~----p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~  366 (514)
                      .|++++|...|++....    | +...|..+..++...|++++|+..++++++.+|+++.++..++.+|...|++++|..
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~   82 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGVE   82 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHHH
Confidence            45566666666654311    2 235566677777777777777777777777777777777777777777777777777


Q ss_pred             HHHHHHhC
Q 040365          367 LRVFMRNK  374 (514)
Q Consensus       367 ~~~~m~~~  374 (514)
                      .+++..+.
T Consensus        83 ~~~~al~~   90 (117)
T 3k9i_A           83 LLLKIIAE   90 (117)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            77766543

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=98.02  E-value=6e-05  Score=73.04  Aligned_cols=90  Identities=12%  Similarity=0.021  Sum_probs=78.3

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY  355 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  355 (514)
                      +...|..+..+|.+.|++++|.+.+++.. ..| +...|..+..++...|++++|+..++++++++|++...+..+..++
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~  351 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVK  351 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            45778888899999999999999998763 334 6788999999999999999999999999999999999999999999


Q ss_pred             HHccChhHHHHH
Q 040365          356 AAARRWKDAASL  367 (514)
Q Consensus       356 ~~~g~~~~a~~~  367 (514)
                      ...++.+++.+.
T Consensus       352 ~~~~~~~~a~k~  363 (370)
T 1ihg_A          352 QKIKAQKDKEKA  363 (370)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHH
Confidence            998888877653

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.01  E-value=0.00015  Score=71.64  Aligned_cols=161  Identities=7%  Similarity=-0.005  Sum_probs=92.9

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHcC-CCCc----HHHHHHHHHHHHhcCCHHHHHHHHHhCC--------CC-ChhH
Q 040365          145 FSSIMPACAHLTTLHLGKQLHGCIIRNG-FDDN----MFIASSLLDMYAKCGNIRLARCIFDKMD--------LH-DIVS  210 (514)
Q Consensus       145 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~----~~~~~~li~~y~k~g~~~~A~~~~~~m~--------~~-d~~~  210 (514)
                      +..+...|...|++++|.+.+..+.+.- -.++    ..+.+.+-..+...|+.+.|.++++...        .+ -..+
T Consensus        58 l~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  137 (434)
T 4b4t_Q           58 ILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSL  137 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHH
Confidence            3445555555555555555555443320 0111    1223333344445566666666665542        11 1245


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHc--CC--CCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcC-C-CC-C--Hh
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKD--GV--KPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYG-I-AP-S--FE  280 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~--g~--~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~-~-~p-~--~~  280 (514)
                      +..+...|...|++++|..++++....  +.  +|. ..++..++..|...|++++|..+++....... + .| .  ..
T Consensus       138 ~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  217 (434)
T 4b4t_Q          138 SIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAE  217 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHH
Confidence            666777777788888888887776542  11  222 24677777888888888888888877644211 1 11 1  34


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNM  305 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m  305 (514)
                      .+..+...+...|++++|...|.+.
T Consensus       218 ~~~~~g~~~~~~~~y~~A~~~~~~a  242 (434)
T 4b4t_Q          218 LDLMSGILHCEDKDYKTAFSYFFES  242 (434)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            5666777777888888887776554

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.01  E-value=4.5e-05  Score=61.08  Aligned_cols=90  Identities=17%  Similarity=0.116  Sum_probs=56.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC-CCCC-H---HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---cchHHHHHHHHH
Q 040365          285 VADLLGRAGKLQEAYEFISNMH-AGPT-E---NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN---MGAYVILSNTYA  356 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~-~~p~-~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~---~~~~~~l~~~~~  356 (514)
                      +...+.+.|++++|.+.|++.. ..|+ .   ..+..+..++...|++++|...++++++..|++   +.++..++.+|.
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~~   87 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQY   87 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHH
Confidence            3444556666666666665542 1122 2   355666666677777777777777777777766   555667777777


Q ss_pred             HccChhHHHHHHHHHHhC
Q 040365          357 AARRWKDAASLRVFMRNK  374 (514)
Q Consensus       357 ~~g~~~~a~~~~~~m~~~  374 (514)
                      ..|++++|...++...+.
T Consensus        88 ~~g~~~~A~~~~~~~~~~  105 (129)
T 2xev_A           88 GEGKNTEAQQTLQQVATQ  105 (129)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHH
Confidence            777777777777766553

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.00  E-value=6.8e-05  Score=62.23  Aligned_cols=62  Identities=18%  Similarity=0.066  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC------CCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDP------NNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p------~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      .++..+...+...|++++|...+++.++..+      .....+..++..|...|++++|.+.+++..+
T Consensus        90 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           90 QSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            3455566666777777777777776665421      1234667788888888888888888877653

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.99  E-value=5.7e-05  Score=60.16  Aligned_cols=96  Identities=11%  Similarity=0.023  Sum_probs=62.8

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHh
Q 040365          247 VAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRV  323 (514)
Q Consensus       247 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~  323 (514)
                      ..+...+.+.|++++|...|+...+.   .| +...|..+..++.+.|++++|...+++.. .. .+...|..+..++..
T Consensus        21 ~~~g~~~~~~g~~~~A~~~~~~al~~---~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           21 MEEGLSMLKLANLAEAALAFEAVCQK---EPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            34445566677777777777766543   44 56666677777777777777777777652 22 356677778888888


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCc
Q 040365          324 HKNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      .|++++|...++++++.+|.+.
T Consensus        98 ~g~~~~A~~~~~~al~~~P~~~  119 (121)
T 1hxi_A           98 EHNANAALASLRAWLLSQPQYE  119 (121)
T ss_dssp             HHHHHHHHHHHHHHHC------
T ss_pred             cCCHHHHHHHHHHHHHhCcCCC
Confidence            8888888888888888777643

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.99  E-value=3.8e-05  Score=63.70  Aligned_cols=62  Identities=11%  Similarity=-0.050  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhc-------CCCCcchH----HHHHHHHHHccChhHHHHHHHHHHh
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMI-------DPNNMGAY----VILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-------~p~~~~~~----~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..|..+..++...|++++|+..+++++++       +|++...|    .....++...|++++|...|++..+
T Consensus        58 ~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           58 FCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHh
Confidence            38888888899999999999999999988       99999899    9999999999999999999998864

>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=97.98  E-value=5.4e-05  Score=60.38  Aligned_cols=106  Identities=7%  Similarity=-0.036  Sum_probs=55.9

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-----CCCC----HHHHHHH
Q 040365          247 VAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-----AGPT----ENVWLTL  317 (514)
Q Consensus       247 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-----~~p~----~~~~~~l  317 (514)
                      ..+...+...|++++|..+|+...+..  +.+...+..+...|...|++++|...+++..     ..++    ..+|..+
T Consensus         8 ~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l   85 (131)
T 1elr_A            8 KELGNDAYKKKDFDTALKHYDKAKELD--PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (131)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHH
Confidence            333444444444444444444443321  1133444444555555555555555554431     0112    4566677


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH
Q 040365          318 LSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY  355 (514)
Q Consensus       318 l~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  355 (514)
                      ..++...|+++.|...++++++..| ++.....+..+.
T Consensus        86 a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~l~~~~  122 (131)
T 1elr_A           86 GNSYFKEEKYKDAIHFYNKSLAEHR-TPDVLKKCQQAE  122 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCC-CHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhCC-CHHHHHHHHHHH
Confidence            7777777788888888877777776 455555544443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.94  E-value=5.7e-05  Score=58.37  Aligned_cols=92  Identities=9%  Similarity=-0.092  Sum_probs=45.6

Q ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCC---CC--ChhHHHHHHHHHH
Q 040365           44 LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLP---VK--DAISWNSIIAGCV  118 (514)
Q Consensus        44 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~---~~--d~~~~~~li~~~~  118 (514)
                      +..+...+...|++++|...+..+++.. +.+..++..+...|.+.|++++|...|++..   ..  +...|..+...+.
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~~~   87 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADALR   87 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHHHH
Confidence            3333344444444444444444444432 2333444445555555555555555554432   12  3455556666666


Q ss_pred             HC-CChhHHHHHHHHHHHC
Q 040365          119 QN-GLFDEGLKFFRQMLIA  136 (514)
Q Consensus       119 ~~-g~~~~A~~l~~~m~~~  136 (514)
                      +. |++++|++.|++....
T Consensus        88 ~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           88 YIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             TCSSCSHHHHHHHHHHGGG
T ss_pred             HHhCCHHHHHHHHHHHhhc
Confidence            66 6666666666666554

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.94  E-value=0.00023  Score=56.78  Aligned_cols=100  Identities=16%  Similarity=0.021  Sum_probs=60.6

Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC----HHHHHHHHHHHHh
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT----ENVWLTLLSACRV  323 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~----~~~~~~ll~~~~~  323 (514)
                      ...+...|++++|...|+.+.+...-.| ....+..+...+.+.|++++|...+++.. ..|+    ...+..+..++..
T Consensus         9 a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~~~~   88 (129)
T 2xev_A            9 AFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLSQYG   88 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHH
Confidence            3445556666666666666544311111 01355556666666677777766666542 1222    4566777777888


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHH
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYV  349 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~  349 (514)
                      .|++++|...++++++..|+++....
T Consensus        89 ~g~~~~A~~~~~~~~~~~p~~~~~~~  114 (129)
T 2xev_A           89 EGKNTEAQQTLQQVATQYPGSDAARV  114 (129)
T ss_dssp             TTCHHHHHHHHHHHHHHSTTSHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHCCCChHHHH
Confidence            88888888888888888887654433

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.91  E-value=7.1e-05  Score=62.10  Aligned_cols=96  Identities=15%  Similarity=0.063  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC----CCCC----HH
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP----SFEHYAAVADLLGRAGKLQEAYEFISNMH----AGPT----EN  312 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~~p~----~~  312 (514)
                      ++..+...+...|++++|..+++...+...-.+    ....+..+...+...|++++|.+.+++..    ..++    ..
T Consensus        51 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  130 (164)
T 3ro3_A           51 AYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGR  130 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHH
Confidence            344444455555555555555554432211011    12344555555666666666666555431    0111    24


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFMI  340 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~  340 (514)
                      ++..+...+...|++++|...+++.+++
T Consensus       131 ~~~~la~~~~~~g~~~~A~~~~~~a~~~  158 (164)
T 3ro3_A          131 ACWSLGNAYTALGNHDQAMHFAEKHLEI  158 (164)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            5666777777788888888887777654

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.89  E-value=5e-05  Score=63.84  Aligned_cols=76  Identities=16%  Similarity=0.076  Sum_probs=60.7

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCc-chHHHHHHH
Q 040365          279 FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNM-GAYVILSNT  354 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~-~~~~~l~~~  354 (514)
                      ...|..+..+|.+.|++++|...+++..  .+.+...|..+..++...|++++|...++++++++|+++ .....+..+
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~l~~~  141 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAAASVVAREMKIV  141 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            4677788888889999999998888753  234678899999999999999999999999999999887 334444333

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.89  E-value=3.5e-05  Score=73.79  Aligned_cols=147  Identities=8%  Similarity=-0.087  Sum_probs=82.7

Q ss_pred             hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHH
Q 040365          208 IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       208 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  287 (514)
                      ...|..+...+.+.|++++|+..|++....  .|+...       +...++.+++...+.           ...|..+..
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l~-----------~~~~~nla~  238 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAVK-----------NPCHLNIAA  238 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHHH-----------THHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHHH-----------HHHHHHHHH
Confidence            345777777788889999999999988764  455432       233444444433221           136778888


Q ss_pred             HHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHH-HHccChhHH
Q 040365          288 LLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTY-AAARRWKDA  364 (514)
Q Consensus       288 ~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~-~~~g~~~~a  364 (514)
                      +|.+.|++++|...+++..  .+.+...|..+..++...|++++|+..|+++++++|++...+..|..+. ...+..+.+
T Consensus       239 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a  318 (338)
T 2if4_A          239 CLIKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQ  318 (338)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999888763  2346788999999999999999999999999999999888888887774 445667778


Q ss_pred             HHHHHHHHhC
Q 040365          365 ASLRVFMRNK  374 (514)
Q Consensus       365 ~~~~~~m~~~  374 (514)
                      .+.+..|...
T Consensus       319 ~~~~~~~l~~  328 (338)
T 2if4_A          319 KEMYKGIFKG  328 (338)
T ss_dssp             ----------
T ss_pred             HHHHHHhhCC
Confidence            8888877654

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.83  E-value=5.2e-05  Score=62.87  Aligned_cols=71  Identities=14%  Similarity=0.018  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC-C-------CCC-HHHH----HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcch
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNMH-A-------GPT-ENVW----LTLLSACRVHKNVELAGKVAEKIFMIDPNNMGA  347 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m~-~-------~p~-~~~~----~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~  347 (514)
                      .|..+..++.+.|++++|+..+++.. .       .|+ ...|    .....++...|++++|+..|+++++++|.+...
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            56666666666666666666655432 2       564 5678    899999999999999999999999999988765


Q ss_pred             HHHH
Q 040365          348 YVIL  351 (514)
Q Consensus       348 ~~~l  351 (514)
                      +.-+
T Consensus       139 ~~~~  142 (159)
T 2hr2_A          139 TPGK  142 (159)
T ss_dssp             CTTH
T ss_pred             HHHH
Confidence            5443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.83  E-value=3.6e-05  Score=60.80  Aligned_cols=91  Identities=14%  Similarity=0.137  Sum_probs=55.0

Q ss_pred             cCCHHHHHHHHHHhHHhcCC-CC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHH
Q 040365          256 AGLIDKAWSYFNSMTKDYGI-AP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAG  331 (514)
Q Consensus       256 ~g~~~~a~~~~~~m~~~~~~-~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~  331 (514)
                      .|++++|+..|++..+. +. .| +...+..+...|.+.|++++|.+.+++..  .+.+..++..+..++...|++++|+
T Consensus         3 ~g~~~~A~~~~~~al~~-~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIAS-GLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ----CCCHHHHHHHHSS-CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHc-CCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHH
Confidence            35555566666655421 10 13 34556666666667777777777666642  2234666777777778888888888


Q ss_pred             HHHHHHHhcCCCCcch
Q 040365          332 KVAEKIFMIDPNNMGA  347 (514)
Q Consensus       332 ~~~~~~~~~~p~~~~~  347 (514)
                      ..++++++..|+++..
T Consensus        82 ~~~~~al~~~p~~~~~   97 (117)
T 3k9i_A           82 ELLLKIIAETSDDETI   97 (117)
T ss_dssp             HHHHHHHHHHCCCHHH
T ss_pred             HHHHHHHHhCCCcHHH
Confidence            8888888777776543

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.82  E-value=6.7e-05  Score=58.12  Aligned_cols=92  Identities=11%  Similarity=-0.056  Sum_probs=72.7

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------cchHH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN------MGAYV  349 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~------~~~~~  349 (514)
                      +...+..+...+.+.|++++|.+.+++..  .+.+...|..+..++...|++++|+..++++++++|++      ...+.
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~   82 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIRSKLQY   82 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence            34566777778888888888888887753  23467888899999999999999999999999999988      66777


Q ss_pred             HHHHHHHHccChhHHHHHHH
Q 040365          350 ILSNTYAAARRWKDAASLRV  369 (514)
Q Consensus       350 ~l~~~~~~~g~~~~a~~~~~  369 (514)
                      .+..++...|+++.|...++
T Consensus        83 ~~~~~~~~~~~~~~a~~~~~  102 (111)
T 2l6j_A           83 RLELAQGAVGSVQIPVVEVD  102 (111)
T ss_dssp             HHHHHHHHHHCCCCCSSSSS
T ss_pred             HHHHHHHHHHhHhhhHhHHH
Confidence            78888888887776655443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.82  E-value=0.0001  Score=56.27  Aligned_cols=66  Identities=21%  Similarity=0.181  Sum_probs=60.7

Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          309 PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .+...|..+...+...|++++|+..++++++++|+++.+|..++.+|...|++++|.+.+++..+.
T Consensus         5 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            5 EDPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            467889999999999999999999999999999999999999999999999999999999987653

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.81  E-value=0.00014  Score=72.93  Aligned_cols=125  Identities=11%  Similarity=0.078  Sum_probs=96.8

Q ss_pred             HHHccCCHHHHHHHHHHhHHhcC--CC---C-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC---------CCCCH-HHHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYG--IA---P-SFEHYAAVADLLGRAGKLQEAYEFISNMH---------AGPTE-NVWL  315 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~--~~---p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~---------~~p~~-~~~~  315 (514)
                      .+...|++++|..++++..+...  +.   | ...+++.|..+|...|++++|..++++..         ..|+. .+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            35578899999888877655422  12   2 24678888999999999999998887652         23443 5689


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh-----cCCCCcc---hHHHHHHHHHHccChhHHHHHHHHHHhCCC
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFM-----IDPNNMG---AYVILSNTYAAARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~-----~~p~~~~---~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  376 (514)
                      .|...|...|++++|+.+++++++     ++|+.+.   ....|..++...|++++|..++.+++++-.
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~~~  466 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAAL  466 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999886     4566544   456788889999999999999999987543

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.81  E-value=0.0012  Score=67.59  Aligned_cols=167  Identities=8%  Similarity=0.004  Sum_probs=124.9

Q ss_pred             HHHHHHHHHhCC---CCChhHHHHHHHHHHhCCC----------hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccC--
Q 040365          193 IRLARCIFDKMD---LHDIVSWTAVIMGNALHGN----------AHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAG--  257 (514)
Q Consensus       193 ~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~----------~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g--  257 (514)
                      -++|.+.++.+.   ..+...|+.--..+...|+          ++++++.++++.+... -+...|..-...+.+.+  
T Consensus        45 ~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~p-K~y~aW~hR~w~l~~l~~~  123 (567)
T 1dce_A           45 DESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNP-KSYGTWHHRCWLLSRLPEP  123 (567)
T ss_dssp             SHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTCSSC
T ss_pred             CHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcccc
Confidence            355666666664   3345667766666666665          7888888888887532 25567777777777888  


Q ss_pred             CHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcC-CHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhc---------
Q 040365          258 LIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAG-KLQEAYEFISNMH-AG-PTENVWLTLLSACRVH---------  324 (514)
Q Consensus       258 ~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g-~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~---------  324 (514)
                      ++++++..++.+.+.   .| +...|+.-.-.+.+.| ..+++++.++++. .. -|...|+.....+...         
T Consensus       124 ~~~~el~~~~k~l~~---d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~~~  200 (567)
T 1dce_A          124 NWARELELCARFLEA---DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQ  200 (567)
T ss_dssp             CHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSC
T ss_pred             cHHHHHHHHHHHHhh---ccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhccccccccc
Confidence            678899998888764   44 5667777667777788 8888999888874 22 4678888877776653         


Q ss_pred             -----CCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhH
Q 040365          325 -----KNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKD  363 (514)
Q Consensus       325 -----~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  363 (514)
                           +.++++.+.+.+++..+|++..+|..+...+.+.++.++
T Consensus       201 ~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          201 GRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             ccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCCccc
Confidence                 567999999999999999999999999999998888555

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.79  E-value=9e-05  Score=70.88  Aligned_cols=149  Identities=10%  Similarity=-0.011  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhCC--CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 040365          177 MFIASSLLDMYAKCGNIRLARCIFDKMD--LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACS  254 (514)
Q Consensus       177 ~~~~~~li~~y~k~g~~~~A~~~~~~m~--~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~  254 (514)
                      ...+..+...|.+.|++++|...|++..  .|+..       .+...|+.+++...+.          ...|..+..++.
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~-------~~~~~~~~~~~~~~l~----------~~~~~nla~~~~  241 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDF-------MFQLYGKYQDMALAVK----------NPCHLNIAACLI  241 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHH-------HHTCCHHHHHHHHHHH----------THHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccch-------hhhhcccHHHHHHHHH----------HHHHHHHHHHHH
Confidence            4557778889999999999999999865  22222       1223344444433221          136677777888


Q ss_pred             ccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHH-HHhcCCHHHH
Q 040365          255 HAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSA-CRVHKNVELA  330 (514)
Q Consensus       255 ~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~-~~~~~~~~~a  330 (514)
                      +.|++++|+..++...+.   .| +...|..+..+|...|++++|.+.|++.. ..| +...+..|... ....+..+.+
T Consensus       242 ~~g~~~~A~~~~~~al~~---~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a  318 (338)
T 2if4_A          242 KLKRYDEAIGHCNIVLTE---EEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQ  318 (338)
T ss_dssp             TTTCCHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            888888888888887653   45 57788888888888899999988888864 334 34455555544 3445667788


Q ss_pred             HHHHHHHHhcCCCCc
Q 040365          331 GKVAEKIFMIDPNNM  345 (514)
Q Consensus       331 ~~~~~~~~~~~p~~~  345 (514)
                      ...+++++...|.++
T Consensus       319 ~~~~~~~l~~~p~~~  333 (338)
T 2if4_A          319 KEMYKGIFKGKDEGG  333 (338)
T ss_dssp             ---------------
T ss_pred             HHHHHHhhCCCCCCC
Confidence            888888888887654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.75  E-value=0.0002  Score=53.04  Aligned_cols=81  Identities=21%  Similarity=0.245  Sum_probs=64.3

Q ss_pred             HhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          279 FEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                      ...+..+...+.+.|++++|.+.+++..  .+.+..+|..+..++...|++++|...++++++.+|.++..+..+..++.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~   88 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQ   88 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            4566667777788888888888877652  23467788888889999999999999999999999998888888888876


Q ss_pred             Hcc
Q 040365          357 AAR  359 (514)
Q Consensus       357 ~~g  359 (514)
                      ..|
T Consensus        89 ~~g   91 (91)
T 1na3_A           89 KQG   91 (91)
T ss_dssp             HHC
T ss_pred             hcC
Confidence            654

>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=97.67  E-value=0.00056  Score=68.28  Aligned_cols=85  Identities=9%  Similarity=-0.007  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSA  320 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~  320 (514)
                      ..|..+..++.+.|++++|+..++...+.   .| +...|..+..+|...|++++|...|++.. ..| +...|..+..+
T Consensus       318 ~~~~nla~~~~~~g~~~~A~~~~~~al~~---~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~  394 (457)
T 1kt0_A          318 AAFLNLAMCYLKLREYTKAVECCDKALGL---DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMC  394 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhc---CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            34444444555555555555555544432   22 34445555555555555555555555432 222 23344445555


Q ss_pred             HHhcCCHHHHH
Q 040365          321 CRVHKNVELAG  331 (514)
Q Consensus       321 ~~~~~~~~~a~  331 (514)
                      +...++.+++.
T Consensus       395 ~~~~~~~~~a~  405 (457)
T 1kt0_A          395 QKKAKEHNERD  405 (457)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555554443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.65  E-value=0.00018  Score=56.35  Aligned_cols=77  Identities=17%  Similarity=0.056  Sum_probs=62.6

Q ss_pred             HHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          298 AYEFISNM-HAG-PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       298 A~~~~~~m-~~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      |.+.+++. ... .+...|..+...+...|++++|+..++++++.+|.++..|..++.+|...|++++|...+++..+.
T Consensus         4 a~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   82 (115)
T 2kat_A            4 ITERLEAMLAQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLAA   82 (115)
T ss_dssp             HHHHHHHHHTTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            44555543 222 467788888888999999999999999999999998889999999999999999999999887653

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.64  E-value=0.00038  Score=67.35  Aligned_cols=113  Identities=9%  Similarity=-0.007  Sum_probs=81.3

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRV  323 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~  323 (514)
                      ..+..+...+.+.|++++|...|+...+..   |..          ......+++.+    . .+.+..+|..+..++..
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~---~~~----------~~~~~~~~~~~----~-~~~~~~~~~nla~~~~~  285 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYV---EGS----------RAAAEDADGAK----L-QPVALSCVLNIGACKLK  285 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHH---HHH----------HHHSCHHHHGG----G-HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHh---hcC----------ccccChHHHHH----H-HHHHHHHHHHHHHHHHh
Confidence            345566666667777777777776664320   000          00001111110    0 01245788999999999


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          324 HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .|++++|+..++++++++|+++.+|..++.+|...|++++|.+.+++..+.
T Consensus       286 ~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l  336 (370)
T 1ihg_A          286 MSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  336 (370)
T ss_dssp             TTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            999999999999999999999999999999999999999999999988764

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.54  E-value=0.00012  Score=60.50  Aligned_cols=85  Identities=13%  Similarity=0.037  Sum_probs=64.5

Q ss_pred             hcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCC----------HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 040365          291 RAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKN----------VELAGKVAEKIFMIDPNNMGAYVILSNTYAAA  358 (514)
Q Consensus       291 ~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~----------~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  358 (514)
                      |.+.+++|.+.++...  .+.+...|..+..++...++          +++|+..|+++++++|++..+|..+.++|.+.
T Consensus        14 r~~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~l   93 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSF   93 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHh
Confidence            4455666666665542  22355666666666665554          56999999999999999999999999999987


Q ss_pred             c-----------ChhHHHHHHHHHHhCC
Q 040365          359 R-----------RWKDAASLRVFMRNKG  375 (514)
Q Consensus       359 g-----------~~~~a~~~~~~m~~~g  375 (514)
                      |           ++++|.+.|++..+..
T Consensus        94 g~l~P~~~~a~g~~~eA~~~~~kAl~l~  121 (158)
T 1zu2_A           94 AFLTPDETEAKHNFDLATQFFQQAVDEQ  121 (158)
T ss_dssp             HHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccCcchhhhhccHHHHHHHHHHHHHhC
Confidence            5           8999999999887653

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.42  E-value=0.00057  Score=52.63  Aligned_cols=66  Identities=8%  Similarity=-0.105  Sum_probs=61.4

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      +...|..+...+...|++++|+..++++++.+|.++..+..++.+|...|++++|.+.+++..+..
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   68 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYT   68 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            566788899999999999999999999999999999999999999999999999999999987653

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.39  E-value=0.0012  Score=49.44  Aligned_cols=70  Identities=13%  Similarity=0.156  Sum_probs=60.7

Q ss_pred             CCCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCc
Q 040365          308 GPTENVWLTLLSACRVHKN---VELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       308 ~p~~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  377 (514)
                      ++|...+..+..++...++   .++|..+++++++.+|+++.+...+...+.+.|++++|...++++.+..-.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~   75 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP   75 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            3567788888888765555   799999999999999999999999999999999999999999999886543

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.36  E-value=0.0028  Score=51.43  Aligned_cols=109  Identities=16%  Similarity=0.065  Sum_probs=50.6

Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHh----cCCHHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGR----AGKLQEA  298 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A  298 (514)
                      ++++|+++|++..+.| .|+..    +...|...+.+++|..+|+...+.    -++..+..|..+|..    .+++++|
T Consensus        10 d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~----g~~~a~~~Lg~~y~~G~g~~~d~~~A   80 (138)
T 1klx_A           10 DLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACEL----NSGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             CHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcC----CCHHHHHHHHHHHHcCCCCCccHHHH
Confidence            4556666666666554 22322    444444455555555555555332    233444444444444    4444555


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhc
Q 040365          299 YEFISNMHAGPTENVWLTLLSACRV----HKNVELAGKVAEKIFMI  340 (514)
Q Consensus       299 ~~~~~~m~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~  340 (514)
                      .++|++.-...+...+..|...|..    .+|.++|...+++..+.
T Consensus        81 ~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~  126 (138)
T 1klx_A           81 AQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRL  126 (138)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHC
Confidence            4444443322334444444444444    34444444444444433

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.31  E-value=0.0007  Score=67.77  Aligned_cols=119  Identities=8%  Similarity=-0.045  Sum_probs=69.2

Q ss_pred             ccCChHHHHHHHHHHHHc-----C-CCC-cHHHHHHHHHHHHhcCCHHHHHHHHHhCC----------CCC-hhHHHHHH
Q 040365          154 HLTTLHLGKQLHGCIIRN-----G-FDD-NMFIASSLLDMYAKCGNIRLARCIFDKMD----------LHD-IVSWTAVI  215 (514)
Q Consensus       154 ~~~~~~~a~~~~~~~~~~-----~-~~~-~~~~~~~li~~y~k~g~~~~A~~~~~~m~----------~~d-~~~~~~li  215 (514)
                      ..|++++|..++.+.++.     | -.| ...+++.|...|...|++++|..++++..          .|+ ..+++.|.
T Consensus       321 ~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  400 (490)
T 3n71_A          321 SEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMRAG  400 (490)
T ss_dssp             TTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence            445555555555555432     1 011 23456666666666666666666665542          122 24677777


Q ss_pred             HHHHhCCChHHHHHHHHHHHH-----cCC-CCCH-HHHHHHHHHHHccCCHHHHHHHHHHhHHh
Q 040365          216 MGNALHGNAHDAISLFEQMEK-----DGV-KPNS-VAFVAVLTACSHAGLIDKAWSYFNSMTKD  272 (514)
Q Consensus       216 ~~~~~~g~~~~A~~l~~~m~~-----~g~-~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~  272 (514)
                      ..|...|++++|+.++++...     .|. .|+. .+...+-.++...+.+++|...+..+.+.
T Consensus       401 ~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          401 LTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777777777777776543     121 2332 23445555666777888888888877654

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.22  E-value=0.0006  Score=56.32  Aligned_cols=51  Identities=20%  Similarity=0.238  Sum_probs=36.3

Q ss_pred             HHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhc-----------CCHHHHHHHHHHHHhcCCCCc
Q 040365          295 LQEAYEFISNMH-AGP-TENVWLTLLSACRVH-----------KNVELAGKVAEKIFMIDPNNM  345 (514)
Q Consensus       295 ~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~-----------~~~~~a~~~~~~~~~~~p~~~  345 (514)
                      +++|+..|++.. ..| +..+|..+..+|...           |++++|+..|+++++++|++.
T Consensus        62 ~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~  125 (158)
T 1zu2_A           62 IQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNT  125 (158)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHhCCCCH
Confidence            346666666542 223 455666677776655           589999999999999999875

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.21  E-value=0.0068  Score=49.11  Aligned_cols=113  Identities=15%  Similarity=0.036  Sum_probs=91.8

Q ss_pred             CCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHH
Q 040365          257 GLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRV----HKNVELAGK  332 (514)
Q Consensus       257 g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~----~~~~~~a~~  332 (514)
                      ++.++|..+|+...+. | .|...    |..+|...+.+++|.++|++.-...+...+..|...|..    .+|+++|..
T Consensus         9 ~d~~~A~~~~~~aa~~-g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~   82 (138)
T 1klx_A            9 KDLKKAIQYYVKACEL-N-EMFGC----LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHHHT-T-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             cCHHHHHHHHHHHHcC-C-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            4678899999888653 4 33332    777788888899999999887656788888888888887    889999999


Q ss_pred             HHHHHHhcCCCCcchHHHHHHHHHH----ccChhHHHHHHHHHHhCCCc
Q 040365          333 VAEKIFMIDPNNMGAYVILSNTYAA----ARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       333 ~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~g~~  377 (514)
                      .+++..+.  .++.++..|..+|..    .+++++|.+.+++..+.|..
T Consensus        83 ~~~~Aa~~--g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~  129 (138)
T 1klx_A           83 YYSKACGL--NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGSE  129 (138)
T ss_dssp             HHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcC--CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCCH
Confidence            99998877  456788899999998    88999999999998888753

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.19  E-value=0.0026  Score=49.50  Aligned_cols=65  Identities=8%  Similarity=-0.020  Sum_probs=42.3

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      +...+..+...|.+.|++++|.+.+++..  .+.+...|..+..++...|++++|...+++++++.|
T Consensus        18 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~   84 (115)
T 2kat_A           18 NMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLAAAQ   84 (115)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcc
Confidence            45556666666666666666666666542  223456677777777777777777777777776655

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.17  E-value=0.016  Score=59.32  Aligned_cols=148  Identities=10%  Similarity=0.046  Sum_probs=118.5

Q ss_pred             CCChHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHccCC----------HHHHHHHHHHhHHhcCCCC-CHhHHHHHHHH
Q 040365          221 HGNAHDAISLFEQMEKDGVKPNS-VAFVAVLTACSHAGL----------IDKAWSYFNSMTKDYGIAP-SFEHYAAVADL  288 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~~~~g~----------~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~  288 (514)
                      ....++|++.++++...  .|+. ..|+.--.++.+.|+          ++++...++.+.+.   .| +...|..-.-+
T Consensus        42 ~~~~eeal~~~~~~l~~--nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~---~pK~y~aW~hR~w~  116 (567)
T 1dce_A           42 GELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV---NPKSYGTWHHRCWL  116 (567)
T ss_dssp             TCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHh---CCCCHHHHHHHHHH
Confidence            34467889999999985  5654 445555555555566          89999999999765   45 67777777777


Q ss_pred             HHhcC--CHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc-----
Q 040365          289 LGRAG--KLQEAYEFISNMH--AGPTENVWLTLLSACRVHK-NVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA-----  358 (514)
Q Consensus       289 ~~~~g--~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~-~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~-----  358 (514)
                      +.+.|  ++++++++++++.  ...|...|+.-..+....| .++++.+.++++++.+|.|..+|.....++.+.     
T Consensus       117 l~~l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~  196 (567)
T 1dce_A          117 LSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPD  196 (567)
T ss_dssp             HHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCC
T ss_pred             HHHcccccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhccccc
Confidence            88889  7799999999874  3458889999888888888 899999999999999999999999988888774     


Q ss_pred             ---------cChhHHHHHHHHHHh
Q 040365          359 ---------RRWKDAASLRVFMRN  373 (514)
Q Consensus       359 ---------g~~~~a~~~~~~m~~  373 (514)
                               ++++++.+.++....
T Consensus       197 ~~~~~~~~~~~~~eel~~~~~ai~  220 (567)
T 1dce_A          197 SGPQGRLPENVLLKELELVQNAFF  220 (567)
T ss_dssp             SSSCCSSCHHHHHHHHHHHHHHHH
T ss_pred             ccccccccHHHHHHHHHHHHHHHh
Confidence                     567888888877654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.16  E-value=0.0021  Score=47.23  Aligned_cols=82  Identities=15%  Similarity=0.111  Sum_probs=53.8

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHH
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLIN   84 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (514)
                      +...|..+...+.+.|++++|+..|++..... +.+...+..+...+...|++++|...+..+++.. +.+..++..+..
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            34566777777777778888887777776643 2345566666677777777777777777777664 444555555555


Q ss_pred             HHHH
Q 040365           85 MYAK   88 (514)
Q Consensus        85 ~~~~   88 (514)
                      .+.+
T Consensus        86 ~~~~   89 (91)
T 1na3_A           86 AKQK   89 (91)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            5543

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.14  E-value=0.0012  Score=64.95  Aligned_cols=116  Identities=9%  Similarity=-0.042  Sum_probs=85.2

Q ss_pred             HHHHHhcCCHHHHHHHHHhCC---------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-----CCCC---cch
Q 040365          286 ADLLGRAGKLQEAYEFISNMH---------AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMI-----DPNN---MGA  347 (514)
Q Consensus       286 i~~~~~~g~~~~A~~~~~~m~---------~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~p~~---~~~  347 (514)
                      +..+.+.|++++|++++++..         ..|+ ..+++.|..+|...|++++|+.+++++++.     +|+.   ..+
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            445667788888888887642         1122 357888999999999999999999988763     3443   457


Q ss_pred             HHHHHHHHHHccChhHHHHHHHHHHhCCCccCCcccEEEECCEEEEEEeCCCCCCChHHHHHHHHHHHHHHH
Q 040365          348 YVILSNTYAAARRWKDAASLRVFMRNKGMKKTPACSWIEVKNKAYAFVAGDKSHPFYHRINEALKELLERME  419 (514)
Q Consensus       348 ~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~  419 (514)
                      ++.|+..|...|++++|..++++..+--..                  .-...||...++...|.+...+|+
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~------------------~lG~~Hp~~~~~~~~l~~~~~e~~  427 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFDIMRV------------------THGREHSLIEDLILLLEECDANIR  427 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHH------------------HTCTTSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHH------------------hcCCCChHHHHHHHHHHHHHHHHh
Confidence            888999999999999999999887642110                  001348988888888877777765

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.06  E-value=0.02  Score=61.39  Aligned_cols=153  Identities=14%  Similarity=0.125  Sum_probs=101.0

Q ss_pred             HHhcCChhHHHH-HHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHH
Q 040365           16 LARNGLYEEALN-IVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVED   94 (514)
Q Consensus        16 ~~~~g~~~~A~~-l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~   94 (514)
                      ....+++++|.+ ++..+      |+......++..+.+.|..+.|.++.+.         .   ..-......+|++++
T Consensus       609 ~~~~~~~~~a~~~~l~~i------~~~~~~~~~~~~l~~~~~~~~a~~~~~~---------~---~~~f~~~l~~~~~~~  670 (814)
T 3mkq_A          609 LTLRGEIEEAIENVLPNV------EGKDSLTKIARFLEGQEYYEEALNISPD---------Q---DQKFELALKVGQLTL  670 (814)
T ss_dssp             HHHTTCHHHHHHHTGGGC------CCHHHHHHHHHHHHHTTCHHHHHHHCCC---------H---HHHHHHHHHHTCHHH
T ss_pred             HHHhCCHHHHHHHHHhcC------CchHHHHHHHHHHHhCCChHHheecCCC---------c---chheehhhhcCCHHH
Confidence            345778888876 44221      2122336677777788888887765531         1   122445677899999


Q ss_pred             HHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCC
Q 040365           95 SHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFD  174 (514)
Q Consensus        95 A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  174 (514)
                      |.++.+.+.  +...|..+...+.+.|+++.|.+.|.++..         |..+...+...++.+...++-+.....|  
T Consensus       671 A~~~~~~~~--~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~~--  737 (814)
T 3mkq_A          671 ARDLLTDES--AEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETTG--  737 (814)
T ss_dssp             HHHHHTTCC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHTT--
T ss_pred             HHHHHHhhC--cHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHcC--
Confidence            999988774  567899999999999999999999998743         3344445555777776666665555554  


Q ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040365          175 DNMFIASSLLDMYAKCGNIRLARCIFDKM  203 (514)
Q Consensus       175 ~~~~~~~~li~~y~k~g~~~~A~~~~~~m  203 (514)
                          -++.-..+|.++|++++|.+++.++
T Consensus       738 ----~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          738 ----KFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             ----CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             ----chHHHHHHHHHcCCHHHHHHHHHHc
Confidence                1233444566777777777665443

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.84  E-value=0.032  Score=59.69  Aligned_cols=42  Identities=12%  Similarity=0.060  Sum_probs=21.8

Q ss_pred             HHCCCHHHHHH-HHccCCCCChhHHHHHHHHHHHCCChhHHHHHH
Q 040365           87 AKCARVEDSHR-LFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFF  130 (514)
Q Consensus        87 ~~~g~~~~A~~-~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~  130 (514)
                      ...+++++|.+ ++..++.  ......++..+.+.|.+++|+++.
T Consensus       610 ~~~~~~~~a~~~~l~~i~~--~~~~~~~~~~l~~~~~~~~a~~~~  652 (814)
T 3mkq_A          610 TLRGEIEEAIENVLPNVEG--KDSLTKIARFLEGQEYYEEALNIS  652 (814)
T ss_dssp             HHTTCHHHHHHHTGGGCCC--HHHHHHHHHHHHHTTCHHHHHHHC
T ss_pred             HHhCCHHHHHHHHHhcCCc--hHHHHHHHHHHHhCCChHHheecC
Confidence            34566666666 5544330  112255555566666666666544

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.83  E-value=0.0054  Score=46.42  Aligned_cols=61  Identities=16%  Similarity=0.150  Sum_probs=29.2

Q ss_pred             hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          208 IVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       208 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      ...|..+...|.+.|++++|+..|++..+.. +.+...|..+..++...|++++|...|+..
T Consensus         7 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~a   67 (100)
T 3ma5_A            7 PFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQG   67 (100)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3444445555555555555555555554431 112334444555555555555555555544

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.79  E-value=0.0017  Score=63.96  Aligned_cols=83  Identities=12%  Similarity=0.013  Sum_probs=65.4

Q ss_pred             hcCCHHHHHHHHHhCC---------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhc-----CCC---CcchHHHHH
Q 040365          291 RAGKLQEAYEFISNMH---------AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMI-----DPN---NMGAYVILS  352 (514)
Q Consensus       291 ~~g~~~~A~~~~~~m~---------~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~p~---~~~~~~~l~  352 (514)
                      ..|++++|+.++++..         ..|+ ..+++.|..+|...|++++|+.+++++++.     +|+   ...+|+.|+
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            3467888888776541         2233 357889999999999999999999998863     444   445788999


Q ss_pred             HHHHHccChhHHHHHHHHHHh
Q 040365          353 NTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       353 ~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      .+|...|++++|..++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            999999999999999998764

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.77  E-value=0.0094  Score=44.61  Aligned_cols=64  Identities=11%  Similarity=0.124  Sum_probs=50.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC-CC-CCHH-HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchH
Q 040365          285 VADLLGRAGKLQEAYEFISNMH-AG-PTEN-VWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAY  348 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~-~~-p~~~-~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~  348 (514)
                      ....+.+.|++++|.+.+++.. .. .+.. .|..+..++...|++++|...++++++++|+++.++
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~   72 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDSPALQ   72 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHH
Confidence            3455677788888888887753 22 3566 788888888999999999999999999999887766

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.69  E-value=0.0051  Score=46.14  Aligned_cols=59  Identities=17%  Similarity=0.241  Sum_probs=54.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCcc-hHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          317 LLSACRVHKNVELAGKVAEKIFMIDPNNMG-AYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       317 ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~-~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      ....+...|++++|...++++++.+|.++. .+..++.+|...|++++|.+.+++..+..
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            455678899999999999999999999999 99999999999999999999999987654

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.67  E-value=0.16  Score=39.91  Aligned_cols=140  Identities=11%  Similarity=0.121  Sum_probs=97.8

Q ss_pred             HhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHH
Q 040365          219 ALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEA  298 (514)
Q Consensus       219 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A  298 (514)
                      ...|..++..++..+....   .+..-|+.++--....-+-+-..+.++.+-+-+.+              ..+|++...
T Consensus        18 ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDi--------------s~C~NlKrV   80 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDL--------------DKCQNLKSV   80 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCG--------------GGCSCTHHH
T ss_pred             HHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhhcCc--------------HhhhcHHHH
Confidence            4467777777777776653   24455666665555555555566666665433322              245555555


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCc
Q 040365          299 YEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       299 ~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  377 (514)
                      ..-+-.+.  .+.......++.....|+.+.-..+...++..+|.++....-++++|.+.|+..+|.+++.+.-++|++
T Consensus        81 i~C~~~~n--~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           81 VECGVINN--TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHTT--CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhc--chHHHHHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            55554443  344455667788889999999999999977777888999999999999999999999999999999985

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.65  E-value=0.014  Score=57.39  Aligned_cols=93  Identities=9%  Similarity=-0.002  Sum_probs=68.8

Q ss_pred             ccCCHHHHHHHHHHhHHhcC--CCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC---------CCCCH-HHHHHHH
Q 040365          255 HAGLIDKAWSYFNSMTKDYG--IAP----SFEHYAAVADLLGRAGKLQEAYEFISNMH---------AGPTE-NVWLTLL  318 (514)
Q Consensus       255 ~~g~~~~a~~~~~~m~~~~~--~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~---------~~p~~-~~~~~ll  318 (514)
                      +.|++++|..++++..+...  +.|    ...+++.|..+|...|++++|+.++++..         ..|+. .+++.|.
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            45778888888877654321  222    24678888888999999999988887652         23544 5688999


Q ss_pred             HHHHhcCCHHHHHHHHHHHHh-----cCCCCcch
Q 040365          319 SACRVHKNVELAGKVAEKIFM-----IDPNNMGA  347 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~-----~~p~~~~~  347 (514)
                      ..|...|++++|+.+++++++     ++|+.+.+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~i~~~~lG~~Hp~~  423 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIAIMEVAHGKDHPYI  423 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHHHHHHcCCCChHH
Confidence            999999999999999999876     35776543

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.59  E-value=0.014  Score=47.53  Aligned_cols=66  Identities=6%  Similarity=-0.035  Sum_probs=45.5

Q ss_pred             CCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhcC-C-CCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          309 PTENVWLTLLSACRVHK---NVELAGKVAEKIFMID-P-NNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~---~~~~a~~~~~~~~~~~-p-~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ++..+.-.+..++.+.+   +.++|+.+++.+.+.+ | .+...+..|+-+|.+.|++++|.+.++.+.+.
T Consensus        30 ~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~i  100 (152)
T 1pc2_A           30 VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQT  100 (152)
T ss_dssp             CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            56666666666777766   5557777777777766 5 34556667777777777777777777777653

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.55  E-value=0.025  Score=55.54  Aligned_cols=100  Identities=9%  Similarity=-0.035  Sum_probs=71.0

Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcC--CCC----CHhHHHHHHHHHHhcCCHHHHHHHHHhCC---------CCCCH-HH
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYG--IAP----SFEHYAAVADLLGRAGKLQEAYEFISNMH---------AGPTE-NV  313 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~--~~p----~~~~~~~li~~~~~~g~~~~A~~~~~~m~---------~~p~~-~~  313 (514)
                      +..+...|++++|..++++......  +.|    ...+++.|...|...|++++|+.++++..         ..|+. .+
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            4455567788888888877754321  222    24667788888888888888888877642         23443 56


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHh-----cCCCCcchHH
Q 040365          314 WLTLLSACRVHKNVELAGKVAEKIFM-----IDPNNMGAYV  349 (514)
Q Consensus       314 ~~~ll~~~~~~~~~~~a~~~~~~~~~-----~~p~~~~~~~  349 (514)
                      ++.|...|...|++++|+.+++++++     ++|+.+.+-.
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~  414 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIED  414 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCChHHHH
Confidence            88899999999999999999998876     4677664443

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.49  E-value=0.1  Score=49.38  Aligned_cols=47  Identities=17%  Similarity=0.133  Sum_probs=29.0

Q ss_pred             CCChhHHHHHHHHHHh--CC---ChHHHHHHHHHHHHcCCCCCH-HHHHHHHHHH
Q 040365          205 LHDIVSWTAVIMGNAL--HG---NAHDAISLFEQMEKDGVKPNS-VAFVAVLTAC  253 (514)
Q Consensus       205 ~~d~~~~~~li~~~~~--~g---~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~  253 (514)
                      ..+..+|...+.+...  .+   ...+|..+|++..+.  .|+- ..+..+..++
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l--DP~~a~A~A~la~a~  243 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS--SPEFTYARAEKALVD  243 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHH
Confidence            4467778877766432  33   357889999998884  6663 3444333333

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.09  E-value=0.14  Score=48.56  Aligned_cols=61  Identities=7%  Similarity=0.047  Sum_probs=31.3

Q ss_pred             ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040365          207 DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSM  269 (514)
Q Consensus       207 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  269 (514)
                      +...|.++...+...|++++|+..+++....+  |+...|..+...+.-.|++++|.+.|++.
T Consensus       276 ~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~A  336 (372)
T 3ly7_A          276 LSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTA  336 (372)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            44444444444444455555555555555542  45444444445555555555555555544

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.85  E-value=0.34  Score=40.44  Aligned_cols=105  Identities=11%  Similarity=0.119  Sum_probs=70.5

Q ss_pred             HHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHH
Q 040365           83 INMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGK  162 (514)
Q Consensus        83 i~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~  162 (514)
                      .+....+|+++.|.++.+.+  .+...|..|.....+.|+++-|.+.|.+...         +..+.-.|.-.|+.+.-.
T Consensus        12 F~LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~   80 (177)
T 3mkq_B           12 FDLALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLS   80 (177)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHH
Confidence            34456788888888887766  3567899999999999999999888887643         334444455567776666


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040365          163 QLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD  204 (514)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~  204 (514)
                      .+-......| .     ++.-...+.-.|+++++.++|.+..
T Consensus        81 kla~iA~~~g-~-----~n~af~~~l~lGdv~~~i~lL~~~~  116 (177)
T 3mkq_B           81 KMQNIAQTRE-D-----FGSMLLNTFYNNSTKERSSIFAEGG  116 (177)
T ss_dssp             HHHHHHHHTT-C-----HHHHHHHHHHHTCHHHHHHHHHHTT
T ss_pred             HHHHHHHHCc-c-----HHHHHHHHHHcCCHHHHHHHHHHCC
Confidence            6655555554 1     2333444556677777777776554

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.73  E-value=0.11  Score=38.51  Aligned_cols=77  Identities=13%  Similarity=-0.041  Sum_probs=56.5

Q ss_pred             CCHhHHHHHHHHHHhcCC---HHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          277 PSFEHYAAVADLLGRAGK---LQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       277 p~~~~~~~li~~~~~~g~---~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      +++..+..+..++...++   .++|..++++..  .+.++..+..+...+.+.|+++.|+..|+++++.+|++ .....+
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~~-~~~~~i   82 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDPN-LDRVTI   82 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCTT-CCHHHH
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCC-ccHHHH
Confidence            466777777777765544   688888888763  33467778888888999999999999999999999883 334444


Q ss_pred             HHH
Q 040365          352 SNT  354 (514)
Q Consensus       352 ~~~  354 (514)
                      ...
T Consensus        83 ~~~   85 (93)
T 3bee_A           83 IES   85 (93)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.71  E-value=0.074  Score=40.37  Aligned_cols=74  Identities=14%  Similarity=0.063  Sum_probs=53.2

Q ss_pred             CHhHHHHHHHHHHhcCCHHHHHHHHHhCC---------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchH
Q 040365          278 SFEHYAAVADLLGRAGKLQEAYEFISNMH---------AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAY  348 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~---------~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~  348 (514)
                      +..-+..|...+.+.|+++.|...++...         ..+...++..|..++.+.|+++.|...++++++++|++..+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~~~~~~   83 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRAN   83 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHH
Confidence            33444556666666666666666665531         123467788999999999999999999999999999987664


Q ss_pred             HHH
Q 040365          349 VIL  351 (514)
Q Consensus       349 ~~l  351 (514)
                      ..+
T Consensus        84 ~n~   86 (104)
T 2v5f_A           84 GNL   86 (104)
T ss_dssp             HHH
T ss_pred             hhH
Confidence            443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.59  E-value=0.34  Score=40.48  Aligned_cols=129  Identities=16%  Similarity=0.157  Sum_probs=76.7

Q ss_pred             HHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040365          185 DMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWS  264 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~  264 (514)
                      +...++|+++.|.++.+.+  .+...|..+......+|+++-|.+.|.+...         |..+.-.|.-.|+.+.-..
T Consensus        13 ~LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~k   81 (177)
T 3mkq_B           13 DLALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSK   81 (177)
T ss_dssp             HHHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHH
Confidence            4456778888888877766  4566788888888888888888888877542         3334444555666655444


Q ss_pred             HHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040365          265 YFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKI  337 (514)
Q Consensus       265 ~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  337 (514)
                      +-+....+ |      -++.-...+.-.|+++++.+++.+...-|...      -....+|-.+.|.++.+.+
T Consensus        82 la~iA~~~-g------~~n~af~~~l~lGdv~~~i~lL~~~~r~~eA~------~~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           82 MQNIAQTR-E------DFGSMLLNTFYNNSTKERSSIFAEGGSLPLAY------AVAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHHT-T------CHHHHHHHHHHHTCHHHHHHHHHHTTCHHHHH------HHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHC-c------cHHHHHHHHHHcCCHHHHHHHHHHCCChHHHH------HHHHHcCcHHHHHHHHHHh
Confidence            43333211 1      23444455666778888887777665222111      1123355566666665543

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=95.13  E-value=0.082  Score=48.05  Aligned_cols=87  Identities=10%  Similarity=0.051  Sum_probs=68.7

Q ss_pred             HHHHHHHHHhC-CCCCC---HHHHHHHHHHHHh-----cCCHHHHHHHHHHHHhcCCCC-cchHHHHHHHHHHc-cChhH
Q 040365          295 LQEAYEFISNM-HAGPT---ENVWLTLLSACRV-----HKNVELAGKVAEKIFMIDPNN-MGAYVILSNTYAAA-RRWKD  363 (514)
Q Consensus       295 ~~~A~~~~~~m-~~~p~---~~~~~~ll~~~~~-----~~~~~~a~~~~~~~~~~~p~~-~~~~~~l~~~~~~~-g~~~~  363 (514)
                      ..+|...+++. ...|+   ...|..|...|.+     .|+.++|.+.|+++++++|+. ..+++..+..++.. |+.++
T Consensus       179 l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~  258 (301)
T 3u64_A          179 VHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAG  258 (301)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHH
T ss_pred             HHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHH
Confidence            34555555554 23455   5678888888888     499999999999999999974 99999999999885 99999


Q ss_pred             HHHHHHHHHhCCCccCCc
Q 040365          364 AASLRVFMRNKGMKKTPA  381 (514)
Q Consensus       364 a~~~~~~m~~~g~~~~~~  381 (514)
                      +.+.+++.........|+
T Consensus       259 a~~~L~kAL~a~p~~~P~  276 (301)
T 3u64_A          259 FDEALDRALAIDPESVPH  276 (301)
T ss_dssp             HHHHHHHHHHCCGGGCSS
T ss_pred             HHHHHHHHHcCCCCCCCC
Confidence            999999998877664453

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=94.52  E-value=0.19  Score=40.87  Aligned_cols=70  Identities=17%  Similarity=0.106  Sum_probs=46.5

Q ss_pred             CCHhHHHHHHHHHHhcC---CHHHHHHHHHhCC-CC-C--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc
Q 040365          277 PSFEHYAAVADLLGRAG---KLQEAYEFISNMH-AG-P--TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG  346 (514)
Q Consensus       277 p~~~~~~~li~~~~~~g---~~~~A~~~~~~m~-~~-p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~  346 (514)
                      ++..+...+.-++.+++   +++++..++++.- .. |  +...+..|.-++.+.|++++|.+.++.+++.+|++.-
T Consensus        30 ~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~~~lL~ieP~n~Q  106 (152)
T 1pc2_A           30 VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLLQTEPQNNQ  106 (152)
T ss_dssp             CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHH
Confidence            34444445555555555   3445555555432 11 3  2455667778889999999999999999999998753

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=94.50  E-value=0.25  Score=38.63  Aligned_cols=87  Identities=17%  Similarity=0.036  Sum_probs=41.4

Q ss_pred             CCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHH---HHHHHHhCCCC--C--CHHHHHHHHHHHHhcCCHHH
Q 040365          257 GLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQE---AYEFISNMHAG--P--TENVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       257 g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~---A~~~~~~m~~~--p--~~~~~~~ll~~~~~~~~~~~  329 (514)
                      ..+..+.+-|...... |. |+..+-..+.-++.++....+   +..++++.-..  |  .......|.-++.+.|+++.
T Consensus        15 ~~l~~~~~~y~~e~~~-~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~   92 (126)
T 1nzn_A           15 EDLLKFEKKFQSEKAA-GS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEK   92 (126)
T ss_dssp             HHHHHHHHHHHHHHHH-SC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhcc-CC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHH
Confidence            3344444444443222 21 444444455555555554444   55555554311  2  11223334445555666666


Q ss_pred             HHHHHHHHHhcCCCCc
Q 040365          330 AGKVAEKIFMIDPNNM  345 (514)
Q Consensus       330 a~~~~~~~~~~~p~~~  345 (514)
                      |.+.++.+++.+|+|.
T Consensus        93 A~~~~~~lL~~eP~n~  108 (126)
T 1nzn_A           93 ALKYVRGLLQTEPQNN  108 (126)
T ss_dssp             HHHHHHHHHHHCTTCH
T ss_pred             HHHHHHHHHHhCCCCH
Confidence            6666666666665553

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=94.42  E-value=5.1  Score=40.97  Aligned_cols=309  Identities=7%  Similarity=0.009  Sum_probs=158.9

Q ss_pred             HHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHh-CCCCchhHHHHHHHHHHHCCCHHH
Q 040365           16 LARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRH-GLDANVCIGSSLINMYAKCARVED   94 (514)
Q Consensus        16 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~-g~~~~~~~~~~li~~~~~~g~~~~   94 (514)
                      ..+.|++..+..+...+...-+. .-..|..+...... ....   ++-..+.+. |.+.....-+.-+..+++.+++..
T Consensus        16 a~~~~~~~~~~~l~~~l~~~pL~-~yl~y~~l~~~l~~-~~~~---ev~~Fl~~~~~~p~~~~Lr~~~l~~l~~~~~w~~   90 (618)
T 1qsa_A           16 AWDNRQMDVVEQMMPGLKDYPLY-PYLEYRQITDDLMN-QPAV---TVTNFVRANPTLPPARTLQSRFVNELARREDWRG   90 (618)
T ss_dssp             HHHTTCHHHHHHHSGGGTTSTTH-HHHHHHHHHHTGGG-CCHH---HHHHHHHHCTTCHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHCCCHHHHHHHHHhhcCCCcH-HHHHHHHHHhCccc-CCHH---HHHHHHHHCCCChhHHHHHHHHHHHHHhCCCHHH
Confidence            34568888877776666433221 11234443332221 1233   444444443 223333444666777888999999


Q ss_pred             HHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH--HHHHHHHHHHcC
Q 040365           95 SHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHL--GKQLHGCIIRNG  172 (514)
Q Consensus        95 A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~--a~~~~~~~~~~~  172 (514)
                      ....+.. +..+...-.....+....|+..+|....+.+-..| .........++..+.+.|.+..  ..+=+..+...|
T Consensus        91 ~l~~~~~-~p~~~~~~c~~~~A~~~~G~~~~a~~~~~~lW~~~-~~~p~~c~~l~~~~~~~g~lt~~~~~~R~~~al~~~  168 (618)
T 1qsa_A           91 LLAFSPE-KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG-KSQPNACDKLFSVWRASGKQDPLAYLERIRLAMKAG  168 (618)
T ss_dssp             HHHHCCS-CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS-SCCCTHHHHHHHHHHHTTCSCHHHHHHHHHHHHHTT
T ss_pred             HHHhccC-CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC
Confidence            9998877 44455555567777888899888888777776655 3344556666766665554422  222222222222


Q ss_pred             -----------CCCcH-HHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhH---HHHHHHHHHhCCChHHHHHHHHHHHHc
Q 040365          173 -----------FDDNM-FIASSLLDMYAKCGNIRLARCIFDKMDLHDIVS---WTAVIMGNALHGNAHDAISLFEQMEKD  237 (514)
Q Consensus       173 -----------~~~~~-~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~---~~~li~~~~~~g~~~~A~~l~~~m~~~  237 (514)
                                 ++++. .....++..+.+-..+   ....... .++...   ...-+.-+++ .+.+.|..+|......
T Consensus       169 ~~~~a~~l~~~l~~~~~~~a~~~~al~~~p~~~---~~~~~~~-~~~~~~~~~~~~~~~rlar-~d~~~A~~~~~~~~~~  243 (618)
T 1qsa_A          169 NTGLVTVLAGQMPADYQTIASAIISLANNPNTV---LTFARTT-GATDFTRQMAAVAFASVAR-QDAENARLMIPSLAQA  243 (618)
T ss_dssp             CHHHHHHHHHTCCGGGHHHHHHHHHHHHCGGGH---HHHHHHS-CCCHHHHHHHHHHHHHHHH-HCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhCCHHHHHHHHHHHHHHhChHhH---HHHHhcc-CCChhhHHHHHHHHHHHHh-cCHHHHHHHHHhhhhc
Confidence                       11111 1112222222221111   1111111 111111   1111222333 3778888888887654


Q ss_pred             C-CCCCHH--HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCC-C-HH
Q 040365          238 G-VKPNSV--AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGP-T-EN  312 (514)
Q Consensus       238 g-~~p~~~--t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p-~-~~  312 (514)
                      + +.+...  ....+.......+...++...+......   .++.....-.+....+.|+++.|...|+.|+..+ + ..
T Consensus       244 ~~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~e~~~r~Alr~~d~~~a~~~~~~l~~~~~~~~r  320 (618)
T 1qsa_A          244 QQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMR---SQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEKDE  320 (618)
T ss_dssp             TTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHT---CCCHHHHHHHHHHHHHHTCHHHHHHHHHHSCTTGGGSHH
T ss_pred             cCCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhcccc---CCChHHHHHHHHHHHHCCCHHHHHHHHHHccccccccHh
Confidence            3 222221  1222222333445244555555554322   2333333344444557799999999999887542 2 22


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFM  339 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~  339 (514)
                      -.-=+..+....|+.++|..+|+++..
T Consensus       321 ~~YW~~ra~~~~g~~~~a~~~~~~~a~  347 (618)
T 1qsa_A          321 WRYWQADLLLERGREAEAKEILHQLMQ  347 (618)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            222244567778999999999888865

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=93.35  E-value=0.039  Score=53.66  Aligned_cols=211  Identities=11%  Similarity=0.133  Sum_probs=116.9

Q ss_pred             cchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHH
Q 040365            6 LVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINM   85 (514)
Q Consensus         6 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (514)
                      ...|+.|..+..+.++..+|++.|-+.      -|+..|..++.++.+.|.+++-...+..+.+.  ..++.+=+.|+-+
T Consensus        54 p~VWs~LgkAqL~~~~v~eAIdsyIkA------~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~--~ke~~IDteLi~a  125 (624)
T 3lvg_A           54 PAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFA  125 (624)
T ss_dssp             CCCSSSHHHHTTTSSSCTTTTTSSCCC------SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTT--CCSTTTTHHHHHH
T ss_pred             ccHHHHHHHHHHccCchHHHHHHHHhC------CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccHHHHHHH
Confidence            456777888888888777777655321      25556777888888888888777777666554  3344555678888


Q ss_pred             HHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHC--------------------CCCCCHHHH
Q 040365           86 YAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIA--------------------KIKPRHVSF  145 (514)
Q Consensus        86 ~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--------------------g~~p~~~t~  145 (514)
                      |+|.+++.+-++++.   .||+.-...+.+-|...|.++.|.-+|..+...                    .-.-+..||
T Consensus       126 yAk~~rL~elEefl~---~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktW  202 (624)
T 3lvg_A          126 LAKTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTW  202 (624)
T ss_dssp             HHTSCSSSTTTSTTS---CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSH
T ss_pred             HHhhCcHHHHHHHHc---CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHH
Confidence            888777665444332   233333333444444444444444333332110                    001234455


Q ss_pred             HHHHHHHhccCChH------------------------------HHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHH
Q 040365          146 SSIMPACAHLTTLH------------------------------LGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRL  195 (514)
Q Consensus       146 ~~ll~~~~~~~~~~------------------------------~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~  195 (514)
                      -.+-.+|...+.+.                              +-..+++.-+.. -.....+++-|.-.|+|-. .++
T Consensus       203 KeV~~ACvd~~EfrLAqicGLniIvhadeL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaILYsKY~-PeK  280 (624)
T 3lvg_A          203 KEVCFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK-PQK  280 (624)
T ss_dssp             HHHTHHHHHSCTTTTTTHHHHHHHCCSSCCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHHHHHSSC-TTH
T ss_pred             HHHHHHHhCchHHHHHHHhcchhcccHHHHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHhcC-HHH
Confidence            55555555544444                              333333333211 1334567777777777753 333


Q ss_pred             HHHHHHh----CCCC-------ChhHHHHHHHHHHhCCChHHHHH
Q 040365          196 ARCIFDK----MDLH-------DIVSWTAVIMGNALHGNAHDAIS  229 (514)
Q Consensus       196 A~~~~~~----m~~~-------d~~~~~~li~~~~~~g~~~~A~~  229 (514)
                      -.+-++.    +.-|       ....|.-++-.|.+-.+++.|..
T Consensus       281 lmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~l  325 (624)
T 3lvg_A          281 MREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAII  325 (624)
T ss_dssp             HHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHH
Confidence            3333322    2222       34568888888888888887753

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=93.31  E-value=0.46  Score=49.66  Aligned_cols=54  Identities=13%  Similarity=0.025  Sum_probs=50.3

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHH
Q 040365          319 SACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMR  372 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  372 (514)
                      .-|...|+++.|+.+++++...-|.+..+|..|+.+|...|+|+.|+-.++.+.
T Consensus       345 ~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          345 NFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            346788999999999999999999999999999999999999999999999884

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=93.25  E-value=0.39  Score=36.22  Aligned_cols=65  Identities=11%  Similarity=-0.067  Sum_probs=54.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC-------CCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMID-------PNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-------p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +..-...|...+...++++.|...++.+++..       +..+..+..|+.+|.+.|+++.|...+++..+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            44456678889999999999999999998753       334567899999999999999999999988763

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=93.00  E-value=1.1  Score=43.19  Aligned_cols=69  Identities=14%  Similarity=0.081  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh-----CCCccCCc
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN-----KGMKKTPA  381 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~g~~~~~~  381 (514)
                      +...++.++...|+.+++...++.+...+|-+...|..|+.+|.+.|+..+|.+.|+...+     .|+.|.|.
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~  246 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPT  246 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence            3455677888899999999999999999999999999999999999999999999988754     48887764

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=92.94  E-value=0.0016  Score=63.06  Aligned_cols=237  Identities=12%  Similarity=0.129  Sum_probs=159.8

Q ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhc
Q 040365           75 NVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH  154 (514)
Q Consensus        75 ~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~  154 (514)
                      .+.+|..|..++.+.|++.+|.+-|-+  ..|+..|..+|....+.|.+++-+..+...++..-.|  ..=+.++-+|++
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsyIk--A~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~--~IDteLi~ayAk  128 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARES--YVETELIFALAK  128 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSSCC--CSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCST--TTTHHHHHHHHT
T ss_pred             CccHHHHHHHHHHccCchHHHHHHHHh--CCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccc--ccHHHHHHHHHh
Confidence            456788888888888888888776643  4466678888898889999999888877665543333  333467888888


Q ss_pred             cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC------------------------CCChhH
Q 040365          155 LTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD------------------------LHDIVS  210 (514)
Q Consensus       155 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~------------------------~~d~~~  210 (514)
                      .+++.+-++++.       .||+.-...+.+-+...|.++.|.-+|..+.                        ..++.+
T Consensus       129 ~~rL~elEefl~-------~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~kt  201 (624)
T 3lvg_A          129 TNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRT  201 (624)
T ss_dssp             SCSSSTTTSTTS-------CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCS
T ss_pred             hCcHHHHHHHHc-------CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhH
Confidence            888766554432       4666566677788888888888888887764                        125678


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCC-CCHhHHHHHHHHH
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA-PSFEHYAAVADLL  289 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~-p~~~~~~~li~~~  289 (514)
                      |-.+-.+|...+.+.-|.-.--.+.   +.||.  ...++..|...|-+++-+.+++.-.   |++ .....|+-|.-+|
T Consensus       202 WKeV~~ACvd~~EfrLAqicGLniI---vhade--L~elv~~YE~~G~f~ELIsLlEagl---glErAHmGmFTELaILY  273 (624)
T 3lvg_A          202 WKEVCFACVDGKEFRLAQMCGLHIV---VHADE--LEELINYYQDRGYFEELITMLEAAL---GLERAHMGMFTELAILY  273 (624)
T ss_dssp             HHHHTHHHHHSCTTTTTTHHHHHHH---CCSSC--CSGGGSSSSTTCCCTTSTTTHHHHT---TSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCchHHHHHHHhcchhc---ccHHH--HHHHHHHHHhCCCHHHHHHHHHHHh---CCCchhHHHHHHHHHHH
Confidence            8888888888888776655444433   22221  2235566777788888887777543   443 3677788888777


Q ss_pred             HhcCCHHHHHHHHHhCCCC----------CCHHHHHHHHHHHHhcCCHHHHH
Q 040365          290 GRAGKLQEAYEFISNMHAG----------PTENVWLTLLSACRVHKNVELAG  331 (514)
Q Consensus       290 ~~~g~~~~A~~~~~~m~~~----------p~~~~~~~ll~~~~~~~~~~~a~  331 (514)
                      ++- ++++.++.++..-.+          .....|.-|+-.|....+++.|.
T Consensus       274 sKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~  324 (624)
T 3lvg_A          274 SKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAI  324 (624)
T ss_dssp             HSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHH
T ss_pred             Hhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHH
Confidence            765 455555555443211          22345777777777777777664

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=92.19  E-value=3.5  Score=32.52  Aligned_cols=83  Identities=13%  Similarity=-0.007  Sum_probs=58.4

Q ss_pred             CCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 040365           89 CARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCI  168 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  168 (514)
                      ||++......+-.+. .+....+..++.....|.-++-.+++..+.. +.+|++.....+..||.+.|+..++.+++.++
T Consensus        74 C~NlKrVi~C~~~~n-~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~A  151 (172)
T 1wy6_A           74 CQNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEA  151 (172)
T ss_dssp             CSCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            455554444444432 3444566677788888888888888888544 34677888888888888888888888888888


Q ss_pred             HHcCC
Q 040365          169 IRNGF  173 (514)
Q Consensus       169 ~~~~~  173 (514)
                      -+.|+
T Consensus       152 C~kG~  156 (172)
T 1wy6_A          152 CKKGE  156 (172)
T ss_dssp             HHTTC
T ss_pred             HHhhh
Confidence            88775

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=91.92  E-value=4  Score=32.51  Aligned_cols=65  Identities=9%  Similarity=-0.033  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHHhcCC---HHHHHHHHHHHHhcCCCCc-chHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          309 PTENVWLTLLSACRVHKN---VELAGKVAEKIFMIDPNNM-GAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~~---~~~a~~~~~~~~~~~p~~~-~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      |+..+--.+..++.+..+   ..+++.+++.+...+|.+. .....|+-+|.+.|++++|++..+.+.+
T Consensus        37 vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~  105 (144)
T 1y8m_A           37 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  105 (144)
T ss_dssp             SCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            444444444444444432   3455666666665555332 2334556666666666666666666654

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=91.32  E-value=2.1  Score=34.43  Aligned_cols=99  Identities=14%  Similarity=0.211  Sum_probs=62.3

Q ss_pred             CCCCCcchHHHHHHHHHhcCCh------hHHHHHHHHHhhCCCCCChh----hHHHHHHHH---hCCCChHHHHHHHHHH
Q 040365            1 MPVSDLVSWNTVIVGLARNGLY------EEALNIVRQMGNVNLKPDSF----TLSSVLPIF---ADYVDVIKGKEIHGYA   67 (514)
Q Consensus         1 m~~~~~~~~~~li~~~~~~g~~------~~A~~l~~~m~~~g~~p~~~----t~~~ll~~~---~~~~~~~~a~~~~~~~   67 (514)
                      |...|..+|-..+.-.-+.|++      ++.+++|++.... ++|+..    .|.-+.--|   ...+++++|+++|..+
T Consensus         8 ~~p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a   86 (161)
T 4h7y_A            8 MMANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMA   86 (161)
T ss_dssp             --CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            3456788898888888888998      7888888887763 566531    122111111   1236777788888877


Q ss_pred             HHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHcc
Q 040365           68 IRHGLDANVCIGSSLINMYAKCARVEDSHRLFCL  101 (514)
Q Consensus        68 ~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~  101 (514)
                      ++.+ ..=..+|......=.+.|+++.|++++..
T Consensus        87 ~~~h-KkFAKiwi~~AqFEiRqgnl~kARkILg~  119 (161)
T 4h7y_A           87 RANC-KKFAFVHISFAQFELSQGNVKKSKQLLQK  119 (161)
T ss_dssp             HHHC-TTBHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHh-HHHHHHHHHHHHHHHHcccHHHHHHHHHH
Confidence            7653 22255666666666667777777776654

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=91.21  E-value=3.6  Score=32.09  Aligned_cols=80  Identities=8%  Similarity=-0.006  Sum_probs=46.0

Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHH---HHHHHHHhHHhcCCCC--CHhHHHHHHHHHHhcCCHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDK---AWSYFNSMTKDYGIAP--SFEHYAAVADLLGRAGKLQE  297 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~---a~~~~~~m~~~~~~~p--~~~~~~~li~~~~~~g~~~~  297 (514)
                      ....+.+-|.+....|. |+..+-..+..++.++.....   ++.++..+.+.  -.|  .....-.|.-++.+.|++++
T Consensus        16 ~l~~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~--~~p~~~Rd~lY~LAvg~yklg~Y~~   92 (126)
T 1nzn_A           16 DLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPK--GSKEEQRDYVFYLAVGNYRLKEYEK   92 (126)
T ss_dssp             HHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTT--SCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHhhhHHH
Confidence            34445555555544443 555555556666666665544   77777766543  123  22333345556777777777


Q ss_pred             HHHHHHhC
Q 040365          298 AYEFISNM  305 (514)
Q Consensus       298 A~~~~~~m  305 (514)
                      |.+.++.+
T Consensus        93 A~~~~~~l  100 (126)
T 1nzn_A           93 ALKYVRGL  100 (126)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77777765

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=90.97  E-value=11  Score=40.46  Aligned_cols=20  Identities=20%  Similarity=0.112  Sum_probs=10.4

Q ss_pred             HHHhCCChHHHHHHHHHHHH
Q 040365          217 GNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       217 ~~~~~g~~~~A~~l~~~m~~  236 (514)
                      +|+-.|+......+++.+..
T Consensus       569 AyaGTGn~~aIq~LL~~~~~  588 (963)
T 4ady_A          569 AYAGTGNNSAVKRLLHVAVS  588 (963)
T ss_dssp             HTTTSCCHHHHHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHHHHHhcc
Confidence            34455555444445555554

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=90.26  E-value=3.7  Score=30.23  Aligned_cols=87  Identities=15%  Similarity=0.120  Sum_probs=63.4

Q ss_pred             CChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          156 TTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      ...++|..|-+.+...+.  ...+--.-+..+...|++++|..+.+....||+.+|-++-.  .+.|..+++..-+.++.
T Consensus        21 H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la   96 (116)
T 2p58_C           21 HYHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCE--YRLGLGSALESRLNRLA   96 (116)
T ss_dssp             TCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH--HHHTCHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHH
Confidence            356778888777777653  33333334556778999999999999999999999988765  46688888887777777


Q ss_pred             HcCCCCCHHHHH
Q 040365          236 KDGVKPNSVAFV  247 (514)
Q Consensus       236 ~~g~~p~~~t~~  247 (514)
                      .+| .|....|.
T Consensus        97 ~sg-~p~~q~Fa  107 (116)
T 2p58_C           97 RSQ-DPRIQTFV  107 (116)
T ss_dssp             TCC-CHHHHHHH
T ss_pred             hCC-CHHHHHHH
Confidence            765 55555554

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=90.15  E-value=4.3  Score=29.84  Aligned_cols=89  Identities=13%  Similarity=0.027  Sum_probs=65.1

Q ss_pred             CCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHH
Q 040365           54 YVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQM  133 (514)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m  133 (514)
                      ....++|.-+-+.+...|-  ...+--.-+..+...|++++|..+.+....||.+.|-+|-..  +.|..+++..-+.++
T Consensus        19 ~H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce~--rlGl~s~le~rL~~l   94 (115)
T 2uwj_G           19 QHCHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCEW--HLGLGAALDRRLAGL   94 (115)
T ss_dssp             TTCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHHH--HTTCHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHHH--hcccHHHHHHHHHHH
Confidence            3456778777777776653  333333334556789999999999999999999999887654  788888888888788


Q ss_pred             HHCCCCCCHHHHHH
Q 040365          134 LIAKIKPRHVSFSS  147 (514)
Q Consensus       134 ~~~g~~p~~~t~~~  147 (514)
                      ...| .|....|..
T Consensus        95 a~sg-~p~~q~Fa~  107 (115)
T 2uwj_G           95 GGSS-DPALADFAA  107 (115)
T ss_dssp             HTCS-SHHHHHHHH
T ss_pred             HhCC-CHHHHHHHH
Confidence            7776 565555543

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=89.90  E-value=3.7  Score=33.04  Aligned_cols=38  Identities=16%  Similarity=0.310  Sum_probs=27.9

Q ss_pred             CCChhHHHHHHHHHHHCCCh------hHHHHHHHHHHHCCCCCCH
Q 040365          104 VKDAISWNSIIAGCVQNGLF------DEGLKFFRQMLIAKIKPRH  142 (514)
Q Consensus       104 ~~d~~~~~~li~~~~~~g~~------~~A~~l~~~m~~~g~~p~~  142 (514)
                      ..|..+|=..+...-+.|++      ++..++|++.... ++|+.
T Consensus        10 p~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k   53 (161)
T 4h7y_A           10 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDK   53 (161)
T ss_dssp             CCSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGG
T ss_pred             CCCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccc
Confidence            45777887777777777888      7778888877664 56653

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=89.89  E-value=3.5  Score=30.32  Aligned_cols=88  Identities=13%  Similarity=0.037  Sum_probs=64.8

Q ss_pred             CChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHH
Q 040365          156 TTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQME  235 (514)
Q Consensus       156 ~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~  235 (514)
                      ...++|..|-+.+...+.  ...+--.-+..+...|++++|..+.+....||+.+|-++-.  .+.|..+++..-+.++.
T Consensus        20 H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la   95 (115)
T 2uwj_G           20 HCHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLG   95 (115)
T ss_dssp             TCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHH
Confidence            346778888777777653  33333334556778999999999999999999999988755  46788888888887887


Q ss_pred             HcCCCCCHHHHHH
Q 040365          236 KDGVKPNSVAFVA  248 (514)
Q Consensus       236 ~~g~~p~~~t~~~  248 (514)
                      .+| .|....|..
T Consensus        96 ~sg-~p~~q~Fa~  107 (115)
T 2uwj_G           96 GSS-DPALADFAA  107 (115)
T ss_dssp             TCS-SHHHHHHHH
T ss_pred             hCC-CHHHHHHHH
Confidence            776 555555543

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=89.86  E-value=4.6  Score=29.74  Aligned_cols=89  Identities=11%  Similarity=0.041  Sum_probs=64.3

Q ss_pred             CCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHH
Q 040365           54 YVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQM  133 (514)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m  133 (514)
                      ....++|.-+-+.+...|-  ...+--.-+..+...|++++|..+.+....||.+.|-+|-..  +.|..+++..-+.++
T Consensus        20 ~H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce~--rlGl~s~le~rL~~l   95 (116)
T 2p58_C           20 NHYHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCEY--RLGLGSALESRLNRL   95 (116)
T ss_dssp             TTCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHHH--HHTCHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHHH--hcccHHHHHHHHHHH
Confidence            3456778777777776653  333333334556789999999999999999999999888664  678888888888787


Q ss_pred             HHCCCCCCHHHHHH
Q 040365          134 LIAKIKPRHVSFSS  147 (514)
Q Consensus       134 ~~~g~~p~~~t~~~  147 (514)
                      ...| .|....|..
T Consensus        96 a~sg-~p~~q~Fa~  108 (116)
T 2p58_C           96 ARSQ-DPRIQTFVN  108 (116)
T ss_dssp             TTCC-CHHHHHHHH
T ss_pred             HhCC-CHHHHHHHH
Confidence            7766 555555543

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=89.32  E-value=2.7  Score=34.46  Aligned_cols=29  Identities=10%  Similarity=0.077  Sum_probs=20.1

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhCCCC
Q 040365          280 EHYAAVADLLGRAGKLQEAYEFISNMHAG  308 (514)
Q Consensus       280 ~~~~~li~~~~~~g~~~~A~~~~~~m~~~  308 (514)
                      +.---+..+|.+.|+.++|+.+++.+|.+
T Consensus       123 Elkykia~C~~~l~~~~~Ai~~Le~Ip~k  151 (167)
T 3ffl_A          123 EVKYKLAECYTVLKQDKDAIAILDGIPSR  151 (167)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHTSCGG
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHhcCCch
Confidence            34444666777788888888888877644

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=88.54  E-value=15  Score=33.98  Aligned_cols=167  Identities=14%  Similarity=0.110  Sum_probs=105.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHH----HHHHHcCCCCCHHHHHHHHHHHH
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLF----EQMEKDGVKPNSVAFVAVLTACS  254 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~----~~m~~~g~~p~~~t~~~ll~a~~  254 (514)
                      .+.++..-|.+.+++++|.+++..-           ...+.++|+...|.++-    +-..+.++++|..+...++..+.
T Consensus        37 ~~RTi~~Ry~~~k~y~eAidLL~~G-----------A~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~L~~  105 (336)
T 3lpz_A           37 ETRLVAARYSKQGNWAAAVDILASV-----------SQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLGCLR  105 (336)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH-----------HHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHH-----------HHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            4455667789999999998875432           33456677776666654    45556788899888877777776


Q ss_pred             ccCC--HHHHHHHHHHhH---HhcCCCC--CHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 040365          255 HAGL--IDKAWSYFNSMT---KDYGIAP--SFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNV  327 (514)
Q Consensus       255 ~~g~--~~~a~~~~~~m~---~~~~~~p--~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~  327 (514)
                      ....  .+. ..+.+.+.   .++|-.|  ++.....+...|.+.+++.+|+..|- ....+++..+..++.-+...+..
T Consensus       106 ~~~~~~p~r-~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~i-lg~~~s~~~~a~mL~ew~~~~~~  183 (336)
T 3lpz_A          106 LFQPGEPVR-KRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLV-LGTKESPEVLARMEYEWYKQDES  183 (336)
T ss_dssp             TSCTTCHHH-HHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHT-TSCTTHHHHHHHHHHHHHHTSCG
T ss_pred             hCCCCCcHH-HHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH-hcCCchHHHHHHHHHHHHHhcCC
Confidence            5543  211 22222221   2234323  67778889999999999999998873 23233446666655554444332


Q ss_pred             HHHHHHHHHHHhcCCCCcchHH-HHHHHHHHccChhHHHHHHHHHHh
Q 040365          328 ELAGKVAEKIFMIDPNNMGAYV-ILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       328 ~~a~~~~~~~~~~~p~~~~~~~-~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                                     .....|. ..+--|...++...|..+++...+
T Consensus       184 ---------------~e~dlfiaRaVL~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          184 ---------------HTAPLYCARAVLPYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             ---------------GGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ---------------ccHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence                           2222332 345557788899999998877664

>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=87.86  E-value=1.5  Score=39.79  Aligned_cols=89  Identities=6%  Similarity=-0.095  Sum_probs=53.6

Q ss_pred             HHHHHHHccCCC--CC---hhHHHHHHHHHHH-----CCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc-CChHHH
Q 040365           93 EDSHRLFCLLPV--KD---AISWNSIIAGCVQ-----NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHL-TTLHLG  161 (514)
Q Consensus        93 ~~A~~~f~~~~~--~d---~~~~~~li~~~~~-----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~-~~~~~a  161 (514)
                      ..|+..+++..+  |+   -..|..|...|.+     .|+.++|.+.|++..+.+..-+..++......++.. ++.+.+
T Consensus       180 ~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a  259 (301)
T 3u64_A          180 HAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGF  259 (301)
T ss_dssp             HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHH
Confidence            445555554432  32   3467777777777     377777777777777643111255555666666663 777777


Q ss_pred             HHHHHHHHHcCCC--CcHHHHH
Q 040365          162 KQLHGCIIRNGFD--DNMFIAS  181 (514)
Q Consensus       162 ~~~~~~~~~~~~~--~~~~~~~  181 (514)
                      .+.+++.++....  |+....|
T Consensus       260 ~~~L~kAL~a~p~~~P~~~lan  281 (301)
T 3u64_A          260 DEALDRALAIDPESVPHNKLLV  281 (301)
T ss_dssp             HHHHHHHHHCCGGGCSSCHHHH
T ss_pred             HHHHHHHHcCCCCCCCChhHHH
Confidence            7777777776544  5544444

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=87.59  E-value=18  Score=33.57  Aligned_cols=168  Identities=10%  Similarity=0.009  Sum_probs=101.7

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHH----HHHHHCCCCCCHHHHHHHHHHHh
Q 040365           78 IGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFF----RQMLIAKIKPRHVSFSSIMPACA  153 (514)
Q Consensus        78 ~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~----~~m~~~g~~p~~~t~~~ll~~~~  153 (514)
                      .+.++..-|.+.+++++|.+++-.           =...+.+.|+...|-++-    +-..+.++++|..+..-++..+.
T Consensus        37 ~~RTi~~Ry~~~k~y~eAidLL~~-----------GA~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~L~~  105 (336)
T 3lpz_A           37 ETRLVAARYSKQGNWAAAVDILAS-----------VSQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLGCLR  105 (336)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHH-----------HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHH-----------HHHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            456677778999999999988643           223455667766555443    55566778888888887877776


Q ss_pred             ccCChH-HHHHHHHHH----HHcC--CCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHH
Q 040365          154 HLTTLH-LGKQLHGCI----IRNG--FDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHD  226 (514)
Q Consensus       154 ~~~~~~-~a~~~~~~~----~~~~--~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~  226 (514)
                      ....-+ .=..+.+.+    .+.|  -.-|......+...|.+.|++.+|+.-|-.-..+.+..+..|+--+...+...+
T Consensus       106 ~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~ilg~~~s~~~~a~mL~ew~~~~~~~e  185 (336)
T 3lpz_A          106 LFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLVLGTKESPEVLARMEYEWYKQDESHT  185 (336)
T ss_dssp             TSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHTTSCTTHHHHHHHHHHHHHHTSCGGG
T ss_pred             hCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHhcCCchHHHHHHHHHHHHHhcCCcc
Confidence            655422 112233333    3333  234667778889999999999999988843222233555555444433332211


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHH
Q 040365          227 AISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTK  271 (514)
Q Consensus       227 A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  271 (514)
                                    +|.+.-.+++ -|...+++..|..+|+...+
T Consensus       186 --------------~dlfiaRaVL-~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          186 --------------APLYCARAVL-PYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             --------------HHHHHHHHHH-HHHHTTCHHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHHH-HHHHhCCHHHHHHHHHHHHH
Confidence                          1222223333 34556788888887766654

>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=87.53  E-value=3.7  Score=30.37  Aligned_cols=64  Identities=17%  Similarity=0.175  Sum_probs=50.7

Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADL  288 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~  288 (514)
                      +.-++.+-++.+....+-|+.....+.|.||.+.+++..|.++|+.+..+.  .+...+|..+++-
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~--~~~~~iY~~~lqE   88 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA--GPHKEIYPYVIQE   88 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh--cCchhhHHHHHHH
Confidence            455677777777778889999999999999999999999999999886543  3445567777653

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=86.25  E-value=20  Score=32.88  Aligned_cols=169  Identities=9%  Similarity=0.039  Sum_probs=104.7

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHH----HHHHHHCCCCCCHHHHHHHHHHHh
Q 040365           78 IGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKF----FRQMLIAKIKPRHVSFSSIMPACA  153 (514)
Q Consensus        78 ~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l----~~~m~~~g~~p~~~t~~~ll~~~~  153 (514)
                      .|.++..-|.+.+++++|.+++..           -...+.+.|+...|-++    .+...+.++++|..+..-++..+.
T Consensus        35 ~~Rtl~~Ry~~~~~~~eAidlL~~-----------ga~~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~l~~  103 (312)
T 2wpv_A           35 TLRTIANRYVRSKSYEHAIELISQ-----------GALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIA  103 (312)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHH-----------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHH-----------HHHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            456777888999999999988643           22345567776665554    455566788888888888887776


Q ss_pred             ccCCh-----HHHHHHHHHHHHcCC--CCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhC---CC
Q 040365          154 HLTTL-----HLGKQLHGCIIRNGF--DDNMFIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALH---GN  223 (514)
Q Consensus       154 ~~~~~-----~~a~~~~~~~~~~~~--~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~---g~  223 (514)
                      ....-     .-..+......+.|-  .-++.....+...|.+.|++.+|+.-|-.-...|...+..|+--+...   |.
T Consensus       104 ~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~~~~s~~~~a~~l~~w~~~~~~~~  183 (312)
T 2wpv_A          104 ELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIE  183 (312)
T ss_dssp             TCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTCCC
T ss_pred             HCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhCCCccHHHHHHHHHHHHHhcCCCC
Confidence            54321     222233333333332  246788888999999999999999887643333455555555444333   43


Q ss_pred             hHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHh
Q 040365          224 AHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKD  272 (514)
Q Consensus       224 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~  272 (514)
                      ..++              |...-.+++ -|...+++..|..+|+...+.
T Consensus       184 ~~e~--------------dlf~~RaVL-~yL~l~n~~~A~~~~~~f~~~  217 (312)
T 2wpv_A          184 DSTV--------------AEFFSRLVF-NYLFISNISFAHESKDIFLER  217 (312)
T ss_dssp             HHHH--------------HHHHHHHHH-HHHHTTBHHHHHHHHHHHHHH
T ss_pred             cchH--------------HHHHHHHHH-HHHHhcCHHHHHHHHHHHHHH
Confidence            3332              112122233 344568888888888876543

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=86.15  E-value=20  Score=32.85  Aligned_cols=169  Identities=9%  Similarity=0.017  Sum_probs=102.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHH----HHHHHHcCCCCCHHHHHHHHHHHH
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISL----FEQMEKDGVKPNSVAFVAVLTACS  254 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l----~~~m~~~g~~p~~~t~~~ll~a~~  254 (514)
                      .|.++..-|.+.+++++|.+++..-           ...+.++|+...|.++    .+...+.++++|......++..+.
T Consensus        35 ~~Rtl~~Ry~~~~~~~eAidlL~~g-----------a~~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~l~~  103 (312)
T 2wpv_A           35 TLRTIANRYVRSKSYEHAIELISQG-----------ALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIA  103 (312)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH-----------HHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-----------HHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            4456667788888999888875432           3345667887666665    444455688888888777777665


Q ss_pred             ccCCHH-HHHHHHHHhH---HhcCCC--CCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc---C
Q 040365          255 HAGLID-KAWSYFNSMT---KDYGIA--PSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVH---K  325 (514)
Q Consensus       255 ~~g~~~-~a~~~~~~m~---~~~~~~--p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~---~  325 (514)
                      .-..-+ .=.++.+.+.   .+.|-.  -++.....+...|.+.|++.+|+..|-- ....|...+..++.-+...   |
T Consensus       104 ~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~-~~~~s~~~~a~~l~~w~~~~~~~  182 (312)
T 2wpv_A          104 ELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFML-GTHDSMIKYVDLLWDWLCQVDDI  182 (312)
T ss_dssp             TCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHh-CCCccHHHHHHHHHHHHHhcCCC
Confidence            532111 1122222222   122222  3778888999999999999999987752 2112455565555544444   4


Q ss_pred             CHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          326 NVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ...++-...              ...+--|...|+...|..+++...+
T Consensus       183 ~~~e~dlf~--------------~RaVL~yL~l~n~~~A~~~~~~f~~  216 (312)
T 2wpv_A          183 EDSTVAEFF--------------SRLVFNYLFISNISFAHESKDIFLE  216 (312)
T ss_dssp             CHHHHHHHH--------------HHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred             CcchHHHHH--------------HHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            443332221              1234456678899999999887754

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=84.11  E-value=14  Score=29.05  Aligned_cols=65  Identities=9%  Similarity=-0.033  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhcCCCC-cchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          309 PTENVWLTLLSACRVHK---NVELAGKVAEKIFMIDPNN-MGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       309 p~~~~~~~ll~~~~~~~---~~~~a~~~~~~~~~~~p~~-~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      |+..+--.+..++.+..   +..+|+.+++.+...+|.. -.....|+-++.+.|++++|++..+.+.+
T Consensus        38 vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~  106 (134)
T 3o48_A           38 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  106 (134)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHT
T ss_pred             CChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            44444434444444333   2345666666666655532 33444566666666666666666666654

>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=83.41  E-value=7.3  Score=28.86  Aligned_cols=48  Identities=17%  Similarity=0.146  Sum_probs=36.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHH
Q 040365          305 MHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILS  352 (514)
Q Consensus       305 m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~  352 (514)
                      +..-|++.+..+.+.||++.+|+..|.++++-+...-.+....|-.++
T Consensus        39 ~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~l   86 (109)
T 1v54_E           39 YDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVI   86 (109)
T ss_dssp             SSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHH
Confidence            334589999999999999999999999999988765443344565544

>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=83.03  E-value=9.8  Score=36.38  Aligned_cols=68  Identities=18%  Similarity=0.185  Sum_probs=41.5

Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHH----hcCCCCCHhH
Q 040365          213 AVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTK----DYGIAPSFEH  281 (514)
Q Consensus       213 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~----~~~~~p~~~~  281 (514)
                      .++..+...|++.+|+..+..+... -+-+...+..++.++...|+..+|.+.|+...+    +.|+.|+..+
T Consensus       176 ~~~~~~l~~g~~~~a~~~l~~~~~~-~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          176 AKAEAEIACGRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            3455556666666666666666553 123555666777777777777777766665432    3577776544

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=82.99  E-value=5.2  Score=31.37  Aligned_cols=64  Identities=17%  Similarity=0.183  Sum_probs=50.4

Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADL  288 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~  288 (514)
                      +.-+..+-++.+....+-|+.....+.|.+|.+.+++..|.++|+.+..+  ..+...+|..+++-
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K--~~~~~~iY~y~lqE  131 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK--AGPHKEIYPYVIQE  131 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh--cCCchhhHHHHHHH
Confidence            34466667777777788999999999999999999999999999988654  34446667777653

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=82.83  E-value=27  Score=38.80  Aligned_cols=165  Identities=10%  Similarity=-0.002  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 040365           79 GSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTL  158 (514)
Q Consensus        79 ~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~  158 (514)
                      ...++..+.+.+..+.|.++..-.+ .+...--.+..+|...|++++|.+.|.+.. .|+..+....          ...
T Consensus       815 ~~~l~~~l~~~~~~~~~~~l~~~~~-~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa-~~~~~~~~l~----------~~~  882 (1139)
T 4fhn_B          815 VTELVEKLFLFKQYNACMQLIGWLN-SDPIAVYLKALIYLKSKEAVKAVRCFKTTS-LVLYSHTSQF----------AVL  882 (1139)
T ss_dssp             HHHHHHHHHHHSCTTHHHHHHHHSC-CCHHHHHHHHHHHHHTTCHHHHHHHHHTCC-CSCTTCCCSC----------SSH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcc-CCcHHHHHHHHHHHhcCCHHHHHHHHHHHh-hhhcccchhh----------hhh
Confidence            3446666677788877777665554 344444566778888999999999997752 2222221100          000


Q ss_pred             HHHHHHHHHHHHcC--CCCcHHHHHHHHHHHHhcCCHHHHHHHHHh----CCCCCh----hHHHHHHHHHHhCCChHHHH
Q 040365          159 HLGKQLHGCIIRNG--FDDNMFIASSLLDMYAKCGNIRLARCIFDK----MDLHDI----VSWTAVIMGNALHGNAHDAI  228 (514)
Q Consensus       159 ~~a~~~~~~~~~~~--~~~~~~~~~~li~~y~k~g~~~~A~~~~~~----m~~~d~----~~~~~li~~~~~~g~~~~A~  228 (514)
                      ..    ...+....  ...-..-|..++..+-+.|.++.+.++-..    ....+.    ..|..+..++...|++++|.
T Consensus       883 ~~----~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay  958 (1139)
T 4fhn_B          883 RE----FQEIAEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAH  958 (1139)
T ss_dssp             HH----HHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGG
T ss_pred             cc----cccccccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHH
Confidence            00    01111110  111234456666777777776666544332    222222    25888999999999999999


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHH
Q 040365          229 SLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDK  261 (514)
Q Consensus       229 ~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  261 (514)
                      ..+-.+.....+  ...+..++...+..|..+.
T Consensus       959 ~aL~~~pd~~~r--~~cLr~LV~~lce~~~~~~  989 (1139)
T 4fhn_B          959 VALMVLSTTPLK--KSCLLDFVNQLTKQGKINQ  989 (1139)
T ss_dssp             HHHHHHHHSSSC--HHHHHHHHHHHHHHCCHHH
T ss_pred             HHHHhCCCHHHH--HHHHHHHHHHHHhCCChhh
Confidence            999888765443  3456666666666555443

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=82.67  E-value=6.1  Score=41.29  Aligned_cols=48  Identities=13%  Similarity=-0.074  Sum_probs=22.6

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA  358 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  358 (514)
                      +..-|..|.....+.+++++|..+|+..+... -++.+..-|+..|.+.
T Consensus       612 s~lEWEiLGlla~RL~h~~EA~~a~~~~l~~R-Fs~ka~~kLLeiY~~~  659 (754)
T 4gns_B          612 SGLEWELLGLIMLRTWHWEDAVACLRTSIVAR-FDPVSCQQLLKIYLQP  659 (754)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHSSS-CCHHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc-cCHHHHHHHHHHHHhc
Confidence            33445555554444555555555555544322 2344444555555443

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=81.19  E-value=37  Score=37.67  Aligned_cols=141  Identities=13%  Similarity=0.050  Sum_probs=83.0

Q ss_pred             HHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCCC---------C------------
Q 040365          149 MPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDLH---------D------------  207 (514)
Q Consensus       149 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~~---------d------------  207 (514)
                      +..+...+..+.+.++...     .+.+....-.+..+|..+|++++|.+.|.+....         .            
T Consensus       819 ~~~l~~~~~~~~~~~l~~~-----~~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~~~~~~  893 (1139)
T 4fhn_B          819 VEKLFLFKQYNACMQLIGW-----LNSDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEIAEKYH  893 (1139)
T ss_dssp             HHHHHHHSCTTHHHHHHHH-----SCCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHHHHTTT
T ss_pred             HHHHHHhhhHHHHHHHhhh-----ccCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhccccccccccc
Confidence            3344444555554443322     2334444445677788899999999999876311         0            


Q ss_pred             -----hhHHHHHHHHHHhCCChHHHHHHHHHHHHcCC-C-CCHH--HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC
Q 040365          208 -----IVSWTAVIMGNALHGNAHDAISLFEQMEKDGV-K-PNSV--AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS  278 (514)
Q Consensus       208 -----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~-p~~~--t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~  278 (514)
                           ..-|..++..|-++|.++.++++-+...+... . ++..  .|..+..++...|++++|...+-.+... .  --
T Consensus       894 ~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~-~--~r  970 (1139)
T 4fhn_B          894 HQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTT-P--LK  970 (1139)
T ss_dssp             SCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHS-S--SC
T ss_pred             ccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCH-H--HH
Confidence                 01255666777778888888777766655321 1 1111  3566777888888888888777766321 2  23


Q ss_pred             HhHHHHHHHHHHhcCCHHH
Q 040365          279 FEHYAAVADLLGRAGKLQE  297 (514)
Q Consensus       279 ~~~~~~li~~~~~~g~~~~  297 (514)
                      ......||..++..|.+++
T Consensus       971 ~~cLr~LV~~lce~~~~~~  989 (1139)
T 4fhn_B          971 KSCLLDFVNQLTKQGKINQ  989 (1139)
T ss_dssp             HHHHHHHHHHHHHHCCHHH
T ss_pred             HHHHHHHHHHHHhCCChhh
Confidence            4455666666666555444

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=80.03  E-value=22  Score=29.08  Aligned_cols=63  Identities=11%  Similarity=0.015  Sum_probs=42.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHhhC-CCCCCh-------hhHHHHHHHHhCCCChHHHHHHHHHHHHh
Q 040365            8 SWNTVIVGLARNGLYEEALNIVRQMGNV-NLKPDS-------FTLSSVLPIFADYVDVIKGKEIHGYAIRH   70 (514)
Q Consensus         8 ~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~-------~t~~~ll~~~~~~~~~~~a~~~~~~~~~~   70 (514)
                      .+-.-+..+...|.++.|+-+...+... +..|+.       .++..+..++...+++..|...|.++++.
T Consensus        22 ~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~   92 (167)
T 3ffl_A           22 NVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQ   92 (167)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHH
Confidence            3444567788888888888877765432 123332       24566777888889999999888887543

---

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	514
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.91
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.88
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.58
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.57
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.16
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.05
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.02
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.02
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.0
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.97
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.95
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.94
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.86
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.78
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.52
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.51
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.45
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.43
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.41
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.4
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.4
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.38
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.35
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.32
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.28
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.24
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.15
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.12
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.07
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.02
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.0
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.96
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.92
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.92
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.88
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.82
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.81
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.8
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.76
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.71
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.7
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.69
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.44
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.36
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.26
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.24
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.19
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.19
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.17
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.07
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.99
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.95
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.86
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.49
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	95.59
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	94.26
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	93.37
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.23
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	92.71
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	91.65
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	89.52
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	87.28
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	85.13
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	81.71

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=2.1e-20  Score=181.11  Aligned_cols=355  Identities=15%  Similarity=0.068  Sum_probs=286.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCC
Q 040365           12 VIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCAR   91 (514)
Q Consensus        12 li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~   91 (514)
                      +...+.+.|++++|+..|+++.+.. +-+...+..+...+...|++++|...+..+++.. |.+..++..+...|.+.|+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~   82 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcc
Confidence            3456778999999999999998753 3356678888889999999999999999999986 5677889999999999999


Q ss_pred             HHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 040365           92 VEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCI  168 (514)
Q Consensus        92 ~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  168 (514)
                      +++|...+....   ..+...+..........+....+........... .................+....+.......
T Consensus        83 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (388)
T d1w3ba_          83 LQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGNLLKALGRLEEAKACYLKA  161 (388)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccc-cccccccccccccccccchhhhhHHHHHHh
Confidence            999999998765   3344555556666666677777776666665543 334444445555666777778888777777


Q ss_pred             HHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHH
Q 040365          169 IRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVA  245 (514)
Q Consensus       169 ~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  245 (514)
                      .... +.+...+..+...+...|++++|...+++..   +.+..+|..+...+...|++++|+..|++....+ ..+...
T Consensus       162 ~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  239 (388)
T d1w3ba_         162 IETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVV  239 (388)
T ss_dssp             HHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHH
T ss_pred             hccC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHH
Confidence            7664 5566777888889999999999999988764   4466788888999999999999999999988753 345667


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHH
Q 040365          246 FVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACR  322 (514)
Q Consensus       246 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~  322 (514)
                      +..+...+...|++++|...|+...+   +.| +...+..+...+...|++++|.+.++...  .+.+...+..+...+.
T Consensus       240 ~~~l~~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  316 (388)
T d1w3ba_         240 HGNLACVYYEQGLIDLAIDTYRRAIE---LQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKR  316 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---TCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHH
Confidence            77788888999999999999998764   355 57788889999999999999999988763  3457788888999999


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          323 VHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ..|++++|+..++++++.+|+++.++..++.+|.+.|++++|.+.+++..+.
T Consensus       317 ~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l  368 (388)
T d1w3ba_         317 EQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             TTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999887653

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=4e-19  Score=171.97  Aligned_cols=348  Identities=11%  Similarity=0.024  Sum_probs=287.3

Q ss_pred             CcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHH
Q 040365            5 DLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLIN   84 (514)
Q Consensus         5 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (514)
                      ++..|..+...|.+.|++++|+..|++..+.. +-+..++..+...+...|++++|...+..+.+.. +.+.........
T Consensus        32 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~  109 (388)
T d1w3ba_          32 NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLK-PDFIDGYINLAA  109 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhccccccccccccccccc-cccccccccccc
Confidence            57789999999999999999999999998754 3356688889999999999999999999999886 444444555555


Q ss_pred             HHHHCCCHHHHHHHHccC---CCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHH
Q 040365           85 MYAKCARVEDSHRLFCLL---PVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLG  161 (514)
Q Consensus        85 ~~~~~g~~~~A~~~f~~~---~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a  161 (514)
                      .+...+....+.......   .......+..........+....+...+.+..... +-+...+..+...+...+.++.|
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A  188 (388)
T d1w3ba_         110 ALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLA  188 (388)
T ss_dssp             HHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccC-cchhHHHHhhcccccccCcHHHH
Confidence            555555555444443332   23455566667777788888899988888877653 34566777788888999999999


Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC
Q 040365          162 KQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG  238 (514)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  238 (514)
                      ...+...++.. +.+...+..+...|...|++++|...|++..   ..+...|..+...+.+.|++++|+..|++..+. 
T Consensus       189 ~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-  266 (388)
T d1w3ba_         189 IHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL-  266 (388)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-
T ss_pred             HHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-
Confidence            99999998875 5567788999999999999999999998865   456678888999999999999999999999884 


Q ss_pred             CCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHH
Q 040365          239 VKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWL  315 (514)
Q Consensus       239 ~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~  315 (514)
                       .|+ ..++..+..++...|++++|...++.....  .+.+...+..+...+.+.|++++|.+.+++.. ..| +..+|.
T Consensus       267 -~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~  343 (388)
T d1w3ba_         267 -QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHS  343 (388)
T ss_dssp             -CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHH
T ss_pred             -CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhcc--CCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence             454 567888999999999999999999988654  34467888899999999999999999999863 345 577899


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC
Q 040365          316 TLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR  360 (514)
Q Consensus       316 ~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  360 (514)
                      .+..++...|++++|...++++++++|+++.+|..|+.+|.+.|+
T Consensus       344 ~la~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~lg~~~~~~~D  388 (388)
T d1w3ba_         344 NLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            999999999999999999999999999999999999999988875

>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=99.58  E-value=2e-13  Score=128.57  Aligned_cols=240  Identities=11%  Similarity=0.001  Sum_probs=169.1

Q ss_pred             HHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC
Q 040365          112 SIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG  191 (514)
Q Consensus       112 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g  191 (514)
                      -....+.+.|++++|+..|++..+.. +-+..+|..+..++...|+++.|...+.++++.. +.+...+..+...|.+.|
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~  101 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNES  101 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccc
Confidence            34556778888888888888887753 3345667777777788888888888888777764 445666667777777777


Q ss_pred             CHHHHHHHHHhCCC--CCh-hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040365          192 NIRLARCIFDKMDL--HDI-VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNS  268 (514)
Q Consensus       192 ~~~~A~~~~~~m~~--~d~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~  268 (514)
                      ++++|.+.++....  |+. ..+........                    ..+.......+..+...+..+++...|..
T Consensus       102 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  161 (323)
T d1fcha_         102 LQRQACEILRDWLRYTPAYAHLVTPAEEGAG--------------------GAGLGPSKRILGSLLSDSLFLEVKELFLA  161 (323)
T ss_dssp             CHHHHHHHHHHHHHTSTTTGGGCC-----------------------------------CTTHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccchhhHHHhccchHHHHHhhhhhhh--------------------hcccccchhhHHHHHHhhHHHHHHHHHHH
Confidence            77777777766531  111 00000000000                    00000111112223344567778888877


Q ss_pred             hHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc
Q 040365          269 MTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG  346 (514)
Q Consensus       269 m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~  346 (514)
                      ..+...-.++...+..+...+...|++++|...+++..  .+.+..+|..+...+...|++++|...++++++++|+++.
T Consensus       162 al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~  241 (323)
T d1fcha_         162 AVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIR  241 (323)
T ss_dssp             HHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHH
Confidence            76543334467788888899999999999999998753  2346788999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          347 AYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       347 ~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      +|..++.+|.+.|++++|.+.+++..+
T Consensus       242 a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         242 SRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999999999999999999998765

>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=99.57  E-value=5.6e-13  Score=125.41  Aligned_cols=265  Identities=10%  Similarity=0.006  Sum_probs=192.3

Q ss_pred             HHHHHHHHCCCHHHHHHHHccCC---CCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC
Q 040365           81 SLINMYAKCARVEDSHRLFCLLP---VKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTT  157 (514)
Q Consensus        81 ~li~~~~~~g~~~~A~~~f~~~~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~  157 (514)
                      .....|.+.|++++|...|+...   ..+..+|..+...|...|++++|+..|.+..+.. +-+...+..+...+...|+
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-ccccccccccccccccccc
Confidence            35667889999999999999875   3367789999999999999999999999988753 3356777788889999999


Q ss_pred             hHHHHHHHHHHHHcCCCCcHH-HHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHH
Q 040365          158 LHLGKQLHGCIIRNGFDDNMF-IASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEK  236 (514)
Q Consensus       158 ~~~a~~~~~~~~~~~~~~~~~-~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~  236 (514)
                      +++|.+.+..+.+..  |+.. ..........                ..+.......+..+...+...+|.+.|.+...
T Consensus       103 ~~~A~~~~~~~~~~~--~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~  164 (323)
T d1fcha_         103 QRQACEILRDWLRYT--PAYAHLVTPAEEGAG----------------GAGLGPSKRILGSLLSDSLFLEVKELFLAAVR  164 (323)
T ss_dssp             HHHHHHHHHHHHHTS--TTTGGGCC-------------------------------CTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccchhhHHHhc--cchHHHHHhhhhhhh----------------hcccccchhhHHHHHHhhHHHHHHHHHHHHHH
Confidence            999999999988754  2211 1100000000                00111111122233445667788888888776


Q ss_pred             cC-CCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHH
Q 040365          237 DG-VKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TEN  312 (514)
Q Consensus       237 ~g-~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~  312 (514)
                      .. -.++...+..+...+...|++++|...|+.....   .| +...|..+...|.+.|++++|.+.+++.. ..| +..
T Consensus       165 ~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~  241 (323)
T d1fcha_         165 LDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSV---RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIR  241 (323)
T ss_dssp             HSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HhhcccccccchhhHHHHHHHHHHhhhhccccccccc---ccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHH
Confidence            42 2345667788888899999999999999988654   45 57788889999999999999999998763 233 677


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcch-----------HHHHHHHHHHccChhHHHHH
Q 040365          313 VWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGA-----------YVILSNTYAAARRWKDAASL  367 (514)
Q Consensus       313 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~-----------~~~l~~~~~~~g~~~~a~~~  367 (514)
                      +|..+..+|...|++++|+..|+++++++|++...           |..+..++...|+.+.+...
T Consensus       242 a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~~~  307 (323)
T d1fcha_         242 SRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAA  307 (323)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            89999999999999999999999999988776543           34556666667776655433

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.16  E-value=1.5e-08  Score=94.91  Aligned_cols=260  Identities=13%  Similarity=0.001  Sum_probs=170.6

Q ss_pred             HHHHHHCCChhHHHHHHHHHHHCCCCCC----HHHHHHHHHHHhccCChHHHHHHHHHHHHcC--CC---CcHHHHHHHH
Q 040365          114 IAGCVQNGLFDEGLKFFRQMLIAKIKPR----HVSFSSIMPACAHLTTLHLGKQLHGCIIRNG--FD---DNMFIASSLL  184 (514)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g~~p~----~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~---~~~~~~~~li  184 (514)
                      ...+...|++++|++++++..+.....+    ...+..+..++...|++++|...+...++..  ..   .....+..+.
T Consensus        19 A~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~   98 (366)
T d1hz4a_          19 AQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQS   98 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHH
Confidence            3445566777777777766655321111    1234445556666777777777776665431  11   1123445566


Q ss_pred             HHHHhcCCHHHHHHHHHhCC-------CC----ChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCC----CCCHHHHHHH
Q 040365          185 DMYAKCGNIRLARCIFDKMD-------LH----DIVSWTAVIMGNALHGNAHDAISLFEQMEKDGV----KPNSVAFVAV  249 (514)
Q Consensus       185 ~~y~k~g~~~~A~~~~~~m~-------~~----d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~----~p~~~t~~~l  249 (514)
                      ..|...|++..|...+....       .+    ....+..+...+...|+++.+...+.+......    .....++...
T Consensus        99 ~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (366)
T d1hz4a_          99 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAML  178 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence            67777788777777666542       11    113455566777888888888888888776322    2223455566


Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCC-----CHhHHHHHHHHHHhcCCHHHHHHHHHhCCC-C-----CCHHHHHHHH
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAP-----SFEHYAAVADLLGRAGKLQEAYEFISNMHA-G-----PTENVWLTLL  318 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p-----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~-----p~~~~~~~ll  318 (514)
                      ...+...+....+...+........-..     ....+..+...+...|++++|...++.... .     .....+..+.
T Consensus       179 ~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la  258 (366)
T d1hz4a_         179 IQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIA  258 (366)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHH
Confidence            6667778888888887776644322211     123455667778889999999999987631 1     1245667788


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhc------CCCCcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          319 SACRVHKNVELAGKVAEKIFMI------DPNNMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~------~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      .++...|+++.|...+++++..      .|....++..++.+|...|++++|.+.+++..+
T Consensus       259 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         259 RAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            8999999999999999988743      255567888999999999999999999987654

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=99.05  E-value=2.8e-09  Score=95.91  Aligned_cols=221  Identities=10%  Similarity=-0.062  Sum_probs=137.7

Q ss_pred             hhHHHHHHHHHHHCCC-CC--CHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHH
Q 040365          123 FDEGLKFFRQMLIAKI-KP--RHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCI  199 (514)
Q Consensus       123 ~~~A~~l~~~m~~~g~-~p--~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~  199 (514)
                      .+.++.-+.+...... .+  ...+|..+..++.+.|++++|.+.+.+.++.. +.+..+++.+..+|.+.|++++|.+.
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~   93 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEA   93 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhh
Confidence            3455555555554321 11  12345555667777888888888888887764 55677888888888888888888888


Q ss_pred             HHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCC
Q 040365          200 FDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIA  276 (514)
Q Consensus       200 ~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~  276 (514)
                      |++..   +.+..+|..+...|...|++++|++.|++..+.. +.+......+..++.+.+..+....+......   ..
T Consensus        94 ~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~  169 (259)
T d1xnfa_          94 FDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK---SD  169 (259)
T ss_dssp             HHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH---SC
T ss_pred             hhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhc---cc
Confidence            88775   3356678888888888999999999999888753 22344444444445555555555555554432   12


Q ss_pred             CCHhHHHHHHHHHHhcCCHHHHHHHH-HhCC----CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHH
Q 040365          277 PSFEHYAAVADLLGRAGKLQEAYEFI-SNMH----AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYV  349 (514)
Q Consensus       277 p~~~~~~~li~~~~~~g~~~~A~~~~-~~m~----~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~  349 (514)
                      +....+. ++..+............. ....    ..|+ ..+|..|...+...|++++|...+++++..+|++...|.
T Consensus       170 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~  247 (259)
T d1xnfa_         170 KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFVEHR  247 (259)
T ss_dssp             CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTCHHHH
T ss_pred             hhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHH
Confidence            2222222 222222222222211111 1111    1122 346777888999999999999999999999998765554

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.02  E-value=2.5e-08  Score=92.29  Aligned_cols=185  Identities=12%  Similarity=0.106  Sum_probs=123.7

Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCCC---CC-hhHHHHHHHHHHhCCChHHHHHHHH
Q 040365          157 TLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMDL---HD-IVSWTAVIMGNALHGNAHDAISLFE  232 (514)
Q Consensus       157 ~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~~---~d-~~~~~~li~~~~~~g~~~~A~~l~~  232 (514)
                      ..+.+..+++..++...+.+...+..++..+.+.|+++.|+.+|+++..   .+ ...|...+....+.|+.++|.++|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            3466777777777655555666777777788888888888888877642   22 2367777777777888888888888


Q ss_pred             HHHHcCCCCCHHHHHHHHH-HHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC----C
Q 040365          233 QMEKDGVKPNSVAFVAVLT-ACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH----A  307 (514)
Q Consensus       233 ~m~~~g~~p~~~t~~~ll~-a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~  307 (514)
                      ++.+.+.. +...|..... -+...|+.+.|..+|+.+.+.+  +.+...|...++.+.+.|++++|..+|++..    .
T Consensus       159 ~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~--p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~  235 (308)
T d2onda1         159 KAREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  235 (308)
T ss_dssp             HHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSS
T ss_pred             HHHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhh--hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC
Confidence            87765322 2233333222 2334577788888888776542  2246677777777778888888877777641    2


Q ss_pred             CC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 040365          308 GP--TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN  344 (514)
Q Consensus       308 ~p--~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~  344 (514)
                      .|  ....|...+.--..+|+.+.+..+.+++.+..|.+
T Consensus       236 ~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~~~  274 (308)
T d2onda1         236 PPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREE  274 (308)
T ss_dssp             CGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTT
T ss_pred             ChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCccc
Confidence            22  24567777777777788888877777777766654

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.02  E-value=9.9e-08  Score=89.16  Aligned_cols=220  Identities=10%  Similarity=-0.019  Sum_probs=122.4

Q ss_pred             HHHHHhccCChHHHHHHHHHHHHc----CCC--C-cHHHHHHHHHHHHhcCCHHHHHHHHHhCC--------CCChhHHH
Q 040365          148 IMPACAHLTTLHLGKQLHGCIIRN----GFD--D-NMFIASSLLDMYAKCGNIRLARCIFDKMD--------LHDIVSWT  212 (514)
Q Consensus       148 ll~~~~~~~~~~~a~~~~~~~~~~----~~~--~-~~~~~~~li~~y~k~g~~~~A~~~~~~m~--------~~d~~~~~  212 (514)
                      +...+...+++..+...+......    +..  + ....+..+...|...|+++.|...+....        .....++.
T Consensus        97 ~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  176 (366)
T d1hz4a_          97 QSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLA  176 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHH
Confidence            333444555555555555444321    111  1 12234445556666666666666665542        11223444


Q ss_pred             HHHHHHHhCCChHHHHHHHHHHHHc----CCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC--CHhHHHH
Q 040365          213 AVIMGNALHGNAHDAISLFEQMEKD----GVKPN--SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP--SFEHYAA  284 (514)
Q Consensus       213 ~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p--~~~~~~~  284 (514)
                      .+...+...|+..++...+.+....    +..+.  ...+..+...+...|+.++|...+....+...-.+  ....+..
T Consensus       177 ~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  256 (366)
T d1hz4a_         177 MLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRN  256 (366)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHH
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHH
Confidence            4555566667777777766665431    11111  12344555566777888888888776643211111  2344555


Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC-------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC---------Ccch
Q 040365          285 VADLLGRAGKLQEAYEFISNMH-------AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPN---------NMGA  347 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~-------~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~---------~~~~  347 (514)
                      +...+...|++++|.+.+++..       ..|+ ..+|..+...+...|++++|...+++++++.+.         ....
T Consensus       257 la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~~~~~~~~~~~~~~~~  336 (366)
T d1hz4a_         257 IARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTGFISHFVIEGEA  336 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCCCHHHHTTHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhhcCcHHHHHHHHHH
Confidence            6777888888888888777642       1222 346677778888888888888888888775421         1122


Q ss_pred             HHHHHHHHHHccChhHHHHH
Q 040365          348 YVILSNTYAAARRWKDAASL  367 (514)
Q Consensus       348 ~~~l~~~~~~~g~~~~a~~~  367 (514)
                      ...++..+...++.+++.+-
T Consensus       337 ~~~~~~~l~~~~~l~e~e~~  356 (366)
T d1hz4a_         337 MAQQLRQLIQLNTLPELEQH  356 (366)
T ss_dssp             HHHHHHHHHHTTCSCHHHHH
T ss_pred             HHHHHHHHHhcCCChHHHHH
Confidence            33455556666776666543

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.00  E-value=3e-08  Score=92.03  Aligned_cols=211  Identities=11%  Similarity=0.130  Sum_probs=109.3

Q ss_pred             HHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHH-HHHHHHHHHhccC-ChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 040365          109 SWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHV-SFSSIMPACAHLT-TLHLGKQLHGCIIRNGFDDNMFIASSLLDM  186 (514)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  186 (514)
                      +++.+...+.+.+.+++|+++++++.+.  .|+.. .|.....++...+ ++++|...++.+++.. +-+.         
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~l--nP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~---------  112 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIEL--NAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNY---------  112 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCH---------
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHH--CCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-Hhhh---------
Confidence            4555555566666666666666666653  33332 3334444444433 2455555555554443 3334         


Q ss_pred             HHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040365          187 YAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYF  266 (514)
Q Consensus       187 y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  266 (514)
                                            .+|+.+...+.+.|++++|++.|+++.+.. +-+...|..+...+.+.|++++|+..+
T Consensus       113 ----------------------~a~~~~~~~~~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~  169 (315)
T d2h6fa1         113 ----------------------QVWHHRRVLVEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYV  169 (315)
T ss_dssp             ----------------------HHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHH
T ss_pred             ----------------------hHHHHHhHHHHhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHH
Confidence                                  444444444555555555555555555431 113344555555555555555555555


Q ss_pred             HHhHHhcCCCC-CHhHHHHHHHHHHhcCC------HHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 040365          267 NSMTKDYGIAP-SFEHYAAVADLLGRAGK------LQEAYEFISNM-HAG-PTENVWLTLLSACRVHKNVELAGKVAEKI  337 (514)
Q Consensus       267 ~~m~~~~~~~p-~~~~~~~li~~~~~~g~------~~~A~~~~~~m-~~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~  337 (514)
                      +.+.+.   .| +...|+.+...+.+.+.      +++|.+.+.+. ... .+...|..+...+.. ...+++...++.+
T Consensus       170 ~~al~~---~p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~  245 (315)
T d2h6fa1         170 DQLLKE---DVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQD-RGLSKYPNLLNQL  245 (315)
T ss_dssp             HHHHHH---CTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTT-TCGGGCHHHHHHH
T ss_pred             HHHHHH---CCccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHh-cChHHHHHHHHHH
Confidence            555432   33 33444444444443333      45666666553 222 356777777665544 3457778888888


Q ss_pred             HhcCCCC--cchHHHHHHHHHHc
Q 040365          338 FMIDPNN--MGAYVILSNTYAAA  358 (514)
Q Consensus       338 ~~~~p~~--~~~~~~l~~~~~~~  358 (514)
                      .++.|..  +..+..++..|...
T Consensus       246 ~~l~~~~~~~~~~~~l~~~y~~~  268 (315)
T d2h6fa1         246 LDLQPSHSSPYLIAFLVDIYEDM  268 (315)
T ss_dssp             HHHTTTCCCHHHHHHHHHHHHHH
T ss_pred             HHhCCCcCCHHHHHHHHHHHHHH
Confidence            8877654  33445666666543

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.97  E-value=2.3e-09  Score=100.71  Aligned_cols=231  Identities=9%  Similarity=-0.031  Sum_probs=163.3

Q ss_pred             HHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccC--ChHHHHHHHHHHHHcCCCCcHHHH-HHHHHHHHhcCCHH
Q 040365          118 VQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLT--TLHLGKQLHGCIIRNGFDDNMFIA-SSLLDMYAKCGNIR  194 (514)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~-~~li~~y~k~g~~~  194 (514)
                      ...|++++|+.++++..+.. +-+...+..+..++...+  +.+++...+..+++.. +++...+ ..+...+...|..+
T Consensus        84 ~~~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~  161 (334)
T d1dcea1          84 ESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPA  161 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHH
T ss_pred             HHHHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccH
Confidence            34455778888888887653 334445555555555554  4788888888888775 3444444 34556777889999


Q ss_pred             HHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHH
Q 040365          195 LARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTK  271 (514)
Q Consensus       195 ~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  271 (514)
                      +|...++...   ..+..+|+.+...+.+.|++++|...+++....  .|+..   .+...+...+..+++...+.....
T Consensus       162 ~Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~---~~~~~~~~l~~~~~a~~~~~~~l~  236 (334)
T d1dcea1         162 EELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENV--LLKEL---ELVQNAFFTDPNDQSAWFYHRWLL  236 (334)
T ss_dssp             HHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHH--HHHHH---HHHHHHHHHCSSCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHh--HHHHH---HHHHHHHHhcchhHHHHHHHHHHH
Confidence            9999998876   346778999989999999888887666554432  22222   222334455666677777776644


Q ss_pred             hcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHH
Q 040365          272 DYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYV  349 (514)
Q Consensus       272 ~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~  349 (514)
                      .  -.++...+..+...+...|+.++|.+.+.+.. ..| +..+|..+..++...|+.++|...++++++++|.+...|.
T Consensus       237 ~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~~~~y~~  314 (334)
T d1dcea1         237 G--RAEPLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLD  314 (334)
T ss_dssp             S--CCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHHH
T ss_pred             h--CcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcccHHHHH
Confidence            2  23345566667778888899999999888764 334 4567888999999999999999999999999999888888


Q ss_pred             HHHHHHHH
Q 040365          350 ILSNTYAA  357 (514)
Q Consensus       350 ~l~~~~~~  357 (514)
                      .|...+.-
T Consensus       315 ~L~~~~~~  322 (334)
T d1dcea1         315 DLRSKFLL  322 (334)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhH
Confidence            88776653

>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=98.95  E-value=4.1e-08  Score=91.09  Aligned_cols=143  Identities=8%  Similarity=-0.026  Sum_probs=81.0

Q ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCC-CHHHHHHHHccCC---CCChhHHHHHHHHHHH
Q 040365           44 LSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCA-RVEDSHRLFCLLP---VKDAISWNSIIAGCVQ  119 (514)
Q Consensus        44 ~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g-~~~~A~~~f~~~~---~~d~~~~~~li~~~~~  119 (514)
                      |+.+-..+.+.+..++|.++++.+++.. |.+..+|+.....+...| ++++|...++...   ..+..+|+.+...+.+
T Consensus        46 ~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~~~  124 (315)
T d2h6fa1          46 YDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLVEW  124 (315)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHHHh
Confidence            3444445556666666777776666664 445556666666666554 3666666665543   2355566666666666


Q ss_pred             CCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh
Q 040365          120 NGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK  189 (514)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k  189 (514)
                      .|++++|++.|.++.+.. +-+...|..+...+...+++++|.+.++.+++.. +.+...|+.+...+.+
T Consensus       125 l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~-p~n~~a~~~r~~~l~~  192 (315)
T d2h6fa1         125 LRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISN  192 (315)
T ss_dssp             HTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             hccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHC-CccHHHHHHHHHHHHH
Confidence            666666666666666542 2345555555555666666666666666665553 3344444444443333

>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=98.94  E-value=1.5e-07  Score=86.94  Aligned_cols=163  Identities=11%  Similarity=0.036  Sum_probs=65.5

Q ss_pred             hhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 040365          107 AISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDM  186 (514)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~  186 (514)
                      ...|...+..+.+.|++++|..+|+++...........|...+..+.+.++++.|++++..+++.+ +.+...+......
T Consensus        99 ~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~-~~~~~~~~~~a~~  177 (308)
T d2onda1          99 MLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALM  177 (308)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCcHHHHHHHHHH
Confidence            334444444444455555555555544432211112234444444444444445555544444433 1122222222211


Q ss_pred             -HHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcC-CCCC--HHHHHHHHHHHHccCCH
Q 040365          187 -YAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDG-VKPN--SVAFVAVLTACSHAGLI  259 (514)
Q Consensus       187 -y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~--~~t~~~ll~a~~~~g~~  259 (514)
                       +...|+.+.|..+|+.+.   ..+...|...+..+.+.|+.+.|..+|++..... ..|+  ...|...+.--...|+.
T Consensus       178 e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~  257 (308)
T d2onda1         178 EYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDL  257 (308)
T ss_dssp             HHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCH
T ss_pred             HHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCH
Confidence             122344444444444443   1233344444444444444444444444443321 2222  12333333333344444


Q ss_pred             HHHHHHHHHhH
Q 040365          260 DKAWSYFNSMT  270 (514)
Q Consensus       260 ~~a~~~~~~m~  270 (514)
                      +.+..+++++.
T Consensus       258 ~~~~~~~~r~~  268 (308)
T d2onda1         258 ASILKVEKRRF  268 (308)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            44444444443

>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=98.86  E-value=3.1e-08  Score=88.84  Aligned_cols=211  Identities=13%  Similarity=-0.003  Sum_probs=143.7

Q ss_pred             HHHHHHHHHHHHcCC-CC--cHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHH
Q 040365          159 HLGKQLHGCIIRNGF-DD--NMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFE  232 (514)
Q Consensus       159 ~~a~~~~~~~~~~~~-~~--~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~  232 (514)
                      +.+..-+++++.... .+  ...++..+...|.+.|++++|.+.|++..   +.+..+|+.+..+|.+.|++++|++.|+
T Consensus        16 e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~   95 (259)
T d1xnfa_          16 EVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFD   95 (259)
T ss_dssp             HHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhh
Confidence            444444555554321 11  23566778899999999999999999875   4578899999999999999999999999


Q ss_pred             HHHHcCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC
Q 040365          233 QMEKDGVKPN-SVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP  309 (514)
Q Consensus       233 ~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p  309 (514)
                      +..+.  .|+ ..++..+..++...|++++|...|+...+.   .| +......+...+.+.+..+.+..+..... ..+
T Consensus        96 ~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (259)
T d1xnfa_          96 SVLEL--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD---DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDK  170 (259)
T ss_dssp             HHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCC
T ss_pred             HHHHH--HhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhh---ccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccch
Confidence            99985  444 567888889999999999999999988764   44 44444444455556665555544443321 112


Q ss_pred             CHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          310 TENVWLTLLSACRV----HKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       310 ~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      +...++ ++..+..    .+..+.+...+.......|....+|..|+..|...|++++|.+.+++.....
T Consensus       171 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~  239 (259)
T d1xnfa_         171 EQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANN  239 (259)
T ss_dssp             CSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             hhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            211222 2222211    1223333333333334446666788899999999999999999999887643

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.78  E-value=1.2e-08  Score=95.77  Aligned_cols=254  Identities=6%  Similarity=-0.059  Sum_probs=177.1

Q ss_pred             HHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHH-H---HHHHHHh-------ccCChHHHHHHHHHHHHcCCCCcHHH
Q 040365          111 NSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSF-S---SIMPACA-------HLTTLHLGKQLHGCIIRNGFDDNMFI  179 (514)
Q Consensus       111 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~-~---~ll~~~~-------~~~~~~~a~~~~~~~~~~~~~~~~~~  179 (514)
                      ..++......+..++|++++.+..+.  .|+..+. +   .++....       ..+.++++..+++.+++.. +.+...
T Consensus        33 ~~~~~~~~~~~~~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~  109 (334)
T d1dcea1          33 QAVFQKRQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGT  109 (334)
T ss_dssp             HHHHHHHHTTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHH
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHH
Confidence            33433333444558899999988874  4665543 2   2222222       3345778888888888765 556777


Q ss_pred             HHHHHHHHHhcC--CHHHHHHHHHhCC---CCChhHHHHH-HHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040365          180 ASSLLDMYAKCG--NIRLARCIFDKMD---LHDIVSWTAV-IMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTAC  253 (514)
Q Consensus       180 ~~~li~~y~k~g--~~~~A~~~~~~m~---~~d~~~~~~l-i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~  253 (514)
                      +..+..++...+  ++++|...+.++.   .++...|... ...+...|.+++|+..+++...... -+...|..+..++
T Consensus       110 ~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~~  188 (334)
T d1dcea1         110 WHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLL  188 (334)
T ss_dssp             HHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHH
T ss_pred             HHHhhHHHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHHHHHHHHHHH
Confidence            777776766665  4789998888874   4456666544 4667778999999999998877532 2566788888888


Q ss_pred             HccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCCHHHHH
Q 040365          254 SHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNM--HAGPTENVWLTLLSACRVHKNVELAG  331 (514)
Q Consensus       254 ~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m--~~~p~~~~~~~ll~~~~~~~~~~~a~  331 (514)
                      ...|++++|...+....+.   .|.   ...+...+...+..+++...+...  ..+++...+..+...+...++.++|.
T Consensus       189 ~~~~~~~~A~~~~~~~~~~---~~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~  262 (334)
T d1dcea1         189 PQLHPQPDSGPQGRLPENV---LLK---ELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELESC  262 (334)
T ss_dssp             HHHSCCCCSSSCCSSCHHH---HHH---HHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHhHHh---HHH---HHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHH
Confidence            8888887776655544322   121   112333445566666777666554  22344555667777888889999999


Q ss_pred             HHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          332 KVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       332 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ..+.+....+|.+..++..++.+|...|++++|.+.+++..+.
T Consensus       263 ~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l  305 (334)
T d1dcea1         263 KELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  305 (334)
T ss_dssp             HHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998764

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.52  E-value=4.6e-07  Score=77.48  Aligned_cols=111  Identities=7%  Similarity=-0.074  Sum_probs=65.0

Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHH
Q 040365          241 PNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTL  317 (514)
Q Consensus       241 p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~l  317 (514)
                      |+...+......+.+.|++++|+..|......   .| +...|..+..+|.+.|++++|...|++.. ..| +..+|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~---~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITR---NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHH
Confidence            55556666666666666666666666665433   34 45556666666666666666666666542 223 35556666


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 040365          318 LSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNT  354 (514)
Q Consensus       318 l~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  354 (514)
                      ..++...|++++|...++++++++|++...+...+..
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~l~p~~~~~~~~~~~~  115 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPS  115 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCCSHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            6666666666666666666666655444433333333

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.51  E-value=1.3e-06  Score=67.50  Aligned_cols=102  Identities=20%  Similarity=0.122  Sum_probs=64.1

Q ss_pred             HHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCC
Q 040365          250 LTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKN  326 (514)
Q Consensus       250 l~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~  326 (514)
                      ...+...|++++|+..|+...+.   .| +...|..+..+|...|++++|++.++...  .+.+...|..+..++...|+
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~---~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~   86 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKL---DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNR   86 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhc---CCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccC
Confidence            34555666666666666666543   34 45566666666666666666666666542  23456666667777777777


Q ss_pred             HHHHHHHHHHHHhcCCCCcchHHHHHHH
Q 040365          327 VELAGKVAEKIFMIDPNNMGAYVILSNT  354 (514)
Q Consensus       327 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~  354 (514)
                      +++|+..++++++++|+++..+..+.++
T Consensus        87 ~~~A~~~~~~a~~~~p~~~~~~~~l~~l  114 (117)
T d1elwa_          87 FEEAKRTYEEGLKHEANNPQLKEGLQNM  114 (117)
T ss_dssp             HHHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            7777777777777777766555555443

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.45  E-value=5.5e-06  Score=70.16  Aligned_cols=141  Identities=10%  Similarity=-0.074  Sum_probs=99.3

Q ss_pred             HHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040365          184 LDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAW  263 (514)
Q Consensus       184 i~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  263 (514)
                      ...+...|+++.|.+.|+++.+++...|..+...|...|++++|++.|++..+.. +-+...|..+..++.+.|++++|.
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~   90 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAI   90 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHH
Confidence            4557788999999999999888888888889999999999999999999988753 224567888888888999999998


Q ss_pred             HHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          264 SYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       264 ~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      ..|+.....  ..++...      .+...|           ...++ ...++..+..++...|+++.|.+.+++++++.|
T Consensus        91 ~~~~kAl~~--~~~n~~~------~~~~~~-----------~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~  151 (192)
T d1hh8a_          91 KDLKEALIQ--LRGNQLI------DYKILG-----------LQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKS  151 (192)
T ss_dssp             HHHHHHHHT--TTTCSEE------ECGGGT-----------BCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHh--CccCchH------HHHHhh-----------hhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            888877542  1111100      000000           00011 124555667778888888888888888888777


Q ss_pred             CC
Q 040365          343 NN  344 (514)
Q Consensus       343 ~~  344 (514)
                      ..
T Consensus       152 ~~  153 (192)
T d1hh8a_         152 EP  153 (192)
T ss_dssp             SG
T ss_pred             Cc
Confidence            64

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.43  E-value=1.6e-06  Score=66.93  Aligned_cols=91  Identities=11%  Similarity=0.025  Sum_probs=82.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChh
Q 040365          285 VADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWK  362 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  362 (514)
                      -...+.+.|++++|+..|++..  .+.+...|..+..++...|++++|+..++++++++|+++..|..++.+|...|+++
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHH
Confidence            3566889999999999999863  34578889999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCC
Q 040365          363 DAASLRVFMRNKG  375 (514)
Q Consensus       363 ~a~~~~~~m~~~g  375 (514)
                      +|...++...+..
T Consensus        89 ~A~~~~~~a~~~~  101 (117)
T d1elwa_          89 EAKRTYEEGLKHE  101 (117)
T ss_dssp             HHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999988653

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.41  E-value=9.7e-07  Score=75.38  Aligned_cols=90  Identities=7%  Similarity=-0.082  Sum_probs=42.5

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHH
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLL  289 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~  289 (514)
                      .......|.+.|++++|+..|++..... +-+...|..+..+|.+.|++++|+..|+...   .+.| +...|..+..+|
T Consensus         7 l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al---~l~p~~~~a~~~lg~~~   82 (201)
T d2c2la1           7 LKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRAL---ELDGQSVKAHFFLGQCQ   82 (201)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHT---TSCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHH---HhCCCcHHHHHHHHHHH
Confidence            3334444555555555555555544431 1133344444455555555555555555443   3344 344444555555


Q ss_pred             HhcCCHHHHHHHHHh
Q 040365          290 GRAGKLQEAYEFISN  304 (514)
Q Consensus       290 ~~~g~~~~A~~~~~~  304 (514)
                      .+.|++++|...|++
T Consensus        83 ~~l~~~~~A~~~~~~   97 (201)
T d2c2la1          83 LEMESYDEAIANLQR   97 (201)
T ss_dssp             HHTTCHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHH
Confidence            555555555555443

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.40  E-value=4.6e-06  Score=68.25  Aligned_cols=116  Identities=9%  Similarity=0.001  Sum_probs=92.4

Q ss_pred             HHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC
Q 040365          249 VLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHK  325 (514)
Q Consensus       249 ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~  325 (514)
                      -...|.+.|++++|...|+...+.   .| +...|..+..+|...|++++|.+.|++..  .+.+..+|..+..++...|
T Consensus        16 ~gn~~~~~~~y~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g   92 (159)
T d1a17a_          16 QANDYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALG   92 (159)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHhhhcccc---chhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcC
Confidence            455677888999999999888654   45 67888888889999999999999988763  2346788999999999999


Q ss_pred             CHHHHHHHHHHHHhcCCCCcchHHHHHHHH--HHccChhHHHHH
Q 040365          326 NVELAGKVAEKIFMIDPNNMGAYVILSNTY--AAARRWKDAASL  367 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~--~~~g~~~~a~~~  367 (514)
                      ++++|...+++++.++|+++..+..+..+.  ...+.+++|...
T Consensus        93 ~~~eA~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~~~a~~~  136 (159)
T d1a17a_          93 KFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAG  136 (159)
T ss_dssp             CHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            999999999999999999988877766554  344456666554

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.40  E-value=3.5e-06  Score=76.63  Aligned_cols=189  Identities=14%  Similarity=0.027  Sum_probs=123.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCCC-----CC----hhHHHHHHHHHHhCCChHHHHHHHHHHHHcC---CCCC--HHHHHH
Q 040365          183 LLDMYAKCGNIRLARCIFDKMDL-----HD----IVSWTAVIMGNALHGNAHDAISLFEQMEKDG---VKPN--SVAFVA  248 (514)
Q Consensus       183 li~~y~k~g~~~~A~~~~~~m~~-----~d----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g---~~p~--~~t~~~  248 (514)
                      ....|...|++++|.+.|.+..+     .+    ..+|+.+...|.+.|++++|++.+++..+.-   -.+.  ..++..
T Consensus        43 aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~  122 (290)
T d1qqea_          43 AATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFE  122 (290)
T ss_dssp             HHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHH
Confidence            35667788888888888876631     11    3578888888888999999998888765421   1111  244556


Q ss_pred             HHHHHH-ccCCHHHHHHHHHHhHHhcC---CCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CC---C----CH-HHH
Q 040365          249 VLTACS-HAGLIDKAWSYFNSMTKDYG---IAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AG---P----TE-NVW  314 (514)
Q Consensus       249 ll~a~~-~~g~~~~a~~~~~~m~~~~~---~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~---p----~~-~~~  314 (514)
                      +...|. ..|++++|...++...+-..   -.+ ...++..+...|...|++++|.+.++++. ..   +    .. ..+
T Consensus       123 l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~  202 (290)
T d1qqea_         123 LGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYF  202 (290)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHH
T ss_pred             HHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHH
Confidence            666664 46999999999987754221   111 13557778889999999999999998752 11   1    11 234


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc-----hHHHHHHHHHH--ccChhHHHHHHHHH
Q 040365          315 LTLLSACRVHKNVELAGKVAEKIFMIDPNNMG-----AYVILSNTYAA--ARRWKDAASLRVFM  371 (514)
Q Consensus       315 ~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~-----~~~~l~~~~~~--~g~~~~a~~~~~~m  371 (514)
                      ..++..+...|+++.|...+++..+.+|.-..     ....|+.+|..  .+++++|.+.|+.+
T Consensus       203 ~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~  266 (290)
T d1qqea_         203 LKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNF  266 (290)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            44555677889999999999999998875332     33455666654  34577887777543

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.38  E-value=1.1e-06  Score=67.43  Aligned_cols=88  Identities=16%  Similarity=0.101  Sum_probs=79.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccCh
Q 040365          284 AVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRW  361 (514)
Q Consensus       284 ~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  361 (514)
                      .+...+.+.|++++|...|++.. ..| +..+|..+..++...|++++|+..++++++++|+++.++..|+..|...|++
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~~  100 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNA  100 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCCCH
Confidence            45667888999999999998863 334 6889999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHH
Q 040365          362 KDAASLRVFM  371 (514)
Q Consensus       362 ~~a~~~~~~m  371 (514)
                      ++|.+.+++.
T Consensus       101 ~~A~~~l~~~  110 (112)
T d1hxia_         101 NAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999875

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=7.7e-06  Score=69.20  Aligned_cols=119  Identities=12%  Similarity=0.057  Sum_probs=83.3

Q ss_pred             HHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHH
Q 040365          252 ACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVEL  329 (514)
Q Consensus       252 a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~  329 (514)
                      .+...|++++|++.|..+     .+|+...|..+..+|...|++++|++.|++..  .+.+...|..+..++.+.|++++
T Consensus        14 ~~~~~~d~~~Al~~~~~i-----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~   88 (192)
T d1hh8a_          14 LAADKKDWKGALDAFSAV-----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDL   88 (192)
T ss_dssp             HHHHTTCHHHHHHHHHTS-----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHCCCHHHHHHHHHhc-----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHH
Confidence            345566777777766643     13455666667777777777777777776642  23456677777777788888888


Q ss_pred             HHHHHHHHHhcCCCC----------------cchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          330 AGKVAEKIFMIDPNN----------------MGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       330 a~~~~~~~~~~~p~~----------------~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      |...|++++...|.+                ..++..++.+|.+.|++++|.+.++...+..
T Consensus        89 A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~  150 (192)
T d1hh8a_          89 AIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  150 (192)
T ss_dssp             HHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            888887777654432                2356678899999999999999998876654

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.32  E-value=3.5e-05  Score=69.72  Aligned_cols=57  Identities=4%  Similarity=-0.229  Sum_probs=31.8

Q ss_pred             HHHHHHHCCChhHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHhccCChHHHHHHHHHHH
Q 040365          113 IIAGCVQNGLFDEGLKFFRQMLIA----KIKP-RHVSFSSIMPACAHLTTLHLGKQLHGCII  169 (514)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~~~~~~~~~~~a~~~~~~~~  169 (514)
                      ....|...|++++|++.|.+..+.    +-++ -..+|..+..+|.+.|++++|.+.+...+
T Consensus        43 aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~  104 (290)
T d1qqea_          43 AATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAI  104 (290)
T ss_dssp             HHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhh
Confidence            455666777777777777666441    1111 12345555556666666666666555544

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.28  E-value=4.5e-06  Score=68.33  Aligned_cols=91  Identities=13%  Similarity=-0.000  Sum_probs=82.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChh
Q 040365          285 VADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWK  362 (514)
Q Consensus       285 li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  362 (514)
                      ....|.+.|++++|...|++..  .+.+...|..+..++...|+++.|...|+++++++|.+..+|..++.+|...|+++
T Consensus        16 ~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~~~   95 (159)
T d1a17a_          16 QANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFR   95 (159)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCCHH
Confidence            4556889999999999999863  34578899999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCC
Q 040365          363 DAASLRVFMRNKG  375 (514)
Q Consensus       363 ~a~~~~~~m~~~g  375 (514)
                      +|...+++.....
T Consensus        96 eA~~~~~~a~~~~  108 (159)
T d1a17a_          96 AALRDYETVVKVK  108 (159)
T ss_dssp             HHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHcC
Confidence            9999999887653

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=2e-05  Score=65.06  Aligned_cols=133  Identities=14%  Similarity=0.005  Sum_probs=93.2

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHH
Q 040365          210 SWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLL  289 (514)
Q Consensus       210 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~  289 (514)
                      .+......+.+.|++++|+..|++....-  |..            .+..+.-......+        ....|+.+..+|
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~--~~~------------~~~~~~~~~~~~~~--------~~~~~~nla~~y   72 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWL--EYE------------SSFSNEEAQKAQAL--------RLASHLNLAMCH   72 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHT--TTC------------CCCCSHHHHHHHHH--------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHh--hhc------------cccchHHHhhhchh--------HHHHHHHHHHHH
Confidence            34445566777788888888877766531  100            00000000111111        123566788889


Q ss_pred             HhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHH
Q 040365          290 GRAGKLQEAYEFISNMH-AGP-TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDA  364 (514)
Q Consensus       290 ~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a  364 (514)
                      .+.|++++|+..++... ..| ++.+|..+..++...|+++.|...|+++++++|+++.+...+..+....+...+.
T Consensus        73 ~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~~~~~~  149 (170)
T d1p5qa1          73 LKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAR  149 (170)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999998763 334 7889999999999999999999999999999999999998888887766665544

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.15  E-value=1.4e-05  Score=61.89  Aligned_cols=104  Identities=19%  Similarity=0.057  Sum_probs=80.4

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCH---HHHHHHHHhCC-CCCCH---HHHHHHH
Q 040365          247 VAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKL---QEAYEFISNMH-AGPTE---NVWLTLL  318 (514)
Q Consensus       247 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~---~~A~~~~~~m~-~~p~~---~~~~~ll  318 (514)
                      ..+++.+...+++++|.+.|+...+.   .| ++.++..+..++.+.++.   ++|..+++++. ..|+.   .+|..|.
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~---~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg   79 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAA---GSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLA   79 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH---SCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhh---CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHH
Confidence            35677788888999999999888653   45 677888888888775554   46888888864 23433   3788899


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHH
Q 040365          319 SACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSN  353 (514)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~  353 (514)
                      .+|...|++++|+..|+++++++|++..+...+..
T Consensus        80 ~~y~~~g~~~~A~~~~~~aL~~~P~~~~A~~l~~~  114 (122)
T d1nzna_          80 VGNYRLKEYEKALKYVRGLLQTEPQNNQAKELERL  114 (122)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHHHHHHhCcCCHHHHHHHHH
Confidence            99999999999999999999999998766555443

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.12  E-value=0.00066  Score=59.88  Aligned_cols=226  Identities=12%  Similarity=-0.014  Sum_probs=126.2

Q ss_pred             ChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhc----cCChHHHHHHHHHHHHcCCCCcHHHHH
Q 040365          106 DAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH----LTTLHLGKQLHGCIIRNGFDDNMFIAS  181 (514)
Q Consensus       106 d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  181 (514)
                      |+..+..|...+.+.+++++|++.|++..+.|   |...+..|-..+..    ..+...+...+....+.+         
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---------   68 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---------   68 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---------
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---------
Confidence            44556666666777777777777777776655   23333333333332    334555555555554443         


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHh----CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH----
Q 040365          182 SLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNAL----HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTAC----  253 (514)
Q Consensus       182 ~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~----  253 (514)
                                               +...+..+...+..    .++.+.|...+++....|..+.   ...+...+    
T Consensus        69 -------------------------~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a---~~~l~~~~~~~~  120 (265)
T d1ouva_          69 -------------------------YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEG---CASLGGIYHDGK  120 (265)
T ss_dssp             -------------------------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHH---HHHHHHHHHHCS
T ss_pred             -------------------------ccchhhccccccccccccchhhHHHHHHHhhhhhhhhhhH---HHhhcccccCCC
Confidence                                     22222222222221    3345555566655555442211   11111111    


Q ss_pred             HccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHh----cCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cC
Q 040365          254 SHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGR----AGKLQEAYEFISNMHAGPTENVWLTLLSACRV----HK  325 (514)
Q Consensus       254 ~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~----~~  325 (514)
                      ........+...+.....    ..+...+..|...|..    ..+...+..+++......+......|...+..    ..
T Consensus       121 ~~~~~~~~a~~~~~~~~~----~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~  196 (265)
T d1ouva_         121 VVTRDFKKAVEYFTKACD----LNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATK  196 (265)
T ss_dssp             SSCCCHHHHHHHHHHHHH----TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCC
T ss_pred             cccchhHHHHHHhhhhhc----ccccchhhhhhhhhccCCCcccccccchhhhhccccccccccccchhhhcccCccccc
Confidence            123345555555554422    2344555555555553    34556666666655444566666666655554    56


Q ss_pred             CHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH----ccChhHHHHHHHHHHhCCCc
Q 040365          326 NVELAGKVAEKIFMIDPNNMGAYVILSNTYAA----ARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~g~~  377 (514)
                      +++.|...|++..+.+  ++..+..|+.+|..    ..+.++|.+.|++..+.|-.
T Consensus       197 d~~~A~~~~~~aa~~g--~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~~  250 (265)
T d1ouva_         197 NFKEALARYSKACELE--NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAK  250 (265)
T ss_dssp             CHHHHHHHHHHHHHTT--CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             chhhhhhhHhhhhccc--CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHCcCH
Confidence            8899999999988875  45677888888875    34788899999988877743

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=98.07  E-value=6.3e-05  Score=61.81  Aligned_cols=94  Identities=15%  Similarity=0.058  Sum_probs=76.2

Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH
Q 040365          280 EHYAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAA  357 (514)
Q Consensus       280 ~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  357 (514)
                      ..|..+..+|.+.|++++|+..++...  .+.+..+|..+..++...|++++|...++++++++|+++.+...+..+...
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~  144 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQKK  144 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            356667788899999999999998763  345788999999999999999999999999999999999988888888777


Q ss_pred             ccChh-HHHHHHHHHHh
Q 040365          358 ARRWK-DAASLRVFMRN  373 (514)
Q Consensus       358 ~g~~~-~a~~~~~~m~~  373 (514)
                      .+... ...+++..|-+
T Consensus       145 ~~~~~e~~kk~~~~~f~  161 (168)
T d1kt1a1         145 AKEHNERDRRTYANMFK  161 (168)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHh
Confidence            66554 34555555543

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.02  E-value=8.8e-05  Score=61.01  Aligned_cols=111  Identities=14%  Similarity=0.019  Sum_probs=79.3

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 040365          245 AFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVH  324 (514)
Q Consensus       245 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~  324 (514)
                      .+......+.+.|++++|+..|..........+....              .+ ......+    -..+|+.+..+|.+.
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~--------------~~-~~~~~~~----~~~~~~nla~~y~k~   75 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSN--------------EE-AQKAQAL----RLASHLNLAMCHLKL   75 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCS--------------HH-HHHHHHH----HHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccch--------------HH-Hhhhchh----HHHHHHHHHHHHHhh
Confidence            3444455667777777777777766543222211100              00 0000000    124577788899999


Q ss_pred             CCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          325 KNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       325 ~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      |++++|+..++++++++|+++.+|..++.+|...|++++|...++...+.
T Consensus        76 ~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          76 QAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999998764

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.00  E-value=2.2e-05  Score=60.63  Aligned_cols=92  Identities=8%  Similarity=-0.014  Sum_probs=76.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHHHhcCCCC--cchHHHHHHHH
Q 040365          283 AAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHK---NVELAGKVAEKIFMIDPNN--MGAYVILSNTY  355 (514)
Q Consensus       283 ~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~---~~~~a~~~~~~~~~~~p~~--~~~~~~l~~~~  355 (514)
                      ..++..+...+++++|.+.|++..  .+.+..++..+..++...+   +.++|+.+++++++.+|.+  ..++..|+.+|
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            457788889999999999999863  3457788888998887644   5567999999999988754  34788999999


Q ss_pred             HHccChhHHHHHHHHHHhC
Q 040365          356 AAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       356 ~~~g~~~~a~~~~~~m~~~  374 (514)
                      .+.|++++|.+.+++..+.
T Consensus        83 ~~~g~~~~A~~~~~~aL~~  101 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQT  101 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhHHHHHHHHHHHHh
Confidence            9999999999999999874

>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=97.96  E-value=0.00015  Score=58.39  Aligned_cols=63  Identities=21%  Similarity=0.077  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .+|..+..++.+.|++++|+..++++++++|.++.+|..++.+|...|++++|...|+...+.
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l  130 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASL  130 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh
Confidence            467778888899999999999999999999999999999999999999999999999887654

>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=97.92  E-value=0.0001  Score=59.47  Aligned_cols=127  Identities=10%  Similarity=-0.074  Sum_probs=89.9

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHH
Q 040365          209 VSWTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADL  288 (514)
Q Consensus       209 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~  288 (514)
                      ..+......+.+.|++.+|+..|.+....-  |...           ...-.........        ....+|..+..+
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~--~~~~-----------~~~~~~~~~~~~~--------~~~~~~~Nla~~   76 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDFF--IHTE-----------EWDDQILLDKKKN--------IEISCNLNLATC   76 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTT--TTCT-----------TCCCHHHHHHHHH--------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--cchh-----------hhhhHHHHHhhhh--------HHHHHHhhHHHH
Confidence            456666777888888888888888877521  1000           0000000000000        123467778889


Q ss_pred             HHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 040365          289 LGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYA  356 (514)
Q Consensus       289 ~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  356 (514)
                      |.+.|++++|++.++...  .+.+..+|..+..++...|+++.|...|+++++++|+|+.+...+..+..
T Consensus        77 ~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~  146 (153)
T d2fbna1          77 YNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVN  146 (153)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            999999999999998853  33478899999999999999999999999999999999887776655543

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.92  E-value=6.6e-05  Score=61.71  Aligned_cols=131  Identities=11%  Similarity=-0.005  Sum_probs=90.7

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHH
Q 040365          211 WTAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLL  289 (514)
Q Consensus       211 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~  289 (514)
                      +......+...|++++|++.|.+..+.            +...........          ...+.| ....|..+..+|
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~------------~~~~~~~~~~~~----------~~~~~~~~~~~~~nla~~~   87 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRY------------VEGSRAAAEDAD----------GAKLQPVALSCVLNIGACK   87 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH------------HHHHHHHSCHHH----------HGGGHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh------------hhhhhhhhhhHH----------HHHhChhhHHHHHHHHHHH
Confidence            444455667778888888887776531            000000000000          001223 455677788889


Q ss_pred             HhcCCHHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhH
Q 040365          290 GRAGKLQEAYEFISNMH-AG-PTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKD  363 (514)
Q Consensus       290 ~~~g~~~~A~~~~~~m~-~~-p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  363 (514)
                      .+.|++++|+..+++.. .. .+...|..+..++...|+++.|+..|+++++++|++..++..|..++.+.....+
T Consensus        88 ~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~~~~~~l~~~~~~l~~~~~  163 (169)
T d1ihga1          88 LKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKD  163 (169)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999998763 33 4678899999999999999999999999999999998888888777665544444

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.88  E-value=3.4e-05  Score=60.25  Aligned_cols=92  Identities=12%  Similarity=0.103  Sum_probs=73.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc-------hHHHHH
Q 040365          282 YAAVADLLGRAGKLQEAYEFISNMH--AGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG-------AYVILS  352 (514)
Q Consensus       282 ~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~-------~~~~l~  352 (514)
                      +..+...+.+.|++++|++.|++..  .+.+..+|..+..+|...|+++.|+..++++++++|.++.       +|..+.
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            3456677888888888888887753  2346888999999999999999999999999998877665       455566


Q ss_pred             HHHHHccChhHHHHHHHHHHh
Q 040365          353 NTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       353 ~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..+...+++++|.+.+++-..
T Consensus        87 ~~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          87 NSYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHh
Confidence            777888899999999987654

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.82  E-value=0.0001  Score=60.57  Aligned_cols=65  Identities=12%  Similarity=0.031  Sum_probs=60.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          310 TENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       310 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      +...|..+..++.+.|++++|+..++++++++|+++.+|..++.+|...|++++|.+.++...+.
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l  140 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI  140 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh
Confidence            45577888899999999999999999999999999999999999999999999999999988774

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.81  E-value=2.8e-06  Score=83.65  Aligned_cols=111  Identities=8%  Similarity=-0.083  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCC-CHHHHHHHHHHH
Q 040365          244 VAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMH-AGP-TENVWLTLLSAC  321 (514)
Q Consensus       244 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p-~~~~~~~ll~~~  321 (514)
                      ..+..+...+.+.|+.++|...+......   .| ...+..+.+.+...|++++|...|++.. ..| +...|+.|...+
T Consensus       121 ~~~~~lg~~~~~~~~~~~A~~~~~~al~~---~~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~  196 (497)
T d1ya0a1         121 VKSSQLGIISNKQTHTSAIVKPQSSSCSY---IC-QHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILA  196 (497)
T ss_dssp             ----------------------CCHHHHH---HH-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHH
T ss_pred             HHHHHhHHHHHhCCCHHHHHHHHHHHhCC---CH-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHH
Confidence            44555555666666666666655544321   11 2345566666777777777777766642 223 446677777777


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHc
Q 040365          322 RVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAA  358 (514)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  358 (514)
                      ...|+..+|...|.+.+..+|+-+.++..|...|.+.
T Consensus       197 ~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~  233 (497)
T d1ya0a1         197 SSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKA  233 (497)
T ss_dssp             HHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence            7777777777777777777766666666666665543

>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=97.80  E-value=4.5e-05  Score=57.89  Aligned_cols=85  Identities=7%  Similarity=-0.107  Sum_probs=38.4

Q ss_pred             HHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHH
Q 040365           14 VGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVE   93 (514)
Q Consensus        14 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~   93 (514)
                      ..+.+.|++++|+..|++..... +-+...|..+..++...+++++|...+..+++.. |.+..++..|...|...|+.+
T Consensus        24 ~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~~~  101 (112)
T d1hxia_          24 LSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHNAN  101 (112)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCCHH
Confidence            34444455555555555444432 1123344444444444455555555554444443 333444444444444444444


Q ss_pred             HHHHHHc
Q 040365           94 DSHRLFC  100 (514)
Q Consensus        94 ~A~~~f~  100 (514)
                      +|.+.|+
T Consensus       102 ~A~~~l~  108 (112)
T d1hxia_         102 AALASLR  108 (112)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            4444443

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.76  E-value=0.011  Score=51.67  Aligned_cols=223  Identities=11%  Similarity=-0.039  Sum_probs=123.3

Q ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHccCCC-CChhHHHHHHHHHHH----CCChhHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040365           75 NVCIGSSLINMYAKCARVEDSHRLFCLLPV-KDAISWNSIIAGCVQ----NGLFDEGLKFFRQMLIAKIKPRHVSFSSIM  149 (514)
Q Consensus        75 ~~~~~~~li~~~~~~g~~~~A~~~f~~~~~-~d~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (514)
                      |+..+..|-..+.+.+++++|.+.|++..+ .|..++..|...|..    ..++..|...+......+. |  .....+.
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~-~--~a~~~l~   77 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNY-S--NGCHLLG   77 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC-H--HHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccc-c--chhhccc
Confidence            455677788888899999999999998753 467777777777776    5688899999988877652 2  2222232


Q ss_pred             HHH----hccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHh----cCCHHHHHHHHHhCC-CCChhHHHHHHHHHHh
Q 040365          150 PAC----AHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAK----CGNIRLARCIFDKMD-LHDIVSWTAVIMGNAL  220 (514)
Q Consensus       150 ~~~----~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k----~g~~~~A~~~~~~m~-~~d~~~~~~li~~~~~  220 (514)
                      ..+    ....+.+.|...+....+.|...   ....|...+..    ......|...+.... ..+..++..+...|..
T Consensus        78 ~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~---a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~L~~~~~~  154 (265)
T d1ouva_          78 NLYYSGQGVSQNTNKALQYYSKACDLKYAE---GCASLGGIYHDGKVVTRDFKKAVEYFTKACDLNDGDGCTILGSLYDA  154 (265)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTTCHH---HHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cccccccccchhhHHHHHHHhhhhhhhhhh---HHHhhcccccCCCcccchhHHHHHHhhhhhcccccchhhhhhhhhcc
Confidence            222    23456788888888887776321   12222222222    233444444444432 2344455555444443


Q ss_pred             ----CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHh----c
Q 040365          221 ----HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGR----A  292 (514)
Q Consensus       221 ----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~----~  292 (514)
                          ..+...+...++...+.|                                       +......|..+|..    .
T Consensus       155 ~~~~~~~~~~~~~~~~~a~~~g---------------------------------------~~~A~~~lg~~y~~g~~~~  195 (265)
T d1ouva_         155 GRGTPKDLKKALASYDKACDLK---------------------------------------DSPGCFNAGNMYHHGEGAT  195 (265)
T ss_dssp             TSSSCCCHHHHHHHHHHHHHTT---------------------------------------CHHHHHHHHHHHHHTCSSC
T ss_pred             CCCcccccccchhhhhcccccc---------------------------------------ccccccchhhhcccCcccc
Confidence                123333333333333322                                       22222223222322    3


Q ss_pred             CCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHHHhcCC
Q 040365          293 GKLQEAYEFISNMHAGPTENVWLTLLSACRV----HKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       293 g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~p  342 (514)
                      .++++|..+|+.....-++..+..|...|..    ..|.+.|...|+++.+.+.
T Consensus       196 ~d~~~A~~~~~~aa~~g~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~  249 (265)
T d1ouva_         196 KNFKEALARYSKACELENGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGA  249 (265)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTC
T ss_pred             cchhhhhhhHhhhhcccCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHCcC
Confidence            4556666666554333345555555555543    3366677777777666653

>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=97.71  E-value=0.00011  Score=60.90  Aligned_cols=121  Identities=12%  Similarity=0.032  Sum_probs=85.6

Q ss_pred             HHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCH
Q 040365          248 AVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENVWLTLLSACRVHKNV  327 (514)
Q Consensus       248 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~  327 (514)
                      .........|++++|.+.|.....-+.-.+-..        +...........-++.    .....+..+..++...|++
T Consensus        16 ~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~~--------~~~~~w~~~~r~~l~~----~~~~a~~~la~~~~~~g~~   83 (179)
T d2ff4a2          16 TAGVHAAAAGRFEQASRHLSAALREWRGPVLDD--------LRDFQFVEPFATALVE----DKVLAHTAKAEAEIACGRA   83 (179)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGG--------GTTSTTHHHHHHHHHH----HHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhCccccccc--------CcchHHHHHHHHHHHH----HHHHHHHHHHHHHHHCCCc
Confidence            334567788999999999988764322111000        0000011111111111    1245678899999999999


Q ss_pred             HHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHh-----CCCccCC
Q 040365          328 ELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRN-----KGMKKTP  380 (514)
Q Consensus       328 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~g~~~~~  380 (514)
                      ++|...++++++.+|.+...|..++.+|...|++++|.+.|++..+     .|+.|.+
T Consensus        84 ~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~  141 (179)
T d2ff4a2          84 SAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGP  141 (179)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCH
T ss_pred             hHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCH
Confidence            9999999999999999999999999999999999999999998853     5887654

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.70  E-value=0.00064  Score=55.47  Aligned_cols=63  Identities=11%  Similarity=0.018  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          312 NVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       312 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      .+|..+..++...|++++|+..++++++++|.+..+|..++.+|...|++++|...++...+.
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l  127 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV  127 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            456778888999999999999999999999999999999999999999999999999998764

>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=97.69  E-value=0.017  Score=52.10  Aligned_cols=136  Identities=12%  Similarity=0.021  Sum_probs=53.8

Q ss_pred             CChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHH
Q 040365           39 PDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCV  118 (514)
Q Consensus        39 p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~  118 (514)
                      ||..-...+..-|.+.|.++.|..++..+.         -|..++..|.+.+++..|.+++....  +..+|..+...+.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~---------d~~rl~~~~v~l~~~~~avd~~~k~~--~~~~~k~~~~~l~   80 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVS---------NFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACV   80 (336)
T ss_dssp             C----------------CTTTHHHHHHHTT---------CHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCC---------CHHHHHHHHHhhccHHHHHHHHHHcC--CHHHHHHHHHHHH
Confidence            333334444445555555555555554321         12344445555555555555544332  3345555555555


Q ss_pred             HCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcC
Q 040365          119 QNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCG  191 (514)
Q Consensus       119 ~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g  191 (514)
                      +.....-|     .+.......+......++..|-..|.+++...+++..... -..+..+++-|+..|++.+
T Consensus        81 ~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_          81 DGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             HTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTC
T ss_pred             hCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhC
Confidence            44433322     1111222233334444555555555555555555544322 1334445555555555543

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.44  E-value=0.00019  Score=57.17  Aligned_cols=44  Identities=23%  Similarity=0.246  Sum_probs=32.4

Q ss_pred             CHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCC
Q 040365          326 NVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  376 (514)
                      +++.|...|+++++++|++...+..|...       ..|.+++.+..+.|+
T Consensus       101 ~~~~A~~~~~kal~l~P~~~~~~~~L~~~-------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         101 NFDLATQFFQQAVDEQPDNTHYLKSLEMT-------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHHHHHHHHHHHHHCTTCHHHHHHHHHH-------HTHHHHHHHHHHSSS
T ss_pred             hHHHhhhhhhcccccCCCHHHHHHHHHHH-------HHHHHHHHHHHHHhc
Confidence            46889999999999999987666555544       456667776666654

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.36  E-value=0.0016  Score=50.19  Aligned_cols=92  Identities=10%  Similarity=0.063  Sum_probs=46.0

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC-----HhHHHHHH
Q 040365          212 TAVIMGNALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS-----FEHYAAVA  286 (514)
Q Consensus       212 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~-----~~~~~~li  286 (514)
                      ..+...|.+.|++++|+..|.+.++.+ +.+...+..+..+|.+.|++++|+..++.+.+-..-.+.     ..+|..+.
T Consensus         8 k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg   86 (128)
T d1elra_           8 KELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIG   86 (128)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHH
Confidence            344455556666666666666665542 123455555666666666666666666655432100010     12334444


Q ss_pred             HHHHhcCCHHHHHHHHHh
Q 040365          287 DLLGRAGKLQEAYEFISN  304 (514)
Q Consensus       287 ~~~~~~g~~~~A~~~~~~  304 (514)
                      ..+...+++++|.+.|+.
T Consensus        87 ~~~~~~~~~~~A~~~~~k  104 (128)
T d1elra_          87 NSYFKEEKYKDAIHFYNK  104 (128)
T ss_dssp             HHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHH
Confidence            444455555555555543

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.26  E-value=0.0011  Score=48.03  Aligned_cols=73  Identities=12%  Similarity=0.048  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC--------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHH
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNMH--------AGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVIL  351 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m~--------~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l  351 (514)
                      .+--+...+.+.|++++|...|++..        ..++ ..++..|..++.+.|++++|+..++++++++|+++.++..+
T Consensus         7 dc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~~~~a~~Nl   86 (95)
T d1tjca_           7 DSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGNL   86 (95)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcCCHHHHHHH
Confidence            34455666677777777777666541        1122 56788999999999999999999999999999998887776


Q ss_pred             HH
Q 040365          352 SN  353 (514)
Q Consensus       352 ~~  353 (514)
                      ..
T Consensus        87 ~~   88 (95)
T d1tjca_          87 KY   88 (95)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.24  E-value=0.00092  Score=53.69  Aligned_cols=63  Identities=13%  Similarity=-0.081  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-------C----CcchHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDP-------N----NMGAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p-------~----~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      ..+|+.+..++...|++++|...+++.+++.|       +    ...+|..++.+|...|++++|...|++..+
T Consensus        55 a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          55 AFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            35677788888888888888888888776532       1    123577889999999999999999998764

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.19  E-value=0.0003  Score=55.95  Aligned_cols=50  Identities=18%  Similarity=0.172  Sum_probs=42.2

Q ss_pred             CCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccC-----------hhHHHHHHHHHHhC
Q 040365          325 KNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARR-----------WKDAASLRVFMRNK  374 (514)
Q Consensus       325 ~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~-----------~~~a~~~~~~m~~~  374 (514)
                      +.+++|+..++++++++|+++.+|..++.+|...|+           +++|.+.|++..+.
T Consensus        55 ~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l  115 (145)
T d1zu2a1          55 QMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE  115 (145)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhccccc
Confidence            456889999999999999999999999999988764           57788888777653

>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=97.19  E-value=0.004  Score=51.06  Aligned_cols=56  Identities=14%  Similarity=0.259  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHhCCChHHHHHHHHHH
Q 040365          179 IASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNALHGNAHDAISLFEQM  234 (514)
Q Consensus       179 ~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~~g~~~~A~~l~~~m  234 (514)
                      .+..+...+.+.|++++|...++++.   ..+...|..++.+|...|+..+|++.|+++
T Consensus        69 a~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~  127 (179)
T d2ff4a2          69 AHTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRV  127 (179)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            44455556666666666666665553   234455666666666666666666666554

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.17  E-value=0.00012  Score=71.62  Aligned_cols=106  Identities=9%  Similarity=-0.064  Sum_probs=44.3

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHhcCCHHHHHHHHHhCC---CCChhHHHHHHHHHHh
Q 040365          144 SFSSIMPACAHLTTLHLGKQLHGCIIRNGFDDNMFIASSLLDMYAKCGNIRLARCIFDKMD---LHDIVSWTAVIMGNAL  220 (514)
Q Consensus       144 t~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~li~~y~k~g~~~~A~~~~~~m~---~~d~~~~~~li~~~~~  220 (514)
                      .+..+...+.+.++.+.|...+....+..  + ...+..|.+.+...|++++|...|++..   +.+..+|+.+...|..
T Consensus       122 ~~~~lg~~~~~~~~~~~A~~~~~~al~~~--~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~  198 (497)
T d1ya0a1         122 KSSQLGIISNKQTHTSAIVKPQSSSCSYI--C-QHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASS  198 (497)
T ss_dssp             ---------------------CCHHHHHH--H-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHhCCCHHHHHHHHHHHhCCC--H-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHHHH
Confidence            34444444555555555555544443321  1 2334445566666666666666665543   2344566666666666


Q ss_pred             CCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 040365          221 HGNAHDAISLFEQMEKDGVKPNSVAFVAVLTAC  253 (514)
Q Consensus       221 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~  253 (514)
                      .|+..+|+..|.+..... .|-..++..|...+
T Consensus       199 ~~~~~~A~~~y~ral~~~-~~~~~a~~nL~~~~  230 (497)
T d1ya0a1         199 KGDHLTTIFYYCRSIAVK-FPFPAASTNLQKAL  230 (497)
T ss_dssp             TTCHHHHHHHHHHHHSSS-BCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhCC-CCCHHHHHHHHHHH
Confidence            666666666666655532 33444455554443

>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=97.07  E-value=0.097  Score=47.01  Aligned_cols=280  Identities=10%  Similarity=0.005  Sum_probs=145.8

Q ss_pred             CCcchHHHHHHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHH
Q 040365            4 SDLVSWNTVIVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLI   83 (514)
Q Consensus         4 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (514)
                      ||..--..+..-|-+.|.++.|..+|..+..         |..++..+.+.++++.|.++....      .+..+|..+.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d---------~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~   76 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------FGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVC   76 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTC---------HHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC---------HHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHH
Confidence            4444444556667788999999999986643         777888888889988877765432      3566888888


Q ss_pred             HHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHH
Q 040365           84 NMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQ  163 (514)
Q Consensus        84 ~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~  163 (514)
                      ..+.+......|.-+ ......+......++..|-..|.+++...++...... -.++...++-++..+++.+.    .+
T Consensus        77 ~~l~~~~e~~la~i~-~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~~----~k  150 (336)
T d1b89a_          77 FACVDGKEFRLAQMC-GLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFKP----QK  150 (336)
T ss_dssp             HHHHHTTCHHHHHHT-TTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTCH----HH
T ss_pred             HHHHhCcHHHHHHHH-HHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhCh----HH
Confidence            888888777665432 2222235555567889999999999999998876543 24566677778888877542    23


Q ss_pred             HHHHHHHcCCCCcH----------HHHHHHHHHHHhcCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCChHHHHHHHHH
Q 040365          164 LHGCIIRNGFDDNM----------FIASSLLDMYAKCGNIRLARCIFDKMDLHDIVSWTAVIMGNALHGNAHDAISLFEQ  233 (514)
Q Consensus       164 ~~~~~~~~~~~~~~----------~~~~~li~~y~k~g~~~~A~~~~~~m~~~d~~~~~~li~~~~~~g~~~~A~~l~~~  233 (514)
                      +.+.+...+-..|.          ..|.-++-.|.+.|+++.|..+.-.= .+++.....++..+.+.++++...++...
T Consensus       151 l~e~l~~~s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~-~~~~~~~~~f~e~~~k~~N~e~~~~~i~~  229 (336)
T d1b89a_         151 MREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNH-PTDAWKEGQFKDIITKVANVELYYRAIQF  229 (336)
T ss_dssp             HHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHS-TTTTCCHHHHHHHHHHCSSTHHHHHHHHH
T ss_pred             HHHHHHhccccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHc-chhhhhHHHHHHHHHccCChHHHHHHHHH
Confidence            34444332111111          12233444455555555544332221 11222233344555555555544444443


Q ss_pred             HHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHH
Q 040365          234 MEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFISNMHAGPTENV  313 (514)
Q Consensus       234 m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~  313 (514)
                      ..+.  .|+.  .+.++......-+..+                       +++.+.+.+++.-...+++......+..+
T Consensus       230 yL~~--~p~~--i~~lL~~v~~~~d~~r-----------------------~V~~~~k~~~l~li~p~Le~v~~~n~~~v  282 (336)
T d1b89a_         230 YLEF--KPLL--LNDLLMVLSPRLDHTR-----------------------AVNYFSKVKQLPLVKPYLRSVQNHNNKSV  282 (336)
T ss_dssp             HHHH--CGGG--HHHHHHHHGGGCCHHH-----------------------HHHHHHHTTCTTTTHHHHHHHHTTCCHHH
T ss_pred             HHHc--CHHH--HHHHHHHhccCCCHHH-----------------------HHHHHHhcCCcHHHHHHHHHHHHcChHHH
Confidence            3332  2322  1233333333333333                       33334444444444445544333344556


Q ss_pred             HHHHHHHHHhcCCHHHHHH
Q 040365          314 WLTLLSACRVHKNVELAGK  332 (514)
Q Consensus       314 ~~~ll~~~~~~~~~~~a~~  332 (514)
                      .++|...|...+|++.-+.
T Consensus       283 n~al~~lyie~~d~~~l~~  301 (336)
T d1b89a_         283 NESLNNLFITEEDYQALRT  301 (336)
T ss_dssp             HHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHhCcchhHHHHH
Confidence            6677777777776554433

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.99  E-value=0.001  Score=58.52  Aligned_cols=123  Identities=13%  Similarity=0.064  Sum_probs=66.8

Q ss_pred             HhCCChHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCC-HhHHHHHHHHHHhcCCHH
Q 040365          219 ALHGNAHDAISLFEQMEKDGVKP-NSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPS-FEHYAAVADLLGRAGKLQ  296 (514)
Q Consensus       219 ~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~-~~~~~~li~~~~~~g~~~  296 (514)
                      .+.|++++|+..+++.++.  .| |...+..+...++..|++++|...|+...+.   .|+ ...+..+...+...+..+
T Consensus         7 L~~G~l~eAl~~l~~al~~--~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l---~P~~~~~~~~l~~ll~a~~~~~   81 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKA--SPKDASLRSSFIELLCIDGDFERADEQLMQSIKL---FPEYLPGASQLRHLVKAAQARK   81 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHT--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHhccccH
Confidence            3457777777777777664  33 4456666777777777777777777766533   453 333334444443333333


Q ss_pred             HHHHHHHhC--CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcc
Q 040365          297 EAYEFISNM--HAGPT-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMG  346 (514)
Q Consensus       297 ~A~~~~~~m--~~~p~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~  346 (514)
                      ++..-....  ...|+ ...+......+...|+.++|...++++.+..|..+.
T Consensus        82 ~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p~~~~  134 (264)
T d1zbpa1          82 DFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEKGF  134 (264)
T ss_dssp             HHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCCE
T ss_pred             HHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCc
Confidence            332221111  11122 222333344566667777777777777776666543

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.95  E-value=0.0067  Score=48.30  Aligned_cols=62  Identities=13%  Similarity=-0.062  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhCC--------CCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 040365          281 HYAAVADLLGRAGKLQEAYEFISNMH--------AGPT-----ENVWLTLLSACRVHKNVELAGKVAEKIFMIDP  342 (514)
Q Consensus       281 ~~~~li~~~~~~g~~~~A~~~~~~m~--------~~p~-----~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p  342 (514)
                      .|+.+..+|...|++++|.+.+++..        ..++     ...+..+..++...|++++|+..|++++++.|
T Consensus        57 ~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~  131 (156)
T d2hr2a1          57 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIE  131 (156)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            34445555555555555554444321        1121     22466778888899999999999998888754

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.86  E-value=0.00053  Score=60.44  Aligned_cols=119  Identities=12%  Similarity=0.099  Sum_probs=83.5

Q ss_pred             HccCCHHHHHHHHHHhHHhcCCCC-CHhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHH
Q 040365          254 SHAGLIDKAWSYFNSMTKDYGIAP-SFEHYAAVADLLGRAGKLQEAYEFISNMH-AGPT-ENVWLTLLSACRVHKNVELA  330 (514)
Q Consensus       254 ~~~g~~~~a~~~~~~m~~~~~~~p-~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~-~~~~~~ll~~~~~~~~~~~a  330 (514)
                      .+.|++++|+..++..++.   .| +...+..+...|+..|++++|.+.++... ..|+ ...+..+...+...+..+++
T Consensus         7 L~~G~l~eAl~~l~~al~~---~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~~~~~a   83 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKA---SPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHT---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHHH
Confidence            4679999999999998764   66 78999999999999999999999998863 3454 45555555554443333332


Q ss_pred             HHHHHHHHhc-CCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCC
Q 040365          331 GKVAEKIFMI-DPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKG  375 (514)
Q Consensus       331 ~~~~~~~~~~-~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  375 (514)
                      .......... +|++...+...+..+...|++++|.+.+++..+..
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~  129 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELR  129 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC
Confidence            2211111111 24444555667788899999999999999987643

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.49  E-value=0.0099  Score=42.69  Aligned_cols=64  Identities=9%  Similarity=-0.092  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-------cchHHHHHHHHHHccChhHHHHHHHHHHhC
Q 040365          311 ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNN-------MGAYVILSNTYAAARRWKDAASLRVFMRNK  374 (514)
Q Consensus       311 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~-------~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  374 (514)
                      ...+-.+...+.+.|+++.|...+++++++.|.+       +.++..|+.+|.+.|++++|...+++..+.
T Consensus         5 addc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l   75 (95)
T d1tjca_           5 AEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (95)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh
Confidence            3345567888999999999999999998875432       457889999999999999999999998764

>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=95.59  E-value=0.27  Score=36.21  Aligned_cols=141  Identities=11%  Similarity=0.105  Sum_probs=97.2

Q ss_pred             HHhCCChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHH
Q 040365          218 NALHGNAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQE  297 (514)
Q Consensus       218 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~  297 (514)
                      +...|..++..++..+....   .+..-|+.++--....-+-+...+.++.+-+-+.+.|              ++++..
T Consensus        12 ~ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~--------------C~Nlk~   74 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDK--------------CQNLKS   74 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGG--------------CSCTHH
T ss_pred             HHHhhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhhcCchh--------------hhcHHH
Confidence            34567777778877777653   2445566666555555666666666666644333333              344444


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHHHhCCCc
Q 040365          298 AYEFISNMHAGPTENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFMRNKGMK  377 (514)
Q Consensus       298 A~~~~~~m~~~p~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  377 (514)
                      ...-+-.+.  .+....+..++...+.|+-+.-..+++.+++.+..++....-++++|-+.|...++..++.+.-++|++
T Consensus        75 vv~C~~~~n--~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          75 VVECGVINN--TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHTT--CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHhc--chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            443333332  234445666788888999999999999988877777889999999999999999999999999999975

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=94.26  E-value=2.1  Score=39.66  Aligned_cols=117  Identities=9%  Similarity=0.061  Sum_probs=69.0

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCC--ChHHHHHHHHHHHHhCC-CCchhHHHHHHHHHHHC
Q 040365           13 IVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYV--DVIKGKEIHGYAIRHGL-DANVCIGSSLINMYAKC   89 (514)
Q Consensus        13 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~--~~~~a~~~~~~~~~~g~-~~~~~~~~~li~~~~~~   89 (514)
                      +.-..+.|+..++..+...+...   | -..|...-..-...+  ...   ++...+.+..- +.........+..+++.
T Consensus        13 a~~a~~~~~~~~~~~~~~~L~dy---p-L~pYl~~~~l~~~~~~~~~~---~i~~Fl~~~p~~P~~~~lr~~~l~~L~~~   85 (450)
T d1qsaa1          13 IKQAWDNRQMDVVEQMMPGLKDY---P-LYPYLEYRQITDDLMNQPAV---TVTNFVRANPTLPPARTLQSRFVNELARR   85 (450)
T ss_dssp             HHHHHHTTCHHHHHHHSGGGTTS---T-THHHHHHHHHHHTGGGCCHH---HHHHHHHHCTTCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCHHHHHHHHhhhcCC---C-CHHHHHHHHHHhccccCCHH---HHHHHHHHCCCChhHHHHHHHHHHHHHhc
Confidence            34456778888888887776432   3 333443332222222  333   33333434311 11122234456778889


Q ss_pred             CCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCC
Q 040365           90 ARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAK  137 (514)
Q Consensus        90 g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  137 (514)
                      +++......+..-+ .+...-.....+..+.|+..+|...+..+-..|
T Consensus        86 ~~w~~~~~~~~~~p-~~~~~~c~~~~A~~~~g~~~~a~~~~~~lW~~~  132 (450)
T d1qsaa1          86 EDWRGLLAFSPEKP-GTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG  132 (450)
T ss_dssp             TCHHHHHHHCCSCC-SSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS
T ss_pred             cCHHHHHHhccCCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcC
Confidence            99998888776433 345545567788888999999988888776554

>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=93.37  E-value=0.89  Score=34.01  Aligned_cols=46  Identities=4%  Similarity=-0.066  Sum_probs=24.7

Q ss_pred             ChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHHcC
Q 040365          122 LFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCIIRNG  172 (514)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~~  172 (514)
                      ++++|+++|++..+.|..   .....+.  .....+.++|.+.+....+.|
T Consensus         8 d~~~A~~~~~kaa~~g~~---~a~~~l~--~~~~~~~~~a~~~~~~aa~~g   53 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEM---FGCLSLV--SNSQINKQKLFQYLSKACELN   53 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCT---THHHHHH--TCTTSCHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHCCCh---hhhhhhc--cccccCHHHHHHHHhhhhccc
Confidence            566777777777666522   1121221  223345666666666666655

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=93.23  E-value=1.1  Score=32.96  Aligned_cols=83  Identities=13%  Similarity=0.003  Sum_probs=56.2

Q ss_pred             CCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 040365           89 CARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAHLTTLHLGKQLHGCI  168 (514)
Q Consensus        89 ~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~  168 (514)
                      |+++......|-.+. .+....+..++...++|.-+.-.++++.+.+.+ +|++.....+..||.+.|+..++.+++.+.
T Consensus        69 C~Nlk~vv~C~~~~n-~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~A  146 (161)
T d1wy6a1          69 CQNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEA  146 (161)
T ss_dssp             CSCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             hhcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            444444444333332 233445666777888888888888888866643 677777778888888888888888888888


Q ss_pred             HHcCC
Q 040365          169 IRNGF  173 (514)
Q Consensus       169 ~~~~~  173 (514)
                      -+.|+
T Consensus       147 Ce~G~  151 (161)
T d1wy6a1         147 CKKGE  151 (161)
T ss_dssp             HHTTC
T ss_pred             HHHhH
Confidence            77774

>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=92.71  E-value=1.1  Score=33.53  Aligned_cols=49  Identities=16%  Similarity=0.082  Sum_probs=26.9

Q ss_pred             CHHHHHHHHHHHHhcCCCCcchHHHHHHHHHH----ccChhHHHHHHHHHHhCCC
Q 040365          326 NVELAGKVAEKIFMIDPNNMGAYVILSNTYAA----ARRWKDAASLRVFMRNKGM  376 (514)
Q Consensus       326 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~g~  376 (514)
                      |.+.|.+.|++..+.+  ++.....|..+|..    ..+.++|.+.+++..+.|.
T Consensus        74 d~~~A~~~~~~aa~~g--~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_          74 DLRKAAQYYSKACGLN--DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             CHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             hhHHHHHHHhhhhccC--cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCC
Confidence            4555666666655543  23445555555554    2456666666666655554

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.65  E-value=0.38  Score=35.62  Aligned_cols=47  Identities=11%  Similarity=0.002  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHhcCCCCc-chHHHHHHHHHHccChhHHHHHHHHHHh
Q 040365          327 VELAGKVAEKIFMIDPNNM-GAYVILSNTYAAARRWKDAASLRVFMRN  373 (514)
Q Consensus       327 ~~~a~~~~~~~~~~~p~~~-~~~~~l~~~~~~~g~~~~a~~~~~~m~~  373 (514)
                      .++|+.+++.+...+|.+. ..+..|+.+|.+.|++++|.+.++.+.+
T Consensus        54 ~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~  101 (124)
T d2pqrb1          54 ERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  101 (124)
T ss_dssp             HHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            3455555555555444432 2444555555555555555555555543

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=89.52  E-value=7.7  Score=35.53  Aligned_cols=332  Identities=9%  Similarity=-0.065  Sum_probs=169.9

Q ss_pred             HHHHHhcCChhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCC-----------------CCc
Q 040365           13 IVGLARNGLYEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGL-----------------DAN   75 (514)
Q Consensus        13 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~-----------------~~~   75 (514)
                      +..+.+.++++..+..+.     ..+++...-...+.+....|+...|......+-..|.                 ..+
T Consensus        79 l~~L~~~~~w~~~~~~~~-----~~p~~~~~~c~~~~A~~~~g~~~~a~~~~~~lW~~~~~~p~~c~~l~~~~~~~~~lt  153 (450)
T d1qsaa1          79 VNELARREDWRGLLAFSP-----EKPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPNACDKLFSVWRASGKQD  153 (450)
T ss_dssp             HHHHHHTTCHHHHHHHCC-----SCCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCSSCCCTHHHHHHHHHHHTTCSC
T ss_pred             HHHHHhccCHHHHHHhcc-----CCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCCchHHHHHHHHHHhcCCCC
Confidence            445666777665444331     1223333333455566666776666665555544331                 122


Q ss_pred             hhHHHHHHHHHHHCCCHHHHHHHHccCCCCChhHHHHHHHHHHHCCChhHHHHHHHHHHHCCCCCCHHHHHHHHHHHhc-
Q 040365           76 VCIGSSLINMYAKCARVEDSHRLFCLLPVKDAISWNSIIAGCVQNGLFDEGLKFFRQMLIAKIKPRHVSFSSIMPACAH-  154 (514)
Q Consensus        76 ~~~~~~li~~~~~~g~~~~A~~~f~~~~~~d~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~-  154 (514)
                      ...+-.-+......|+...|..+...++..........+....   ++..+......     ..++......+..+..+ 
T Consensus       154 ~~~~~~R~~~~l~~~~~~~a~~l~~~l~~~~~~~~~a~~~l~~---~p~~~~~~~~~-----~~~~~~~~~~~~~~l~rl  225 (450)
T d1qsaa1         154 PLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLAN---NPNTVLTFART-----TGATDFTRQMAAVAFASV  225 (450)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHTCCGGGHHHHHHHHHHHH---CGGGHHHHHHH-----SCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChhhHHHHHhhCChhHHHHHHHHHHHHh---ChHhHHHHHhc-----CCCChhhhHHHHHHHHHH
Confidence            2222233444455667777777777666444444444444432   23333332221     12333333333333333 


Q ss_pred             -cCChHHHHHHHHHHHHcCCCCcHHH---HHHHHHHHHhcCCHHHHHHHHHhCC--CCChhHHHHHHHHHHhCCChHHHH
Q 040365          155 -LTTLHLGKQLHGCIIRNGFDDNMFI---ASSLLDMYAKCGNIRLARCIFDKMD--LHDIVSWTAVIMGNALHGNAHDAI  228 (514)
Q Consensus       155 -~~~~~~a~~~~~~~~~~~~~~~~~~---~~~li~~y~k~g~~~~A~~~~~~m~--~~d~~~~~~li~~~~~~g~~~~A~  228 (514)
                       ..+.+.+..++..............   ...+...+...+..+.|...+....  ..+.....-.+......+++..+.
T Consensus       226 a~~d~~~a~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~w~~~~al~~~~~~~~~  305 (450)
T d1qsaa1         226 ARQDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSLIERRVRMALGTGDRRGLN  305 (450)
T ss_dssp             HHHCHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             hccChhHHHHHHHhhhhcccccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccccchHHHHHHHHHHHHcCChHHHH
Confidence             2466777777776655432222111   1222233334566666766665543  223333233444455667888888


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHHHHHhcCCHHHHHHHH-HhCCC
Q 040365          229 SLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVADLLGRAGKLQEAYEFI-SNMHA  307 (514)
Q Consensus       229 ~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~~~~~~g~~~~A~~~~-~~m~~  307 (514)
                      ..|..|... ..-...-.--+..+....|+.++|..+|.....    .++  -|.-|...  +.|..-   .+- ...+.
T Consensus       306 ~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~----~~~--fYG~LAa~--~Lg~~~---~~~~~~~~~  373 (450)
T d1qsaa1         306 TWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLMQ----QRG--FYPMVAAQ--RIGEEY---ELKIDKAPQ  373 (450)
T ss_dssp             HHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT----SCS--HHHHHHHH--HTTCCC---CCCCCCCCS
T ss_pred             HHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc----CCC--hHHHHHHH--HcCCCC---CCCcCCCCc
Confidence            888776432 111233344566778888888888888887742    233  33333211  222110   000 00011


Q ss_pred             CCCH-HH---HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHccChhHHHHHHHHH
Q 040365          308 GPTE-NV---WLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGAYVILSNTYAAARRWKDAASLRVFM  371 (514)
Q Consensus       308 ~p~~-~~---~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  371 (514)
                      .++. ..   -..-+..+...|....|...+..+....  ++.-...++....+.|.++.|.......
T Consensus       374 ~~~~~~~~~~~~~ra~~L~~~g~~~~A~~e~~~l~~~~--~~~~~~~la~lA~~~g~~~~aI~a~~~~  439 (450)
T d1qsaa1         374 NVDSALTQGPEMARVRELMYWNLDNTARSEWANLVKSK--SKTEQAQLARYAFNNQWWDLSVQATIAG  439 (450)
T ss_dssp             CCCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHHHTTC--CHHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             cHHHhhhcChHHHHHHHHHHcCCchHHHHHHHHHHhCC--CHHHHHHHHHHHHHCCChhHHHHHHHHH
Confidence            1111 11   1122455678899999999888876543  3456677888888999999888776655

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=87.28  E-value=1.4  Score=30.58  Aligned_cols=63  Identities=17%  Similarity=0.193  Sum_probs=50.2

Q ss_pred             ChHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhHHhcCCCCCHhHHHHHHH
Q 040365          223 NAHDAISLFEQMEKDGVKPNSVAFVAVLTACSHAGLIDKAWSYFNSMTKDYGIAPSFEHYAAVAD  287 (514)
Q Consensus       223 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~p~~~~~~~li~  287 (514)
                      +.-++.+-+..+....+-|+.....+.+.||.+.+++..|.++|+....+.  .++...|..+++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~--~~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA--GPHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh--cCcHHHHHHHHH
Confidence            455777777777778889999999999999999999999999999886543  344567766654

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.13  E-value=5.4  Score=29.08  Aligned_cols=70  Identities=11%  Similarity=0.119  Sum_probs=45.1

Q ss_pred             CHhHHHHHHHHHHhcC---CHHHHHHHHHhCC-CCC-C-HHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCcch
Q 040365          278 SFEHYAAVADLLGRAG---KLQEAYEFISNMH-AGP-T-ENVWLTLLSACRVHKNVELAGKVAEKIFMIDPNNMGA  347 (514)
Q Consensus       278 ~~~~~~~li~~~~~~g---~~~~A~~~~~~m~-~~p-~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~p~~~~~  347 (514)
                      ++.+--...-++.++.   ++++++.++++.- ..| + ...|..|.-+|.+.|+++.|.+.++++++.+|++..+
T Consensus        34 s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~n~qA  109 (124)
T d2pqrb1          34 TIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQV  109 (124)
T ss_dssp             CHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             CcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCCcHHH
Confidence            3333333344444433   3445666665542 123 3 2567778888999999999999999999999988643

>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=81.71  E-value=6.3  Score=27.23  Aligned_cols=62  Identities=13%  Similarity=0.051  Sum_probs=43.7

Q ss_pred             hhHHHHHHHHHhhCCCCCChhhHHHHHHHHhCCCChHHHHHHHHHHHHhCCCCchhHHHHHHH
Q 040365           22 YEEALNIVRQMGNVNLKPDSFTLSSVLPIFADYVDVIKGKEIHGYAIRHGLDANVCIGSSLIN   84 (514)
Q Consensus        22 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~~~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (514)
                      .-++.+-++.+....+.|++....+.++||.+.+++..|.++++-+.... .++...|..++.
T Consensus        22 ~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yilq   83 (105)
T d1v54e_          22 AWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   83 (105)
T ss_dssp             HHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHHH
Confidence            33555566666667788888888888888888888888888888776543 334556665543