Citrus Sinensis ID: 011236

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490
Protein Sequence
MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK
Secondary Structure (PSIPRED)
ccHHHHHHHHHcccccHHHHHHHHHHHHcccccccHHHHHHHHccccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcHHcccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHccccccHHHHHHHHHHccccccccHHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHcccccEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccEHHHHHHHHHHHHcccHHHHHHHHHHHHHHccHHccccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHHccHHHHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
MASKLFSTIFNnkrnftktNLEIFTRAYRAVKPvarnnlysrisplgdpdvsltpvlDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSewmsgqglafsvHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGsfgsalnyNGIMCLytntgqhekipdvlldmkengvppdnfsyRICINSYGARSELSSMENVLQEMEsqshismdwgtySTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELScycydfrvpniillgysqkgMIEKADAVLKEIVKkgktptpnswSIIAAGYADKNNMEKAFECMKEALAVHeenkfwrpkpslVSSILdwlgdnrdvEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQEVDGLLesmkaddidedk
Flexible Loop (DISEMBL)
masklfstifnnkrnftktnleIFTRAYRAVKPVARNNLYSrisplgdpdvSLTPVLDQWVLegqkiseleLQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVkkgktptpnswsIIAAGYADKNNMEKAFECMKEALAVHeenkfwrpkpsLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEahirsgqevdgllesmkaddidedk
Low Complexity Region (SEG)
MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGeleeaekmleewelSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK
Disordered region (IsUnstruct)
*****FSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGA******************HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHI**********************
Disordered Region (DISOPRED)
MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDIDED*
Disordered Region (DISEMBL)
MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK
Disordered Region (DISPRO)
MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADD*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADxxxxxxxxxxxxxxxxxxxxxKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	490	2.2.26 [Sep-21-2011]
Q84JR3	492	Pentatricopeptide repeat-	yes	no	0.940	0.936	0.513	1e-133
Q9SKU6	490	Pentatricopeptide repeat-	no	no	0.820	0.820	0.371	2e-75
O22714	491	Pentatricopeptide repeat-	no	no	0.934	0.932	0.298	5e-70
Q8LPS6	524	Pentatricopeptide repeat-	no	no	0.853	0.797	0.347	8e-70
Q3E911	491	Pentatricopeptide repeat-	no	no	0.920	0.918	0.339	1e-67
Q9SY07	532	Pentatricopeptide repeat-	no	no	0.916	0.843	0.315	2e-60
Q93WC5	502	Pentatricopeptide repeat-	no	no	0.928	0.906	0.307	3e-58
Q9FZ24	537	Pentatricopeptide repeat-	no	no	0.873	0.797	0.312	8e-56
Q9C7F1	566	Putative pentatricopeptid	no	no	0.893	0.773	0.284	2e-48
Q94B59	409	Pentatricopeptide repeat-	no	no	0.644	0.772	0.310	1e-38

>sp|Q84JR3|PP334_ARATH Pentatricopeptide repeat-containing protein At4g21705, mitochondrial OS=Arabidopsis thaliana GN=At4g21705 PE=2 SV=1

 Score =  476 bits (1225), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 240/467 (51%), Positives = 326/467 (69%), Gaps = 6/467 (1%)

Query: 28  YRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKH 87
           Y     V +  LYS+ISPLGDP  S+ P L  WV  G+K+S  EL R++  LR RKRF H
Sbjct: 16  YYYTNRVKKTTLYSKISPLGDPKSSVYPELQNWVQCGKKVSVAELIRIVHDLRRRKRFLH 75

Query: 88  ALQVSEWMSGQGLA-FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNC 146
           AL+VS+WM+  G+  FS  +HAV LDLIG+V G  +AE YF +L ++ K DK YGALLNC
Sbjct: 76  ALEVSKWMNETGVCVFSPTEHAVHLDLIGRVYGFVTAEEYFENLKEQYKNDKTYGALLNC 135

Query: 147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPD 206
           YVR+  V++SL   +KMKEMG   S+L YN IMCLYTN GQHEK+P VL +MKE  V PD
Sbjct: 136 YVRQQNVEKSLLHFEKMKEMGFVTSSLTYNNIMCLYTNIGQHEKVPKVLEEMKEENVAPD 195

Query: 207 NFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYL 266
           N+SYRICIN++GA  +L  +   L++ME +  I+MDW TY+  A +YI  G  ++A+  L
Sbjct: 196 NYSYRICINAFGAMYDLERIGGTLRDMERRQDITMDWNTYAVAAKFYIDGGDCDRAVELL 255

Query: 267 KKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVK 326
           K  E+ + K KD  GYNHLI+ YA LG K E+++ W L+K  CK+++N+DY+T+L SLVK
Sbjct: 256 KMSENRLEK-KDGEGYNHLITLYARLGKKIEVLRLWDLEKDVCKRRINQDYLTVLQSLVK 314

Query: 327 IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNS 386
           I  L EAE++L EW+ S  CYDFRVPN ++ GY  K M EKA+A+L+++ ++GK  TP S
Sbjct: 315 IDALVEAEEVLTEWKSSGNCYDFRVPNTVIRGYIGKSMEEKAEAMLEDLARRGKATTPES 374

Query: 387 WSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAF 446
           W ++A  YA+K  +E AF+CMK AL V   ++ WRP  +LV+S+L W+GD   ++EVE+F
Sbjct: 375 WELVATAYAEKGTLENAFKCMKTALGVEVGSRKWRPGLTLVTSVLSWVGDEGSLKEVESF 434

Query: 447 VSSLK--IKVQKRNMYHALTEAHIR-SGQEVDGLLESMKADDIDEDK 490
           V+SL+  I V K+ MYHAL +A IR  G+ +D LL+ MK D I+ D+
Sbjct: 435 VASLRNCIGVNKQ-MYHALVKADIREGGRNIDTLLQRMKDDKIEIDE 480

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SKU6|PP166_ARATH Pentatricopeptide repeat-containing protein At2g20710, mitochondrial OS=Arabidopsis thaliana GN=At2g20710 PE=2 SV=1

 Score =  283 bits (723), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 151/406 (37%), Positives = 239/406 (58%), Gaps = 4/406 (0%)

Query: 37  NNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMS 96
           + L  R++  GDP  S+  VLD W+ +G  +   EL  +I+ LR   RF HALQ+S+WMS
Sbjct: 38  DTLQRRVARSGDPSASIIKVLDGWLDQGNLVKTSELHSIIKMLRKFSRFSHALQISDWMS 97

Query: 97  GQGL-AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDE 155
              +   S  D A++LDLI KV GL  AE +F ++  E +   LYGALLNCY  + ++ +
Sbjct: 98  EHRVHEISEGDVAIRLDLIAKVGGLGEAEKFFETIPMERRNYHLYGALLNCYASKKVLHK 157

Query: 156 SLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICIN 215
           +  + Q+MKE+G     L YN ++ LY  TG++  +  +L +M++  V PD F+    ++
Sbjct: 158 AEQVFQEMKELGFLKGCLPYNVMLNLYVRTGKYTMVEKLLREMEDETVKPDIFTVNTRLH 217

Query: 216 SYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK 275
           +Y   S++  ME  L   E+   + +DW TY+  AN YI AGL EKA+  L+K E +V+ 
Sbjct: 218 AYSVVSDVEGMEKFLMRCEADQGLHLDWRTYADTANGYIKAGLTEKALEMLRKSEQMVNA 277

Query: 276 SKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEK 335
            K    Y  L+S Y + G K+E+ + W L K +     N  YI+++ +L+K+ ++EE EK
Sbjct: 278 QKRKHAYEVLMSFYGAAGKKEEVYRLWSLYK-ELDGFYNTGYISVISALLKMDDIEEVEK 336

Query: 336 MLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA 395
           ++EEWE     +D R+P++++ GY +KGM+EKA+ V+  +V+K +    ++W  +A GY 
Sbjct: 337 IMEEWEAGHSLFDIRIPHLLITGYCKKGMMEKAEEVVNILVQKWRVEDTSTWERLALGYK 396

Query: 396 DKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVE 441
               MEKA E  K A+ V +    WRP   ++ S +D+L   RD+E
Sbjct: 397 MAGKMEKAVEKWKRAIEVSKPG--WRPHQVVLMSCVDYLEGQRDME 440

Arabidopsis thaliana (taxid: 3702)

>sp|O22714|PPR86_ARATH Pentatricopeptide repeat-containing protein At1g60770 OS=Arabidopsis thaliana GN=At1g60770 PE=2 SV=1

 Score =  265 bits (677), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 138/462 (29%), Positives = 258/462 (55%), Gaps = 4/462 (0%)

Query: 29  RAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHA 88
           R+ K      LY+R+   G  +V +   L+Q++   + + + E+   I++LR+R  +  A
Sbjct: 15  RSTKKYIEEPLYNRLFKDGGTEVKVRQQLNQFLKGTKHVFKWEVGDTIKKLRNRGLYYPA 74

Query: 89  LQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYV 148
           L++SE M  +G+  +V D A+ LDL+ K R + + E YF  L +  K +  YG+LLNCY 
Sbjct: 75  LKLSEVMEERGMNKTVSDQAIHLDLVAKAREITAGENYFVDLPETSKTELTYGSLLNCYC 134

Query: 149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNF 208
           +E L +++  L+ KMKE+    S+++YN +M LYT TG+ EK+P ++ ++K   V PD++
Sbjct: 135 KELLTEKAEGLLNKMKELNITPSSMSYNSLMTLYTKTGETEKVPAMIQELKAENVMPDSY 194

Query: 209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK 268
           +Y + + +  A +++S +E V++EM     ++ DW TYS +A+ Y+ AGL +KA   L++
Sbjct: 195 TYNVWMRALAATNDISGVERVIEEMNRDGRVAPDWTTYSNMASIYVDAGLSQKAEKALQE 254

Query: 269 CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG 328
            E + +  +D   Y  LI+ Y  LG   E+ + W   ++   K  N  Y+ M+  LVK+ 
Sbjct: 255 LE-MKNTQRDFTAYQFLITLYGRLGKLTEVYRIWRSLRLAIPKTSNVAYLNMIQVLVKLN 313

Query: 329 ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS 388
           +L  AE + +EW+ +C  YD R+ N+++  Y+Q+G+I+KA+ + ++  ++G      +W 
Sbjct: 314 DLPGAETLFKEWQANCSTYDIRIVNVLIGAYAQEGLIQKANELKEKAPRRGGKLNAKTWE 373

Query: 389 IIAAGYADKNNMEKAFECMKEALAVHE-ENKFWRPKPSLVSSILDWLGDNRDVEEVEAFV 447
           I    Y    +M +A ECM +A+++ + +   W P P  V +++ +    +DV   E  +
Sbjct: 374 IFMDYYVKSGDMARALECMSKAVSIGKGDGGKWLPSPETVRALMSYFEQKKDVNGAENLL 433

Query: 448 SSLKIKVQK--RNMYHALTEAHIRSGQEVDGLLESMKADDID 487
             LK         ++  L   +  +G+    +   +K ++++
Sbjct: 434 EILKNGTDNIGAEIFEPLIRTYAAAGKSHPAMRRRLKMENVE 475

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LPS6|PPR3_ARATH Pentatricopeptide repeat-containing protein At1g02150 OS=Arabidopsis thaliana GN=At1g02150 PE=2 SV=2

 Score =  265 bits (676), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 147/423 (34%), Positives = 247/423 (58%), Gaps = 5/423 (1%)

Query: 32  KPVAR-NNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQ 90
           +P+ + N +Y +IS +  P++    VL+QW   G+K+++ EL RV+++LR  KR   AL+
Sbjct: 61  RPIVQWNAIYKKISLMEKPELGAASVLNQWEKAGRKLTKWELCRVVKELRKYKRANQALE 120

Query: 91  VSEWMSGQGLAF--SVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYV 148
           V +WM+ +G  F  S  D A+QLDLIGKVRG+  AE +F  L +  K  ++YG+LLN YV
Sbjct: 121 VYDWMNNRGERFRLSASDAAIQLDLIGKVRGIPDAEEFFLQLPENFKDRRVYGSLLNAYV 180

Query: 149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNF 208
           R    +++ +L+  M++ G     L +N +M LY N  +++K+  ++ +MK+  +  D +
Sbjct: 181 RAKSREKAEALLNTMRDKGYALHPLPFNVMMTLYMNLREYDKVDAMVFEMKQKDIRLDIY 240

Query: 209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK 268
           SY I ++S G+   +  ME V Q+M+S   I  +W T+ST+A  YI  G  EKA   L+K
Sbjct: 241 SYNIWLSSCGSLGSVEKMELVYQQMKSDVSIYPNWTTFSTMATMYIKMGETEKAEDALRK 300

Query: 269 CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG 328
            E  ++  ++ + Y++L+S Y SLGNK E+ + W + K       N  Y  ++ SLV++G
Sbjct: 301 VEARIT-GRNRIPYHYLLSLYGSLGNKKELYRVWHVYKSVVPSIPNLGYHALVSSLVRMG 359

Query: 329 ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS 388
           ++E AEK+ EEW      YD R+PN+++  Y +   +E A+ +   +V+ G  P+ ++W 
Sbjct: 360 DIEGAEKVYEEWLPVKSSYDPRIPNLLMNAYVKNDQLETAEGLFDHMVEMGGKPSSSTWE 419

Query: 389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVS 448
           I+A G+  K  + +A  C++ A +  E +  WRPK  ++S       +  DV   EA + 
Sbjct: 420 ILAVGHTRKRCISEALTCLRNAFSA-EGSSNWRPKVLMLSGFFKLCEEESDVTSKEAVLE 478

Query: 449 SLK 451
            L+
Sbjct: 479 LLR 481

Arabidopsis thaliana (taxid: 3702)

>sp|Q3E911|PP400_ARATH Pentatricopeptide repeat-containing protein At5g27460 OS=Arabidopsis thaliana GN=At5g27460 PE=2 SV=1

 Score =  257 bits (657), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 156/459 (33%), Positives = 253/459 (55%), Gaps = 8/459 (1%)

Query: 34  VARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSE 93
           VA  N    I     P  S+T +L + +  G  +S  EL+ + ++L    R+  ALQ+ E
Sbjct: 35  VANRNSLKEILRKNGPRRSVTSLLQERIDSGHAVSLSELRLISKRLIRSNRYDLALQMME 94

Query: 94  WMSGQ-GLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED---KVDK-LYGALLNCYV 148
           WM  Q  + FSV+D A++LDLI K  GL+  E YF  L       +V K  Y  LL  YV
Sbjct: 95  WMENQKDIEFSVYDIALRLDLIIKTHGLKQGEEYFEKLLHSSVSMRVAKSAYLPLLRAYV 154

Query: 149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNF 208
           +  +V E+ +LM+K+  +G   +   +N +M LY  +GQ+EK+  V+  MK N +P +  
Sbjct: 155 KNKMVKEAEALMEKLNGLGFLVTPHPFNEMMKLYEASGQYEKVVMVVSMMKGNKIPRNVL 214

Query: 209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK 268
           SY + +N+    S ++++E V +EM     + + W +  T+AN YI +G  EKA + L+ 
Sbjct: 215 SYNLWMNACCEVSGVAAVETVYKEMVGDKSVEVGWSSLCTLANVYIKSGFDEKARLVLED 274

Query: 269 CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG 328
            E ++++S + LGY  LI+ YASLGNK+ +++ W + K  C +    +YI +L SLVK G
Sbjct: 275 AEKMLNRS-NRLGYFFLITLYASLGNKEGVVRLWEVSKSVCGRISCVNYICVLSSLVKTG 333

Query: 329 ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS 388
           +LEEAE++  EWE  C+ YD RV N++L  Y + G I KA+++   ++++G TP   +W 
Sbjct: 334 DLEEAERVFSEWEAQCFNYDVRVSNVLLGAYVRNGEIRKAESLHGCVLERGGTPNYKTWE 393

Query: 389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVS 448
           I+  G+    NMEKA + M +   +      WRP  ++V +I ++      +EE  A+V 
Sbjct: 394 ILMEGWVKCENMEKAIDAMHQVFVLMRRCH-WRPSHNIVMAIAEYFEKEEKIEEATAYVR 452

Query: 449 SL-KIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDI 486
            L ++ +    +Y  L   H  + +    + E MK D +
Sbjct: 453 DLHRLGLASLPLYRLLLRMHEHAKRPAYDIYEMMKLDKL 491

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SY07|PP302_ARATH Pentatricopeptide repeat-containing protein At4g02820, mitochondrial OS=Arabidopsis thaliana GN=At4g02820 PE=2 SV=1

 Score =  233 bits (594), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 144/457 (31%), Positives = 248/457 (54%), Gaps = 8/457 (1%)

Query: 35  ARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEW 94
            R+ L  R+  L     S    + +W  EG  + + EL R++R+LR  KR+KHAL++ EW
Sbjct: 59  GRDTLGGRLLSLVYTKRSAVVTIRKWKEEGHSVRKYELNRIVRELRKIKRYKHALEICEW 118

Query: 95  MSGQ-GLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLV 153
           M  Q  +     D+AV LDLI K+RGL SAE +F  + D+ +      +LL+ YV+  L 
Sbjct: 119 MVVQEDIKLQAGDYAVHLDLISKIRGLNSAEKFFEDMPDQMRGHAACTSLLHSYVQNKLS 178

Query: 154 DESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRIC 213
           D++ +L +KM E G   S L YN ++ +Y + GQ EK+P ++ ++K     PD  +Y + 
Sbjct: 179 DKAEALFEKMGECGFLKSCLPYNHMLSMYISRGQFEKVPVLIKELKIR-TSPDIVTYNLW 237

Query: 214 INSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIV 273
           + ++ + +++   E V  + + +  ++ DW TYS + N Y      EKA + LK+ E +V
Sbjct: 238 LTAFASGNDVEGAEKVYLKAKEEK-LNPDWVTYSVLTNLYAKTDNVEKARLALKEMEKLV 296

Query: 274 SKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEA 333
           SK K+ + Y  LIS +A+LG+KD +   W   K   KK  + +Y++M+ ++VK+GE E+A
Sbjct: 297 SK-KNRVAYASLISLHANLGDKDGVNLTWKKVKSSFKKMNDAEYLSMISAVVKLGEFEQA 355

Query: 334 EKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG 393
           + + +EWE      D R+PN+IL  Y  +  +   +   + IV+KG  P+ ++W I+   
Sbjct: 356 KGLYDEWESVSGTGDARIPNLILAEYMNRDEVLLGEKFYERIVEKGINPSYSTWEILTWA 415

Query: 394 YADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSL-KI 452
           Y  + +MEK  +C  +A+   +  K W     LV      L +  +V+  E  ++ L K 
Sbjct: 416 YLKRKDMEKVLDCFGKAI---DSVKKWTVNVRLVKGACKELEEQGNVKGAEKLMTLLQKA 472

Query: 453 KVQKRNMYHALTEAHIRSGQEVDGLLESMKADDIDED 489
                 +Y++L   + ++G+    + E M  D+++ D
Sbjct: 473 GYVNTQLYNSLLRTYAKAGEMALIVEERMAKDNVELD 509

Arabidopsis thaliana (taxid: 3702)

>sp|Q93WC5|PP300_ARATH Pentatricopeptide repeat-containing protein At4g01990, mitochondrial OS=Arabidopsis thaliana GN=At4g01990 PE=2 SV=1

 Score =  226 bits (576), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 144/468 (30%), Positives = 249/468 (53%), Gaps = 13/468 (2%)

Query: 14  RNFTKT----NLEIFTRAYRAVKPVARNN--LYSRISPLGDPDVS-LTPVLDQWVLEGQK 66
           R F  T      EI   A  +V   A+ +  +Y ++S LG      +   L+Q+V+EG  
Sbjct: 10  RRFCATLATATAEISGEAAASVPTKAKKHRSIYKKLSSLGTRGGGKMEETLNQFVMEGVP 69

Query: 67  ISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETY 126
           + + +L R  + LR  ++ + AL++ EWM  + +AF+  DHA++L+LI K +GLE+AETY
Sbjct: 70  VKKHDLIRYAKDLRKFRQPQRALEIFEWMERKEIAFTGSDHAIRLNLIAKSKGLEAAETY 129

Query: 127 FNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTG 186
           FNSL+D  K    YG+LLNCY  E    ++ +  + M ++    ++L +N +M +Y   G
Sbjct: 130 FNSLDDSIKNQSTYGSLLNCYCVEKEEVKAKAHFENMVDLNHVSNSLPFNNLMAMYMGLG 189

Query: 187 QHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTY 246
           Q EK+P +++ MKE  + P + +Y + I S G+  +L  +E VL EM+++      W T+
Sbjct: 190 QPEKVPALVVAMKEKSITPCDITYSMWIQSCGSLKDLDGVEKVLDEMKAEGEGIFSWNTF 249

Query: 247 STVANYYIIAGLKEKAIIYLKKCEDIVSKS-KDALGYNHLISHYASLGNKDEMMKFWGLQ 305
           + +A  YI  GL  KA   LK  E+ ++   +D   Y+ LI+ Y  + N  E+ + W L 
Sbjct: 250 ANLAAIYIKVGLYGKAEEALKSLENNMNPDVRDC--YHFLINLYTGIANASEVYRVWDLL 307

Query: 306 KIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMI 365
           K +     N  Y+TML +L K+ +++  +K+  EWE +C+ YD R+ N+ +  Y ++ M 
Sbjct: 308 KKRYPNVNNSSYLTMLRALSKLDDIDGVKKVFAEWESTCWTYDMRMANVAISSYLKQNMY 367

Query: 366 EKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS 425
           E+A+AV    +KK K     +  ++       +  + A +  +   AV +++K W     
Sbjct: 368 EEAEAVFNGAMKKCKGQFSKARQLLMMHLLKNDQADLALKHFEA--AVLDQDKNWTWSSE 425

Query: 426 LVSSILDWLGDNRDVEEVEAFVSSL-KIKVQKRNMYHALTEAHIRSGQ 472
           L+SS      + +DV+  E F  +L K        Y  L + ++ +G+
Sbjct: 426 LISSFFLHFEEAKDVDGAEEFCKTLTKWSPLSSETYTLLMKTYLAAGK 473

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FZ24|PPR4_ARATH Pentatricopeptide repeat-containing protein At1g02370, mitochondrial OS=Arabidopsis thaliana GN=At1g02370 PE=2 SV=1

 Score =  218 bits (555), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 137/439 (31%), Positives = 235/439 (53%), Gaps = 11/439 (2%)

Query: 15  NFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQR 74
           N  +T++   T A R      +  LY ++S L     ++   L+Q+++EG  + + +L R
Sbjct: 55  NGVRTSVAAPTVASR------QRELYKKLSMLSVTGGTVAETLNQFIMEGITVRKDDLFR 108

Query: 75  VIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED 134
             + LR  +R +HA ++ +WM  + + FSV DHA+ LDLIGK +GLE+AE YFN+L+   
Sbjct: 109 CAKTLRKFRRPQHAFEIFDWMEKRKMTFSVSDHAICLDLIGKTKGLEAAENYFNNLDPSA 168

Query: 135 KVDK-LYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPD 193
           K  +  YGAL+NCY  E   +++ +  + M E+    ++L +N +M +Y    Q EK+P 
Sbjct: 169 KNHQSTYGALMNCYCVELEEEKAKAHFEIMDELNFVNNSLPFNNMMSMYMRLSQPEKVPV 228

Query: 194 VLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYY 253
           ++  MK+ G+ P   +Y I + S G+ ++L  +E ++ EM   S     W T+S +A  Y
Sbjct: 229 LVDAMKQRGISPCGVTYSIWMQSCGSLNDLDGLEKIIDEMGKDSEAKTTWNTFSNLAAIY 288

Query: 254 IIAGLKEKAIIYLKKCEDIVS-KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQ 312
             AGL EKA   LK  E+ ++  ++D+  ++ L+S YA +    E+ + W   K    + 
Sbjct: 289 TKAGLYEKADSALKSMEEKMNPNNRDS--HHFLMSLYAGISKGPEVYRVWESLKKARPEV 346

Query: 313 LNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVL 372
            N  Y+ ML ++ K+G+L+  +K+  EWE  C+ YD R+ NI +  Y +  M E+A+ +L
Sbjct: 347 NNLSYLVMLQAMSKLGDLDGIKKIFTEWESKCWAYDMRLANIAINTYLKGNMYEEAEKIL 406

Query: 373 KEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENK-FWRPKPSLVSSIL 431
              +KK K P   +  ++     + +  + A + ++ A++   ENK  W     LVS   
Sbjct: 407 DGAMKKSKGPFSKARQLLMIHLLENDKADLAMKHLEAAVSDSAENKDEWGWSSELVSLFF 466

Query: 432 DWLGDNRDVEEVEAFVSSL 450
                 +DV+  E F   L
Sbjct: 467 LHFEKAKDVDGAEDFCKIL 485

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C7F1|PPR61_ARATH Putative pentatricopeptide repeat-containing protein At1g28020 OS=Arabidopsis thaliana GN=At1g28020 PE=3 SV=2

 Score =  193 bits (491), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 135/475 (28%), Positives = 236/475 (49%), Gaps = 37/475 (7%)

Query: 42  RISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLA 101
           RI+     +  + PVL+QW  +G +++   ++ +I++LR   +   ALQVSEWMS + + 
Sbjct: 41  RITDALHRNAQIIPVLEQWRQQGNQVNPSHVRVIIKKLRDSDQSLQALQVSEWMSKEKIC 100

Query: 102 FSV-HDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESL--- 157
             +  D A +L LI  V GLE AE +F S+    + D +Y +LLN Y R    D++L   
Sbjct: 101 NLIPEDFAARLHLIENVVGLEEAEKFFESIPKNARGDSVYTSLLNSYARS---DKTLCKA 157

Query: 158 -SLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINS 216
            +  QKM+++G     + YN +M LY+     EK+ ++LL+MK+N V  DN +    +  
Sbjct: 158 EATFQKMRDLGLLLRPVPYNAMMSLYSALKNREKVEELLLEMKDNDVEADNVTVNNVLKL 217

Query: 217 YGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS 276
           Y A  +++ ME  L + E    I ++W T   +A  Y+ A    KA+  L+  E +V + 
Sbjct: 218 YSAVCDVTEMEKFLNKWEGIHGIKLEWHTTLDMAKAYLRARSSGKAMKMLRLTEQLVDQK 277

Query: 277 KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM 336
                Y+HL+  Y   GN++E+++ W L K K  ++ N  Y T++ SL+K+ ++  AE++
Sbjct: 278 SLKSAYDHLMKLYGEAGNREEVLRVWKLYKSKIGERDNNGYRTVIRSLLKVDDIVGAEEI 337

Query: 337 LEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK------TPTPNSWS-- 388
            + WE     +D R+P ++  GY  +GM EKA+ ++     K +      TP    W   
Sbjct: 338 YKVWESLPLEFDHRIPTMLASGYRDRGMTEKAEKLMNSKTIKDRRMNKPVTPLLEQWGDQ 397

Query: 389 -------IIAAGYADKNNMEKAF---ECMKEALAVHEENKFWRPKPSLVSSILDWLGDNR 438
                   +     D     KA    E M E    +   + +  +  L  ++L       
Sbjct: 398 MKPSDLKCLIKNLRDSKQFSKALQVSEWMGEKQVCNLYLEDYAARLYLTENVL------- 450

Query: 439 DVEEVEAFVSSLKIKVQKRNMYHALTEAHIRS----GQEVDGLLESMKADDIDED 489
            +EE E +  ++   ++  ++Y AL  ++ +S    G  VD +L  M+ +++D D
Sbjct: 451 GLEEAEKYFENIPENMKDYSVYVALLSSYAKSDKNLGNMVDEILREMEENNVDPD 505

Arabidopsis thaliana (taxid: 3702)

>sp|Q94B59|PP372_ARATH Pentatricopeptide repeat-containing protein At5g09450, mitochondrial OS=Arabidopsis thaliana GN=At5g09450 PE=2 SV=1

 Score =  161 bits (407), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 104/335 (31%), Positives = 188/335 (56%), Gaps = 19/335 (5%)

Query: 24  FTRAYRAVKPVA---------RNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQR 74
           F+++Y A   +          +++L SRI  L  P  S T VL++W+ EG +++  EL+ 
Sbjct: 33  FSKSYNADAAIGNSLVEESEEKDDLKSRIFRLRLPKRSATTVLEKWIGEGNQMTINELRE 92

Query: 75  VIRQLRSRKRFKHALQVSEWM-SGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDE 133
           + ++LR  +R+KHAL+V+EWM   +    S  D+A ++DLI KV G+++AE YF  L+ +
Sbjct: 93  ISKELRRTRRYKHALEVTEWMVQHEESKISDADYASRIDLISKVFGIDAAERYFEGLDID 152

Query: 134 DKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGS--FGSALNYNGIMCLYTNTGQHEKI 191
            K  + Y +LL+ Y      + + +L +++ E  S  FG A+ YN +M LY + GQ EK+
Sbjct: 153 SKTAETYTSLLHAYAASKQTERAEALFKRIIESDSLTFG-AITYNEMMTLYMSVGQVEKV 211

Query: 192 PDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVAN 251
           P+V+  +K+  V PD F+Y + ++S  A   +  +  +L+EM   +  +  W  Y  + +
Sbjct: 212 PEVIEVLKQKKVSPDIFTYNLWLSSCAATFNIDELRKILEEMRHDASSNEGWVRYIDLTS 271

Query: 252 YYIIAGLKEKAIIYLK-KCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK 310
            YI +     A   L  + E  +S+ ++ + Y+ L+  +  LGNK  + + W  + ++  
Sbjct: 272 IYINSSRVTNAESTLPVEAEKSISQ-REWITYDFLMILHTGLGNKVMIDQIW--KSLRNT 328

Query: 311 KQL--NRDYITMLGSLVKIGELEEAEKMLEEWELS 343
            Q+  +R YI +L S + +G L EAE+++ +W+ S
Sbjct: 329 NQILSSRSYICVLSSYLMLGHLREAEEIIHQWKES 363

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	490
255573349	502	pentatricopeptide repeat-containing prot	0.991	0.968	0.654	0.0
302143027	687	unnamed protein product [Vitis vinifera]	0.991	0.707	0.641	0.0
225461407	504	PREDICTED: pentatricopeptide repeat-cont	0.991	0.964	0.641	0.0
224114960	437	predicted protein [Populus trichocarpa]	0.887	0.995	0.674	1e-174
359483464	506	PREDICTED: pentatricopeptide repeat-cont	0.995	0.964	0.591	1e-167
147807263	506	hypothetical protein VITISV_006333 [Viti	0.995	0.964	0.585	1e-165
356514762	492	PREDICTED: pentatricopeptide repeat-cont	0.924	0.920	0.600	1e-159
449431834	492	PREDICTED: pentatricopeptide repeat-cont	0.961	0.957	0.581	1e-158
356555227	486	PREDICTED: pentatricopeptide repeat-cont	0.948	0.956	0.555	1e-151
255556039	485	pentatricopeptide repeat-containing prot	0.951	0.960	0.565	1e-150

>gi|255573349|ref|XP_002527601.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223533018|gb|EEF34782.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  655 bits (1691), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/492 (65%), Positives = 393/492 (79%), Gaps = 6/492 (1%)

Query: 1   MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQW 60
           MAS  F TI   KR  + T   I TR Y      A N L++RISPLG+PD+SL PVLD W
Sbjct: 1   MASTRFFTIL--KRTQSLTANAILTRRYYNKARTASNTLFARISPLGEPDISLVPVLDNW 58

Query: 61  VLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLA-FSVHDHAVQLDLIGKVRG 119
           V EG+KI   ELQ++IR LR  +R+  ALQVSEWM+G+G + FS  DHAVQLDLIG+VRG
Sbjct: 59  VQEGKKIRGFELQKIIRDLRCHRRYTQALQVSEWMNGKGQSGFSPADHAVQLDLIGRVRG 118

Query: 120 LESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIM 179
           LESAE+YF +L ++D+ DK YGALLNCYVREGLVD+SL  MQKMKE+G   S LNYN +M
Sbjct: 119 LESAESYFQNLVNQDRNDKTYGALLNCYVREGLVDKSLYHMQKMKELGFASSPLNYNDLM 178

Query: 180 CLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHI 239
           CLYT TGQ EK+ DVL +MKENG+ PD FSYRIC++S  ARS+L  +E +L+EME+QSHI
Sbjct: 179 CLYTRTGQLEKVTDVLSEMKENGITPDLFSYRICMSSCAARSDLKGVEEILEEMENQSHI 238

Query: 240 SMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMM 299
           S+DW TYSTVA+ Y+ A LKEKA+IYLKKCE  V++  DALGYNHLIS  ASLG KDE+M
Sbjct: 239 SIDWVTYSTVASIYVKASLKEKALIYLKKCEQKVNR--DALGYNHLISLNASLGIKDEVM 296

Query: 300 KFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGY 359
           + WGL K KCKKQ+NRDYITMLG+LVK+ ELEEA+K+L+EWE SC CYDFRVPN++L+GY
Sbjct: 297 RLWGLVKTKCKKQVNRDYITMLGALVKLEELEEADKLLQEWESSCQCYDFRVPNVLLIGY 356

Query: 360 SQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKF 419
            Q+G+IEKA+A+LK+IVKK K PTPNSW+IIAAGY +K NMEKAF CMKEAL V  ENK 
Sbjct: 357 CQQGLIEKAEAMLKDIVKKQKNPTPNSWAIIAAGYVNKQNMEKAFNCMKEALTVQAENKG 416

Query: 420 WRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSGQEVDGLL 478
           WRPK +L+SSIL WLG+N DVE+VEAFV+ L+ KV K R +YH L +A+IR G++VDG+L
Sbjct: 417 WRPKANLISSILSWLGENGDVEDVEAFVNLLETKVPKDREIYHTLIKAYIRGGKQVDGVL 476

Query: 479 ESMKADDIDEDK 490
           E+M A+ IDED+
Sbjct: 477 ENMTANKIDEDE 488

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143027|emb|CBI20322.3| unnamed protein product [Vitis vinifera]

 Score =  645 bits (1664), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 317/494 (64%), Positives = 396/494 (80%), Gaps = 8/494 (1%)

Query: 1   MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKP--VARNNLYSRISPLGDPDVSLTPVLD 58
           MAS +F+ + +N R+ ++T +     + R+V     A  NLYSRISPLG P++SL PVLD
Sbjct: 1   MASSIFNRLKSN-RHVSQTLISNVC-SVRSVYTGRFANINLYSRISPLGTPNLSLVPVLD 58

Query: 59  QWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLA-FSVHDHAVQLDLIGKV 117
           QWV EG+K+ ++EL R+IR LRSRKR+  AL+VSEWMS + L  FS    AVQLDLIG+V
Sbjct: 59  QWVEEGKKVRDVELHRIIRDLRSRKRYAQALEVSEWMSSKELCPFSPSARAVQLDLIGQV 118

Query: 118 RGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNG 177
           RGLESAE YFN+++ E+K+DK+YGALLNCYVRE ++D+SLS +QKMKE+G   + L YNG
Sbjct: 119 RGLESAENYFNNMSAEEKIDKMYGALLNCYVRERVIDKSLSHLQKMKELGFASTPLPYNG 178

Query: 178 IMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQS 237
           +MCLY NT Q EKIPDVL +M+ENG+ PDNFSYR+CINSYGARS+L+SME +L+EMES+S
Sbjct: 179 LMCLYINTDQLEKIPDVLSEMQENGISPDNFSYRLCINSYGARSDLNSMEKILEEMESKS 238

Query: 238 HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE 297
           HI +DW TYS VAN+YI AGL EKA+ +LKK E  + K  D LGYNHLIS YASLG+K E
Sbjct: 239 HIHIDWMTYSMVANFYIKAGLNEKALFFLKKAETKLHK--DPLGYNHLISLYASLGSKAE 296

Query: 298 MMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILL 357
           MM+ W  +K   KK +NRDYITMLGSLVK+GELE+ E +L+EWE S  CYDFRVPN +L+
Sbjct: 297 MMRLWERRKTASKKLINRDYITMLGSLVKLGELEDTEALLKEWESSGNCYDFRVPNTLLI 356

Query: 358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEEN 417
           G+ QKG+IEKA+++L++IV++GKTPTPNSWSI+AAGY +K NMEKAFECMKEA+AV  EN
Sbjct: 357 GFCQKGLIEKAESMLRDIVEEGKTPTPNSWSIVAAGYIEKQNMEKAFECMKEAIAVLAEN 416

Query: 418 KFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV-QKRNMYHALTEAHIRSGQEVDG 476
           K WRPKP ++SSIL WLGDNRDVEEVE FVS+LK  +   R MYHA   A IR+G+EVDG
Sbjct: 417 KGWRPKPKVISSILSWLGDNRDVEEVETFVSALKAVIPMDREMYHAQIRASIRAGKEVDG 476

Query: 477 LLESMKADDIDEDK 490
           +L+SMKAD IDED+
Sbjct: 477 ILDSMKADKIDEDE 490

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225461407|ref|XP_002282230.1| PREDICTED: pentatricopeptide repeat-containing protein At4g21705, mitochondrial [Vitis vinifera]

 Score =  643 bits (1658), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 317/494 (64%), Positives = 396/494 (80%), Gaps = 8/494 (1%)

Query: 1   MASKLFSTIFNNKRNFTKTNLEIFTRAYRAVKP--VARNNLYSRISPLGDPDVSLTPVLD 58
           MAS +F+ + +N R+ ++T +     + R+V     A  NLYSRISPLG P++SL PVLD
Sbjct: 1   MASSIFNRLKSN-RHVSQTLISNVC-SVRSVYTGRFANINLYSRISPLGTPNLSLVPVLD 58

Query: 59  QWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLA-FSVHDHAVQLDLIGKV 117
           QWV EG+K+ ++EL R+IR LRSRKR+  AL+VSEWMS + L  FS    AVQLDLIG+V
Sbjct: 59  QWVEEGKKVRDVELHRIIRDLRSRKRYAQALEVSEWMSSKELCPFSPSARAVQLDLIGQV 118

Query: 118 RGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNG 177
           RGLESAE YFN+++ E+K+DK+YGALLNCYVRE ++D+SLS +QKMKE+G   + L YNG
Sbjct: 119 RGLESAENYFNNMSAEEKIDKMYGALLNCYVRERVIDKSLSHLQKMKELGFASTPLPYNG 178

Query: 178 IMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQS 237
           +MCLY NT Q EKIPDVL +M+ENG+ PDNFSYR+CINSYGARS+L+SME +L+EMES+S
Sbjct: 179 LMCLYINTDQLEKIPDVLSEMQENGISPDNFSYRLCINSYGARSDLNSMEKILEEMESKS 238

Query: 238 HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE 297
           HI +DW TYS VAN+YI AGL EKA+ +LKK E  + K  D LGYNHLIS YASLG+K E
Sbjct: 239 HIHIDWMTYSMVANFYIKAGLNEKALFFLKKAETKLHK--DPLGYNHLISLYASLGSKAE 296

Query: 298 MMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILL 357
           MM+ W  +K   KK +NRDYITMLGSLVK+GELE+ E +L+EWE S  CYDFRVPN +L+
Sbjct: 297 MMRLWERRKTASKKLINRDYITMLGSLVKLGELEDTEALLKEWESSGNCYDFRVPNTLLI 356

Query: 358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEEN 417
           G+ QKG+IEKA+++L++IV++GKTPTPNSWSI+AAGY +K NMEKAFECMKEA+AV  EN
Sbjct: 357 GFCQKGLIEKAESMLRDIVEEGKTPTPNSWSIVAAGYIEKQNMEKAFECMKEAIAVLAEN 416

Query: 418 KFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV-QKRNMYHALTEAHIRSGQEVDG 476
           K WRPKP ++SSIL WLGDNRDVEEVE FVS+LK  +   R MYHA   A IR+G+EVDG
Sbjct: 417 KGWRPKPKVISSILSWLGDNRDVEEVETFVSALKAVIPMDREMYHAQIRASIRAGKEVDG 476

Query: 477 LLESMKADDIDEDK 490
           +L+SMKAD IDED+
Sbjct: 477 ILDSMKADKIDEDE 490

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114960|ref|XP_002316903.1| predicted protein [Populus trichocarpa] gi|222859968|gb|EEE97515.1| predicted protein [Populus trichocarpa]

 Score =  619 bits (1596), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 296/439 (67%), Positives = 365/439 (83%), Gaps = 4/439 (0%)

Query: 38  NLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSG 97
           NLYSRISPLGDP +SL PVLDQWV EG+K+ + EL+ +++ LR RKRFK AL+VS+WMS 
Sbjct: 1   NLYSRISPLGDPRISLAPVLDQWVEEGKKVKDYELRTIVKGLRERKRFKQALEVSQWMSS 60

Query: 98  QGLA-FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDES 156
             L  FS  D AV+LDLIGKV GLESAE+YF +L+++DK+ K YGALLNCYVR GLV++S
Sbjct: 61  NRLCNFSPSDDAVRLDLIGKVHGLESAESYFKNLDEKDKIHKTYGALLNCYVRGGLVEKS 120

Query: 157 LSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINS 216
           LS +QKMKE+G F +ALNYN +MCLY NTG  EK+PDVL DMKENG+ PD FSYRIC+ S
Sbjct: 121 LSHVQKMKELGFFSTALNYNDLMCLYVNTGLLEKVPDVLSDMKENGISPDLFSYRICLKS 180

Query: 217 YGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS 276
           YG RS+  ++E +L+EMESQSHISMDW T++TVAN Y+ AGLKEKA++YLKKCE+ V+K 
Sbjct: 181 YGERSDFDNVEKILREMESQSHISMDWRTFATVANIYLEAGLKEKALVYLKKCEEKVNK- 239

Query: 277 KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM 336
            +ALGYNHLIS YASLGNKDEMM+ W L K  CKKQLNRDYIT+LGSLVK+G LEEAEK+
Sbjct: 240 -NALGYNHLISLYASLGNKDEMMRLWELAKANCKKQLNRDYITILGSLVKLGHLEEAEKL 298

Query: 337 LEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD 396
           L++WE SC  YDFRVPN++L+GYS+KG+ EKA+A+L++I++K K   P+SWSII+AGY D
Sbjct: 299 LQDWESSCQYYDFRVPNVVLIGYSRKGLPEKAEAMLQDIIEKQKMKNPSSWSIISAGYMD 358

Query: 397 KNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK 456
           K NMEKAFECMKEALA   EN  WRPKP+++S+IL+WLGDNRD +EVEAFV  L+ KV K
Sbjct: 359 KQNMEKAFECMKEALAAETENNGWRPKPAMISNILNWLGDNRDAQEVEAFVGLLETKVPK 418

Query: 457 -RNMYHALTEAHIRSGQEV 474
            R MYHAL +++IR G+EV
Sbjct: 419 SREMYHALIKSYIRCGKEV 437

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359483464|ref|XP_003632962.1| PREDICTED: pentatricopeptide repeat-containing protein At4g21705, mitochondrial-like [Vitis vinifera]

 Score =  595 bits (1533), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 293/495 (59%), Positives = 371/495 (74%), Gaps = 7/495 (1%)

Query: 1   MASKLFSTIFNNKRNFTKTNLE---IFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVL 57
           M S+LFS +  + + + ++ +    I  R Y   +   + +LY++ISPLGDP+ S+ P L
Sbjct: 1   MDSRLFSLLRQSIQQYPQSLIRKNPISNRTYYTSR-YGKISLYNKISPLGDPNTSVVPEL 59

Query: 58  DQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGL-AFSVHDHAVQLDLIGK 116
           D WV  G K+   ELQR+I  LR RKRF  AL++SEWMS +G+ AFS  +HAVQLDLIG+
Sbjct: 60  DNWVQNGNKVWVAELQRIIHDLRKRKRFSQALEISEWMSKKGICAFSPTEHAVQLDLIGR 119

Query: 117 VRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYN 176
           VRG  SAE+YFNSL + DK DK YGALLNCYVR+   D+SLS +QKMKEMG   S L YN
Sbjct: 120 VRGFLSAESYFNSLQNHDKTDKTYGALLNCYVRQRQTDKSLSHLQKMKEMGFASSPLTYN 179

Query: 177 GIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQ 236
            IMCLYTN GQHEK+PDVL +MK++ V PDNFSYRICINSYGA+S++  MENVL+EME Q
Sbjct: 180 DIMCLYTNVGQHEKVPDVLTEMKQSNVYPDNFSYRICINSYGAQSDIQGMENVLKEMERQ 239

Query: 237 SHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKD 296
            HI MDW TY+  AN+YI AGL +KAI  LKK E+ + K +D LGYNHLIS YASLGNK 
Sbjct: 240 PHIVMDWNTYAVAANFYIKAGLPDKAIEALKKSEERLDK-RDGLGYNHLISLYASLGNKA 298

Query: 297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIIL 356
           E+++ W L+K  CK+ +NRDYITML SLV++GELEEAEK+L EWE S  CYDFRVPNI++
Sbjct: 299 EVLRLWSLEKSACKRNINRDYITMLESLVRLGELEEAEKVLREWESSGNCYDFRVPNIVI 358

Query: 357 LGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEE 416
           +GYS+KG+ EKA+A+LKE+++KGK  TPNSW  +A+GY D+  MEKA ECMK A+++H  
Sbjct: 359 IGYSEKGLFEKAEAMLKELMEKGKITTPNSWGTVASGYMDEGEMEKAVECMKAAISLHVN 418

Query: 417 NKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV-QKRNMYHALTEAHIRSGQEVD 475
           NK  +P   +++ IL WLGD   VE+VEAFV SL+I +   R MYH L  A+IR+G+EVD
Sbjct: 419 NKGRKPNSRVIAGILSWLGDKGRVEDVEAFVGSLRIVIPMNRRMYHTLIMANIRAGKEVD 478

Query: 476 GLLESMKADDIDEDK 490
           GLL SMKAD I ED+
Sbjct: 479 GLLASMKADKIVEDE 493

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147807263|emb|CAN64166.1| hypothetical protein VITISV_006333 [Vitis vinifera]

 Score =  588 bits (1516), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 290/495 (58%), Positives = 369/495 (74%), Gaps = 7/495 (1%)

Query: 1   MASKLFSTIFNNKRNFTKTNLE---IFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVL 57
           M S+LFS +  + + + ++ +    I  R Y   +   + +LY++ISPLGDP+ S+ P L
Sbjct: 1   MDSRLFSLLRQSIQQYPQSLIRKNPISNRTYYTSR-YGKISLYNKISPLGDPNTSVVPEL 59

Query: 58  DQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGL-AFSVHDHAVQLDLIGK 116
           D WV  G K+   ELQR+I  LR RKRF  AL++SEWMS +G+ AFS  +HAVQLDLIG+
Sbjct: 60  DNWVQNGNKVWVAELQRIIHDLRKRKRFSQALEISEWMSKKGICAFSPTEHAVQLDLIGR 119

Query: 117 VRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYN 176
           VRG  SAE+YFNSL + DK DK YGALLNCYVR+   D+SLS +QKMKEMG   S L YN
Sbjct: 120 VRGFLSAESYFNSLQNHDKTDKTYGALLNCYVRQRQTDKSLSHLQKMKEMGFASSPLTYN 179

Query: 177 GIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQ 236
            IMCLYTN GQHEK+PDVL +MK++ V PDNFSYRICINSY A+S++  ME VL+EME Q
Sbjct: 180 DIMCLYTNVGQHEKVPDVLTEMKQSHVYPDNFSYRICINSYAAQSDIQGMEKVLKEMERQ 239

Query: 237 SHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKD 296
            HI MDW TY+  AN+YI AGL +KAI  LKK E+ + K +D LGYNHLIS YASLGNK 
Sbjct: 240 PHIVMDWNTYAVAANFYIKAGLPDKAIEALKKSEERLDK-RDGLGYNHLISLYASLGNKA 298

Query: 297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIIL 356
           E+++ W L+K  CK+ +NRDYITML SLV++GELEEAEK+L EWE S  CYDFRVPNI++
Sbjct: 299 EVLRLWSLEKSACKRNINRDYITMLESLVRLGELEEAEKVLREWESSGNCYDFRVPNIVI 358

Query: 357 LGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEE 416
           +GYS+KG+ EKA+A+LKE+++KGK  TP+SW  +A+GY D+  MEKA ECMK A+++H  
Sbjct: 359 IGYSEKGLFEKAEAMLKELMEKGKITTPDSWGTVASGYMDEGEMEKAVECMKAAISLHVN 418

Query: 417 NKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV-QKRNMYHALTEAHIRSGQEVD 475
           NK  +P   +++ IL WLGD   VE+VEAFV SL+I +   R MYH L  A+IR+G+EVD
Sbjct: 419 NKGRKPNSRVIAGILSWLGDKGRVEDVEAFVGSLRIVIPMNRRMYHTLIMANIRAGKEVD 478

Query: 476 GLLESMKADDIDEDK 490
           GLL SMKAD I ED+
Sbjct: 479 GLLASMKADKIVEDE 493

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356514762|ref|XP_003526072.1| PREDICTED: pentatricopeptide repeat-containing protein At4g21705, mitochondrial-like [Glycine max]

 Score =  567 bits (1460), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 274/456 (60%), Positives = 350/456 (76%), Gaps = 3/456 (0%)

Query: 36  RNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWM 95
           R NLYSRISPLGDP +S+ PVLD+W+ EG  +    L  +I+ LR+R R   AL+VSEWM
Sbjct: 31  RRNLYSRISPLGDPSISVVPVLDEWIEEGNAVDGPHLHHIIKILRTRNRNTQALEVSEWM 90

Query: 96  SGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDE 155
           S +GL  S  D AVQLDLIG+V G+ESAE Y  SL+D DK  K++GALLNCYVREGLVD+
Sbjct: 91  SSKGLPISSRDQAVQLDLIGRVHGVESAERYLQSLSDGDKTWKVHGALLNCYVREGLVDK 150

Query: 156 SLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICIN 215
           SLSLMQKMK+MG F S LNYN IM LYT T Q+EK+P VL  MK++GVPP+ FSYRICIN
Sbjct: 151 SLSLMQKMKDMG-FVSFLNYNNIMSLYTQTQQYEKVPGVLEQMKKDGVPPNIFSYRICIN 209

Query: 216 SYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK 275
           SY  R +L+++E +L+EME + HI +DW TYS V N+YI A ++EKA++ L KCE    +
Sbjct: 210 SYCVRGDLANVEKLLEEMEREPHIGIDWITYSMVTNFYIKADMREKALVCLMKCEKKTHR 269

Query: 276 SKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEK 335
             + + YNHLISH A+L +K  MM+ W LQK  CKKQLNR+YITMLG LVK+GEL++AEK
Sbjct: 270 G-NTVAYNHLISHNAALRSKGGMMRAWKLQKANCKKQLNREYITMLGCLVKLGELDKAEK 328

Query: 336 MLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA 395
           +L EWELS    DFRVPNI+L+GY Q+G++EKA+A+L+++V +GKTP PNSWSI+A+GY 
Sbjct: 329 VLGEWELSGNTCDFRVPNILLIGYCQRGLVEKAEALLRKMVAEGKTPIPNSWSIVASGYV 388

Query: 396 DKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLK-IKV 454
            K NMEKAF+CMKEA+AVH +NK WRPK  ++SSI  W+ +NRD+EE E FV+S K +  
Sbjct: 389 AKENMEKAFQCMKEAVAVHAQNKRWRPKVDVISSIFSWVTNNRDIEEAEDFVNSWKSVNA 448

Query: 455 QKRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK 490
             R MY +L +  IR G+ VDG+LESMKAD+I+ D+
Sbjct: 449 MNRGMYLSLMKMCIRYGKHVDGILESMKADNIEIDE 484

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449431834|ref|XP_004133705.1| PREDICTED: pentatricopeptide repeat-containing protein At4g21705, mitochondrial-like [Cucumis sativus] gi|449478158|ref|XP_004155237.1| PREDICTED: pentatricopeptide repeat-containing protein At4g21705, mitochondrial-like [Cucumis sativus]

 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 286/492 (58%), Positives = 370/492 (75%), Gaps = 21/492 (4%)

Query: 2   ASKLFSTIFNNKRNFTKT---NLEIFT----RAYRAVKPVARNNLYSRISPLGDPDVSLT 54
           AS +F  +  +    T+T     + F     R Y   +   R NLY+RISPLGDP+ ++ 
Sbjct: 4   ASAMFKILSRSSSGCTRTLRPETDAFCFVALRLYSTRRSCDRRNLYARISPLGDPECTVV 63

Query: 55  PVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGL-AFSVHDHAVQLDL 113
           PVL+QW+ EG+ I + EL+R++R LR+ +R++ AL+VSEWM  +GL + +  D A+QLDL
Sbjct: 64  PVLNQWIEEGRNIKDFELRRIVRDLRTCRRYRQALEVSEWMCSKGLFSLTTRDFAIQLDL 123

Query: 114 IGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSAL 173
           IG+VRGL+SAE YF S++++ ++ KLYGALLNCYVREGL+D+SL+ MQKMKEMG   S L
Sbjct: 124 IGQVRGLDSAEKYFGSVSNQKEIGKLYGALLNCYVREGLIDKSLAHMQKMKEMGLASSPL 183

Query: 174 NYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEM 233
            YN IMCLY NTGQ +K+P+VL +MKENGV PDNFSYRICI+SYGARS++ SMENVL+EM
Sbjct: 184 CYNDIMCLYLNTGQADKVPNVLSEMKENGVLPDNFSYRICISSYGARSDVISMENVLKEM 243

Query: 234 ESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG 293
           E Q+HISMDW TYS VA ++I AG+ +KA+ YL+KCED V   +DALG+NHLISHY +LG
Sbjct: 244 EGQTHISMDWTTYSMVAGFFIKAGMHDKAMNYLRKCEDKV--DEDALGFNHLISHYTNLG 301

Query: 294 NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPN 353
           +K+E+M+ W L K K KKQLNRDYITMLGSLVK+  LEEAE ++ EWE SC CYDFRVPN
Sbjct: 302 HKNEVMRLWALLK-KGKKQLNRDYITMLGSLVKLELLEEAENLVMEWESSCQCYDFRVPN 360

Query: 354 IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAV 413
           ++L+GYSQKG+IEKA+ +L+ I+  G  P+PNSW IIA+GY +K N+EKAFECMKEALAV
Sbjct: 361 VVLIGYSQKGLIEKAEKMLRNIIVNGMIPSPNSWGIIASGYLEKQNLEKAFECMKEALAV 420

Query: 414 HEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSGQE 473
             +NK WRPKP+++SSIL WL +NR  EE++ F+SSLK      +M   L  A       
Sbjct: 421 KGQNKVWRPKPNVLSSILRWLSENRRYEEMKEFMSSLKTVP---SMDEKLNNA------- 470

Query: 474 VDGLLESMKADD 485
           +D LLE M  DD
Sbjct: 471 LDELLEIMANDD 482

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356555227|ref|XP_003545936.1| PREDICTED: pentatricopeptide repeat-containing protein At4g21705, mitochondrial-like [Glycine max]

 Score =  540 bits (1391), Expect = e-151,   Method: Compositional matrix adjust.
 Identities = 264/475 (55%), Positives = 345/475 (72%), Gaps = 10/475 (2%)

Query: 21  LEIFTRAY---RAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIR 77
           + + +R+Y   R+ KP    +LYS+ISPLG+P+ S+ PVLD WV +G K+   ELQR+IR
Sbjct: 6   IAVVSRSYYTSRSKKP----SLYSKISPLGNPNTSVVPVLDDWVFKGNKLRVAELQRIIR 61

Query: 78  QLRSRKRFKHALQVSEWMSGQGLA-FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV 136
            LR R RF  ALQ+SEWM  +G+  FS  ++AV LDLIGKV G  SAETYF++L D+ K 
Sbjct: 62  DLRKRSRFSQALQISEWMHNKGVCIFSPTEYAVHLDLIGKVHGFSSAETYFDALKDQHKT 121

Query: 137 DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLL 196
           +K YGALLNCYVR+   D++LS +QKMK++G   S L YN IMCLYTN GQHEK+PDVL 
Sbjct: 122 NKTYGALLNCYVRQRQTDKALSHLQKMKDLGFASSPLTYNDIMCLYTNIGQHEKVPDVLR 181

Query: 197 DMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIA 256
           +MK+N V PDNFSYRICINSYG RS+   +E VL+EME+Q +I MDW TYS  AN+YI A
Sbjct: 182 EMKQNQVLPDNFSYRICINSYGVRSDFGGVERVLKEMETQPNIVMDWNTYSIAANFYIKA 241

Query: 257 GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRD 316
           GL   A+  L+K E+ +  +KD  GYNHLIS YA LG K+E+M+ W L+K  CK+ +NRD
Sbjct: 242 GLTRDAVCALRKSEERLD-NKDGQGYNHLISLYAQLGLKNEVMRIWDLEKNACKRCINRD 300

Query: 317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIV 376
           + T+L SLVK+GEL+EAEK+L+EWE S  CYDF +P+I+++GYSQKG+ EKA A+L+E+ 
Sbjct: 301 FTTLLESLVKLGELDEAEKILKEWESSDNCYDFGIPSIVIIGYSQKGLHEKALAMLEELQ 360

Query: 377 KKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD 436
            K K  TPN WSI+A GY  K  MEKAF+C K AL+++ ENK W+P   +++ +L W+GD
Sbjct: 361 NKEKVTTPNCWSIVAGGYIHKGEMEKAFKCFKTALSLYVENKGWKPNAKVIAELLRWIGD 420

Query: 437 NRDVEEVEAFVSSLKIKVQ-KRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK 490
           N  VE+ E  VS L+  V   R MYH L + +IR G+EVD LL  M+ D IDE+K
Sbjct: 421 NGSVEDAEVLVSLLRNAVPVNRQMYHTLIKTYIRGGKEVDDLLGRMEKDGIDENK 475

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556039|ref|XP_002519054.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis] gi|223541717|gb|EEF43265.1| pentatricopeptide repeat-containing protein, putative [Ricinus communis]

 Score =  537 bits (1383), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 266/470 (56%), Positives = 344/470 (73%), Gaps = 4/470 (0%)

Query: 23  IFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSR 82
           + +R Y A +   +  LYS+ISPLGDP+ SL P LD WV +G K+   ELQR+IR LR R
Sbjct: 1   MISRYYYANR-TKKVTLYSKISPLGDPNTSLVPELDNWVQDGNKVRVGELQRIIRDLRKR 59

Query: 83  KRFKHALQVSEWMSGQGLA-FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYG 141
            RF  AL+VSEWM+ +G+  FS  +HAVQLDLIGKVRG  SAE YFN+L D DK DK YG
Sbjct: 60  NRFTQALEVSEWMNKKGICIFSSTEHAVQLDLIGKVRGFLSAENYFNNLMDHDKTDKTYG 119

Query: 142 ALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKEN 201
           ALLNCYVR+   D S+S  QKMKEMG   S L YN IMCLY N G +EK+  VL +MKEN
Sbjct: 120 ALLNCYVRQRQTDRSISHWQKMKEMGLASSPLAYNDIMCLYINLGLYEKVLHVLTEMKEN 179

Query: 202 GVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEK 261
            + PDNFSYRICINSYGARS++  ME VL EME +   +MDW TY+ VAN+YI AGL +K
Sbjct: 180 KISPDNFSYRICINSYGARSDIQGMEKVLNEMECRLGNAMDWNTYAVVANFYIKAGLADK 239

Query: 262 AIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML 321
           A+  L+K E+ + K KD +GYNHLIS YA+LG K E+++ W LQK  CK+++NRD++TML
Sbjct: 240 AVDALRKSEEKLDK-KDGIGYNHLISLYATLGIKSEVLRIWDLQKSVCKRRINRDFVTML 298

Query: 322 GSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT 381
            SLVK+G+LEEAEK+L+EWE S   YD R+PNI+++GYS+ G+ EKA+A L+ +++KG+ 
Sbjct: 299 ESLVKLGDLEEAEKVLKEWESSGNFYDVRIPNIVVVGYSKNGLHEKAEASLEALMEKGRA 358

Query: 382 PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVE 441
            TPNSW++IA+GY +K    KAFECMK A +++ E K W+P P +V  IL WLGD    E
Sbjct: 359 TTPNSWAMIASGYLEKGEKAKAFECMKAAFSLNVEKKGWKPNPRVVMDILIWLGDEGSPE 418

Query: 442 EVEAFVSSLKIKVQ-KRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK 490
           +VEAFV+SL + +   R +YHAL +A IRSG++   +L+ MK D IDED+
Sbjct: 419 DVEAFVASLSVAIPLNRQIYHALLKAKIRSGRDAHEILDRMKTDKIDEDE 468

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	490
TAIR|locus:504955535	492	AT4G21705 "AT4G21705" [Arabido	0.953	0.949	0.498	2.3e-119
TAIR|locus:2051379	490	AT2G20710 [Arabidopsis thalian	0.820	0.820	0.352	2.8e-66
TAIR|locus:2036586	491	AT1G60770 [Arabidopsis thalian	0.932	0.930	0.293	3.7e-64
TAIR|locus:2204793	524	AT1G02150 [Arabidopsis thalian	0.853	0.797	0.330	1.4e-62
TAIR|locus:2146390	491	AT5G27460 "AT5G27460" [Arabido	0.920	0.918	0.322	3.9e-60
TAIR|locus:2140220	532	AT4G02820 "AT4G02820" [Arabido	0.916	0.843	0.301	9.6e-57
TAIR|locus:2141360	502	AT4G01990 [Arabidopsis thalian	0.948	0.926	0.298	8.6e-56
TAIR|locus:2204808	537	AT1G02370 "AT1G02370" [Arabido	0.838	0.765	0.311	3.8e-53
TAIR|locus:2010459	566	AT1G28020 "AT1G28020" [Arabido	0.904	0.782	0.285	1.1e-46
TAIR|locus:2034215	596	PPR596 "AT1G80270" [Arabidopsi	0.881	0.724	0.276	3.6e-41

TAIR|locus:504955535 AT4G21705 "AT4G21705" [Arabidopsis thaliana (taxid:3702)]

 Score = 1175 (418.7 bits), Expect = 2.3e-119, P = 2.3e-119
 Identities = 237/475 (49%), Positives = 322/475 (67%)

Query:    20 NLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQL 79
             NL I +R Y   + V +  LYS+ISPLGDP  S+ P L  WV  G+K+S  EL R++  L
Sbjct:    10 NL-IASRYYYTNR-VKKTTLYSKISPLGDPKSSVYPELQNWVQCGKKVSVAELIRIVHDL 67

Query:    80 RSRKRFKHALQVSEWMSGQGLA-FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDK 138
             R RKRF HAL+VS+WM+  G+  FS  +HAV LDLIG+V G  +AE YF +L ++ K DK
Sbjct:    68 RRRKRFLHALEVSKWMNETGVCVFSPTEHAVHLDLIGRVYGFVTAEEYFENLKEQYKNDK 127

Query:   139 LYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDM 198
              YGALLNCYVR+  V++SL   +KMKEMG   S+L YN IMCLYTN GQHEK+P VL +M
Sbjct:   128 TYGALLNCYVRQQNVEKSLLHFEKMKEMGFVTSSLTYNNIMCLYTNIGQHEKVPKVLEEM 187

Query:   199 KENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGL 258
             KE  V PDN+SYRICIN++GA  +L  +   L++ME +  I+MDW TY+  A +YI  G 
Sbjct:   188 KEENVAPDNYSYRICINAFGAMYDLERIGGTLRDMERRQDITMDWNTYAVAAKFYIDGGD 247

Query:   259 KEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYI 318
              ++A+  LK  E+ + K KD  GYNHLI+ YA LG K E+++ W L+K  CK+++N+DY+
Sbjct:   248 CDRAVELLKMSENRLEK-KDGEGYNHLITLYARLGKKIEVLRLWDLEKDVCKRRINQDYL 306

Query:   319 TMLGSLVKIGXXXXXXXXXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK 378
             T+L SLVKI               S  CYDFRVPN ++ GY  K M EKA+A+L+++ ++
Sbjct:   307 TVLQSLVKIDALVEAEEVLTEWKSSGNCYDFRVPNTVIRGYIGKSMEEKAEAMLEDLARR 366

Query:   379 GKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNR 438
             GK  TP SW ++A  YA+K  +E AF+CMK AL V   ++ WRP  +LV+S+L W+GD  
Sbjct:   367 GKATTPESWELVATAYAEKGTLENAFKCMKTALGVEVGSRKWRPGLTLVTSVLSWVGDEG 426

Query:   439 DVEEVEAFVSSLK--IKVQKRNMYHALTEAHIRSG-QEVDGLLESMKADDIDEDK 490
              ++EVE+FV+SL+  I V K+ MYHAL +A IR G + +D LL+ MK D I+ D+
Sbjct:   427 SLKEVESFVASLRNCIGVNKQ-MYHALVKADIREGGRNIDTLLQRMKDDKIEIDE 480

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2051379 AT2G20710 [Arabidopsis thaliana (taxid:3702)]

 Score = 674 (242.3 bits), Expect = 2.8e-66, P = 2.8e-66
 Identities = 143/406 (35%), Positives = 227/406 (55%)

Query:    37 NNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMS 96
             + L  R++  GDP  S+  VLD W+ +G  +   EL  +I+ LR   RF HALQ+S+WMS
Sbjct:    38 DTLQRRVARSGDPSASIIKVLDGWLDQGNLVKTSELHSIIKMLRKFSRFSHALQISDWMS 97

Query:    97 GQGL-AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDE 155
                +   S  D A++LDLI KV GL  AE +F ++  E +   LYGALLNCY  + ++ +
Sbjct:    98 EHRVHEISEGDVAIRLDLIAKVGGLGEAEKFFETIPMERRNYHLYGALLNCYASKKVLHK 157

Query:   156 SLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICIN 215
             +  + Q+MKE+G     L YN ++ LY  TG++  +  +L +M++  V PD F+    ++
Sbjct:   158 AEQVFQEMKELGFLKGCLPYNVMLNLYVRTGKYTMVEKLLREMEDETVKPDIFTVNTRLH 217

Query:   216 SYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK 275
             +Y   S++  ME  L   E+   + +DW TY+  AN YI AGL EKA+  L+K E +V+ 
Sbjct:   218 AYSVVSDVEGMEKFLMRCEADQGLHLDWRTYADTANGYIKAGLTEKALEMLRKSEQMVNA 277

Query:   276 SKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGXXXXXXX 335
              K    Y  L+S Y + G K+E+ + W L K +     N  YI+++ +L+K+        
Sbjct:   278 QKRKHAYEVLMSFYGAAGKKEEVYRLWSLYK-ELDGFYNTGYISVISALLKMDDIEEVEK 336

Query:   336 XXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA 395
                        +D R+P++++ GY +KGM+EKA+ V+  +V+K +    ++W  +A GY 
Sbjct:   337 IMEEWEAGHSLFDIRIPHLLITGYCKKGMMEKAEEVVNILVQKWRVEDTSTWERLALGYK 396

Query:   396 DKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVE 441
                 MEKA E  K A+ V +    WRP   ++ S +D+L   RD+E
Sbjct:   397 MAGKMEKAVEKWKRAIEVSKPG--WRPHQVVLMSCVDYLEGQRDME 440

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

TAIR|locus:2036586 AT1G60770 [Arabidopsis thaliana (taxid:3702)]

 Score = 654 (235.3 bits), Expect = 3.7e-64, P = 3.7e-64
 Identities = 136/463 (29%), Positives = 251/463 (54%)

Query:    29 RAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQK-ISELELQRVIRQLRSRKRFKH 87
             R+ K      LY+R+   G  +V +   L+Q+ L+G K + + E+   I++LR+R  +  
Sbjct:    15 RSTKKYIEEPLYNRLFKDGGTEVKVRQQLNQF-LKGTKHVFKWEVGDTIKKLRNRGLYYP 73

Query:    88 ALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCY 147
             AL++SE M  +G+  +V D A+ LDL+ K R + + E YF  L +  K +  YG+LLNCY
Sbjct:    74 ALKLSEVMEERGMNKTVSDQAIHLDLVAKAREITAGENYFVDLPETSKTELTYGSLLNCY 133

Query:   148 VREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDN 207
              +E L +++  L+ KMKE+    S+++YN +M LYT TG+ EK+P ++ ++K   V PD+
Sbjct:   134 CKELLTEKAEGLLNKMKELNITPSSMSYNSLMTLYTKTGETEKVPAMIQELKAENVMPDS 193

Query:   208 FSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLK 267
             ++Y + + +  A +++S +E V++EM     ++ DW TYS +A+ Y+ AGL +KA   L+
Sbjct:   194 YTYNVWMRALAATNDISGVERVIEEMNRDGRVAPDWTTYSNMASIYVDAGLSQKAEKALQ 253

Query:   268 KCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI 327
             + E + +  +D   Y  LI+ Y  LG   E+ + W   ++   K  N  Y+ M+  LVK+
Sbjct:   254 ELE-MKNTQRDFTAYQFLITLYGRLGKLTEVYRIWRSLRLAIPKTSNVAYLNMIQVLVKL 312

Query:   328 GXXXXXXXXXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSW 387
                            +C  YD R+ N+++  Y+Q+G+I+KA+ + ++  ++G      +W
Sbjct:   313 NDLPGAETLFKEWQANCSTYDIRIVNVLIGAYAQEGLIQKANELKEKAPRRGGKLNAKTW 372

Query:   388 SIIAAGYADKNNMEKAFECMKEALAVHE-ENKFWRPKPSLVSSILDWLGDNRDVEEVEAF 446
              I    Y    +M +A ECM +A+++ + +   W P P  V +++ +    +DV   E  
Sbjct:   373 EIFMDYYVKSGDMARALECMSKAVSIGKGDGGKWLPSPETVRALMSYFEQKKDVNGAENL 432

Query:   447 VSSLKIKVQK--RNMYHALTEAHIRSGQEVDGLLESMKADDID 487
             +  LK         ++  L   +  +G+    +   +K ++++
Sbjct:   433 LEILKNGTDNIGAEIFEPLIRTYAAAGKSHPAMRRRLKMENVE 475

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2204793 AT1G02150 [Arabidopsis thaliana (taxid:3702)]

 Score = 639 (230.0 bits), Expect = 1.4e-62, P = 1.4e-62
 Identities = 140/423 (33%), Positives = 237/423 (56%)

Query:    32 KPVAR-NNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQ 90
             +P+ + N +Y +IS +  P++    VL+QW   G+K+++ EL RV+++LR  KR   AL+
Sbjct:    61 RPIVQWNAIYKKISLMEKPELGAASVLNQWEKAGRKLTKWELCRVVKELRKYKRANQALE 120

Query:    91 VSEWMSGQGLAF--SVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYV 148
             V +WM+ +G  F  S  D A+QLDLIGKVRG+  AE +F  L +  K  ++YG+LLN YV
Sbjct:   121 VYDWMNNRGERFRLSASDAAIQLDLIGKVRGIPDAEEFFLQLPENFKDRRVYGSLLNAYV 180

Query:   149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNF 208
             R    +++ +L+  M++ G     L +N +M LY N  +++K+  ++ +MK+  +  D +
Sbjct:   181 RAKSREKAEALLNTMRDKGYALHPLPFNVMMTLYMNLREYDKVDAMVFEMKQKDIRLDIY 240

Query:   209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK 268
             SY I ++S G+   +  ME V Q+M+S   I  +W T+ST+A  YI  G  EKA   L+K
Sbjct:   241 SYNIWLSSCGSLGSVEKMELVYQQMKSDVSIYPNWTTFSTMATMYIKMGETEKAEDALRK 300

Query:   269 CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG 328
              E  ++  ++ + Y++L+S Y SLGNK E+ + W + K       N  Y  ++ SLV++G
Sbjct:   301 VEARIT-GRNRIPYHYLLSLYGSLGNKKELYRVWHVYKSVVPSIPNLGYHALVSSLVRMG 359

Query:   329 XXXXXXXXXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS 388
                               YD R+PN+++  Y +   +E A+ +   +V+ G  P+ ++W 
Sbjct:   360 DIEGAEKVYEEWLPVKSSYDPRIPNLLMNAYVKNDQLETAEGLFDHMVEMGGKPSSSTWE 419

Query:   389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVS 448
             I+A G+  K  + +A  C++ A +  E +  WRPK  ++S       +  DV   EA + 
Sbjct:   420 ILAVGHTRKRCISEALTCLRNAFSA-EGSSNWRPKVLMLSGFFKLCEEESDVTSKEAVLE 478

Query:   449 SLK 451
              L+
Sbjct:   479 LLR 481

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0006364 "rRNA processing" evidence=RCA

GO:0006399 "tRNA metabolic process" evidence=RCA

GO:0009658 "chloroplast organization" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

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

TAIR|locus:2146390 AT5G27460 "AT5G27460" [Arabidopsis thaliana (taxid:3702)]

 Score = 616 (221.9 bits), Expect = 3.9e-60, P = 3.9e-60
 Identities = 148/459 (32%), Positives = 242/459 (52%)

Query:    34 VARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSE 93
             VA  N    I     P  S+T +L + +  G  +S  EL+ + ++L    R+  ALQ+ E
Sbjct:    35 VANRNSLKEILRKNGPRRSVTSLLQERIDSGHAVSLSELRLISKRLIRSNRYDLALQMME 94

Query:    94 WMSGQ-GLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED---KVDK-LYGALLNCYV 148
             WM  Q  + FSV+D A++LDLI K  GL+  E YF  L       +V K  Y  LL  YV
Sbjct:    95 WMENQKDIEFSVYDIALRLDLIIKTHGLKQGEEYFEKLLHSSVSMRVAKSAYLPLLRAYV 154

Query:   149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNF 208
             +  +V E+ +LM+K+  +G   +   +N +M LY  +GQ+EK+  V+  MK N +P +  
Sbjct:   155 KNKMVKEAEALMEKLNGLGFLVTPHPFNEMMKLYEASGQYEKVVMVVSMMKGNKIPRNVL 214

Query:   209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK 268
             SY + +N+    S ++++E V +EM     + + W +  T+AN YI +G  EKA + L+ 
Sbjct:   215 SYNLWMNACCEVSGVAAVETVYKEMVGDKSVEVGWSSLCTLANVYIKSGFDEKARLVLED 274

Query:   269 CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG 328
              E ++++S + LGY  LI+ YASLGNK+ +++ W + K  C +    +YI +L SLVK G
Sbjct:   275 AEKMLNRS-NRLGYFFLITLYASLGNKEGVVRLWEVSKSVCGRISCVNYICVLSSLVKTG 333

Query:   329 XXXXXXXXXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS 388
                            C+ YD RV N++L  Y + G I KA+++   ++++G TP   +W 
Sbjct:   334 DLEEAERVFSEWEAQCFNYDVRVSNVLLGAYVRNGEIRKAESLHGCVLERGGTPNYKTWE 393

Query:   389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVS 448
             I+  G+    NMEKA + M +   +      WRP  ++V +I ++      +EE  A+V 
Sbjct:   394 ILMEGWVKCENMEKAIDAMHQVFVLMRRCH-WRPSHNIVMAIAEYFEKEEKIEEATAYVR 452

Query:   449 SL-KIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDI 486
              L ++ +    +Y  L   H  + +    + E MK D +
Sbjct:   453 DLHRLGLASLPLYRLLLRMHEHAKRPAYDIYEMMKLDKL 491

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2140220 AT4G02820 "AT4G02820" [Arabidopsis thaliana (taxid:3702)]

 Score = 584 (210.6 bits), Expect = 9.6e-57, P = 9.6e-57
 Identities = 138/457 (30%), Positives = 239/457 (52%)

Query:    36 RNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWM 95
             R+ L  R+  L     S    + +W  EG  + + EL R++R+LR  KR+KHAL++ EWM
Sbjct:    60 RDTLGGRLLSLVYTKRSAVVTIRKWKEEGHSVRKYELNRIVRELRKIKRYKHALEICEWM 119

Query:    96 SGQ-GLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVD 154
               Q  +     D+AV LDLI K+RGL SAE +F  + D+ +      +LL+ YV+  L D
Sbjct:   120 VVQEDIKLQAGDYAVHLDLISKIRGLNSAEKFFEDMPDQMRGHAACTSLLHSYVQNKLSD 179

Query:   155 ESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICI 214
             ++ +L +KM E G   S L YN ++ +Y + GQ EK+P ++ ++K     PD  +Y + +
Sbjct:   180 KAEALFEKMGECGFLKSCLPYNHMLSMYISRGQFEKVPVLIKELKIR-TSPDIVTYNLWL 238

Query:   215 NSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVS 274
              ++ + +++   E V  + + +  ++ DW TYS + N Y      EKA + LK+ E +VS
Sbjct:   239 TAFASGNDVEGAEKVYLKAKEEK-LNPDWVTYSVLTNLYAKTDNVEKARLALKEMEKLVS 297

Query:   275 KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGXXXXXX 334
             K K+ + Y  LIS +A+LG+KD +   W   K   KK  + +Y++M+ ++VK+G      
Sbjct:   298 K-KNRVAYASLISLHANLGDKDGVNLTWKKVKSSFKKMNDAEYLSMISAVVKLGEFEQAK 356

Query:   335 XXXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY 394
                          D R+PN+IL  Y  +  +   +   + IV+KG  P+ ++W I+   Y
Sbjct:   357 GLYDEWESVSGTGDARIPNLILAEYMNRDEVLLGEKFYERIVEKGINPSYSTWEILTWAY 416

Query:   395 ADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSL-KIK 453
               + +MEK  +C  +A+   +  K W     LV      L +  +V+  E  ++ L K  
Sbjct:   417 LKRKDMEKVLDCFGKAI---DSVKKWTVNVRLVKGACKELEEQGNVKGAEKLMTLLQKAG 473

Query:   454 VQKRNMYHALTEAHIRSGQEVDGLLESMKADDIDEDK 490
                  +Y++L   + ++G+    + E M  D+++ D+
Sbjct:   474 YVNTQLYNSLLRTYAKAGEMALIVEERMAKDNVELDE 510

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0008150 "biological_process" evidence=ND

GO:0006606 "protein import into nucleus" evidence=RCA

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

TAIR|locus:2141360 AT4G01990 [Arabidopsis thaliana (taxid:3702)]

 Score = 575 (207.5 bits), Expect = 8.6e-56, P = 8.6e-56
 Identities = 142/476 (29%), Positives = 247/476 (51%)

Query:    22 EIFTRAYRAVKPVARNN--LYSRISPLGDPDVS-LTPVLDQWVLEGQKISELELQRVIRQ 78
             EI   A  +V   A+ +  +Y ++S LG      +   L+Q+V+EG  + + +L R  + 
Sbjct:    22 EISGEAAASVPTKAKKHRSIYKKLSSLGTRGGGKMEETLNQFVMEGVPVKKHDLIRYAKD 81

Query:    79 LRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDK 138
             LR  ++ + AL++ EWM  + +AF+  DHA++L+LI K +GLE+AETYFNSL+D  K   
Sbjct:    82 LRKFRQPQRALEIFEWMERKEIAFTGSDHAIRLNLIAKSKGLEAAETYFNSLDDSIKNQS 141

Query:   139 LYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDM 198
              YG+LLNCY  E    ++ +  + M ++    ++L +N +M +Y   GQ EK+P +++ M
Sbjct:   142 TYGSLLNCYCVEKEEVKAKAHFENMVDLNHVSNSLPFNNLMAMYMGLGQPEKVPALVVAM 201

Query:   199 KENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGL 258
             KE  + P + +Y + I S G+  +L  +E VL EM+++      W T++ +A  YI  GL
Sbjct:   202 KEKSITPCDITYSMWIQSCGSLKDLDGVEKVLDEMKAEGEGIFSWNTFANLAAIYIKVGL 261

Query:   259 KEKAIIYLKKCEDIVSKS-KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDY 317
               KA   LK  E+ ++   +D   Y+ LI+ Y  + N  E+ + W L K +     N  Y
Sbjct:   262 YGKAEEALKSLENNMNPDVRDC--YHFLINLYTGIANASEVYRVWDLLKKRYPNVNNSSY 319

Query:   318 ITMLGSLVKIGXXXXXXXXXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVK 377
             +TML +L K+               +C+ YD R+ N+ +  Y ++ M E+A+AV    +K
Sbjct:   320 LTMLRALSKLDDIDGVKKVFAEWESTCWTYDMRMANVAISSYLKQNMYEEAEAVFNGAMK 379

Query:   378 KGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDN 437
             K K     +  ++       +  + A +   EA AV +++K W     L+SS      + 
Sbjct:   380 KCKGQFSKARQLLMMHLLKNDQADLALKHF-EA-AVLDQDKNWTWSSELISSFFLHFEEA 437

Query:   438 RDVEEVEAFVSSL-KIKVQKRNMYHALTEAHIRSGQEVDGLLESMKADDI--DEDK 490
             +DV+  E F  +L K        Y  L + ++ +G+    + + ++   I  DE++
Sbjct:   438 KDVDGAEEFCKTLTKWSPLSSETYTLLMKTYLAAGKACPDMKKRLEEQGILVDEEQ 493

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

TAIR|locus:2204808 AT1G02370 "AT1G02370" [Arabidopsis thaliana (taxid:3702)]

 Score = 550 (198.7 bits), Expect = 3.8e-53, P = 3.8e-53
 Identities = 131/420 (31%), Positives = 223/420 (53%)

Query:    36 RNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWM 95
             +  LY ++S L     ++   L+Q+++EG  + + +L R  + LR  +R +HA ++ +WM
Sbjct:    70 QRELYKKLSMLSVTGGTVAETLNQFIMEGITVRKDDLFRCAKTLRKFRRPQHAFEIFDWM 129

Query:    96 SGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDK-LYGALLNCYVREGLVD 154
               + + FSV DHA+ LDLIGK +GLE+AE YFN+L+   K  +  YGAL+NCY  E   +
Sbjct:   130 EKRKMTFSVSDHAICLDLIGKTKGLEAAENYFNNLDPSAKNHQSTYGALMNCYCVELEEE 189

Query:   155 ESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLD-MKENGVPPDNFSYRIC 213
             ++ +  + M E+    ++L +N +M +Y    Q EK+P VL+D MK+ G+ P   +Y I 
Sbjct:   190 KAKAHFEIMDELNFVNNSLPFNNMMSMYMRLSQPEKVP-VLVDAMKQRGISPCGVTYSIW 248

Query:   214 INSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIV 273
             + S G+ ++L  +E ++ EM   S     W T+S +A  Y  AGL EKA   LK  E+ +
Sbjct:   249 MQSCGSLNDLDGLEKIIDEMGKDSEAKTTWNTFSNLAAIYTKAGLYEKADSALKSMEEKM 308

Query:   274 S-KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNR-DYITMLGSLVKIGXXX 331
             +  ++D+  ++ L+S YA +    E+ + W   K K + ++N   Y+ ML ++ K+G   
Sbjct:   309 NPNNRDS--HHFLMSLYAGISKGPEVYRVWESLK-KARPEVNNLSYLVMLQAMSKLGDLD 365

Query:   332 XXXXXXXXXXXSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIA 391
                         C+ YD R+ NI +  Y +  M E+A+ +L   +KK K P   +  ++ 
Sbjct:   366 GIKKIFTEWESKCWAYDMRLANIAINTYLKGNMYEEAEKILDGAMKKSKGPFSKARQLLM 425

Query:   392 AGYADKNNMEKAFECMKEALAVHEENKF-WRPKPSLVSSILDWLGDNRDVEEVEAFVSSL 450
                 + +  + A + ++ A++   ENK  W     LVS         +DV+  E F   L
Sbjct:   426 IHLLENDKADLAMKHLEAAVSDSAENKDEWGWSSELVSLFFLHFEKAKDVDGAEDFCKIL 485

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

TAIR|locus:2010459 AT1G28020 "AT1G28020" [Arabidopsis thaliana (taxid:3702)]

 Score = 489 (177.2 bits), Expect = 1.1e-46, P = 1.1e-46
 Identities = 134/470 (28%), Positives = 234/470 (49%)

Query:    42 RISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLA 101
             RI+     +  + PVL+QW  +G +++   ++ +I++LR   +   ALQVSEWMS + + 
Sbjct:    41 RITDALHRNAQIIPVLEQWRQQGNQVNPSHVRVIIKKLRDSDQSLQALQVSEWMSKEKIC 100

Query:   102 FSV-HDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVR-EGLVDESLSL 159
               +  D A +L LI  V GLE AE +F S+    + D +Y +LLN Y R +  + ++ + 
Sbjct:   101 NLIPEDFAARLHLIENVVGLEEAEKFFESIPKNARGDSVYTSLLNSYARSDKTLCKAEAT 160

Query:   160 MQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGA 219
              QKM+++G     + YN +M LY+     EK+ ++LL+MK+N V  DN +    +  Y A
Sbjct:   161 FQKMRDLGLLLRPVPYNAMMSLYSALKNREKVEELLLEMKDNDVEADNVTVNNVLKLYSA 220

Query:   220 RSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA 279
               +++ ME  L + E    I ++W T   +A  Y+ A    KA+  L+  E +V +    
Sbjct:   221 VCDVTEMEKFLNKWEGIHGIKLEWHTTLDMAKAYLRARSSGKAMKMLRLTEQLVDQKSLK 280

Query:   280 LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGXXXXXXXXXXX 339
               Y+HL+  Y   GN++E+++ W L K K  ++ N  Y T++ SL+K+            
Sbjct:   281 SAYDHLMKLYGEAGNREEVLRVWKLYKSKIGERDNNGYRTVIRSLLKVDDIVGAEEIYKV 340

Query:   340 XXXSCYCYDFRVPNIILLGYSQKGMIEKADAVL--KEI----VKKGKTPTPNSWSIIAAG 393
                    +D R+P ++  GY  +GM EKA+ ++  K I    + K  TP    W      
Sbjct:   341 WESLPLEFDHRIPTMLASGYRDRGMTEKAEKLMNSKTIKDRRMNKPVTPLLEQWGDQMKP 400

Query:   394 YADKNNMEKAFECMKE---ALAVHEENKFWRPKPSLVSSILD------WLGDN-RDVEEV 443
              +D   + K     K+   AL V E    W  +  + +  L+      +L +N   +EE 
Sbjct:   401 -SDLKCLIKNLRDSKQFSKALQVSE----WMGEKQVCNLYLEDYAARLYLTENVLGLEEA 455

Query:   444 EAFVSSLKIKVQKRNMYHALTEAHIRS----GQEVDGLLESMKADDIDED 489
             E +  ++   ++  ++Y AL  ++ +S    G  VD +L  M+ +++D D
Sbjct:   456 EKYFENIPENMKDYSVYVALLSSYAKSDKNLGNMVDEILREMEENNVDPD 505

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2034215 PPR596 "AT1G80270" [Arabidopsis thaliana (taxid:3702)]

 Score = 437 (158.9 bits), Expect = 3.6e-41, P = 3.6e-41
 Identities = 123/445 (27%), Positives = 217/445 (48%)

Query:    49 PDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWM-SGQGLAFSVHDH 107
             P +S+   LD+WV EG +I+ +E+ + + QLR R+ +  ALQ+SEW+ + + +  +  D+
Sbjct:   140 PGLSIGSALDKWVEEGNEITRVEIAKAMLQLRRRRMYGRALQMSEWLEANKKIEMTERDY 199

Query:   108 AVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALL-NCYVREGLVDESLSLMQKMKEM 166
             A +LDL  K+RGLE  E     +    K + LY  LL NC V  G V +S  +  KMK++
Sbjct:   200 ASRLDLTVKIRGLEKGEACMQKIPKSFKGEVLYRTLLANC-VAAGNVKKSELVFNKMKDL 258

Query:   167 GSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSM 226
             G   S    + ++ L+    + +KI DVLL M++  + P   +Y+I I+  GA +++S M
Sbjct:   259 GFPLSGFTCDQMLLLHKRIDR-KKIADVLLLMEKENIKPSLLTYKILIDVKGATNDISGM 317

Query:   227 ENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLI 286
             E +L+ M+ +  + +D+ T +  A +Y  AGLK+KA   LK+ E   S   +   +  L+
Sbjct:   318 EQILETMKDEG-VELDFQTQALTARHYSGAGLKDKAEKVLKEMEG-ESLEANRRAFKDLL 375

Query:   287 SHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGXXXXXXXXXXXXXXSCYC 346
             S YASLG +DE+ + W + + K   + +   I   G L K+                   
Sbjct:   376 SIYASLGREDEVKRIWKICESKPYFEESLAAIQAFGKLNKVQEAEAIFEKIVKMDRRASS 435

Query:   347 YDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFEC 406
               +   +++L  Y    M+ K   ++K + + G      +W  +   Y +   +EKA   
Sbjct:   436 STY---SVLLRVYVDHKMLSKGKDLVKRMAESGCRIEATTWDALIKLYVEAGEVEKADSL 492

Query:   407 MKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKR-NMYHALTE 465
             + +A +     K        +       GD  + E++  F+   +     R   + AL +
Sbjct:   493 LDKA-SKQSHTKLMMNSFMYIMDEYSKRGDVHNTEKI--FLKMREAGYTSRLRQFQALMQ 549

Query:   466 AHIRSGQEVDGLLESMKADDIDEDK 490
             A+I +     G+ + +KAD+I  +K
Sbjct:   550 AYINAKSPAYGMRDRLKADNIFPNK 574

GO:0003677 "DNA binding" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0008150 "biological_process" evidence=ND

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q84JR3	PP334_ARATH	No assigned EC number	0.5139	0.9408	0.9369	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00027652001 SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (504 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	490
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-06
COG0457	291	COG0457, NrfG, FOG: TPR repeat [General function p	2e-05
pfam01535	31	pfam01535, PPR, PPR repeat	0.001
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.002
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	0.003
COG0457	291	COG0457, NrfG, FOG: TPR repeat [General function p	0.004

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

 Score = 44.7 bits (107), Expect = 1e-06
 Identities = 12/43 (27%), Positives = 24/43 (55%)

Query: 175 YNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSY 217
           YN ++  Y   G+ E+   +  +MK+ G+ P+ ++Y I I+  
Sbjct: 6   YNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGL 48

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

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

 Score = 46.0 bits (107), Expect = 2e-05
 Identities = 39/200 (19%), Positives = 78/200 (39%), Gaps = 2/200 (1%)

Query: 220 RSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA 279
             EL+    +L+E       S   G    +A   +  G  E+A+  L+K  ++      A
Sbjct: 36  LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLA 95

Query: 280 LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEE 339
               +L     +LG  +E ++               + +  LG+L ++G+ EEA ++ E+
Sbjct: 96  EALLNLGLLLEALGKYEEALELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEK 155

Query: 340 WELSCYCYDFRVPNIILLG--YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK 397
                   +     ++ LG      G  E+A  +L++ +K        +   +   Y   
Sbjct: 156 ALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKL 215

Query: 398 NNMEKAFECMKEALAVHEEN 417
              E+A E  ++AL +  +N
Sbjct: 216 GKYEEALEYYEKALELDPDN 235

Length = 291

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

 Score = 36.3 bits (85), Expect = 0.001
 Identities = 11/28 (39%), Positives = 20/28 (71%)

Query: 140 YGALLNCYVREGLVDESLSLMQKMKEMG 167
           Y +L++ Y + G ++E+L L ++MKE G
Sbjct: 3   YNSLISGYCKAGKLEEALELFKEMKEKG 30

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

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

 Score = 35.8 bits (84), Expect = 0.002
 Identities = 14/44 (31%), Positives = 25/44 (56%)

Query: 353 NIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD 396
           N ++ GY +KG +E+A  +  E+ K+G  P   ++SI+  G   
Sbjct: 7   NTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

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

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

 Score = 34.7 bits (81), Expect = 0.003
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 140 YGALLNCYVREGLVDESLSLMQKMKEMG 167
           Y  L++   + G V+E+L L ++MKE G
Sbjct: 3   YNTLIDGLCKAGRVEEALELFKEMKERG 30

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 = 39.1 bits (89), Expect = 0.004
 Identities = 33/221 (14%), Positives = 76/221 (34%), Gaps = 4/221 (1%)

Query: 198 MKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAG 257
           ++            +   +      L     +L++      +         +       G
Sbjct: 50  LELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALG 109

Query: 258 LKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFW--GLQKIKCKKQLNR 315
             E+A+  L+K   +      A     L +    LG+ +E ++ +   L+      +L  
Sbjct: 110 KYEEALELLEKALALDPDPDLAEALLALGA-LYELGDYEEALELYEKALELDPELNELAE 168

Query: 316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEI 375
             + +   L  +G  EEA ++LE+        D      + L Y + G  E+A    ++ 
Sbjct: 169 ALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKA 228

Query: 376 VKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEE 416
           ++        +   +A    +    E+A E +++AL +  +
Sbjct: 229 LELDP-DNAEALYNLALLLLELGRYEEALEALEKALELDPD 268

Length = 291

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	490
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	100.0
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.95
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.93
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.93
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.93
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.93
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.93
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.93
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.92
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.91
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.9
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.9
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.9
PRK14574	822	hmsH outer membrane protein; Provisional	99.86
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.85
PRK14574	822	hmsH outer membrane protein; Provisional	99.85
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.84
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.83
KOG2003	840	consensus TPR repeat-containing protein [General f	99.82
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.79
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.79
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.77
KOG2076	895	consensus RNA polymerase III transcription factor	99.75
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.74
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.73
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.72
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.72
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.71
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.7
KOG2076	895	consensus RNA polymerase III transcription factor	99.7
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.69
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.68
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.67
KOG2003	840	consensus TPR repeat-containing protein [General f	99.66
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.66
KOG1126	638	consensus DNA-binding cell division cycle control	99.66
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.65
KOG1126	638	consensus DNA-binding cell division cycle control	99.64
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.62
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.62
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.61
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.61
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.6
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.57
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.56
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.51
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.5
PRK12370	553	invasion protein regulator; Provisional	99.49
KOG1129	478	consensus TPR repeat-containing protein [General f	99.49
PRK12370	553	invasion protein regulator; Provisional	99.49
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.48
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.48
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.47
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.46
KOG1129	478	consensus TPR repeat-containing protein [General f	99.46
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.45
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.45
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.43
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.42
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.4
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.4
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.39
PF13041	50	PPR_2: PPR repeat family	99.38
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.38
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.38
PF13041	50	PPR_2: PPR repeat family	99.38
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.37
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.34
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.3
PRK11189	296	lipoprotein NlpI; Provisional	99.28
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.26
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.26
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.26
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.25
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.25
PRK11189	296	lipoprotein NlpI; Provisional	99.25
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.24
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.22
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.21
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.18
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.11
PRK04841	903	transcriptional regulator MalT; Provisional	99.09
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.09
PRK04841	903	transcriptional regulator MalT; Provisional	99.06
KOG1125	579	consensus TPR repeat-containing protein [General f	99.03
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.02
KOG1125	579	consensus TPR repeat-containing protein [General f	99.01
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.0
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	99.0
PLN02789	320	farnesyltranstransferase	98.93
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.93
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.92
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.91
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.91
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.89
PLN02789	320	farnesyltranstransferase	98.88
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.88
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.85
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.85
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.84
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.83
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.82
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.8
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.78
PF12854	34	PPR_1: PPR repeat	98.78
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.77
PF12854	34	PPR_1: PPR repeat	98.76
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.74
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.72
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.71
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.71
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.7
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.7
PRK15359	144	type III secretion system chaperone protein SscB;	98.69
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.69
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.69
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.68
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.63
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.63
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.63
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.61
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.6
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.57
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.57
PRK15359	144	type III secretion system chaperone protein SscB;	98.56
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.54
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.46
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.45
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.37
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.36
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.31
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.27
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.23
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.21
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.2
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.16
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.16
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.14
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.14
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.11
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.1
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	98.1
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	98.08
COG3898	531	Uncharacterized membrane-bound protein [Function u	98.04
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.02
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	98.01
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.01
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.99
KOG0553	304	consensus TPR repeat-containing protein [General f	97.99
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.98
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.93
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.92
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.92
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.91
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.88
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.88
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.88
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.87
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.86
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.86
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.86
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.81
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.81
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.8
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.8
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.79
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.78
KOG0553	304	consensus TPR repeat-containing protein [General f	97.78
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.75
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.74
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.74
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.74
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.7
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.7
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.69
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.67
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.67
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.66
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.65
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.64
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.64
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.62
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.6
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.58
PF12688	120	TPR_5: Tetratrico peptide repeat	97.57
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.56
PF03704	146	BTAD: Bacterial transcriptional activator domain;	97.55
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.55
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.54
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.54
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.53
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.46
PRK10803	263	tol-pal system protein YbgF; Provisional	97.43
PRK11906	458	transcriptional regulator; Provisional	97.4
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.4
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.37
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.35
PF12688	120	TPR_5: Tetratrico peptide repeat	97.29
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.28
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.26
PF13371	73	TPR_9: Tetratricopeptide repeat	97.23
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.21
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.19
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	97.18
PRK10803	263	tol-pal system protein YbgF; Provisional	97.14
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.12
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.1
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.96
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.96
COG4105	254	ComL DNA uptake lipoprotein [General function pred	96.92
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.87
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.83
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.83
PF13371	73	TPR_9: Tetratricopeptide repeat	96.82
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	96.62
KOG1258	577	consensus mRNA processing protein [RNA processing	96.61
KOG4555	175	consensus TPR repeat-containing protein [Function	96.58
PRK15331	165	chaperone protein SicA; Provisional	96.57
COG4105	254	ComL DNA uptake lipoprotein [General function pred	96.52
KOG3941	406	consensus Intermediate in Toll signal transduction	96.43
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.42
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.41
KOG1585	308	consensus Protein required for fusion of vesicles	96.41
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	96.38
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.34
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.33
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.33
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	96.33
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.33
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.27
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	96.27
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.25
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.23
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.2
smart00299	140	CLH Clathrin heavy chain repeat homology.	96.13
PRK15331	165	chaperone protein SicA; Provisional	96.13
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.11
COG3629	280	DnrI DNA-binding transcriptional activator of the	96.07
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.03
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.98
PF13428	44	TPR_14: Tetratricopeptide repeat	95.93
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.91
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	95.87
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.82
KOG2610	491	consensus Uncharacterized conserved protein [Funct	95.76
COG0457	291	NrfG FOG: TPR repeat [General function prediction	95.74
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.68
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	95.61
PF13428	44	TPR_14: Tetratricopeptide repeat	95.58
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	95.57
KOG3941	406	consensus Intermediate in Toll signal transduction	95.54
KOG4555	175	consensus TPR repeat-containing protein [Function	95.53
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	95.5
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.49
COG0457	291	NrfG FOG: TPR repeat [General function prediction	95.42
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	95.42
PRK11906	458	transcriptional regulator; Provisional	95.26
KOG2610	491	consensus Uncharacterized conserved protein [Funct	95.24
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	95.06
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	95.04
PF13512	142	TPR_18: Tetratricopeptide repeat	94.98
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	94.83
PF13512	142	TPR_18: Tetratricopeptide repeat	94.75
COG3629	280	DnrI DNA-binding transcriptional activator of the	94.69
KOG1941	518	consensus Acetylcholine receptor-associated protei	94.67
KOG1941	518	consensus Acetylcholine receptor-associated protei	94.65
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	94.54
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.53
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	94.15
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	94.15
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.88
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	93.72
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	93.7
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	93.5
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	93.33
KOG1258	577	consensus mRNA processing protein [RNA processing	93.28
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	93.16
PF13431	34	TPR_17: Tetratricopeptide repeat	93.09
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.95
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	92.92
COG1747	711	Uncharacterized N-terminal domain of the transcrip	92.89
PF13431	34	TPR_17: Tetratricopeptide repeat	92.88
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	92.8
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	92.79
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	92.78
KOG1550	552	consensus Extracellular protein SEL-1 and related	92.57
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	92.49
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.42
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	92.35
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	92.34
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	92.17
PRK09687	280	putative lyase; Provisional	92.03
PF13929	292	mRNA_stabil: mRNA stabilisation	91.98
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	91.97
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	91.89
KOG1585	308	consensus Protein required for fusion of vesicles	91.82
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	91.75
KOG4234	271	consensus TPR repeat-containing protein [General f	91.59
KOG4234	271	consensus TPR repeat-containing protein [General f	91.46
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	91.36
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	91.36
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.33
COG3947	361	Response regulator containing CheY-like receiver a	91.24
PF13929	292	mRNA_stabil: mRNA stabilisation	91.2
COG4455	273	ImpE Protein of avirulence locus involved in tempe	91.13
KOG4570	418	consensus Uncharacterized conserved protein [Funct	91.09
KOG2063	877	consensus Vacuolar assembly/sorting proteins VPS39	90.81
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	90.73
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	90.65
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	90.4
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	89.82
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	89.75
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	89.71
COG4455	273	ImpE Protein of avirulence locus involved in tempe	89.61
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	89.36
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	89.12
PRK11619	644	lytic murein transglycosylase; Provisional	88.9
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	88.84
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	88.51
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	88.27
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	88.16
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	88.03
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	87.97
COG1747	711	Uncharacterized N-terminal domain of the transcrip	87.8
cd08819	88	CARD_MDA5_2 Caspase activation and recruitment dom	87.69
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	87.45
KOG4648	536	consensus Uncharacterized conserved protein, conta	87.41
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	87.23
KOG4077	149	consensus Cytochrome c oxidase, subunit Va/COX6 [E	87.02
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	86.54
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	86.36
KOG1550	552	consensus Extracellular protein SEL-1 and related	86.15
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	86.01
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	85.62
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	85.42
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	85.07
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	84.87
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	84.48
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	84.47
KOG4648	536	consensus Uncharacterized conserved protein, conta	84.46
KOG0403	645	consensus Neoplastic transformation suppressor Pdc	84.35
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	84.31
PF10579	80	Rapsyn_N: Rapsyn N-terminal myristoylation and lin	84.07
PF09477	116	Type_III_YscG: Bacterial type II secretion system	84.03
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	83.8
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	83.27
PRK09687	280	putative lyase; Provisional	82.77
KOG0686	466	consensus COP9 signalosome, subunit CSN1 [Posttran	82.39
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	82.33
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	81.52
PHA02875	413	ankyrin repeat protein; Provisional	81.41
PF07575	566	Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR0	81.1
COG5159	421	RPN6 26S proteasome regulatory complex component [	80.9
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	80.72
PF07163	309	Pex26: Pex26 protein; InterPro: IPR010797 This fam	80.1

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.8e-67  Score=527.75  Aligned_cols=461  Identities=16%  Similarity=0.157  Sum_probs=430.8

Q ss_pred             chhhhhhhhhccCCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 011236           20 NLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQG   99 (490)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~   99 (490)
                      ++..+.....| +..+|+.++.++++.|+.+.+.. ++++|.+.|..||..+|+.+|.+|++.|+++.|.++|++|.+.|
T Consensus       425 Al~lf~~M~~p-d~~Tyn~LL~a~~k~g~~e~A~~-lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~G  502 (1060)
T PLN03218        425 AFRFAKLIRNP-TLSTFNMLMSVCASSQDIDGALR-VLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAG  502 (1060)
T ss_pred             HHHHHHHcCCC-CHHHHHHHHHHHHhCcCHHHHHH-HHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcC
Confidence            33344333333 78899999999999999888877 99999999999999999999999999999999999999999999


Q ss_pred             CCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC--CChhHHHHHHHHHHhcCChhHHHHHHHHHHh--cCCCCCcchH
Q 011236          100 LAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED--KVDKLYGALLNCYVREGLVDESLSLMQKMKE--MGSFGSALNY  175 (490)
Q Consensus       100 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~--~~~~p~~~~~  175 (490)
                      +.|+..+|+.+|.+|++.|++++|.++|+.|...+  ||..+|+.+|.+|++.|++++|.++|++|..  .|+.||..+|
T Consensus       503 v~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTy  582 (1060)
T PLN03218        503 VEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITV  582 (1060)
T ss_pred             CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHH
Confidence            99999999999999999999999999999998876  8999999999999999999999999999986  6899999999


Q ss_pred             HHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Q 011236          176 NGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII  255 (490)
Q Consensus       176 ~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  255 (490)
                      ++|+.+|++.|++++|.++|++|.+.|+.|+..+|+.+|.+|++.|++++|.++|++|. +.|+.||..+|+.++.+|++
T Consensus       583 naLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~-~~Gv~PD~~TynsLI~a~~k  661 (1060)
T PLN03218        583 GALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMK-KKGVKPDEVFFSALVDVAGH  661 (1060)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHH-HcCCCCCHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999 89999999999999999999


Q ss_pred             cCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011236          256 AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEK  335 (490)
Q Consensus       256 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  335 (490)
                      .|++++|.++|++|.+.+.. ||..+|+.+|.+|++.|++++|.++|++|...+..|+..+|+.||.+|++.|++++|.+
T Consensus       662 ~G~~eeA~~l~~eM~k~G~~-pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAle  740 (1060)
T PLN03218        662 AGDLDKAFEILQDARKQGIK-LGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALE  740 (1060)
T ss_pred             CCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            99999999999999999988 99999999999999999999999999999998889999999999999999999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----c--------------
Q 011236          336 MLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----K--------------  397 (490)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~--------------  397 (490)
                      +|++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+.|+.||..+|+.++..|.+    .              
T Consensus       741 lf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~  820 (1060)
T PLN03218        741 VLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGR  820 (1060)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccc
Confidence            9999999999999999999999999999999999999999999999999999999876432    1              


Q ss_pred             -----CCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc--hhhhHHHHHHHHhc
Q 011236          398 -----NNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK--RNMYHALTEAHIRS  470 (490)
Q Consensus       398 -----~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~l~~~~~~~  470 (490)
                           +..++|..+|++|++     .|+.||..||+.++.++++.+..+.+..+++.|...+..  ..+|++|+.++.+.
T Consensus       821 ~~~~n~w~~~Al~lf~eM~~-----~Gi~Pd~~T~~~vL~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~~~~  895 (1060)
T PLN03218        821 PQIENKWTSWALMVYRETIS-----AGTLPTMEVLSQVLGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEY  895 (1060)
T ss_pred             cccccchHHHHHHHHHHHHH-----CCCCCCHHHHHHHHHHhcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhhccC
Confidence                 224679999999999     999999999999998888999999999999988765544  88999999999665


Q ss_pred             CCcHHHHHHHHHhCCCCCC
Q 011236          471 GQEVDGLLESMKADDIDED  489 (490)
Q Consensus       471 g~~a~~~~~~m~~~~~~pd  489 (490)
                      .++|..++++|.+.|+.||
T Consensus       896 ~~~A~~l~~em~~~Gi~p~  914 (1060)
T PLN03218        896 DPRAFSLLEEAASLGVVPS  914 (1060)
T ss_pred             hHHHHHHHHHHHHcCCCCC
Confidence            5789999999999999997

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=3.5e-67  Score=525.67  Aligned_cols=448  Identities=15%  Similarity=0.159  Sum_probs=426.1

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCC-CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQ-KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQ  110 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  110 (490)
                      +...+..++..+++.|+..+++. ++++|...|+ +++...++.++..|.+.|.+++|+.+|+.|..    |+..+|+.+
T Consensus       369 ~~~~~~~~y~~l~r~G~l~eAl~-Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~----pd~~Tyn~L  443 (1060)
T PLN03218        369 KSPEYIDAYNRLLRDGRIKDCID-LLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRN----PTLSTFNML  443 (1060)
T ss_pred             CchHHHHHHHHHHHCcCHHHHHH-HHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCC----CCHHHHHHH
Confidence            45668889999999999988888 9999999985 57888889999999999999999999999875    799999999


Q ss_pred             HHHHHhhcCHHHHHHHHHHccccC--CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCc
Q 011236          111 LDLIGKVRGLESAETYFNSLNDED--KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQH  188 (490)
Q Consensus       111 ~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  188 (490)
                      +.+|++.|+++.|.++|+.|.+.+  ||..+|++||.+|++.|++++|.++|++|.+.|+.||..+|+.||.+|++.|++
T Consensus       444 L~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~  523 (1060)
T PLN03218        444 MSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQV  523 (1060)
T ss_pred             HHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCH
Confidence            999999999999999999999887  799999999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHh-CCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Q 011236          189 EKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMES-QSHISMDWGTYSTVANYYIIAGLKEKAIIYLK  267 (490)
Q Consensus       189 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~  267 (490)
                      ++|.++|++|.+.|+.||..+|+.+|.+|++.|++++|.++|++|.. ..++.||..+|+++|.+|++.|++++|.++|+
T Consensus       524 eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~  603 (1060)
T PLN03218        524 AKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQ  603 (1060)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999972 26789999999999999999999999999999


Q ss_pred             HHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 011236          268 KCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY  347 (490)
Q Consensus       268 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  347 (490)
                      .|.+.+.. |+..+|+.+|.+|++.|++++|.++|++|...+..||..+|+.++.+|++.|++++|.+++++|.+.|+.|
T Consensus       604 ~M~e~gi~-p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~p  682 (1060)
T PLN03218        604 MIHEYNIK-GTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKL  682 (1060)
T ss_pred             HHHHcCCC-CChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCC
Confidence            99999988 99999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhH
Q 011236          348 DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLV  427 (490)
Q Consensus       348 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~  427 (490)
                      |..+|++||.+|++.|++++|.++|++|.+.|+.||..+|+.||.+|++.|++++|.++|++|..     .|+.||..||
T Consensus       683 d~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~-----~Gi~Pd~~Ty  757 (1060)
T PLN03218        683 GTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKR-----LGLCPNTITY  757 (1060)
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-----cCCCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999998     8999999999


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHhcccc--hhhhHHHHHHHHh----c-------------------C--CcHHHHHHH
Q 011236          428 SSILDWLGDNRDVEEVEAFVSSLKIKVQK--RNMYHALTEAHIR----S-------------------G--QEVDGLLES  480 (490)
Q Consensus       428 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~l~~~~~~----~-------------------g--~~a~~~~~~  480 (490)
                      +.++.+|++.|+++.|.+++++|.+.+..  ..+|++++..|.+    +                   +  +.|..+|++
T Consensus       758 ~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~e  837 (1060)
T PLN03218        758 SILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRE  837 (1060)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHH
Confidence            99999999999999999999999998876  7889999876542    1                   1  469999999


Q ss_pred             HHhCCCCCCC
Q 011236          481 MKADDIDEDK  490 (490)
Q Consensus       481 m~~~~~~pd~  490 (490)
                      |.+.|+.||.
T Consensus       838 M~~~Gi~Pd~  847 (1060)
T PLN03218        838 TISAGTLPTM  847 (1060)
T ss_pred             HHHCCCCCCH
Confidence            9999999983

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=3.1e-63  Score=506.53  Aligned_cols=451  Identities=15%  Similarity=0.115  Sum_probs=397.0

Q ss_pred             ccccchhhhhhhhhccCCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH
Q 011236           16 FTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWM   95 (490)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~   95 (490)
                      ....++..+.....+ +..+|+.++.++++.|+.++++. ++++|...|+.||..+|+.++++|+..+++..+.+++..|
T Consensus       136 ~~~~A~~~f~~m~~~-d~~~~n~li~~~~~~g~~~~A~~-~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~  213 (857)
T PLN03077        136 ELVHAWYVFGKMPER-DLFSWNVLVGGYAKAGYFDEALC-LYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHV  213 (857)
T ss_pred             ChHHHHHHHhcCCCC-CeeEHHHHHHHHHhCCCHHHHHH-HHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHH
Confidence            344455556555555 88999999999999999999888 9999999999999999999999999999999999999999


Q ss_pred             HhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchH
Q 011236           96 SGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNY  175 (490)
Q Consensus        96 ~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~  175 (490)
                      .+.|+.++..+++.++.+|++.|++++|..+|++|..  ||..+||++|.+|++.|++++|+++|++|.+.|+.||..||
T Consensus       214 ~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~--~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty  291 (857)
T PLN03077        214 VRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPR--RDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTI  291 (857)
T ss_pred             HHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCC--CCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHH
Confidence            9999999999999999999999999999999999986  68889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Q 011236          176 NGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII  255 (490)
Q Consensus       176 ~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  255 (490)
                      +.++.+|++.|+.+.+.+++..|.+.|+.||..+|+.|+.+|++.|++++|.++|++|. .    ||..+|+.+|.+|++
T Consensus       292 ~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~-~----~d~~s~n~li~~~~~  366 (857)
T PLN03077        292 TSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRME-T----KDAVSWTAMISGYEK  366 (857)
T ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCC-C----CCeeeHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999996 3    678899999999999


Q ss_pred             cCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011236          256 AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEK  335 (490)
Q Consensus       256 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  335 (490)
                      .|++++|+++|++|...+.. ||..||+.++.+|++.|+++.|.++++.+...+..|+..+|+.|+.+|++.|++++|.+
T Consensus       367 ~g~~~~A~~lf~~M~~~g~~-Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~  445 (857)
T PLN03077        367 NGLPDKALETYALMEQDNVS-PDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALE  445 (857)
T ss_pred             CCCHHHHHHHHHHHHHhCCC-CCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHH
Confidence            99999999999999999988 99999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhh
Q 011236          336 MLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHE  415 (490)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  415 (490)
                      +|++|.+    +|..+|+.+|.+|++.|+.++|..+|++|.. ++.||..||+.++.+|++.|+.+.+.+++..+.+   
T Consensus       446 vf~~m~~----~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~---  517 (857)
T PLN03077        446 VFHNIPE----KDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLR---  517 (857)
T ss_pred             HHHhCCC----CCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHH---
Confidence            9999854    6888999999999999999999999999986 5889999999999888888888888888888777   


Q ss_pred             cCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccchhhhHHHHHHHHhcC--CcHHHHHHHHHhCCCCCC
Q 011236          416 ENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSG--QEVDGLLESMKADDIDED  489 (490)
Q Consensus       416 ~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~~~pd  489 (490)
                        .|+.|+..++++++.+|++.|+.++|.++|+.+   .++..+|+++|.+|++.|  ++|.++|++|.+.|+.||
T Consensus       518 --~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~---~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd  588 (857)
T PLN03077        518 --TGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH---EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPD  588 (857)
T ss_pred             --hCCCccceechHHHHHHHHcCCHHHHHHHHHhc---CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC
Confidence              666666655555555555555555555555554   122555555555555555  555555555555555555

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

Probab=100.00  E-value=2.9e-62  Score=487.92  Aligned_cols=439  Identities=15%  Similarity=0.168  Sum_probs=344.4

Q ss_pred             CCCcccHHHhhccCCCCCCChHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHH
Q 011236           33 PVARNNLYSRISPLGDPDVSLTPVLDQWVLEG-QKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQL  111 (490)
Q Consensus        33 ~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  111 (490)
                      ..+|+.++.++.+.|++.+++. +++.|...+ ..||..+|+.++.+|.+.++++.+.+++..|.+.|+.|+..+++.++
T Consensus        87 ~~~~~~~i~~l~~~g~~~~Al~-~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n~Li  165 (697)
T PLN03081         87 GVSLCSQIEKLVACGRHREALE-LFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMNRVL  165 (697)
T ss_pred             ceeHHHHHHHHHcCCCHHHHHH-HHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHHHHH
Confidence            3479999999999999999888 888888764 78999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcH
Q 011236          112 DLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKI  191 (490)
Q Consensus       112 ~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  191 (490)
                      .+|++.|+++.|.++|++|..  ||..+||+++.+|++.|++++|+++|++|.+.|+.|+..+|+.++.+|++.|+.+.+
T Consensus       166 ~~y~k~g~~~~A~~lf~~m~~--~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~  243 (697)
T PLN03081        166 LMHVKCGMLIDARRLFDEMPE--RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAG  243 (697)
T ss_pred             HHHhcCCCHHHHHHHHhcCCC--CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHH
Confidence            999999999999999999986  789999999999999999999999999999999988888888777777777777777


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhh
Q 011236          192 PDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCED  271 (490)
Q Consensus       192 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  271 (490)
                      .+++..+.+.|+.||..+|+.|+.+|++.|++++|.++|++|. .    +|..+||.+|.+|++.|++++|.++|++|..
T Consensus       244 ~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~-~----~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~  318 (697)
T PLN03081        244 QQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP-E----KTTVAWNSMLAGYALHGYSEEALCLYYEMRD  318 (697)
T ss_pred             HHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCC-C----CChhHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            7777777777777777777777777777777777777777775 2    4666777777777777777777777777777


Q ss_pred             hhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchh
Q 011236          272 IVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRV  351 (490)
Q Consensus       272 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  351 (490)
                      .+.. ||..||+.++.+|++.|++++|.+++..|...+..|+..+|++|+.+|++.|++++|.++|++|.    .||..+
T Consensus       319 ~g~~-pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~~d~~t  393 (697)
T PLN03081        319 SGVS-IDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKNLIS  393 (697)
T ss_pred             cCCC-CCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----CCCeee
Confidence            6666 77777777777777777777777777777777666777777777777777777777777777663    356677


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSIL  431 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~  431 (490)
                      ||+||.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|++.|..++|.++|+.|.+    ..|+.|+..+|+.++
T Consensus       394 ~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~----~~g~~p~~~~y~~li  469 (697)
T PLN03081        394 WNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSE----NHRIKPRAMHYACMI  469 (697)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHH----hcCCCCCccchHhHH
Confidence            7777777777777777777777777777777777777777777777777777777777764    135555555555555


Q ss_pred             HHHHcCCCHHHHH--------------------------------HHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHH
Q 011236          432 DWLGDNRDVEEVE--------------------------------AFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDG  476 (490)
Q Consensus       432 ~~~~~~g~~~~a~--------------------------------~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~  476 (490)
                      .+|++.|++++|.                                .+++++.+..|. ..+|..|++.|++.|  ++|.+
T Consensus       470 ~~l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A~~  549 (697)
T PLN03081        470 ELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAK  549 (697)
T ss_pred             HHHHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHHHH
Confidence            5555555555554                                444555555555 678888888888888  88888


Q ss_pred             HHHHHHhCCCCC
Q 011236          477 LLESMKADDIDE  488 (490)
Q Consensus       477 ~~~~m~~~~~~p  488 (490)
                      +++.|+++|+..
T Consensus       550 v~~~m~~~g~~k  561 (697)
T PLN03081        550 VVETLKRKGLSM  561 (697)
T ss_pred             HHHHHHHcCCcc
Confidence            888898888764

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=2.2e-61  Score=492.97  Aligned_cols=464  Identities=14%  Similarity=0.112  Sum_probs=355.1

Q ss_pred             hhhhhhcCCccccccchhhhhhhhhccCCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC
Q 011236            5 LFSTIFNNKRNFTKTNLEIFTRAYRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKR   84 (490)
Q Consensus         5 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~   84 (490)
                      ++..+.+.+  ....+...|.....+ +..+|+.++.++++.|+.++++. ++++|...|+.||..+|+.++.+|++.|+
T Consensus       228 Li~~y~k~g--~~~~A~~lf~~m~~~-d~~s~n~li~~~~~~g~~~eAl~-lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~  303 (857)
T PLN03077        228 LITMYVKCG--DVVSARLVFDRMPRR-DCISWNAMISGYFENGECLEGLE-LFFTMRELSVDPDLMTITSVISACELLGD  303 (857)
T ss_pred             HHHHHhcCC--CHHHHHHHHhcCCCC-CcchhHHHHHHHHhCCCHHHHHH-HHHHHHHcCCCCChhHHHHHHHHHHhcCC
Confidence            444444433  344556666665555 88999999999999999999988 99999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHH
Q 011236           85 FKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMK  164 (490)
Q Consensus        85 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~  164 (490)
                      ++.|.+++..|.+.|..|+..+++.++.+|++.|++++|.++|++|..  ||..+||++|.+|++.|++++|+++|++|.
T Consensus       304 ~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~--~d~~s~n~li~~~~~~g~~~~A~~lf~~M~  381 (857)
T PLN03077        304 ERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMET--KDAVSWTAMISGYEKNGLPDKALETYALME  381 (857)
T ss_pred             hHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCC--CCeeeHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999975  788899999999999999999999999999


Q ss_pred             hcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHH
Q 011236          165 EMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWG  244 (490)
Q Consensus       165 ~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  244 (490)
                      +.|+.||..||+.++.+|++.|+++.|.++++.|.+.|+.|+..+|+.|+.+|++.|++++|.++|++|. +    +|..
T Consensus       382 ~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~-~----~d~v  456 (857)
T PLN03077        382 QDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIP-E----KDVI  456 (857)
T ss_pred             HhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCC-C----CCee
Confidence            9999999999999999999999999999999999999999999999999999999999999999999997 4    5667


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSL  324 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  324 (490)
                      +|+.+|.+|++.|+.++|+.+|++|... .. ||..||+.++.+|++.|+++.+.+++..+...+..++..++++|+.+|
T Consensus       457 s~~~mi~~~~~~g~~~eA~~lf~~m~~~-~~-pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y  534 (857)
T PLN03077        457 SWTSIIAGLRLNNRCFEALIFFRQMLLT-LK-PNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLY  534 (857)
T ss_pred             eHHHHHHHHHHCCCHHHHHHHHHHHHhC-CC-CCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHH
Confidence            8999999999999999999999999764 44 888888888777777776666666666666655555555555555555


Q ss_pred             HhcCCHHHHHH------------------------------HHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          325 VKIGELEEAEK------------------------------MLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKE  374 (490)
Q Consensus       325 ~~~~~~~~a~~------------------------------~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  374 (490)
                      ++.|++++|.+                              +|++|.+.|+.||..||+.++.+|++.|++++|.++|+.
T Consensus       535 ~k~G~~~~A~~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~  614 (857)
T PLN03077        535 VRCGRMNYAWNQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHS  614 (857)
T ss_pred             HHcCCHHHHHHHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHH
Confidence            55555555544                              444444444444444444444444444444444444444


Q ss_pred             HH-HcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          375 IV-KKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       375 m~-~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      |. +.|+.|+..+|+.++.+|++.|++++|.+++++|        .++||..+|.+|+.+|...|+.+.++...+++.+.
T Consensus       615 M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m--------~~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l  686 (857)
T PLN03077        615 MEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKM--------PITPDPAVWGALLNACRIHRHVELGELAAQHIFEL  686 (857)
T ss_pred             HHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHC--------CCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhh
Confidence            44 3444444444444444444444444444444443        13344444555555444444444444444444555


Q ss_pred             ccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhCCCCCC
Q 011236          454 VQK-RNMYHALTEAHIRSG--QEVDGLLESMKADDIDED  489 (490)
Q Consensus       454 ~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~~~pd  489 (490)
                      .|. ...|..|.+.|...|  ++|.++.+.|+++|+.++
T Consensus       687 ~p~~~~~y~ll~n~ya~~g~~~~a~~vr~~M~~~g~~k~  725 (857)
T PLN03077        687 DPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVD  725 (857)
T ss_pred             CCCCcchHHHHHHHHHHCCChHHHHHHHHHHHHcCCCCC
Confidence            555 666667777777778  788888888988888875

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

Probab=100.00  E-value=1.9e-58  Score=460.61  Aligned_cols=403  Identities=15%  Similarity=0.182  Sum_probs=382.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCC-CCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC--CChhHHH
Q 011236           65 QKISELELQRVIRQLRSRKRFKHALQVSEWMSGQG-LAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED--KVDKLYG  141 (490)
Q Consensus        65 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~  141 (490)
                      ...+..+|+.+|..+.+.|++++|+++|++|...+ ..|+..+|+.++.+|++.++++.|.+++..|...+  ||..+||
T Consensus        83 ~~~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n  162 (697)
T PLN03081         83 IRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN  162 (697)
T ss_pred             CCCCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHH
Confidence            44567799999999999999999999999999865 57899999999999999999999999999999876  8999999


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccC
Q 011236          142 ALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARS  221 (490)
Q Consensus       142 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g  221 (490)
                      .|+.+|++.|++++|.++|++|.+    ||..+||.++.+|++.|++++|.++|++|.+.|+.||..||+.++.+|++.|
T Consensus       163 ~Li~~y~k~g~~~~A~~lf~~m~~----~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~  238 (697)
T PLN03081        163 RVLLMHVKCGMLIDARRLFDEMPE----RNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLG  238 (697)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcCCC----CCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCC
Confidence            999999999999999999999974    7999999999999999999999999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHH
Q 011236          222 ELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKF  301 (490)
Q Consensus       222 ~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  301 (490)
                      +.+.+.+++..+. +.|+.||..+|+.|+.+|++.|++++|.++|++|..     +|..+|+.++.+|++.|++++|+++
T Consensus       239 ~~~~~~~l~~~~~-~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~-----~~~vt~n~li~~y~~~g~~~eA~~l  312 (697)
T PLN03081        239 SARAGQQLHCCVL-KTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPE-----KTTVAWNSMLAGYALHGYSEEALCL  312 (697)
T ss_pred             cHHHHHHHHHHHH-HhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCC-----CChhHHHHHHHHHHhCCCHHHHHHH
Confidence            9999999999999 899999999999999999999999999999999853     7999999999999999999999999


Q ss_pred             HHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          302 WGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       302 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      |++|...+..||..||+.++.+|++.|++++|.+++..|.+.|+.||..+|++|+++|++.|++++|.++|++|.+    
T Consensus       313 f~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~----  388 (697)
T PLN03081        313 YYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPR----  388 (697)
T ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCC----
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999964    


Q ss_pred             CCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhc-ccc--hh
Q 011236          382 PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK-VQK--RN  458 (490)
Q Consensus       382 p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~--~~  458 (490)
                      ||..+|++||.+|++.|+.++|.++|++|.+     .|+.||..||+.++.+|.+.|+.++|.++|+.|.+. +..  ..
T Consensus       389 ~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~-----~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~  463 (697)
T PLN03081        389 KNLISWNALIAGYGNHGRGTKAVEMFERMIA-----EGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAM  463 (697)
T ss_pred             CCeeeHHHHHHHHHHcCCHHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCcc
Confidence            6999999999999999999999999999999     899999999999999999999999999999999864 333  78


Q ss_pred             hhHHHHHHHHhcC--CcHHHHHHHHHhCCCCCC
Q 011236          459 MYHALTEAHIRSG--QEVDGLLESMKADDIDED  489 (490)
Q Consensus       459 ~~~~l~~~~~~~g--~~a~~~~~~m~~~~~~pd  489 (490)
                      +|+.++++|++.|  ++|.+++++|   ++.||
T Consensus       464 ~y~~li~~l~r~G~~~eA~~~~~~~---~~~p~  493 (697)
T PLN03081        464 HYACMIELLGREGLLDEAYAMIRRA---PFKPT  493 (697)
T ss_pred             chHhHHHHHHhcCCHHHHHHHHHHC---CCCCC
Confidence            9999999999999  9999998876   45565

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

Probab=100.00  E-value=2.2e-29  Score=263.39  Aligned_cols=427  Identities=15%  Similarity=0.105  Sum_probs=253.3

Q ss_pred             CcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 011236           35 ARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLI  114 (490)
Q Consensus        35 ~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  114 (490)
                      .+..+...+...|+.+++.. .+++.... .+.+...+..+...+...|++++|.+.++.+.+.+ +.+...+..+...+
T Consensus       467 ~~~~l~~~~~~~~~~~~A~~-~~~~a~~~-~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~  543 (899)
T TIGR02917       467 LHNLLGAIYLGKGDLAKARE-AFEKALSI-EPDFFPAAANLARIDIQEGNPDDAIQRFEKVLTID-PKNLRAILALAGLY  543 (899)
T ss_pred             HHHHHHHHHHhCCCHHHHHH-HHHHHHhh-CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHH
Confidence            34444444444454444444 33333322 12233444444555555555555555555555443 23444445555555


Q ss_pred             HhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHH
Q 011236          115 GKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPD  193 (490)
Q Consensus       115 ~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  193 (490)
                      .+.|+.++|..+|+++...+| +...+..++..+.+.|++++|..+++.+.... +.+..+|..+..++...|++++|..
T Consensus       544 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~  622 (899)
T TIGR02917       544 LRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAA-PDSPEAWLMLGRAQLAAGDLNKAVS  622 (899)
T ss_pred             HHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            555555555555555544443 34445555555555555555555555555442 2244555666666666666666666


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhh
Q 011236          194 VLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIV  273 (490)
Q Consensus       194 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~  273 (490)
                      .|+.+.+.. +.+...+..+..++...|++++|..+|+++. +... .+..++..++..+...|++++|..+++.+....
T Consensus       623 ~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~-~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  699 (899)
T TIGR02917       623 SFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRAL-ELKP-DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQH  699 (899)
T ss_pred             HHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHH-hcCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            666665532 1234455555566666666666666666655 3332 345555566666666666666666666665544


Q ss_pred             ccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHH
Q 011236          274 SKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPN  353 (490)
Q Consensus       274 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  353 (490)
                      +  .+...+..+...+...|++++|...|+.+....+  +..++..+..++.+.|++++|.+.++.+.+. .+.+...+.
T Consensus       700 ~--~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~-~~~~~~~~~  774 (899)
T TIGR02917       700 P--KAALGFELEGDLYLRQKDYPAAIQAYRKALKRAP--SSQNAIKLHRALLASGNTAEAVKTLEAWLKT-HPNDAVLRT  774 (899)
T ss_pred             c--CChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCC--CchHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHH
Confidence            3  4555566666666666666666666666655443  3355556666666666777776666666664 233555666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILD  432 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~  432 (490)
                      .+...|...|++++|...|+++.+.++. +..+++.+...+...|+ .+|+.+++++..       ..|+ ..++..+..
T Consensus       775 ~la~~~~~~g~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~-------~~~~~~~~~~~~~~  845 (899)
T TIGR02917       775 ALAELYLAQKDYDKAIKHYRTVVKKAPD-NAVVLNNLAWLYLELKD-PRALEYAEKALK-------LAPNIPAILDTLGW  845 (899)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcCc-HHHHHHHHHHHh-------hCCCCcHHHHHHHH
Confidence            6666677777777777777777666543 56667777777777777 667777777766       2233 355666777


Q ss_pred             HHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHH
Q 011236          433 WLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMK  482 (490)
Q Consensus       433 ~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~  482 (490)
                      .+...|++++|..+++++.+.+|. +.++..++.++.+.|  ++|.+++++|.
T Consensus       846 ~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       846 LLVEKGEADRALPLLRKAVNIAPEAAAIRYHLALALLATGRKAEARKELDKLL  898 (899)
T ss_pred             HHHHcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            777788888888888888887777 778888888888888  77888888775

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

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

Probab=100.00  E-value=1.1e-28  Score=258.30  Aligned_cols=430  Identities=12%  Similarity=0.021  Sum_probs=338.9

Q ss_pred             ccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHh
Q 011236           37 NNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGK  116 (490)
Q Consensus        37 ~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  116 (490)
                      ..++..+.+.|+.+++.. +++.+... .+.+...+..+...+...|++++|.+.|+++.+.. +.+...+..+...+..
T Consensus       435 ~~l~~~~~~~~~~~~A~~-~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~  511 (899)
T TIGR02917       435 LLLILSYLRSGQFDKALA-AAKKLEKK-QPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQ  511 (899)
T ss_pred             HHHHHHHHhcCCHHHHHH-HHHHHHHh-CCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHH
Confidence            334455555666655555 55555433 44567778888888888888888888888887765 4556666777778888


Q ss_pred             hcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHH
Q 011236          117 VRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVL  195 (490)
Q Consensus       117 ~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~  195 (490)
                      .|++++|.+.|+.+....| +..++..+...+.+.|+.++|..+++++...+.. +...+..++..+...|++++|..++
T Consensus       512 ~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~  590 (899)
T TIGR02917       512 EGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQ-EIEPALALAQYYLGKGQLKKALAIL  590 (899)
T ss_pred             CCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-chhHHHHHHHHHHHCCCHHHHHHHH
Confidence            8888888888888877766 5677888888888888888888888888776543 6667777888888888888888888


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhcc
Q 011236          196 LDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK  275 (490)
Q Consensus       196 ~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~  275 (490)
                      +.+.+. .+.+..+|..+..++...|++++|...|+++. +.+. .+...+..+..++...|++++|...|+++....+ 
T Consensus       591 ~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~-~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-  666 (899)
T TIGR02917       591 NEAADA-APDSPEAWLMLGRAQLAAGDLNKAVSSFKKLL-ALQP-DSALALLLLADAYAVMKNYAKAITSLKRALELKP-  666 (899)
T ss_pred             HHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-
Confidence            888765 34567788888888888888888888888887 4443 4566777888888888888888888888877554 


Q ss_pred             CCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHH
Q 011236          276 SKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNII  355 (490)
Q Consensus       276 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  355 (490)
                       .+..++..++..+...|++++|.++++.+....+ .+...+..+...+...|++++|...++.+...+  |+..++..+
T Consensus       667 -~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~~l  742 (899)
T TIGR02917       667 -DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHP-KAALGFELEGDLYLRQKDYPAAIQAYRKALKRA--PSSQNAIKL  742 (899)
T ss_pred             -CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc-CChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCchHHHHH
Confidence             5677888888888888888888888887777665 666778888888888999999999999888753  444677778


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHH
Q 011236          356 LLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLG  435 (490)
Q Consensus       356 ~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~  435 (490)
                      ...+.+.|++++|...++++.+..+. +...+..+...|...|++++|.++|+++++.      .+++...+..+...+.
T Consensus       743 ~~~~~~~g~~~~A~~~~~~~l~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~------~p~~~~~~~~l~~~~~  815 (899)
T TIGR02917       743 HRALLASGNTAEAVKTLEAWLKTHPN-DAVLRTALAELYLAQKDYDKAIKHYRTVVKK------APDNAVVLNNLAWLYL  815 (899)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHh------CCCCHHHHHHHHHHHH
Confidence            88888999999999999988887654 7788888888899999999999999999872      2345677888888888


Q ss_pred             cCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhCCC
Q 011236          436 DNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKADDI  486 (490)
Q Consensus       436 ~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~~  486 (490)
                      ..|+ .+|...++++.+..|. +..+..++..+...|  ++|.++++++.+.+.
T Consensus       816 ~~~~-~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~  868 (899)
T TIGR02917       816 ELKD-PRALEYAEKALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAP  868 (899)
T ss_pred             hcCc-HHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            8888 7799999998888888 888888899998888  889999999988654

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.

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

Probab=99.95  E-value=3.3e-25  Score=198.82  Aligned_cols=431  Identities=15%  Similarity=0.112  Sum_probs=297.3

Q ss_pred             cccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011236           36 RNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIG  115 (490)
Q Consensus        36 ~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  115 (490)
                      .-.|...+-+.|+..++.+  .-.|+-..-+.+....-.+-..+.+..+.+.....-....+.. +.-.++|..+...+.
T Consensus        51 ~l~lah~~yq~gd~~~a~~--h~nmv~~~d~t~~~~llll~ai~~q~~r~d~s~a~~~~a~r~~-~q~ae~ysn~aN~~k  127 (966)
T KOG4626|consen   51 RLELAHRLYQGGDYKQAEK--HCNMVGQEDPTNTERLLLLSAIFFQGSRLDKSSAGSLLAIRKN-PQGAEAYSNLANILK  127 (966)
T ss_pred             HHHHHHHHHhccCHHHHHH--HHhHhhccCCCcccceeeehhhhhcccchhhhhhhhhhhhhcc-chHHHHHHHHHHHHH
Confidence            4455555666666665554  2233322223333333333344445555555544444444443 345667777777787


Q ss_pred             hhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcc-hHHHHHHHHHhcCCcCcHHH
Q 011236          116 KVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSAL-NYNGIMCLYTNTGQHEKIPD  193 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~-~~~~l~~~~~~~~~~~~a~~  193 (490)
                      ..|++++|+.+++.+.+..| ....|..+..++...|+.+.|.+.|.+..+.+  |+.. ..+.+.......|+.++|..
T Consensus       128 erg~~~~al~~y~~aiel~p~fida~inla~al~~~~~~~~a~~~~~~alqln--P~l~ca~s~lgnLlka~Grl~ea~~  205 (966)
T KOG4626|consen  128 ERGQLQDALALYRAAIELKPKFIDAYINLAAALVTQGDLELAVQCFFEALQLN--PDLYCARSDLGNLLKAEGRLEEAKA  205 (966)
T ss_pred             HhchHHHHHHHHHHHHhcCchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcC--cchhhhhcchhHHHHhhcccchhHH
Confidence            88888888888888877776 47778888888888888888888887777763  3322 22334444455677888888


Q ss_pred             HHHHHHHCCCCCC-HHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhh
Q 011236          194 VLLDMKENGVPPD-NFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDI  272 (490)
Q Consensus       194 ~~~~m~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  272 (490)
                      .|.+.++.  .|. ...|+.|...+-..|+...|++.|++.. +.++ --...|-.|...|...+.+++|...|.+....
T Consensus       206 cYlkAi~~--qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAv-kldP-~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~l  281 (966)
T KOG4626|consen  206 CYLKAIET--QPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAV-KLDP-NFLDAYINLGNVYKEARIFDRAVSCYLRALNL  281 (966)
T ss_pred             HHHHHHhh--CCceeeeehhcchHHhhcchHHHHHHHHHHhh-cCCC-cchHHHhhHHHHHHHHhcchHHHHHHHHHHhc
Confidence            87777764  232 3457777777777888888888888777 4443 23556777888888888888888888777665


Q ss_pred             hccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhH
Q 011236          273 VSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVP  352 (490)
Q Consensus       273 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  352 (490)
                      .+  .....+..+...|...|.++.|+..|++.+...+ .-...|+.|..++-..|++.+|.+.+.+..... +......
T Consensus       282 rp--n~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P-~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~-p~hadam  357 (966)
T KOG4626|consen  282 RP--NHAVAHGNLACIYYEQGLLDLAIDTYKRALELQP-NFPDAYNNLANALKDKGSVTEAVDCYNKALRLC-PNHADAM  357 (966)
T ss_pred             CC--cchhhccceEEEEeccccHHHHHHHHHHHHhcCC-CchHHHhHHHHHHHhccchHHHHHHHHHHHHhC-CccHHHH
Confidence            44  4567777777777888888888888887777665 455678888888888888888888888877752 2234566


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHH
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSIL  431 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~  431 (490)
                      +.|...|...|.+++|..+|....+-.+. -...++.|...|-++|++++|+..++++++       +.|+. ..|+.+.
T Consensus       358 ~NLgni~~E~~~~e~A~~ly~~al~v~p~-~aaa~nNLa~i~kqqgnl~~Ai~~Ykealr-------I~P~fAda~~NmG  429 (966)
T KOG4626|consen  358 NNLGNIYREQGKIEEATRLYLKALEVFPE-FAAAHNNLASIYKQQGNLDDAIMCYKEALR-------IKPTFADALSNMG  429 (966)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHhhChh-hhhhhhhHHHHHHhcccHHHHHHHHHHHHh-------cCchHHHHHHhcc
Confidence            77788888888888888888877764322 334677888888888888888888888876       66776 6778888


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhCCCCCC
Q 011236          432 DWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKADDIDED  489 (490)
Q Consensus       432 ~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~~~pd  489 (490)
                      ..|...|+.+.|.+.+.++....|. .+.++.|...|...|  .+|+.-++...+  ++||
T Consensus       430 nt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLk--lkPD  488 (966)
T KOG4626|consen  430 NTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALK--LKPD  488 (966)
T ss_pred             hHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc--cCCC
Confidence            8888888888888888888888887 888888888888888  777777776665  4444

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

Probab=99.93  E-value=4.1e-23  Score=185.51  Aligned_cols=384  Identities=15%  Similarity=0.117  Sum_probs=333.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhH-HHHH
Q 011236           65 QKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKL-YGAL  143 (490)
Q Consensus        65 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~-~~~l  143 (490)
                      .+--..+|..+...+...|+++.|+.+++.+++.. +-..+.|.-+..++...|+.+.|.+.|....+.+|+... .+.+
T Consensus       112 ~~q~ae~ysn~aN~~kerg~~~~al~~y~~aiel~-p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~l  190 (966)
T KOG4626|consen  112 NPQGAEAYSNLANILKERGQLQDALALYRAAIELK-PKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDL  190 (966)
T ss_pred             cchHHHHHHHHHHHHHHhchHHHHHHHHHHHHhcC-chhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcch
Confidence            34467789999999999999999999999999987 457788889999999999999999999999999986444 4445


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCC-HHHHHHHHHHHhccCC
Q 011236          144 LNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPD-NFSYRICINSYGARSE  222 (490)
Q Consensus       144 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~g~  222 (490)
                      ...+-..|+.++|...+.+..+.... -...|+.|...+...|+...|++.|++..+.  .|+ ...|-.|...|...+.
T Consensus       191 gnLlka~Grl~ea~~cYlkAi~~qp~-fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl--dP~f~dAYiNLGnV~ke~~~  267 (966)
T KOG4626|consen  191 GNLLKAEGRLEEAKACYLKAIETQPC-FAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL--DPNFLDAYINLGNVYKEARI  267 (966)
T ss_pred             hHHHHhhcccchhHHHHHHHHhhCCc-eeeeehhcchHHhhcchHHHHHHHHHHhhcC--CCcchHHHhhHHHHHHHHhc
Confidence            55566689999999999999887432 4668999999999999999999999999874  444 4578889999999999


Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHH
Q 011236          223 LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFW  302 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  302 (490)
                      ++.|...|.+.. .... ....+|..+...|...|++|.|+..|++..+..+  .=...|+.|..++-..|++.+|.+.|
T Consensus       268 ~d~Avs~Y~rAl-~lrp-n~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P--~F~~Ay~NlanALkd~G~V~ea~~cY  343 (966)
T KOG4626|consen  268 FDRAVSCYLRAL-NLRP-NHAVAHGNLACIYYEQGLLDLAIDTYKRALELQP--NFPDAYNNLANALKDKGSVTEAVDCY  343 (966)
T ss_pred             chHHHHHHHHHH-hcCC-cchhhccceEEEEeccccHHHHHHHHHHHHhcCC--CchHHHhHHHHHHHhccchHHHHHHH
Confidence            999999999987 4433 4567788888999999999999999999988765  34578999999999999999999999


Q ss_pred             HHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC-chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          303 GLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD-FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       303 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      .+...-.+ ......+.|...+...|.+++|..+|....+-  .|. ...++.|...|-+.|++++|+..+++.+.-  .
T Consensus       344 nkaL~l~p-~hadam~NLgni~~E~~~~e~A~~ly~~al~v--~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI--~  418 (966)
T KOG4626|consen  344 NKALRLCP-NHADAMNNLGNIYREQGKIEEATRLYLKALEV--FPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRI--K  418 (966)
T ss_pred             HHHHHhCC-ccHHHHHHHHHHHHHhccchHHHHHHHHHHhh--ChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhc--C
Confidence            99888776 66778899999999999999999999999884  343 456888999999999999999999999884  5


Q ss_pred             CC-HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hh
Q 011236          382 PT-PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RN  458 (490)
Q Consensus       382 p~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~  458 (490)
                      |+ ...|+.+...|-..|+.+.|++.+.+++.       +.|.- ..++.|...|...|+..+|..-++...+..|+ +.
T Consensus       419 P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~-------~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklkPDfpd  491 (966)
T KOG4626|consen  419 PTFADALSNMGNTYKEMGDVSAAIQCYTRAIQ-------INPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLKPDFPD  491 (966)
T ss_pred             chHHHHHHhcchHHHHhhhHHHHHHHHHHHHh-------cCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccCCCCch
Confidence            55 46899999999999999999999999998       66776 78999999999999999999999999999999 88


Q ss_pred             hhHHHHHHHH
Q 011236          459 MYHALTEAHI  468 (490)
Q Consensus       459 ~~~~l~~~~~  468 (490)
                      .|..++.++-
T Consensus       492 A~cNllh~lq  501 (966)
T KOG4626|consen  492 AYCNLLHCLQ  501 (966)
T ss_pred             hhhHHHHHHH
Confidence            8888877653

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.93  E-value=4.9e-23  Score=193.52  Aligned_cols=301  Identities=14%  Similarity=0.099  Sum_probs=209.6

Q ss_pred             HHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCC---cchHHHHHHHHHhcCC
Q 011236          112 DLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGS---ALNYNGIMCLYTNTGQ  187 (490)
Q Consensus       112 ~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~---~~~~~~l~~~~~~~~~  187 (490)
                      ..+...|++++|...|+++...+| +..++..+...+...|++++|..+++.+...+..++   ..++..+...|...|+
T Consensus        43 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~  122 (389)
T PRK11788         43 LNFLLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGL  122 (389)
T ss_pred             HHHHhcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence            344566777777777777777766 455677777777788888888888877776532211   2356677777777788


Q ss_pred             cCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHHcCCHHHHH
Q 011236          188 HEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMD----WGTYSTVANYYIIAGLKEKAI  263 (490)
Q Consensus       188 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~  263 (490)
                      +++|..+|+++.+.. +++..++..++..+.+.|++++|.+.++.+. +.+..+.    ...+..+...+.+.|++++|.
T Consensus       123 ~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  200 (389)
T PRK11788        123 LDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLE-KLGGDSLRVEIAHFYCELAQQALARGDLDAAR  200 (389)
T ss_pred             HHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHH-HhcCCcchHHHHHHHHHHHHHHHhCCCHHHHH
Confidence            888888887777642 2456677777777888888888888888776 4333222    123455666777778888888


Q ss_pred             HHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 011236          264 IYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELS  343 (490)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  343 (490)
                      ..|+++.+..+  .+...+..+...+.+.|++++|.++++++....+.....++..++.+|.+.|++++|...++.+.+.
T Consensus       201 ~~~~~al~~~p--~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~  278 (389)
T PRK11788        201 ALLKKALAADP--QCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEE  278 (389)
T ss_pred             HHHHHHHhHCc--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            88888776543  4556677777778888888888888887776544333456677777888888888888888877765


Q ss_pred             CCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc---cCCHHHHHHHHHHHHHhhhcCcCC
Q 011236          344 CYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD---KNNMEKAFECMKEALAVHEENKFW  420 (490)
Q Consensus       344 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~  420 (490)
                        .|+...+..++..+.+.|++++|..+++++.+.  .|+..+++.++..+..   .|+.++++.+++++++     .++
T Consensus       279 --~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~-----~~~  349 (389)
T PRK11788        279 --YPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVG-----EQL  349 (389)
T ss_pred             --CCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHH-----HHH
Confidence              455556677777788888888888888777765  4677777777766553   4577778888887777     556


Q ss_pred             Ccchh
Q 011236          421 RPKPS  425 (490)
Q Consensus       421 ~p~~~  425 (490)
                      .|++.
T Consensus       350 ~~~p~  354 (389)
T PRK11788        350 KRKPR  354 (389)
T ss_pred             hCCCC
Confidence            66654

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.93  E-value=1.6e-22  Score=190.03  Aligned_cols=299  Identities=14%  Similarity=0.079  Sum_probs=197.7

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCC---HHHHHHHHHHHhcc
Q 011236          144 LNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPD---NFSYRICINSYGAR  220 (490)
Q Consensus       144 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~---~~~~~~li~~~~~~  220 (490)
                      ...+...|++++|+..|+++.+.+.. +..++..+...+...|++++|..+++.+...+..++   ...+..+...|.+.
T Consensus        42 g~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~  120 (389)
T PRK11788         42 GLNFLLNEQPDKAIDLFIEMLKVDPE-TVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKA  120 (389)
T ss_pred             HHHHHhcCChHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHC
Confidence            34455677788888888888776432 555677777777777888888887777776432221   23566677777777


Q ss_pred             CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh----hhHHHHHHHHHhcCChh
Q 011236          221 SELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA----LGYNHLISHYASLGNKD  296 (490)
Q Consensus       221 g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~  296 (490)
                      |++++|..+|+++. +... .+..++..++..+.+.|++++|.+.++.+....+. +..    ..+..+...+...|+++
T Consensus       121 g~~~~A~~~~~~~l-~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~la~~~~~~~~~~  197 (389)
T PRK11788        121 GLLDRAEELFLQLV-DEGD-FAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGD-SLRVEIAHFYCELAQQALARGDLD  197 (389)
T ss_pred             CCHHHHHHHHHHHH-cCCc-chHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCC-cchHHHHHHHHHHHHHHHhCCCHH
Confidence            77777777777776 4433 45667777777777777777777777777665443 211    23445566666777777


Q ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      +|...++++....+ .+...+..+...+.+.|++++|.++++++.+.+......+++.++.+|...|++++|...++++.
T Consensus       198 ~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~  276 (389)
T PRK11788        198 AARALLKKALAADP-QCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRAL  276 (389)
T ss_pred             HHHHHHHHHHhHCc-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            77777777666543 34456666777777777777777777777664322223456667777777777777777777776


Q ss_pred             HcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc---CCCHHHHHHHHHHHHhc
Q 011236          377 KKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD---NRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       377 ~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~  453 (490)
                      +..  |+...+..++..+.+.|++++|..+++++++       ..|+..++..++..+..   .|+.+++..+++++.+.
T Consensus       277 ~~~--p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~-------~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~  347 (389)
T PRK11788        277 EEY--PGADLLLALAQLLEEQEGPEAAQALLREQLR-------RHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLVGE  347 (389)
T ss_pred             HhC--CCchHHHHHHHHHHHhCCHHHHHHHHHHHHH-------hCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHHHH
Confidence            653  4445556677777777777777777777766       24666666666665553   34667777777777665


Q ss_pred             ccc
Q 011236          454 VQK  456 (490)
Q Consensus       454 ~~~  456 (490)
                      ...
T Consensus       348 ~~~  350 (389)
T PRK11788        348 QLK  350 (389)
T ss_pred             HHh
Confidence            443

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

Probab=99.93  E-value=6.5e-21  Score=188.38  Aligned_cols=401  Identities=12%  Similarity=0.032  Sum_probs=289.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHh
Q 011236           71 ELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVR  149 (490)
Q Consensus        71 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~  149 (490)
                      .+......+.+.|++++|+..|++.++..  |++..+..+..++.+.|++++|+..++...+.+| +..+|..+..+|..
T Consensus       129 ~~k~~G~~~~~~~~~~~Ai~~y~~al~~~--p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~a~a~~~  206 (615)
T TIGR00990       129 KLKEKGNKAYRNKDFNKAIKLYSKAIECK--PDPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKALNRRANAYDG  206 (615)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            35566777889999999999999998875  5778888889999999999999999999999887 57789999999999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHC----------------------------
Q 011236          150 EGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKEN----------------------------  201 (490)
Q Consensus       150 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----------------------------  201 (490)
                      .|++++|+.-|......+...+.. ...++..+...    .+........+.                            
T Consensus       207 lg~~~eA~~~~~~~~~~~~~~~~~-~~~~~~~~l~~----~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  281 (615)
T TIGR00990       207 LGKYADALLDLTASCIIDGFRNEQ-SAQAVERLLKK----FAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLE  281 (615)
T ss_pred             cCCHHHHHHHHHHHHHhCCCccHH-HHHHHHHHHHH----HHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhh
Confidence            999999998887665442111111 11111111000    000000000000                            


Q ss_pred             ---CCCCCH-HHHHHHHHH---HhccCChHHHHHHHHHHHhCCC-CCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhh
Q 011236          202 ---GVPPDN-FSYRICINS---YGARSELSSMENVLQEMESQSH-ISM-DWGTYSTVANYYIIAGLKEKAIIYLKKCEDI  272 (490)
Q Consensus       202 ---~~~p~~-~~~~~li~~---~~~~g~~~~a~~~~~~~~~~~~-~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  272 (490)
                         ...|+. ..+..+...   ....+++++|.+.|++.. +.+ ..| ....+..+...+...|++++|+..|++....
T Consensus       282 ~~~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al-~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l  360 (615)
T TIGR00990       282 DSNELDEETGNGQLQLGLKSPESKADESYEEAARAFEKAL-DLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL  360 (615)
T ss_pred             cccccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHH-hcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence               000110 001111111   123467889999999887 433 223 4566778888888999999999999998876


Q ss_pred             hccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhH
Q 011236          273 VSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVP  352 (490)
Q Consensus       273 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  352 (490)
                      .+  .+...|..+...+...|++++|...|+......+ .+...+..+...+...|++++|...|++..+.. +.+...+
T Consensus       361 ~P--~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~-P~~~~~~  436 (615)
T TIGR00990       361 DP--RVTQSYIKRASMNLELGDPDKAEEDFDKALKLNS-EDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLD-PDFIFSH  436 (615)
T ss_pred             CC--CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-ccCHHHH
Confidence            54  4567888888889999999999999998877755 567788888899999999999999999998863 3345667


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchh-hHHHHH
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS-LVSSIL  431 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~-~~~~l~  431 (490)
                      ..+...+.+.|++++|+..|++.++..+. +...|+.+...+...|++++|+..|+++++..++..+..++.. .+...+
T Consensus       437 ~~la~~~~~~g~~~eA~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~  515 (615)
T TIGR00990       437 IQLGVTQYKEGSIASSMATFRRCKKNFPE-APDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKAL  515 (615)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHH
Confidence            77888889999999999999998876543 6778888999999999999999999999884432222222221 222222


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          432 DWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       432 ~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      ..+...|++++|.+++++.....|. ...+..++..+.+.|  ++|+.+|++..+.
T Consensus       516 ~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       516 ALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            3334468999999999998888888 778899999999999  8899988887543

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.93  E-value=8.8e-21  Score=199.47  Aligned_cols=319  Identities=10%  Similarity=0.041  Sum_probs=192.0

Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCC-CHHHH------------HHH
Q 011236          147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPP-DNFSY------------RIC  213 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~------------~~l  213 (490)
                      +...|++++|+..|++..+..+. +...+..+..++.+.|++++|...|++..+..... ....+            ...
T Consensus       279 ~~~~g~~~~A~~~l~~aL~~~P~-~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~  357 (1157)
T PRK11447        279 AVDSGQGGKAIPELQQAVRANPK-DSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQ  357 (1157)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHH
Confidence            34455555555555555554322 44455555555555555555555555555432111 10001            111


Q ss_pred             HHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhh------------
Q 011236          214 INSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALG------------  281 (490)
Q Consensus       214 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~------------  281 (490)
                      ...+.+.|++++|+..|+++. .... .+...+..+..++...|++++|++.|+++.+..+  .+...            
T Consensus       358 g~~~~~~g~~~eA~~~~~~Al-~~~P-~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p--~~~~a~~~L~~l~~~~~  433 (1157)
T PRK11447        358 GDAALKANNLAQAERLYQQAR-QVDN-TDSYAVLGLGDVAMARKDYAAAERYYQQALRMDP--GNTNAVRGLANLYRQQS  433 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHhcC
Confidence            223445555555555555555 3332 3344444455555555555555555555544332  12222            


Q ss_pred             ------------------------------HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHH
Q 011236          282 ------------------------------YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELE  331 (490)
Q Consensus       282 ------------------------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  331 (490)
                                                    +..+...+...|++++|.+.|++.....+ .+...+..+...|.+.|+++
T Consensus       434 ~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~P-~~~~~~~~LA~~~~~~G~~~  512 (1157)
T PRK11447        434 PEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALDP-GSVWLTYRLAQDLRQAGQRS  512 (1157)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHH
Confidence                                          22233445567778888888887776655 45556677777788888888


Q ss_pred             HHHHHHHHHHhcCCCCCchhHHHHH--------------------------------------------HHHHhcCCHHH
Q 011236          332 EAEKMLEEWELSCYCYDFRVPNIIL--------------------------------------------LGYSQKGMIEK  367 (490)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~~~~l~--------------------------------------------~~~~~~g~~~~  367 (490)
                      +|...++++.+... .+...+..+.                                            ..+...|+.++
T Consensus       513 ~A~~~l~~al~~~P-~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~e  591 (1157)
T PRK11447        513 QADALMRRLAQQKP-NDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAE  591 (1157)
T ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHH
Confidence            88888887766421 1222222222                                            22334444444


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCCCHHHHHHH
Q 011236          368 ADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNRDVEEVEAF  446 (490)
Q Consensus       368 A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~  446 (490)
                      |..+++    . .+++...+..+...+.+.|++++|+..|+++++.       .| +...+..+...+...|++++|++.
T Consensus       592 A~~~l~----~-~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~-------~P~~~~a~~~la~~~~~~g~~~eA~~~  659 (1157)
T PRK11447        592 AEALLR----Q-QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTR-------EPGNADARLGLIEVDIAQGDLAAARAQ  659 (1157)
T ss_pred             HHHHHH----h-CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            444443    1 1235556677888888899999999999999882       34 357788888889899999999999


Q ss_pred             HHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          447 VSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       447 ~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      ++.+.+..|. ...+..+..++...|  ++|.++++++.+.
T Consensus       660 l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        660 LAKLPATANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             HHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            9988887777 777888888888888  8899999888764

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.93  E-value=4.3e-21  Score=201.79  Aligned_cols=424  Identities=11%  Similarity=0.001  Sum_probs=279.0

Q ss_pred             ccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCh-hhH------------HHH
Q 011236           44 SPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSV-HDH------------AVQ  110 (490)
Q Consensus        44 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~------------~~l  110 (490)
                      ...|+.+++.. .+++..+. .+-+...+..+...+.+.|++++|++.|++..+....... ..+            ...
T Consensus       280 ~~~g~~~~A~~-~l~~aL~~-~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~  357 (1157)
T PRK11447        280 VDSGQGGKAIP-ELQQAVRA-NPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQ  357 (1157)
T ss_pred             HHCCCHHHHHH-HHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHH
Confidence            34455555554 44444433 2235566666666666667777777777666655421111 100            111


Q ss_pred             HHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcC
Q 011236          111 LDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHE  189 (490)
Q Consensus       111 ~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  189 (490)
                      ...+.+.|++++|+..|+++....| +..++..+...+...|++++|++.|++..+.... +...+..+...+. .++.+
T Consensus       358 g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~-~~~a~~~L~~l~~-~~~~~  435 (1157)
T PRK11447        358 GDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG-NTNAVRGLANLYR-QQSPE  435 (1157)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHH-hcCHH
Confidence            2344566667777777766666655 3555666666666677777777777666655322 3444555555443 34556


Q ss_pred             cHHHHHHHHHHCCCC--------CCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011236          190 KIPDVLLDMKENGVP--------PDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEK  261 (490)
Q Consensus       190 ~a~~~~~~m~~~~~~--------p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~  261 (490)
                      +|..+++.+......        .....+..+...+...|++++|.+.|++.. +..+ -+...+..+...|.+.|++++
T Consensus       436 ~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al-~~~P-~~~~~~~~LA~~~~~~G~~~~  513 (1157)
T PRK11447        436 KALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRL-ALDP-GSVWLTYRLAQDLRQAGQRSQ  513 (1157)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHHcCCHHH
Confidence            666665544221100        001223445566667788888888888877 4443 345566677778888888888


Q ss_pred             HHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCCh---------hhHHHHHHHHHhcCCHHH
Q 011236          262 AIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLN---------RDYITMLGSLVKIGELEE  332 (490)
Q Consensus       262 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---------~~~~~l~~~~~~~~~~~~  332 (490)
                      |...++++....+  .+...+..+...+...++.++|+..++.+......+..         ..+..+...+...|+.++
T Consensus       514 A~~~l~~al~~~P--~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~e  591 (1157)
T PRK11447        514 ADALMRRLAQQKP--NDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAE  591 (1157)
T ss_pred             HHHHHHHHHHcCC--CCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHH
Confidence            8888888776444  34445555555566778888888877754322111111         122345667788899999


Q ss_pred             HHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          333 AEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       333 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      |..+++.     .+.+...+..+...+.+.|++++|+..|++..+..+. +...+..++..|...|++++|++.++...+
T Consensus       592 A~~~l~~-----~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~-~~~a~~~la~~~~~~g~~~eA~~~l~~ll~  665 (1157)
T PRK11447        592 AEALLRQ-----QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPG-NADARLGLIEVDIAQGDLAAARAQLAKLPA  665 (1157)
T ss_pred             HHHHHHh-----CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence            9888772     3456667788999999999999999999999998655 788999999999999999999999998876


Q ss_pred             hhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-h------hhhHHHHHHHHhcC--CcHHHHHHHHH
Q 011236          413 VHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-R------NMYHALTEAHIRSG--QEVDGLLESMK  482 (490)
Q Consensus       413 ~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~------~~~~~l~~~~~~~g--~~a~~~~~~m~  482 (490)
                             ..|+. .++..+..++...|++++|.++++++....+. +      ..+..+...+...|  ++|+..|++..
T Consensus       666 -------~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al  738 (1157)
T PRK11447        666 -------TANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAM  738 (1157)
T ss_pred             -------cCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence                   33443 56677888889999999999999999887654 2      46667788899999  89999998775


Q ss_pred             h-CCCCC
Q 011236          483 A-DDIDE  488 (490)
Q Consensus       483 ~-~~~~p  488 (490)
                      . .|+.|
T Consensus       739 ~~~~~~~  745 (1157)
T PRK11447        739 VASGITP  745 (1157)
T ss_pred             hhcCCCC
Confidence            3 35554

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.92  E-value=1.2e-20  Score=185.77  Aligned_cols=335  Identities=10%  Similarity=-0.051  Sum_probs=272.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHH
Q 011236           70 LELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYV  148 (490)
Q Consensus        70 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~  148 (490)
                      .....++..+.+.|++++|..+++...... +-++.....++.+....|+++.|...|+.+....| +...+..+...+.
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            345567777889999999999999998887 34566666666777789999999999999999888 5778888999999


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHH
Q 011236          149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMEN  228 (490)
Q Consensus       149 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  228 (490)
                      +.|++++|...++++...... +...+..+...+...|++++|...++.+...... +...+..+ ..+...|++++|..
T Consensus       122 ~~g~~~~Ai~~l~~Al~l~P~-~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~-~~~a~~~~-~~l~~~g~~~eA~~  198 (656)
T PRK15174        122 KSKQYATVADLAEQAWLAFSG-NSQIFALHLRTLVLMDKELQAISLARTQAQEVPP-RGDMIATC-LSFLNKSRLPEDHD  198 (656)
T ss_pred             HcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCC-CHHHHHHH-HHHHHcCCHHHHHH
Confidence            999999999999999887433 6778888999999999999999999988765432 23333333 34778899999999


Q ss_pred             HHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhH----HHHHHHH
Q 011236          229 VLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE----MMKFWGL  304 (490)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----a~~~~~~  304 (490)
                      .++.+. .....++...+..+..++...|++++|+..++++....+  .+...+..+...+...|++++    |...|++
T Consensus       199 ~~~~~l-~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p--~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~  275 (656)
T PRK15174        199 LARALL-PFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARGL--DGAALRRSLGLAYYQSGRSREAKLQAAEHWRH  275 (656)
T ss_pred             HHHHHH-hcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHHHHcCCchhhHHHHHHHHHH
Confidence            999987 554334455556667888999999999999999987665  577888889999999999986    8999998


Q ss_pred             HHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH
Q 011236          305 QKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTP  384 (490)
Q Consensus       305 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~  384 (490)
                      .....+ .+...+..+...+...|++++|...+++..+.. +.+...+..+..+|.+.|++++|...|+++.+.++. +.
T Consensus       276 Al~l~P-~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~-P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~-~~  352 (656)
T PRK15174        276 ALQFNS-DNVRIVTLYADALIRTGQNEKAIPLLQQSLATH-PDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGV-TS  352 (656)
T ss_pred             HHhhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-ch
Confidence            888766 577889999999999999999999999998863 234556777889999999999999999999887543 33


Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhh
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  414 (490)
                      ..+..+..++...|+.++|...|+++++..
T Consensus       353 ~~~~~~a~al~~~G~~deA~~~l~~al~~~  382 (656)
T PRK15174        353 KWNRYAAAALLQAGKTSEAESVFEHYIQAR  382 (656)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            445556778899999999999999998844

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.91  E-value=1.8e-20  Score=184.54  Aligned_cols=373  Identities=8%  Similarity=-0.060  Sum_probs=293.6

Q ss_pred             HhcCChhHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHH
Q 011236           80 RSRKRFKHALQVSEWMSGQGL--AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDES  156 (490)
Q Consensus        80 ~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a  156 (490)
                      .+..+|+...-.|....+.--  .-+......++..+.+.|+++.|..+++......| +...+..++.+....|++++|
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~~g~~~~A   95 (656)
T PRK15174         16 LKQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTAKNGRDLLRRWVISPLASSQPDAV   95 (656)
T ss_pred             hhhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhCCCchhHHHHHhhhHhhcCCHHHH
Confidence            345555554444443322211  12344455567778899999999999999988877 466777777888889999999


Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhC
Q 011236          157 LSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQ  236 (490)
Q Consensus       157 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  236 (490)
                      +..++++....+. +...+..+...+...|++++|...+++..+.. +.+...+..+...+...|++++|...++.+. .
T Consensus        96 ~~~l~~~l~~~P~-~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~-~  172 (656)
T PRK15174         96 LQVVNKLLAVNVC-QPEDVLLVASVLLKSKQYATVADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQA-Q  172 (656)
T ss_pred             HHHHHHHHHhCCC-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHH-H
Confidence            9999999998654 67788999999999999999999999998852 2356678889999999999999999999886 4


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhh
Q 011236          237 SHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRD  316 (490)
Q Consensus       237 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  316 (490)
                      ... .+...+..+ ..+...|++++|...++.+....+. ++...+..+..++...|++++|...++......+ .+...
T Consensus       173 ~~P-~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~-~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p-~~~~~  248 (656)
T PRK15174        173 EVP-PRGDMIATC-LSFLNKSRLPEDHDLARALLPFFAL-ERQESAGLAVDTLCAVGKYQEAIQTGESALARGL-DGAAL  248 (656)
T ss_pred             hCC-CCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCC-cchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-CCHHH
Confidence            443 233344333 3488899999999999998776554 4455566667888999999999999999887765 56778


Q ss_pred             HHHHHHHHHhcCCHHH----HHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011236          317 YITMLGSLVKIGELEE----AEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAA  392 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~  392 (490)
                      +..+...+...|++++    |...+++..+.. +.+...+..+...+.+.|++++|...+++..+..+. +...+..+..
T Consensus       249 ~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~-P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~-~~~a~~~La~  326 (656)
T PRK15174        249 RRSLGLAYYQSGRSREAKLQAAEHWRHALQFN-SDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPD-LPYVRAMYAR  326 (656)
T ss_pred             HHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHH
Confidence            8889999999999986    899999998863 335678889999999999999999999999987655 6677888999


Q ss_pred             HHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhh-HHHHHHHHHcCCCHHHHHHHHHHHHhcccc--hhhhHHHHHHHH
Q 011236          393 GYADKNNMEKAFECMKEALAVHEENKFWRPKPSL-VSSILDWLGDNRDVEEVEAFVSSLKIKVQK--RNMYHALTEAHI  468 (490)
Q Consensus       393 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~-~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~l~~~~~  468 (490)
                      ++.+.|++++|...++++..       ..|+... +..+..++...|+.++|...|+++.+..|.  +..|...+..|.
T Consensus       327 ~l~~~G~~~eA~~~l~~al~-------~~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~P~~~~~~~~ea~~~~~  398 (656)
T PRK15174        327 ALRQVGQYTAASDEFVQLAR-------EKGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQARASHLPQSFEEGLLALD  398 (656)
T ss_pred             HHHHCCCHHHHHHHHHHHHH-------hCccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhChhhchhhHHHHHHHHH
Confidence            99999999999999999987       3365533 444567889999999999999999988777  555554444443

>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=99.90  E-value=4.5e-19  Score=175.31  Aligned_cols=402  Identities=9%  Similarity=-0.037  Sum_probs=295.0

Q ss_pred             cHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhh
Q 011236           38 NLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKV  117 (490)
Q Consensus        38 ~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  117 (490)
                      ..-..+.+.|+++.++. .+++.+  ...|+...|..+..++.+.|++++|++.++..++.+ +.....+..+..++...
T Consensus       132 ~~G~~~~~~~~~~~Ai~-~y~~al--~~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~a~a~~~l  207 (615)
T TIGR00990       132 EKGNKAYRNKDFNKAIK-LYSKAI--ECKPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-PDYSKALNRRANAYDGL  207 (615)
T ss_pred             HHHHHHHHcCCHHHHHH-HHHHHH--hcCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHc
Confidence            44456667788888888 666555  356788899999999999999999999999999887 45677888899999999


Q ss_pred             cCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHH-------------HHh-c-------------CCC
Q 011236          118 RGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQK-------------MKE-M-------------GSF  169 (490)
Q Consensus       118 ~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~-------------m~~-~-------------~~~  169 (490)
                      |++++|+..|..+...++ +......++..+........+...++.             ... .             ...
T Consensus       208 g~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  287 (615)
T TIGR00990       208 GKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNELD  287 (615)
T ss_pred             CCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhcccccc
Confidence            999999988876654432 211111111111110001111111110             000 0             000


Q ss_pred             CC-cchHHHHHHHH---HhcCCcCcHHHHHHHHHHCC-CCC-CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCH
Q 011236          170 GS-ALNYNGIMCLY---TNTGQHEKIPDVLLDMKENG-VPP-DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDW  243 (490)
Q Consensus       170 p~-~~~~~~l~~~~---~~~~~~~~a~~~~~~m~~~~-~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  243 (490)
                      |. ...+..+...+   ...+++++|.+.|+...+.+ ..| +...+..+...+...|++++|...|++.. .... -..
T Consensus       288 ~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal-~l~P-~~~  365 (615)
T TIGR00990       288 EETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSI-ELDP-RVT  365 (615)
T ss_pred             cccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HcCC-CcH
Confidence            00 00111111111   12367889999999998765 233 44568888888999999999999999998 5443 446


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHH
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGS  323 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  323 (490)
                      ..|..+..++...|++++|+..|+++....+  .+...|..+...+...|++++|...|++.+...+ .+...+..+..+
T Consensus       366 ~~~~~la~~~~~~g~~~eA~~~~~~al~~~p--~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P-~~~~~~~~la~~  442 (615)
T TIGR00990       366 QSYIKRASMNLELGDPDKAEEDFDKALKLNS--EDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDP-DFIFSHIQLGVT  442 (615)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCc-cCHHHHHHHHHH
Confidence            6888899999999999999999999988665  5788899999999999999999999998888765 566778889999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH------HHHHHHHHHhcc
Q 011236          324 LVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPN------SWSIIAAGYADK  397 (490)
Q Consensus       324 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~------~~~~l~~~~~~~  397 (490)
                      +.+.|++++|...+++..+. .+.+...++.+...+...|++++|...|++.++.....+..      .++.....+...
T Consensus       443 ~~~~g~~~eA~~~~~~al~~-~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~  521 (615)
T TIGR00990       443 QYKEGSIASSMATFRRCKKN-FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWK  521 (615)
T ss_pred             HHHCCCHHHHHHHHHHHHHh-CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHh
Confidence            99999999999999999875 34457788999999999999999999999998865431111      122223334457


Q ss_pred             CCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          398 NNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       398 ~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      |++++|.+++++++.       +.|+. ..+..+...+...|++++|.+.|++..+....
T Consensus       522 ~~~~eA~~~~~kAl~-------l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l~~~  574 (615)
T TIGR00990       522 QDFIEAENLCEKALI-------IDPECDIAVATMAQLLLQQGDVDEALKLFERAAELART  574 (615)
T ss_pred             hhHHHHHHHHHHHHh-------cCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHhcc
Confidence            999999999999988       33555 56888999999999999999999998877654

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.90  E-value=4.8e-19  Score=178.25  Aligned_cols=406  Identities=10%  Similarity=0.024  Sum_probs=265.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHH
Q 011236           65 QKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGAL  143 (490)
Q Consensus        65 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~l  143 (490)
                      .+.+..-..-.+......|+.++|++++....... +.+...+..+...+...|++++|..+|+......| +...+..+
T Consensus        11 ~~~~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~l   89 (765)
T PRK10049         11 SALSNNQIADWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRGL   89 (765)
T ss_pred             cCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            34556666666677777888888888888777633 34555677777788888888888888888777766 46667777


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 011236          144 LNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSEL  223 (490)
Q Consensus       144 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  223 (490)
                      ...+...|++++|+..+++..+..+. +.. +..+..++...|+.++|...++++.+... .+...+..+..++...+..
T Consensus        90 a~~l~~~g~~~eA~~~l~~~l~~~P~-~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P-~~~~~~~~la~~l~~~~~~  166 (765)
T PRK10049         90 ILTLADAGQYDEALVKAKQLVSGAPD-KAN-LLALAYVYKRAGRHWDELRAMTQALPRAP-QTQQYPTEYVQALRNNRLS  166 (765)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCC-CHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCh
Confidence            77788888888888888888776332 444 77777777788888888888888877532 2444555566677777778


Q ss_pred             HHHHHHHHHHHhCCCCCCCH------HHHHHHHHHHH-----HcCCH---HHHHHHHHHHhhhhccCCChh-hHH----H
Q 011236          224 SSMENVLQEMESQSHISMDW------GTYSTVANYYI-----IAGLK---EKAIIYLKKCEDIVSKSKDAL-GYN----H  284 (490)
Q Consensus       224 ~~a~~~~~~~~~~~~~~~~~------~~~~~li~~~~-----~~~~~---~~a~~~~~~~~~~~~~~~~~~-~~~----~  284 (490)
                      +.|++.++... .   .|+.      .....++....     ..+++   ++|+..++.+....+..|+.. .+.    .
T Consensus       167 e~Al~~l~~~~-~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d  242 (765)
T PRK10049        167 APALGAIDDAN-L---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARID  242 (765)
T ss_pred             HHHHHHHHhCC-C---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHH
Confidence            88887777665 2   1221      11122222222     12223   667777777765422212221 111    1


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---CchhHHHHHHHHHh
Q 011236          285 LISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY---DFRVPNIILLGYSQ  361 (490)
Q Consensus       285 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~  361 (490)
                      .+.++...|++++|...|+.+...+..........+..+|...|++++|...|+++.+.....   .......+..++..
T Consensus       243 ~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~  322 (765)
T PRK10049        243 RLGALLARDRYKDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLE  322 (765)
T ss_pred             HHHHHHHhhhHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHh
Confidence            123445667888888888877665432111222334667778888888888888876542211   12334556667778


Q ss_pred             cCCHHHHHHHHHHHHHcCC-----------CCC---HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhH
Q 011236          362 KGMIEKADAVLKEIVKKGK-----------TPT---PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLV  427 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~~~-----------~p~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~  427 (490)
                      .|++++|..+++.+.+..+           .|+   ...+..+...+...|+.++|+++++++....      +-+...+
T Consensus       323 ~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~------P~n~~l~  396 (765)
T PRK10049        323 SENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA------PGNQGLR  396 (765)
T ss_pred             cccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC------CCCHHHH
Confidence            8888888888888776532           122   1244566677778888888888888887722      2334667


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          428 SSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       428 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      ..+...+...|+.++|++.++++....|. ...+..++..+.+.|  ++|..+++++.+.
T Consensus       397 ~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        397 IDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            77777788888888888888888888887 677777777777777  7888888887763

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.90  E-value=1e-19  Score=183.14  Aligned_cols=408  Identities=10%  Similarity=-0.007  Sum_probs=310.5

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQL  111 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  111 (490)
                      ++......+......|+.++++. ++.+... ..+.+...+..+...+...|++++|.++++...+.. +.++.....+.
T Consensus        14 ~~~~~~d~~~ia~~~g~~~~A~~-~~~~~~~-~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la   90 (765)
T PRK10049         14 SNNQIADWLQIALWAGQDAEVIT-VYNRYRV-HMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLI   90 (765)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHH-HHHHHHh-hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            45556667777778888888875 6666654 234556679999999999999999999999999886 46677788888


Q ss_pred             HHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCc
Q 011236          112 DLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEK  190 (490)
Q Consensus       112 ~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  190 (490)
                      .++...|++++|+..++++....| +.. +..+..++...|+.++|+..++++.+..+. +...+..+..++...+..++
T Consensus        91 ~~l~~~g~~~eA~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~-~~~~~~~la~~l~~~~~~e~  168 (765)
T PRK10049         91 LTLADAGQYDEALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQ-TQQYPTEYVQALRNNRLSAP  168 (765)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCCChHH
Confidence            899999999999999999998887 466 888999999999999999999999998654 66666778888888899999


Q ss_pred             HHHHHHHHHHCCCCCCH------HHHHHHHHHHh-----ccCCh---HHHHHHHHHHHhCCCCCCCHH-HH----HHHHH
Q 011236          191 IPDVLLDMKENGVPPDN------FSYRICINSYG-----ARSEL---SSMENVLQEMESQSHISMDWG-TY----STVAN  251 (490)
Q Consensus       191 a~~~~~~m~~~~~~p~~------~~~~~li~~~~-----~~g~~---~~a~~~~~~~~~~~~~~~~~~-~~----~~li~  251 (490)
                      |++.++....   .|+.      .....++....     ..+++   ++|++.++.+.......|+.. .+    ...+.
T Consensus       169 Al~~l~~~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~  245 (765)
T PRK10049        169 ALGAIDDANL---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLG  245 (765)
T ss_pred             HHHHHHhCCC---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHH
Confidence            9998886654   2332      11222233222     22234   778888888873212223321 11    11134


Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCC---ChhhHHHHHHHHHhcC
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQ---LNRDYITMLGSLVKIG  328 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~  328 (490)
                      .+...|++++|+..|+.+...++..|+. .-..+..+|...|++++|+..|+.+....+..   .......+..++...|
T Consensus       246 ~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g  324 (765)
T PRK10049        246 ALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESE  324 (765)
T ss_pred             HHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcc
Confidence            5567799999999999998875421222 22335778999999999999999877654321   1245666777889999


Q ss_pred             CHHHHHHHHHHHHhcCC-----------CCC---chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011236          329 ELEEAEKMLEEWELSCY-----------CYD---FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       329 ~~~~a~~~~~~~~~~~~-----------~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~  394 (490)
                      ++++|.+.++.+.....           .|+   ...+..+...+...|+.++|+++++++....+. +...+..+...+
T Consensus       325 ~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~-n~~l~~~lA~l~  403 (765)
T PRK10049        325 NYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPG-NQGLRIDYASVL  403 (765)
T ss_pred             cHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            99999999999987521           122   123456777889999999999999999988655 788899999999


Q ss_pred             hccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          395 ADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       395 ~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ...|++++|++.+++++.       +.|+. ..+......+...|++++|+.+++.+.+..|.
T Consensus       404 ~~~g~~~~A~~~l~~al~-------l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd  459 (765)
T PRK10049        404 QARGWPRAAENELKKAEV-------LEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQ  459 (765)
T ss_pred             HhcCCHHHHHHHHHHHHh-------hCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCC
Confidence            999999999999999988       44664 56667777888999999999999999999888

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.86  E-value=5.4e-17  Score=160.46  Aligned_cols=424  Identities=10%  Similarity=0.031  Sum_probs=302.6

Q ss_pred             hccCCCCCCChHHHHHHHHHcCCCCCH-HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHH
Q 011236           43 ISPLGDPDVSLTPVLDQWVLEGQKISE-LELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLE  121 (490)
Q Consensus        43 l~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  121 (490)
                      ..+.|+...++. .+++..+.  .|+. .....++..+...|+.++|+..+++..... +........+...+...|+++
T Consensus        44 ~~r~Gd~~~Al~-~L~qaL~~--~P~~~~av~dll~l~~~~G~~~~A~~~~eka~~p~-n~~~~~llalA~ly~~~gdyd  119 (822)
T PRK14574         44 RARAGDTAPVLD-YLQEESKA--GPLQSGQVDDWLQIAGWAGRDQEVIDVYERYQSSM-NISSRGLASAARAYRNEKRWD  119 (822)
T ss_pred             HHhCCCHHHHHH-HHHHHHhh--CccchhhHHHHHHHHHHcCCcHHHHHHHHHhccCC-CCCHHHHHHHHHHHHHcCCHH
Confidence            446788887777 55555433  3332 223388888888899999999999988322 233334444466888889999


Q ss_pred             HHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHH
Q 011236          122 SAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKE  200 (490)
Q Consensus       122 ~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  200 (490)
                      .|+++|+++.+.+| +..++..++..+...++.++|++.++++...  .|+...+-.++..+...++..+|++.++++.+
T Consensus       120 ~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~ekll~  197 (822)
T PRK14574        120 QALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASSEAVR  197 (822)
T ss_pred             HHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHHHHHH
Confidence            99999999999888 5777888888999999999999999998876  34555554444444345556569999999988


Q ss_pred             CCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHH----HHHHHH---------HcCC---HHHHHH
Q 011236          201 NGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYST----VANYYI---------IAGL---KEKAII  264 (490)
Q Consensus       201 ~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~----li~~~~---------~~~~---~~~a~~  264 (490)
                      .. +-+...+..+..+..+.|-...|.++..+-.   +. .+...+.-    .+.-.+         ...+   .+.|+.
T Consensus       198 ~~-P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p---~~-f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~ala  272 (822)
T PRK14574        198 LA-PTSEEVLKNHLEILQRNRIVEPALRLAKENP---NL-VSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKALA  272 (822)
T ss_pred             hC-CCCHHHHHHHHHHHHHcCCcHHHHHHHHhCc---cc-cCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHH
Confidence            64 2356677888888999998888887766543   11 11111110    011111         1122   344555


Q ss_pred             HHHHHhhhhccCCCh-h----hHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          265 YLKKCEDIVSKSKDA-L----GYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEE  339 (490)
Q Consensus       265 ~~~~~~~~~~~~~~~-~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  339 (490)
                      -++.+.......|.. .    +..-.+-++...|+..++++.|+.+...+......+-..+.++|...+++++|..+++.
T Consensus       273 ~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~  352 (822)
T PRK14574        273 DYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSS  352 (822)
T ss_pred             HHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHH
Confidence            556555422221321 1    12234556778899999999999888777656777889999999999999999999999


Q ss_pred             HHhcCC-----CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-------------CCCHH-HHHHHHHHHhccCCH
Q 011236          340 WELSCY-----CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK-------------TPTPN-SWSIIAAGYADKNNM  400 (490)
Q Consensus       340 ~~~~~~-----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~-------------~p~~~-~~~~l~~~~~~~~~~  400 (490)
                      +.....     .++......|.-+|...+++++|..+++++.+..+             .||-. .+..++..+.-.|+.
T Consensus       353 ~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl  432 (822)
T PRK14574        353 LYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDL  432 (822)
T ss_pred             HhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCH
Confidence            876531     22333357788999999999999999999987422             12222 345567778899999


Q ss_pred             HHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHH
Q 011236          401 EKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGL  477 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~  477 (490)
                      .+|++.++++..      .-+-|......+...+...|...+|+..++.+....|. ..+....+.++...|  ++|..+
T Consensus       433 ~~Ae~~le~l~~------~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~~~  506 (822)
T PRK14574        433 PTAQKKLEDLSS------TAPANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQMELL  506 (822)
T ss_pred             HHHHHHHHHHHH------hCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHHHH
Confidence            999999999987      23345678888889999999999999999998888888 888888888888888  888888


Q ss_pred             HHHHHh
Q 011236          478 LESMKA  483 (490)
Q Consensus       478 ~~~m~~  483 (490)
                      .+...+
T Consensus       507 ~~~l~~  512 (822)
T PRK14574        507 TDDVIS  512 (822)
T ss_pred             HHHHHh
Confidence            877765

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.85  E-value=1.7e-16  Score=137.34  Aligned_cols=434  Identities=14%  Similarity=0.125  Sum_probs=293.2

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCC--hh-HHHHHHHHHHhCCCCCChhhHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKR--FK-HALQVSEWMSGQGLAFSVHDHA  108 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~--~~-~a~~~~~~~~~~~~~~~~~~~~  108 (490)
                      ...+-+.|+..+ ..|...++.- +++.|.+.|++.+...-..|++.-+-.+.  +. .-++-|-.|...|- .+..++ 
T Consensus       115 ~V~~E~nL~kmI-S~~EvKDs~i-lY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E-~S~~sW-  190 (625)
T KOG4422|consen  115 QVETENNLLKMI-SSREVKDSCI-LYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGE-DSTSSW-  190 (625)
T ss_pred             hhcchhHHHHHH-hhcccchhHH-HHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhcccccc-cccccc-
Confidence            334445555444 3455566666 77888888877777776666655443322  11 12233333444331 222221 


Q ss_pred             HHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCc
Q 011236          109 VQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQH  188 (490)
Q Consensus       109 ~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  188 (490)
                             +.|.+.+  -+|+..++   +..+|.++|.++|+--+.+.|.+++++-.+...+.+..+||.+|.+-.-.   
T Consensus       191 -------K~G~vAd--L~~E~~PK---T~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~---  255 (625)
T KOG4422|consen  191 -------KSGAVAD--LLFETLPK---TDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYS---  255 (625)
T ss_pred             -------ccccHHH--HHHhhcCC---CchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhh---
Confidence                   2333333  34444432   67789999999999999999999999999888888999999998765432   


Q ss_pred             CcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH----HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHH-HH
Q 011236          189 EKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSS----MENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEK-AI  263 (490)
Q Consensus       189 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~----a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~-a~  263 (490)
                       ...+++.+|.+..+.||..|+|+++.+..+.|+++.    |.+++.+|+ +.|+.|+..+|..+|..+++.++..+ +.
T Consensus       256 -~~K~Lv~EMisqkm~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmK-eiGVePsLsSyh~iik~f~re~dp~k~as  333 (625)
T KOG4422|consen  256 -VGKKLVAEMISQKMTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMK-EIGVEPSLSSYHLIIKNFKRESDPQKVAS  333 (625)
T ss_pred             -ccHHHHHHHHHhhcCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHH-HhCCCcchhhHHHHHHHhcccCCchhhhH
Confidence             238899999999999999999999999999998875    567888998 99999999999999999999888754 55


Q ss_pred             HHHHHHhhhhc-------cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC----CCCh---hhHHHHHHHHHhcCC
Q 011236          264 IYLKKCEDIVS-------KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK----KQLN---RDYITMLGSLVKIGE  329 (490)
Q Consensus       264 ~~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~~~~---~~~~~l~~~~~~~~~  329 (490)
                      .++.++.....       ...|...|...+..|.+..+.+.|.++..-......    .|+.   .-|..+....|+...
T Consensus       334 ~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es  413 (625)
T KOG4422|consen  334 SWINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMES  413 (625)
T ss_pred             HHHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHH
Confidence            55555543211       103456677778888888899999888773333221    1221   236677888888889


Q ss_pred             HHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC-C--------H
Q 011236          330 LEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKN-N--------M  400 (490)
Q Consensus       330 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-~--------~  400 (490)
                      .+.-...|+.|.-+-+-|+..+...++++..-.|.++-.-+++..++..|..-+.....-++..+++.. .        +
T Consensus       414 ~~~~~~~Y~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql  493 (625)
T KOG4422|consen  414 IDVTLKWYEDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQL  493 (625)
T ss_pred             HHHHHHHHHHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHH
Confidence            999999999998887888888889999999999999999999999988876555555555555555443 1        1


Q ss_pred             HHH----HHHHHHHHHhhh-cCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc---hhhhH---HHHHHHHh
Q 011236          401 EKA----FECMKEALAVHE-ENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK---RNMYH---ALTEAHIR  469 (490)
Q Consensus       401 ~~a----~~~~~~~~~~~~-~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~---~~~~~---~l~~~~~~  469 (490)
                      ..+    ...+.+..+..+ ..+.........+.+.-.+.+.|..++|.++|..+.+.+..   ....+   -+++.-.+
T Consensus       494 ~~~~ak~aad~~e~~e~~~~R~r~~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~  573 (625)
T KOG4422|consen  494 QVAFAKCAADIKEAYESQPIRQRAQDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKV  573 (625)
T ss_pred             HHHHHHHHHHHHHHHHhhHHHHHhccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHh
Confidence            111    111111111000 01223345566777888889999999999999988655433   33445   44444444


Q ss_pred             cC--CcHHHHHHHHHhCCC
Q 011236          470 SG--QEVDGLLESMKADDI  486 (490)
Q Consensus       470 ~g--~~a~~~~~~m~~~~~  486 (490)
                      ..  ..|...++-|...+.
T Consensus       574 ~~spsqA~~~lQ~a~~~n~  592 (625)
T KOG4422|consen  574 SNSPSQAIEVLQLASAFNL  592 (625)
T ss_pred             cCCHHHHHHHHHHHHHcCc
Confidence            44  778888888866554

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.85  E-value=1.9e-16  Score=156.67  Aligned_cols=428  Identities=11%  Similarity=0.016  Sum_probs=311.4

Q ss_pred             cccccchhhhhhhhhcc--CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHH
Q 011236           15 NFTKTNLEIFTRAYRAV--KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVS   92 (490)
Q Consensus        15 ~~~~~~~~~~~~~~~~~--~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~   92 (490)
                      +....++..+.......  .+.....++..+...|+..+++. .+++.. ............+...+...|++++|+++|
T Consensus        48 Gd~~~Al~~L~qaL~~~P~~~~av~dll~l~~~~G~~~~A~~-~~eka~-~p~n~~~~~llalA~ly~~~gdyd~Aiely  125 (822)
T PRK14574         48 GDTAPVLDYLQEESKAGPLQSGQVDDWLQIAGWAGRDQEVID-VYERYQ-SSMNISSRGLASAARAYRNEKRWDQALALW  125 (822)
T ss_pred             CCHHHHHHHHHHHHhhCccchhhHHHHHHHHHHcCCcHHHHH-HHHHhc-cCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            33344555555444432  21123477777777888887766 666665 212223333444456788889999999999


Q ss_pred             HHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCc
Q 011236           93 EWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSA  172 (490)
Q Consensus        93 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~  172 (490)
                      +++.+.. +-++..+..++..+...++.++|++.++.+....|+...+..++..+...++..+|++.++++.+..+. +.
T Consensus       126 ~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~P~-n~  203 (822)
T PRK14574        126 QSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEAVRLAPT-SE  203 (822)
T ss_pred             HHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhCCC-CH
Confidence            9999998 456788888889999999999999999999999888666755555555567776799999999998644 77


Q ss_pred             chHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHH------HHHHHHHH---h--ccCC---hHHHHHHHHHHHhCCC
Q 011236          173 LNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFS------YRICINSY---G--ARSE---LSSMENVLQEMESQSH  238 (490)
Q Consensus       173 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~------~~~li~~~---~--~~g~---~~~a~~~~~~~~~~~~  238 (490)
                      ..+..++.++.+.|-...|.++..+-... +.+...-      ....++.-   .  ...+   .+.|+.-++.+....+
T Consensus       204 e~~~~~~~~l~~~~~~~~a~~l~~~~p~~-f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~ala~~~~l~~~~~  282 (822)
T PRK14574        204 EVLKNHLEILQRNRIVEPALRLAKENPNL-VSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKALADYQNLLTRWG  282 (822)
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHhCccc-cCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHHHHHHhhcc
Confidence            77888999999999999998777653321 1111111      11111111   0  1122   3445666666552222


Q ss_pred             CCCCH-HHH----HHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC---
Q 011236          239 ISMDW-GTY----STVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK---  310 (490)
Q Consensus       239 ~~~~~-~~~----~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---  310 (490)
                      ..|.. ..|    .-.+-++...|+..++++.|+.+...+.+ ....+-..+..+|...+++++|+.+|+.+....+   
T Consensus       283 ~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~-~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~  361 (822)
T PRK14574        283 KDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYK-MPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTF  361 (822)
T ss_pred             CCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCC-CCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcccccc
Confidence            22322 222    22455788899999999999999987765 4566888999999999999999999998876542   


Q ss_pred             --CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-----------CCCc---hhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          311 --KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY-----------CYDF---RVPNIILLGYSQKGMIEKADAVLKE  374 (490)
Q Consensus       311 --~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~  374 (490)
                        .++......|..++...+++++|..+++.+.+...           .|+.   ..+..++..+.-.|+..+|++.+++
T Consensus       362 ~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~  441 (822)
T PRK14574        362 RNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLED  441 (822)
T ss_pred             CCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence              12333457899999999999999999999987421           1221   1334567778899999999999999


Q ss_pred             HHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          375 IVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       375 m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      +....+. |......+...+...|.+.+|.+.++.+..       +.|+. .+......++...|++++|..+.+.+.+.
T Consensus       442 l~~~aP~-n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~-------l~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l~~~  513 (822)
T PRK14574        442 LSSTAPA-NQNLRIALASIYLARDLPRKAEQELKAVES-------LAPRSLILERAQAETAMALQEWHQMELLTDDVISR  513 (822)
T ss_pred             HHHhCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHhh-------hCCccHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh
Confidence            9888765 899999999999999999999999988766       45665 66778888889999999999999999998


Q ss_pred             ccc
Q 011236          454 VQK  456 (490)
Q Consensus       454 ~~~  456 (490)
                      .|.
T Consensus       514 ~Pe  516 (822)
T PRK14574        514 SPE  516 (822)
T ss_pred             CCC
Confidence            888

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.84  E-value=4.9e-16  Score=156.92  Aligned_cols=112  Identities=16%  Similarity=0.183  Sum_probs=59.7

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHH
Q 011236          363 GMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVE  441 (490)
Q Consensus       363 g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~  441 (490)
                      |++++|...+++.++..  |+...|..+...+.+.|++++|+..+++++.       ..|+. ..+..+..++...|+++
T Consensus       590 Gr~~eAl~~~~~AL~l~--P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~-------l~Pd~~~a~~nLG~aL~~~G~~e  660 (987)
T PRK09782        590 GQPELALNDLTRSLNIA--PSANAYVARATIYRQRHNVPAAVSDLRAALE-------LEPNNSNYQAALGYALWDSGDIA  660 (987)
T ss_pred             CCHHHHHHHHHHHHHhC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHCCCHH
Confidence            55555555555554432  3344555555555555555555555555555       22333 34444445555555555


Q ss_pred             HHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHh
Q 011236          442 EVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       442 ~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~  483 (490)
                      +|...+++..+..|. +..+..+..++...|  ++|+..+++..+
T Consensus       661 eAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~  705 (987)
T PRK09782        661 QSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVID  705 (987)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            555555555555555 555555555555555  555555555544

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.83  E-value=1.3e-15  Score=153.97  Aligned_cols=400  Identities=10%  Similarity=-0.006  Sum_probs=195.0

Q ss_pred             CCCHHHHHHH-HHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHh-hcCHHHHHHHHHHccccCCChhHHHHH
Q 011236           66 KISELELQRV-IRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGK-VRGLESAETYFNSLNDEDKVDKLYGAL  143 (490)
Q Consensus        66 ~~~~~~~~~l-l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~~~~p~~~~~~~l  143 (490)
                      .|+....... ...+...++|++|++++.++.+.+ +.+......+...|.. .++ +.+..+++...+  .+..++..+
T Consensus       178 ~~~~~vL~L~~~rlY~~l~dw~~Ai~lL~~L~k~~-pl~~~~~~~L~~ay~q~l~~-~~a~al~~~~lk--~d~~l~~al  253 (987)
T PRK09782        178 SPEGKTLRTDLLQRAIYLKQWSQADTLYNEARQQN-TLSAAERRQWFDVLLAGQLD-DRLLALQSQGIF--TDPQSRITY  253 (987)
T ss_pred             CCCcHHHHHHHHHHHHHHhCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhhCH-HHHHHHhchhcc--cCHHHHHHH
Confidence            3345444444 777788888888888888888887 3455555556566666 355 666666553222  356677788


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCC-CCcchHH------------------------------HHHHHHHhcCCcCcHH
Q 011236          144 LNCYVREGLVDESLSLMQKMKEMGSF-GSALNYN------------------------------GIMCLYTNTGQHEKIP  192 (490)
Q Consensus       144 i~~~~~~g~~~~a~~~~~~m~~~~~~-p~~~~~~------------------------------~l~~~~~~~~~~~~a~  192 (490)
                      ...|.+.|+.++|.++++++...... |...+|-                              .++..+.+.++++.+.
T Consensus       254 a~~yi~~G~~~~A~~~L~~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  333 (987)
T PRK09782        254 ATALAYRGEKARLQHYLIENKPLFTTDAQEKSWLYLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQ  333 (987)
T ss_pred             HHHHHHCCCHHHHHHHHHhCcccccCCCccHHHHHHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHH
Confidence            88888888888888888876554222 2222220                              0122222222222222


Q ss_pred             HH-----------------------------HHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHh-CCCCCCC
Q 011236          193 DV-----------------------------LLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMES-QSHISMD  242 (490)
Q Consensus       193 ~~-----------------------------~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~-~~~~~~~  242 (490)
                      ++                             +..|.+. .+-+....-.+.-.....|+.++|.++|+.... ..+...+
T Consensus       334 ~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~y~~-~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  412 (987)
T PRK09782        334 KLLATLPANEMLEERYAVSVATRNKAEALRLARLLYQQ-EPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLS  412 (987)
T ss_pred             HHhcCCCcchHHHHHHhhccccCchhHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccC
Confidence            11                             1111111 001222222222233455556666666555542 1111122


Q ss_pred             HHHHHHHHHHHHHc-------------------------CCHHHHHHHHHHHhhhhccC-C--ChhhHHHHHHHHHhcCC
Q 011236          243 WGTYSTVANYYIIA-------------------------GLKEKAIIYLKKCEDIVSKS-K--DALGYNHLISHYASLGN  294 (490)
Q Consensus       243 ~~~~~~li~~~~~~-------------------------~~~~~a~~~~~~~~~~~~~~-~--~~~~~~~l~~~~~~~~~  294 (490)
                      .....-++..|.+.                         |+..++...++......+.. +  +...|..+..++.. ++
T Consensus       413 ~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~  491 (987)
T PRK09782        413 QTLMARLASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TL  491 (987)
T ss_pred             HHHHHHHHHHHHhCCcccchHHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CC
Confidence            22222333333322                         22222222222222211100 2  34455555555544 55


Q ss_pred             hhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          295 KDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKE  374 (490)
Q Consensus       295 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  374 (490)
                      .++|...+.+.....  |+......+..++...|++++|...++++...  +|+...+..+...+.+.|++++|...+++
T Consensus       492 ~~eAi~a~~~Al~~~--Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~q  567 (987)
T PRK09782        492 PGVALYAWLQAEQRQ--PDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQ  567 (987)
T ss_pred             cHHHHHHHHHHHHhC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            555555555444433  23322223333334556666666666555432  23333344444555555666666666655


Q ss_pred             HHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Q 011236          375 IVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV  454 (490)
Q Consensus       375 m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  454 (490)
                      .++.++. +...+..+.......|++++|...++++++       +.|+...+..+..++.+.|++++|...+++.....
T Consensus       568 AL~l~P~-~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~-------l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~  639 (987)
T PRK09782        568 AEQRGLG-DNALYWWLHAQRYIPGQPELALNDLTRSLN-------IAPSANAYVARATIYRQRHNVPAAVSDLRAALELE  639 (987)
T ss_pred             HHhcCCc-cHHHHHHHHHHHHhCCCHHHHHHHHHHHHH-------hCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            5554322 222222233333344566666666666555       33445555555555556666666666666666655


Q ss_pred             cc-hhhhHHHHHHHHhcC--CcHHHHHHHHHh
Q 011236          455 QK-RNMYHALTEAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       455 ~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~  483 (490)
                      |. +..++.+..++...|  ++|+..+++..+
T Consensus       640 Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~  671 (987)
T PRK09782        640 PNNSNYQAALGYALWDSGDIAQSREMLERAHK  671 (987)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            55 555555555565555  555555555544

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

Probab=99.82  E-value=1.6e-16  Score=138.55  Aligned_cols=388  Identities=12%  Similarity=0.050  Sum_probs=255.9

Q ss_pred             cCChhHHHHHHHHHHhCCCCCChhhHHHH----HHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHH
Q 011236           82 RKRFKHALQVSEWMSGQGLAFSVHDHAVQ----LDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESL  157 (490)
Q Consensus        82 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l----~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~  157 (490)
                      .+.+.+|+++|+..+.+-...+..+...+    ...+.+.|.+++|+.-|+...+..|+..+--.|+-++..-|+-++..
T Consensus       250 kr~fskaikfyrmaldqvpsink~~rikil~nigvtfiq~gqy~dainsfdh~m~~~pn~~a~~nl~i~~f~i~d~ekmk  329 (840)
T KOG2003|consen  250 KREFSKAIKFYRMALDQVPSINKDMRIKILNNIGVTFIQAGQYDDAINSFDHCMEEAPNFIAALNLIICAFAIGDAEKMK  329 (840)
T ss_pred             hhhHHHHHHHHHHHHhhccccchhhHHHHHhhcCeeEEecccchhhHhhHHHHHHhCccHHhhhhhhhhheecCcHHHHH
Confidence            34455555555554444322222222222    22345778889999999988888888665545555566678888888


Q ss_pred             HHHHHHHhcCCCCCcchH--------HHHHHHHH---------hcCC--cCcHHHHHHHHHHCCCCCCHHH---------
Q 011236          158 SLMQKMKEMGSFGSALNY--------NGIMCLYT---------NTGQ--HEKIPDVLLDMKENGVPPDNFS---------  209 (490)
Q Consensus       158 ~~~~~m~~~~~~p~~~~~--------~~l~~~~~---------~~~~--~~~a~~~~~~m~~~~~~p~~~~---------  209 (490)
                      +.|.+|......||..-|        ..|+.-..         +.+.  .+++.-.--.++.--+.||-..         
T Consensus       330 eaf~kli~ip~~~dddkyi~~~ddp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~l  409 (840)
T KOG2003|consen  330 EAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESL  409 (840)
T ss_pred             HHHHHHhcCCCCCCcccccCCcCCcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHH
Confidence            889888765433333222        11111111         1111  1111111111111111111100         


Q ss_pred             ----H--------HHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHH---------------------------
Q 011236          210 ----Y--------RICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVA---------------------------  250 (490)
Q Consensus       210 ----~--------~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li---------------------------  250 (490)
                          +        -.-...+.+.|+++.|.+++.-+. +.+-+.-...-+.|-                           
T Consensus       410 k~s~~~~la~dlei~ka~~~lk~~d~~~aieilkv~~-~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dry  488 (840)
T KOG2003|consen  410 KASQHAELAIDLEINKAGELLKNGDIEGAIEILKVFE-KKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRY  488 (840)
T ss_pred             HHhhhhhhhhhhhhhHHHHHHhccCHHHHHHHHHHHH-hccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhccccc
Confidence                0        011234667888888888877766 322212111111111                           


Q ss_pred             ---------HHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          251 ---------NYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       251 ---------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                               +.....|++++|.+.|++.......  -....-.+.-.+-..|++++|++.|-++...-. .+......+.
T Consensus       489 n~~a~~nkgn~~f~ngd~dka~~~ykeal~ndas--c~ealfniglt~e~~~~ldeald~f~klh~il~-nn~evl~qia  565 (840)
T KOG2003|consen  489 NAAALTNKGNIAFANGDLDKAAEFYKEALNNDAS--CTEALFNIGLTAEALGNLDEALDCFLKLHAILL-NNAEVLVQIA  565 (840)
T ss_pred             CHHHhhcCCceeeecCcHHHHHHHHHHHHcCchH--HHHHHHHhcccHHHhcCHHHHHHHHHHHHHHHH-hhHHHHHHHH
Confidence                     1112457889999999887664332  222222333446678999999999876655433 6777888888


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHH
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNME  401 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  401 (490)
                      ..|....+..+|.+++.+.... ++.|+.+...|...|-+.|+-..|.+.+-.--.. ++-+..+...|...|....-++
T Consensus       566 niye~led~aqaie~~~q~~sl-ip~dp~ilskl~dlydqegdksqafq~~ydsyry-fp~nie~iewl~ayyidtqf~e  643 (840)
T KOG2003|consen  566 NIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRY-FPCNIETIEWLAAYYIDTQFSE  643 (840)
T ss_pred             HHHHHhhCHHHHHHHHHHhccc-CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccc-cCcchHHHHHHHHHHHhhHHHH
Confidence            9999999999999999888775 6778889999999999999999999887655443 3447889999999999999999


Q ss_pred             HHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHH-cCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC-CcHHHHH
Q 011236          402 KAFECMKEALAVHEENKFWRPKPSLVSSILDWLG-DNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG-QEVDGLL  478 (490)
Q Consensus       402 ~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~-~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g-~~a~~~~  478 (490)
                      +++.+|+++.-       ++|+..-|..++..|. +.|++..|..+++...+..|. ......|+..+...| .++.++-
T Consensus       644 kai~y~ekaal-------iqp~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl~d~key~  716 (840)
T KOG2003|consen  644 KAINYFEKAAL-------IQPNQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGLKDAKEYA  716 (840)
T ss_pred             HHHHHHHHHHh-------cCccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccchhHHHHH
Confidence            99999999865       7899999998887665 689999999999999999999 999999999999999 7777776


Q ss_pred             HHHH
Q 011236          479 ESMK  482 (490)
Q Consensus       479 ~~m~  482 (490)
                      +++.
T Consensus       717 ~kle  720 (840)
T KOG2003|consen  717 DKLE  720 (840)
T ss_pred             HHHH
Confidence            6554

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

Probab=99.79  E-value=1.1e-15  Score=145.17  Aligned_cols=416  Identities=12%  Similarity=0.020  Sum_probs=241.8

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcC--CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEG--QKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAV  109 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  109 (490)
                      +|...+.|.+.+.-.++...... +...+....  -..-...|-.+.+++...|++++|...|-+..+.......-.+.-
T Consensus       269 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  269 NPVALNHLANHFYFKKDYERVWH-LAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVG  347 (1018)
T ss_pred             CcHHHHHHHHHHhhcccHHHHHH-HHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccc
Confidence            56667777777777777665555 333333221  112334577778888888888888888888777763222444455


Q ss_pred             HHHHHHhhcCHHHHHHHHHHccccCCC-hhHHHHHHHHHHhcC----ChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 011236          110 QLDLIGKVRGLESAETYFNSLNDEDKV-DKLYGALLNCYVREG----LVDESLSLMQKMKEMGSFGSALNYNGIMCLYTN  184 (490)
Q Consensus       110 l~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~li~~~~~~g----~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  184 (490)
                      +...+.+.|+++.+...|+.+....|+ ..+...|...|+..+    ..+.|..++.+..+.-+. |...|-.+...+-.
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 LGQMYIKRGDLEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPV-DSEAWLELAQLLEQ  426 (1018)
T ss_pred             hhHHHHHhchHHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccc-cHHHHHHHHHHHHh
Confidence            678888888888888888888887774 566666666666664    345666666666655432 66667666666654


Q ss_pred             cCCcCcHHHHHHHHH----HCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCC--CCCCC------HHHHHHHHHH
Q 011236          185 TGQHEKIPDVLLDMK----ENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQS--HISMD------WGTYSTVANY  252 (490)
Q Consensus       185 ~~~~~~a~~~~~~m~----~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~--~~~~~------~~~~~~li~~  252 (490)
                      .. ...++.+|....    ..+-.+.....|.+...+...|+++.|...|+......  ...++      ..+--.+..+
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 TD-PWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARL  505 (1018)
T ss_pred             cC-hHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHH
Confidence            43 333366655443    34545677788888888888888888888888776220  11122      2222235555


Q ss_pred             HHHcCCHHHHHHHHHHHhhhhcc--------------------------------CCChhhHHHHHHHHHhcCChhHHHH
Q 011236          253 YIIAGLKEKAIIYLKKCEDIVSK--------------------------------SKDALGYNHLISHYASLGNKDEMMK  300 (490)
Q Consensus       253 ~~~~~~~~~a~~~~~~~~~~~~~--------------------------------~~~~~~~~~l~~~~~~~~~~~~a~~  300 (490)
                      +-..++.+.|.+.|..+....+.                                ..++..++.+...+.....+..|.+
T Consensus       506 ~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k  585 (1018)
T KOG2002|consen  506 LEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKK  585 (1018)
T ss_pred             HHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhccccc
Confidence            55556666666666665554331                                0222223333333333333333433


Q ss_pred             HHHHHHHhcC-CCChhhHHHHHHHHHh------------cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHH
Q 011236          301 FWGLQKIKCK-KQLNRDYITMLGSLVK------------IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEK  367 (490)
Q Consensus       301 ~~~~~~~~~~-~~~~~~~~~l~~~~~~------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  367 (490)
                      -|........ .+|.++...|.+.|..            .+..++|.++|.++++. .+-|...-|-+...++..|++.+
T Consensus       586 ~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~-dpkN~yAANGIgiVLA~kg~~~~  664 (1018)
T KOG2002|consen  586 KFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRN-DPKNMYAANGIGIVLAEKGRFSE  664 (1018)
T ss_pred             HHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhc-CcchhhhccchhhhhhhccCchH
Confidence            3332222211 2344444444443321            23345566666666654 23355555556666666666666


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHH
Q 011236          368 ADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFV  447 (490)
Q Consensus       368 A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~  447 (490)
                      |..+|.+..+.... +..+|-.+..+|..+|++..|+++|+....    +..-.-++.+...|.+++.+.|++.+|.+.+
T Consensus       665 A~dIFsqVrEa~~~-~~dv~lNlah~~~e~~qy~~AIqmYe~~lk----kf~~~~~~~vl~~Lara~y~~~~~~eak~~l  739 (1018)
T KOG2002|consen  665 ARDIFSQVREATSD-FEDVWLNLAHCYVEQGQYRLAIQMYENCLK----KFYKKNRSEVLHYLARAWYEAGKLQEAKEAL  739 (1018)
T ss_pred             HHHHHHHHHHHHhh-CCceeeeHHHHHHHHHHHHHHHHHHHHHHH----HhcccCCHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            66666666665432 445566666666666666666666666655    1223334456666666666666666666666


Q ss_pred             HHHHhcccc
Q 011236          448 SSLKIKVQK  456 (490)
Q Consensus       448 ~~~~~~~~~  456 (490)
                      .......|.
T Consensus       740 l~a~~~~p~  748 (1018)
T KOG2002|consen  740 LKARHLAPS  748 (1018)
T ss_pred             HHHHHhCCc
Confidence            666666665

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

Probab=99.79  E-value=9.8e-16  Score=145.62  Aligned_cols=370  Identities=13%  Similarity=0.025  Sum_probs=261.0

Q ss_pred             CCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCC--HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHH
Q 011236           33 PVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKIS--ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQ  110 (490)
Q Consensus        33 ~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  110 (490)
                      ..+|-.+-+.+...|+.+.|.. .+-+-.  +..++  +..+..|...+...|+.+.+...|+.+.+.. +-+..+...+
T Consensus       307 aes~Y~~gRs~Ha~Gd~ekA~~-yY~~s~--k~~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iL  382 (1018)
T KOG2002|consen  307 AESFYQLGRSYHAQGDFEKAFK-YYMESL--KADNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKIL  382 (1018)
T ss_pred             HHHHHHHHHHHHhhccHHHHHH-HHHHHH--ccCCCCccccccchhHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHH
Confidence            3446677788888899888877 333222  33333  4456677888999999999999999999887 5667777777


Q ss_pred             HHHHHhhc----CHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHH----hcCCCCCcchHHHHHHH
Q 011236          111 LDLIGKVR----GLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMK----EMGSFGSALNYNGIMCL  181 (490)
Q Consensus       111 ~~~~~~~~----~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~----~~~~~p~~~~~~~l~~~  181 (490)
                      ...|+..+    ..+.|..++.......| |...|-.+...+-...-+ .++.+|....    ..+-.+.+...|.+...
T Consensus       383 G~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e~~d~~-~sL~~~~~A~d~L~~~~~~ip~E~LNNvasl  461 (1018)
T KOG2002|consen  383 GCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWLELAQLLEQTDPW-ASLDAYGNALDILESKGKQIPPEVLNNVASL  461 (1018)
T ss_pred             HhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHhcChH-HHHHHHHHHHHHHHHcCCCCCHHHHHhHHHH
Confidence            77777665    45677777777766655 677777777766554433 3366665543    34445667777888888


Q ss_pred             HHhcCCcCcHHHHHHHHHHC---CCCCCHH-------HHHHHHHHHhcc-------------------------------
Q 011236          182 YTNTGQHEKIPDVLLDMKEN---GVPPDNF-------SYRICINSYGAR-------------------------------  220 (490)
Q Consensus       182 ~~~~~~~~~a~~~~~~m~~~---~~~p~~~-------~~~~li~~~~~~-------------------------------  220 (490)
                      ....|++++|...|......   .-.+|..       -|| +....-..                               
T Consensus       462 hf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YN-larl~E~l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma  540 (1018)
T KOG2002|consen  462 HFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYN-LARLLEELHDTEVAEEMYKSILKEHPGYIDAYLRLGCMA  540 (1018)
T ss_pred             HHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHH-HHHHHHhhhhhhHHHHHHHHHHHHCchhHHHHHHhhHHH
Confidence            88888888888888776553   1122221       122 22222222                               


Q ss_pred             ---CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHh------
Q 011236          221 ---SELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYAS------  291 (490)
Q Consensus       221 ---g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~------  291 (490)
                         +...+|...+.... +.+- .++..++.+...+.+...+..|..-|+.+.+.....+|.++.-.|...|..      
T Consensus       541 ~~k~~~~ea~~~lk~~l-~~d~-~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~  618 (1018)
T KOG2002|consen  541 RDKNNLYEASLLLKDAL-NIDS-SNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPS  618 (1018)
T ss_pred             HhccCcHHHHHHHHHHH-hccc-CCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccc
Confidence               34445555555554 2221 233344446667777777777777777666555443577777677775543      


Q ss_pred             ------cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCH
Q 011236          292 ------LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMI  365 (490)
Q Consensus       292 ------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  365 (490)
                            .+..++|+++|.+.+...+ .+.+.-+-+.-.++..|++..|..+|.+..+... -...+|-.+.++|..+|++
T Consensus       619 rn~ek~kk~~~KAlq~y~kvL~~dp-kN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~-~~~dv~lNlah~~~e~~qy  696 (1018)
T KOG2002|consen  619 RNPEKEKKHQEKALQLYGKVLRNDP-KNMYAANGIGIVLAEKGRFSEARDIFSQVREATS-DFEDVWLNLAHCYVEQGQY  696 (1018)
T ss_pred             cChHHHHHHHHHHHHHHHHHHhcCc-chhhhccchhhhhhhccCchHHHHHHHHHHHHHh-hCCceeeeHHHHHHHHHHH
Confidence                  3456789999998888776 7788888899999999999999999999998744 3556788899999999999


Q ss_pred             HHHHHHHHHHHHc-CCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          366 EKADAVLKEIVKK-GKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       366 ~~A~~~~~~m~~~-~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ..|+++|+...+. ...-++.....|..++.+.|.+.+|.+.+..+..
T Consensus       697 ~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~  744 (1018)
T KOG2002|consen  697 RLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARH  744 (1018)
T ss_pred             HHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            9999999987654 4455788899999999999999999999999988

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.77  E-value=3.9e-14  Score=122.93  Aligned_cols=240  Identities=13%  Similarity=0.135  Sum_probs=161.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC--CChhHHHH
Q 011236           65 QKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED--KVDKLYGA  142 (490)
Q Consensus        65 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~  142 (490)
                      .+.+..+|..+|.++|+.-..+.|.+++++...........+++.+|.+-.-..+    ..++.+|....  ||..++|+
T Consensus       203 ~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqkm~Pnl~TfNa  278 (625)
T KOG4422|consen  203 LPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQKMTPNLFTFNA  278 (625)
T ss_pred             cCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhhcCCchHhHHH
Confidence            4557777888888888887778888888877766667777777777765443222    56666666543  78888888


Q ss_pred             HHHHHHhcCChhH----HHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCc-HHHHHHHHHHC--C--CC---C-CHHH
Q 011236          143 LLNCYVREGLVDE----SLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEK-IPDVLLDMKEN--G--VP---P-DNFS  209 (490)
Q Consensus       143 li~~~~~~g~~~~----a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~-a~~~~~~m~~~--~--~~---p-~~~~  209 (490)
                      ++.+..+.|+++.    |.+++.+|++.|+.|...+|..+|..+++.++..+ +..++.++...  |  ++   | |...
T Consensus       279 lL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~F  358 (625)
T KOG4422|consen  279 LLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKF  358 (625)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHH
Confidence            8888888887654    45677778888888888888888887777777654 33344444321  1  22   2 3345


Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHhCCC---CCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHH
Q 011236          210 YRICINSYGARSELSSMENVLQEMESQSH---ISMD---WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYN  283 (490)
Q Consensus       210 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~---~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  283 (490)
                      |...+..|.+..+.+.|.++..-.....+   +.|+   ..-|..+..+.|.....+.-...|+.|...... |+..+..
T Consensus       359 F~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~-p~~~~m~  437 (625)
T KOG4422|consen  359 FQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYF-PHSQTMI  437 (625)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceec-CCchhHH
Confidence            66677777777777777777665542111   2222   233456667777777777778888887766666 7777777


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhc
Q 011236          284 HLISHYASLGNKDEMMKFWGLQKIKC  309 (490)
Q Consensus       284 ~l~~~~~~~~~~~~a~~~~~~~~~~~  309 (490)
                      .++++....|+++-.-++|..+...+
T Consensus       438 ~~lrA~~v~~~~e~ipRiw~D~~~~g  463 (625)
T KOG4422|consen  438 HLLRALDVANRLEVIPRIWKDSKEYG  463 (625)
T ss_pred             HHHHHHhhcCcchhHHHHHHHHHHhh
Confidence            77777777777777777777666554

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

Probab=99.75  E-value=3.7e-14  Score=134.14  Aligned_cols=380  Identities=15%  Similarity=0.126  Sum_probs=286.4

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHH
Q 011236           70 LELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYV  148 (490)
Q Consensus        70 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~  148 (490)
                      ...-.....+...|++++|.+++.+++++. +..+..|..+...|-..|+.+.+...+-......| |...|..+.....
T Consensus       140 ~~ll~eAN~lfarg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~  218 (895)
T KOG2076|consen  140 RQLLGEANNLFARGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSE  218 (895)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHH
Confidence            333344444555699999999999999998 67889999999999999999999999888777776 6789999999999


Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHH----HHHHHHHHhccCChH
Q 011236          149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFS----YRICINSYGARSELS  224 (490)
Q Consensus       149 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~----~~~li~~~~~~g~~~  224 (490)
                      +.|+++.|.-+|.+..+..+. +...+-.-+..|-+.|+...|...|.++.+...+.|..-    -..+++.+...++-+
T Consensus       219 ~~~~i~qA~~cy~rAI~~~p~-n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e  297 (895)
T KOG2076|consen  219 QLGNINQARYCYSRAIQANPS-NWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERE  297 (895)
T ss_pred             hcccHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHH
Confidence            999999999999999998544 555555667788999999999999999988644223222    234456677777779


Q ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhcc---------------------CCChhhHH
Q 011236          225 SMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK---------------------SKDALGYN  283 (490)
Q Consensus       225 ~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---------------------~~~~~~~~  283 (490)
                      .|.+.++......+-..+...++.++..|.+...++.|......+......                     .++...|.
T Consensus       298 ~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~  377 (895)
T KOG2076|consen  298 RAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYD  377 (895)
T ss_pred             HHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCcc
Confidence            999998887733333466777888999999999999999888877651111                     02222221


Q ss_pred             ----HHHHHHHhcCChhHHHHHHHHHHHhc--CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHH
Q 011236          284 ----HLISHYASLGNKDEMMKFWGLQKIKC--KKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILL  357 (490)
Q Consensus       284 ----~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  357 (490)
                          -+.-++.+....+....+........  +.-+...|.-+..+|...|++.+|..+|..+......-+...|-.+..
T Consensus       378 l~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~  457 (895)
T KOG2076|consen  378 LRVIRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLAR  457 (895)
T ss_pred             chhHhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHH
Confidence                12223344444444444444444444  344556789999999999999999999999998755556778999999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhh---hcCcCCCcchhhHHHHHHHH
Q 011236          358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVH---EENKFWRPKPSLVSSILDWL  434 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~p~~~~~~~l~~~~  434 (490)
                      +|...|..++|...|+..+...+. +...--.|...+.+.|+.++|.+.++.+..-.   .+..+..|+..........+
T Consensus       458 c~~~l~e~e~A~e~y~kvl~~~p~-~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l  536 (895)
T KOG2076|consen  458 CYMELGEYEEAIEFYEKVLILAPD-NLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDIL  536 (895)
T ss_pred             HHHHHhhHHHHHHHHHHHHhcCCC-chhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHH
Confidence            999999999999999999987544 66677788888999999999999999865411   01234566666666777778


Q ss_pred             HcCCCHHHHHHHHHHHHh
Q 011236          435 GDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       435 ~~~g~~~~a~~~~~~~~~  452 (490)
                      ...|+.++-..+...|..
T Consensus       537 ~~~gk~E~fi~t~~~Lv~  554 (895)
T KOG2076|consen  537 FQVGKREEFINTASTLVD  554 (895)
T ss_pred             HHhhhHHHHHHHHHHHHH
Confidence            888998886666555554

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

Probab=99.74  E-value=4e-17  Score=145.32  Aligned_cols=263  Identities=15%  Similarity=0.115  Sum_probs=98.4

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcC-CCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc
Q 011236          142 ALLNCYVREGLVDESLSLMQKMKEMG-SFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGAR  220 (490)
Q Consensus       142 ~li~~~~~~g~~~~a~~~~~~m~~~~-~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  220 (490)
                      .+...+.+.|++++|++++++..... .+.|...|..+...+...++++.|.+.++++...+.. +...+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccc
Confidence            44666667777777777775544333 2224444555555666677777777777777665432 44455556655 577


Q ss_pred             CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHH
Q 011236          221 SELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMK  300 (490)
Q Consensus       221 g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  300 (490)
                      +++++|.++++..- +..  ++...+..++..+...++++++.++++.+........+...|..+...+.+.|+.++|++
T Consensus        91 ~~~~~A~~~~~~~~-~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~  167 (280)
T PF13429_consen   91 GDPEEALKLAEKAY-ERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALR  167 (280)
T ss_dssp             ------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHH
T ss_pred             cccccccccccccc-ccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            77777777776654 222  344555667777777778888777777766433221466677777777778888888888


Q ss_pred             HHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 011236          301 FWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK  380 (490)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  380 (490)
                      .+++.....+ .+......++..+...|+.+++.+++....+.. +.|...+..+..+|...|+.++|+..|++..+..+
T Consensus       168 ~~~~al~~~P-~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~-~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p  245 (280)
T PF13429_consen  168 DYRKALELDP-DDPDARNALAWLLIDMGDYDEAREALKRLLKAA-PDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNP  245 (280)
T ss_dssp             HHHHHHHH-T-T-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH--HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHcCC-CCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHC-cCHHHHHHHHHHHhccccccccccccccccccccc
Confidence            8887777665 456667777777888888888777777777653 55666777788888888888888888888777654


Q ss_pred             CCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          381 TPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       381 ~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      . |+.....+..++...|+.++|.++.+++..
T Consensus       246 ~-d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  246 D-DPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             T--HHHHHHHHHHHT-----------------
T ss_pred             c-cccccccccccccccccccccccccccccc
Confidence            4 777777888888888888888887777654

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

Probab=99.73  E-value=1.3e-12  Score=119.43  Aligned_cols=433  Identities=9%  Similarity=0.056  Sum_probs=256.1

Q ss_pred             HHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHH----HhCCCCCChhhHHHHHHHH
Q 011236           39 LYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWM----SGQGLAFSVHDHAVQLDLI  114 (490)
Q Consensus        39 l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~----~~~~~~~~~~~~~~l~~~~  114 (490)
                      |.-+|++..-++.+-. ++...++ .++-+...|.+-...--.+|+.+....+++.-    ...|+..+.+.+..=...|
T Consensus       412 LwlAlarLetYenAkk-vLNkaRe-~iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~  489 (913)
T KOG0495|consen  412 LWLALARLETYENAKK-VLNKARE-IIPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEAC  489 (913)
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHh-hCCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHH
Confidence            3344444444444333 5554433 35556666665555555666666666665542    3345555555555555566


Q ss_pred             HhhcCHHHHHHHHHHccccCC----ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCc
Q 011236          115 GKVRGLESAETYFNSLNDEDK----VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEK  190 (490)
Q Consensus       115 ~~~~~~~~A~~~~~~~~~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  190 (490)
                      -..|..-.+..+.......+.    -..+|+.-...|.+.+.++-|..+|....+--+ -+...|......--..|..++
T Consensus       490 e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqvfp-~k~slWlra~~~ek~hgt~Es  568 (913)
T KOG0495|consen  490 EDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVFP-CKKSLWLRAAMFEKSHGTRES  568 (913)
T ss_pred             hhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhcc-chhHHHHHHHHHHHhcCcHHH
Confidence            666666666555555554431    234566666666666666666666666655422 244555555555555566666


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Q 011236          191 IPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCE  270 (490)
Q Consensus       191 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  270 (490)
                      ...+|++.... ++-....|-.....+-..|+...|..++.... +.+. -+...|-.-+..-..+.+++.|..+|.+..
T Consensus       569 l~Allqkav~~-~pkae~lwlM~ake~w~agdv~~ar~il~~af-~~~p-nseeiwlaavKle~en~e~eraR~llakar  645 (913)
T KOG0495|consen  569 LEALLQKAVEQ-CPKAEILWLMYAKEKWKAGDVPAARVILDQAF-EANP-NSEEIWLAAVKLEFENDELERARDLLAKAR  645 (913)
T ss_pred             HHHHHHHHHHh-CCcchhHHHHHHHHHHhcCCcHHHHHHHHHHH-HhCC-CcHHHHHHHHHHhhccccHHHHHHHHHHHh
Confidence            66666666554 22233344444455555666666666666665 4443 345555555566666666666666666655


Q ss_pred             hhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCch
Q 011236          271 DIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFR  350 (490)
Q Consensus       271 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  350 (490)
                      ...   ++...|.--+...--.++.++|.+++++.++..+ .-...|..+.+.+-+.++++.|...|..-.+. ++..+.
T Consensus       646 ~~s---gTeRv~mKs~~~er~ld~~eeA~rllEe~lk~fp-~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~-cP~~ip  720 (913)
T KOG0495|consen  646 SIS---GTERVWMKSANLERYLDNVEEALRLLEEALKSFP-DFHKLWLMLGQIEEQMENIEMAREAYLQGTKK-CPNSIP  720 (913)
T ss_pred             ccC---CcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhCC-chHHHHHHHhHHHHHHHHHHHHHHHHHhcccc-CCCCch
Confidence            432   3444444444444445566666666665555543 33345555666666666666666666555443 333444


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcC-------------
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEEN-------------  417 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-------------  417 (490)
                      .|-.|...=-+.|.+-+|..++++..-+++. +...|-..|+.-.+.|+.+.|..++.++++..|..             
T Consensus       721 LWllLakleEk~~~~~rAR~ildrarlkNPk-~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~  799 (913)
T KOG0495|consen  721 LWLLLAKLEEKDGQLVRARSILDRARLKNPK-NALLWLESIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPR  799 (913)
T ss_pred             HHHHHHHHHHHhcchhhHHHHHHHHHhcCCC-cchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccC
Confidence            5555555555566666666666666665554 55666666666666666666666655555522100             


Q ss_pred             -----------cCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHh
Q 011236          418 -----------KFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       418 -----------~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~  483 (490)
                                 ....-|++....+...|....+++.|.+.|.+..+.+|+ -++|.-+...+.++|  ++-.+++++-..
T Consensus       800 ~~rkTks~DALkkce~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev~~~c~~  879 (913)
T KOG0495|consen  800 PQRKTKSIDALKKCEHDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEVLKKCET  879 (913)
T ss_pred             cccchHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence                       123456777788888888999999999999999999999 999999999999999  666667666543

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.72  E-value=6.5e-14  Score=130.42  Aligned_cols=283  Identities=16%  Similarity=0.150  Sum_probs=196.7

Q ss_pred             cCChhHHHHHHHHHHhcCCCCCcch-HHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHH--HHHHHHhccCChHHH
Q 011236          150 EGLVDESLSLMQKMKEMGSFGSALN-YNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYR--ICINSYGARSELSSM  226 (490)
Q Consensus       150 ~g~~~~a~~~~~~m~~~~~~p~~~~-~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~--~li~~~~~~g~~~~a  226 (490)
                      .|+++.|.+.+....+..-  ++.. |.....+..+.|+++.+.+.+.++.+.  .|+...+.  .....+...|+++.|
T Consensus        97 eGd~~~A~k~l~~~~~~~~--~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~A  172 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAE--QPVVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAA  172 (398)
T ss_pred             CCCHHHHHHHHHHHHhccc--chHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHH
Confidence            5888888877776555421  2222 333344446778888888888888763  34443322  335667778888888


Q ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh-------hhHHHHHHHHHhcCChhHHH
Q 011236          227 ENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA-------LGYNHLISHYASLGNKDEMM  299 (490)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~  299 (490)
                      ...++++. +.++ -+...+..+...|.+.|++++|.+++..+.+.... ++.       .+|..++.......+.+...
T Consensus       173 l~~l~~~~-~~~P-~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~  249 (398)
T PRK10747        173 RHGVDKLL-EVAP-RHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVG-DEEHRAMLEQQAWIGLMDQAMADQGSEGLK  249 (398)
T ss_pred             HHHHHHHH-hcCC-CCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHHHhcCHHHHH
Confidence            88888887 5553 55677777888888888888888888888776553 211       12333344344445556666


Q ss_pred             HHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011236          300 KFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG  379 (490)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  379 (490)
                      ++|+...... +.++.....+..++...|+.++|..++++..+.  +|+...  .++.+....++.+++++..+...+..
T Consensus       250 ~~w~~lp~~~-~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk~~  324 (398)
T PRK10747        250 RWWKNQSRKT-RHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERL--VLLIPRLKTNNPEQLEKVLRQQIKQH  324 (398)
T ss_pred             HHHHhCCHHH-hCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHH--HHHHhhccCCChHHHHHHHHHHHhhC
Confidence            6666544333 256777888888888889999998888888774  344322  23444455688888888888888876


Q ss_pred             CCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          380 KTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       380 ~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      +. |+..+..+...|.+.+++++|.+.|+.+.+       ..|+..++..+...+.+.|+.++|.+++++...
T Consensus       325 P~-~~~l~l~lgrl~~~~~~~~~A~~~le~al~-------~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        325 GD-TPLLWSTLGQLLMKHGEWQEASLAFRAALK-------QRPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             CC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-------cCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            55 677788888888889999999999988887       568888888888888889999999888887644

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

Probab=99.72  E-value=1.3e-13  Score=121.63  Aligned_cols=396  Identities=13%  Similarity=0.022  Sum_probs=268.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCC-hhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC-hhHHHHHHHHHHh
Q 011236           72 LQRVIRQLRSRKRFKHALQVSEWMSGQGLAFS-VHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV-DKLYGALLNCYVR  149 (490)
Q Consensus        72 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~li~~~~~  149 (490)
                      +....+-|-++|++++|++.|.+.+...  |+ +.-|.....+|...|+|+...+.-....+.+|+ +.++..-..++-+
T Consensus       118 lK~~GN~~f~~kkY~eAIkyY~~AI~l~--p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~P~Y~KAl~RRA~A~E~  195 (606)
T KOG0547|consen  118 LKTKGNKFFRNKKYDEAIKYYTQAIELC--PDEPIFYSNRAACYESLGDWEKVIEDCTKALELNPDYVKALLRRASAHEQ  195 (606)
T ss_pred             HHhhhhhhhhcccHHHHHHHHHHHHhcC--CCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHh
Confidence            4455566788999999999999999986  45 778888888999999999999998888888886 6677777888888


Q ss_pred             cCChhHHHHHHHHHHhc-CCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHH-CC--CCCCHHHHHHHHHHHh-------
Q 011236          150 EGLVDESLSLMQKMKEM-GSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKE-NG--VPPDNFSYRICINSYG-------  218 (490)
Q Consensus       150 ~g~~~~a~~~~~~m~~~-~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-~~--~~p~~~~~~~li~~~~-------  218 (490)
                      .|++++|+.=+.-..-. |+. |..+--.+=+.+-+.     +..-.++-.+ .+  +-|.....++....+-       
T Consensus       196 lg~~~eal~D~tv~ci~~~F~-n~s~~~~~eR~Lkk~-----a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~  269 (606)
T KOG0547|consen  196 LGKFDEALFDVTVLCILEGFQ-NASIEPMAERVLKKQ-----AMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLF  269 (606)
T ss_pred             hccHHHHHHhhhHHHHhhhcc-cchhHHHHHHHHHHH-----HHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccc
Confidence            89988876433222111 111 111111111111110     1111111111 11  2233322222222211       


Q ss_pred             ----------------c--cC---ChHHHHHHHHHHHhCCCCCC-----CH------HHHHHHHHHHHHcCCHHHHHHHH
Q 011236          219 ----------------A--RS---ELSSMENVLQEMESQSHISM-----DW------GTYSTVANYYIIAGLKEKAIIYL  266 (490)
Q Consensus       219 ----------------~--~g---~~~~a~~~~~~~~~~~~~~~-----~~------~~~~~li~~~~~~~~~~~a~~~~  266 (490)
                                      .  .+   .+..|...+.+-.......+     |.      .+......-+.-.|+.-.|..-|
T Consensus       270 ~~~~~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~  349 (606)
T KOG0547|consen  270 DNKSDKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDF  349 (606)
T ss_pred             cCCCccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhH
Confidence                            0  01   22223222222110111111     11      11111112234467888899999


Q ss_pred             HHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 011236          267 KKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYC  346 (490)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  346 (490)
                      +..+...+.  +...|.-+..+|....+.++....|.+....++ .++.+|..-.+...-.+++++|..=|++..... +
T Consensus       350 ~~~I~l~~~--~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp-~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~-p  425 (606)
T KOG0547|consen  350 DAAIKLDPA--FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDP-ENPDVYYHRGQMRFLLQQYEEAIADFQKAISLD-P  425 (606)
T ss_pred             HHHHhcCcc--cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCC-CCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcC-h
Confidence            998887664  334477788889999999999999998777766 677788888888888899999999999998852 2


Q ss_pred             CCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhh
Q 011236          347 YDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSL  426 (490)
Q Consensus       347 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~  426 (490)
                      -+...|..+..+..+.+++++++..|++.+++=+. .+..|+.....+..+++++.|.+.|+.++++.+...++..+...
T Consensus       426 e~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~-~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v~~~p  504 (606)
T KOG0547|consen  426 ENAYAYIQLCCALYRQHKIAESMKTFEEAKKKFPN-CPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIVNAAP  504 (606)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccccchh
Confidence            25556777777778889999999999999987433 67889999999999999999999999999977665555555433


Q ss_pred             --HHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHH
Q 011236          427 --VSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESM  481 (490)
Q Consensus       427 --~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m  481 (490)
                        ...++..-.+ +++..|..+++++.+.+|. ...|..|...-.+.|  ++|+++|++-
T Consensus       505 lV~Ka~l~~qwk-~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEks  563 (606)
T KOG0547|consen  505 LVHKALLVLQWK-EDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKS  563 (606)
T ss_pred             hhhhhHhhhchh-hhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence              2333333333 8999999999999999999 999999999999999  9999999864

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

Probab=99.71  E-value=1.3e-16  Score=142.05  Aligned_cols=261  Identities=15%  Similarity=0.096  Sum_probs=106.3

Q ss_pred             HHHHHHHhhcCHHHHHHHHHH-cccc-CC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhc
Q 011236          109 VQLDLIGKVRGLESAETYFNS-LNDE-DK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNT  185 (490)
Q Consensus       109 ~l~~~~~~~~~~~~A~~~~~~-~~~~-~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  185 (490)
                      .+...+.+.|+++.|.++++. +... +| +...|..+.......++++.|...++++...+.. ++..+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccc
Confidence            456777788888888888854 3343 34 4566677777777788888888888888877654 66667777776 688


Q ss_pred             CCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011236          186 GQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIY  265 (490)
Q Consensus       186 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~  265 (490)
                      +++++|.+++....+..  ++...+..++..+...++++++..+++.+......+.+...|..+...+.+.|+.++|++.
T Consensus        91 ~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~  168 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRD  168 (280)
T ss_dssp             -----------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHH
T ss_pred             ccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            88888888887765542  4566677788888888899998888888764444556777888888888889999999999


Q ss_pred             HHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 011236          266 LKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY  345 (490)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  345 (490)
                      +++..+..|  .|......++..+...|+.+++.++++......+ .++..+..+..++...|+.++|...+++..+. .
T Consensus       169 ~~~al~~~P--~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~-~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~-~  244 (280)
T PF13429_consen  169 YRKALELDP--DDPDARNALAWLLIDMGDYDEAREALKRLLKAAP-DDPDLWDALAAAYLQLGRYEEALEYLEKALKL-N  244 (280)
T ss_dssp             HHHHHHH-T--T-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-H-TSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHH-S
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCc-CHHHHHHHHHHHhccccccccccccccccccc-c
Confidence            998888766  4677788888888888888888888887666653 56667788888888899999999999988875 3


Q ss_pred             CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011236          346 CYDFRVPNIILLGYSQKGMIEKADAVLKEIVK  377 (490)
Q Consensus       346 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  377 (490)
                      +.|......+.+++...|+.++|..+.++...
T Consensus       245 p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  245 PDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             TT-HHHHHHHHHHHT-----------------
T ss_pred             cccccccccccccccccccccccccccccccc
Confidence            44777778888888889999999888776643

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.70  E-value=1.3e-13  Score=128.34  Aligned_cols=283  Identities=11%  Similarity=0.054  Sum_probs=191.8

Q ss_pred             hcCHHHHHHHHHHccccCCChhHHHHH-HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHH--HHHHHHHhcCCcCcHHH
Q 011236          117 VRGLESAETYFNSLNDEDKVDKLYGAL-LNCYVREGLVDESLSLMQKMKEMGSFGSALNYN--GIMCLYTNTGQHEKIPD  193 (490)
Q Consensus       117 ~~~~~~A~~~~~~~~~~~p~~~~~~~l-i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~--~l~~~~~~~~~~~~a~~  193 (490)
                      .|+++.|.+.+.......+++..+..+ .....+.|+++.|.+.+.++.+.  .|+...+.  .....+...|+++.|.+
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            578888887777665544333333333 34446778888888888887765  33433222  33556777788888888


Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCH-------HHHHHHHHHHHHcCCHHHHHHHH
Q 011236          194 VLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDW-------GTYSTVANYYIIAGLKEKAIIYL  266 (490)
Q Consensus       194 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-------~~~~~li~~~~~~~~~~~a~~~~  266 (490)
                      .++++.+... -+...+..+...|.+.|++++|.+++..+. +.+..++.       .+|..++.......+.+...+++
T Consensus       175 ~l~~~~~~~P-~~~~al~ll~~~~~~~gdw~~a~~~l~~l~-k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w  252 (398)
T PRK10747        175 GVDKLLEVAP-RHPEVLRLAEQAYIRTGAWSSLLDILPSMA-KAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWW  252 (398)
T ss_pred             HHHHHHhcCC-CCHHHHHHHHHHHHHHHhHHHHHHHHHHHH-HcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            8888877542 355667777788888888888888888887 44442222       12223333333444556666666


Q ss_pred             HHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 011236          267 KKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYC  346 (490)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  346 (490)
                      +.+....+  .++.....+...+...|+.++|.+++++.....  ++..  ..++.+....++.+++.+..+...+. .+
T Consensus       253 ~~lp~~~~--~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~--~~~~--l~~l~~~l~~~~~~~al~~~e~~lk~-~P  325 (398)
T PRK10747        253 KNQSRKTR--HQVALQVAMAEHLIECDDHDTAQQIILDGLKRQ--YDER--LVLLIPRLKTNNPEQLEKVLRQQIKQ-HG  325 (398)
T ss_pred             HhCCHHHh--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCHH--HHHHHhhccCCChHHHHHHHHHHHhh-CC
Confidence            66544333  567777888888888888888888888776632  4442  22334444568888888888888876 33


Q ss_pred             CCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          347 YDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       347 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      -|......+...+.+.+++++|.+.|+.+.+.  .|+...+..+...+.+.|+.++|.+++++.+.
T Consensus       326 ~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~--~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~  389 (398)
T PRK10747        326 DTPLLWSTLGQLLMKHGEWQEASLAFRAALKQ--RPDAYDYAWLADALDRLHKPEEAAAMRRDGLM  389 (398)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            45566778888888888888888888888875  57788888888888888888888888888765

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

Probab=99.70  E-value=1.7e-12  Score=123.21  Aligned_cols=400  Identities=15%  Similarity=0.074  Sum_probs=225.2

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCCh--h----HHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVD--K----LYG  141 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~--~----~~~  141 (490)
                      |...|..+.....+.|.+++|.-.|.+.++.. |++....---+..|-+.|+...|...|.++.+..|.+  .    .--
T Consensus       206 d~e~W~~ladls~~~~~i~qA~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~  284 (895)
T KOG2076|consen  206 DYELWKRLADLSEQLGNINQARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIR  284 (895)
T ss_pred             ChHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHH
Confidence            33444444444444444444444444444443 2222222333344444444444444444444433310  0    111


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhc-CCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCC------------------
Q 011236          142 ALLNCYVREGLVDESLSLMQKMKEM-GSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENG------------------  202 (490)
Q Consensus       142 ~li~~~~~~g~~~~a~~~~~~m~~~-~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~------------------  202 (490)
                      ..++.+...++-+.|++.++..... +-.-+...+++++..+.+...++.+......+....                  
T Consensus       285 ~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~  364 (895)
T KOG2076|consen  285 RVAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEP  364 (895)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccc
Confidence            1233333344444444444444331 111234455666666666666666666666555411                  


Q ss_pred             ---------CCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhh
Q 011236          203 ---------VPPDNFSYRICINSYGARSELSSMENVLQEMESQSH--ISMDWGTYSTVANYYIIAGLKEKAIIYLKKCED  271 (490)
Q Consensus       203 ---------~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  271 (490)
                               +.++..++ -+.-++.+....+....+..... ..+  +.-++..|.-+..+|...|.+.+|+.+|..+..
T Consensus       365 ~~~~~~~~~~s~~l~v~-rl~icL~~L~~~e~~e~ll~~l~-~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~  442 (895)
T KOG2076|consen  365 NALCEVGKELSYDLRVI-RLMICLVHLKERELLEALLHFLV-EDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITN  442 (895)
T ss_pred             cccccCCCCCCccchhH-hHhhhhhcccccchHHHHHHHHH-HhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhc
Confidence                     11222221 11122223333333333333333 333  334566777788899999999999999999888


Q ss_pred             hhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh--------c
Q 011236          272 IVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWEL--------S  343 (490)
Q Consensus       272 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--------~  343 (490)
                      .... .+...|-.+..+|...|..++|.+.|+..+...+ .+...-..|...+-+.|+.++|.+.+..+..        .
T Consensus       443 ~~~~-~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p-~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~  520 (895)
T KOG2076|consen  443 REGY-QNAFVWYKLARCYMELGEYEEAIEFYEKVLILAP-DNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEAC  520 (895)
T ss_pred             Cccc-cchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCC-CchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhc
Confidence            7666 6778899999999999999999999998877665 5555666777778889999999999888542        2


Q ss_pred             CCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC--------------------------------------------
Q 011236          344 CYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG--------------------------------------------  379 (490)
Q Consensus       344 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~--------------------------------------------  379 (490)
                      +..|+........+.+.+.|+.++=..+...|+...                                            
T Consensus       521 a~~~e~ri~~~r~d~l~~~gk~E~fi~t~~~Lv~~~~~~~~~f~~~~k~r~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~  600 (895)
T KOG2076|consen  521 AWEPERRILAHRCDILFQVGKREEFINTASTLVDDFLKKRYIFPRNKKKRRRAIAGTTSKRYSELLKQIIRAREKATDDN  600 (895)
T ss_pred             cccHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHhhccccccccchhHHHHHHHHhccCchH
Confidence            234444444555566666776655433332222110                                            


Q ss_pred             -----C-CC-----------CH----HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch---hhHHHHHHHHH
Q 011236          380 -----K-TP-----------TP----NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP---SLVSSILDWLG  435 (490)
Q Consensus       380 -----~-~p-----------~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~---~~~~~l~~~~~  435 (490)
                           . .+           +.    ..+.-++..+++.+++++|+.+...+....   .-..++.   ..-...+.+..
T Consensus       601 ~~~~~l~d~~~~~~~e~~~Lsiddwfel~~e~i~~L~k~~r~qeAl~vv~~a~~~~---~f~~~~~~~k~l~~~~l~~s~  677 (895)
T KOG2076|consen  601 VMEKALSDGTEFRAVELRGLSIDDWFELFRELILSLAKLQRVQEALSVVFTALEAY---IFFQDSEIRKELQFLGLKASL  677 (895)
T ss_pred             HhhhcccchhhhhhhhhccCcHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhh---hhhccHHHHHHHHHHHHHHHH
Confidence                 0 00           00    123455667778888888888888887722   1122222   12234455667


Q ss_pred             cCCCHHHHHHHHHHHHhc-----ccc-hhhhHHHHHHHHhcCCcHH
Q 011236          436 DNRDVEEVEAFVSSLKIK-----VQK-RNMYHALTEAHIRSGQEVD  475 (490)
Q Consensus       436 ~~g~~~~a~~~~~~~~~~-----~~~-~~~~~~l~~~~~~~g~~a~  475 (490)
                      ..+++..|...++.+...     .+- ...|+...+.+.+.|+++.
T Consensus       678 ~~~d~~~a~~~lR~~i~~~~~~~~~~q~~l~n~~~s~~~~~~q~v~  723 (895)
T KOG2076|consen  678 YARDPGDAFSYLRSVITQFQFYLDVYQLNLWNLDFSYFSKYGQRVC  723 (895)
T ss_pred             hcCCHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence            788999999888888777     555 7777777777777774443

>TIGR00540 hemY_coli hemY protein

Probab=99.69  E-value=1.8e-13  Score=128.23  Aligned_cols=293  Identities=10%  Similarity=0.043  Sum_probs=136.8

Q ss_pred             hhcCHHHHHHHHHHccccCCChhH-HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHH
Q 011236          116 KVRGLESAETYFNSLNDEDKVDKL-YGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDV  194 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~~~~p~~~~-~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~  194 (490)
                      ..|+++.|.+.+....+..|+... +-....++.+.|+.+.|.+.+.+..+....+.....-.....+...|+++.|...
T Consensus        96 ~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~  175 (409)
T TIGR00540        96 AEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHG  175 (409)
T ss_pred             hCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHH
Confidence            456666666666665555454222 2333455555666666666666655442221112222235555556666666666


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHH-HHHHHH---HHcCCHHHHHHHHHHHh
Q 011236          195 LLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYS-TVANYY---IIAGLKEKAIIYLKKCE  270 (490)
Q Consensus       195 ~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~-~li~~~---~~~~~~~~a~~~~~~~~  270 (490)
                      ++.+.+... -+...+..+...+...|++++|.+.+..+. +.++ ++...+. ....++   ...+..+++.+.+..+.
T Consensus       176 l~~l~~~~P-~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~-k~~~-~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~  252 (409)
T TIGR00540       176 VDKLLEMAP-RHKEVLKLAEEAYIRSGAWQALDDIIDNMA-KAGL-FDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWW  252 (409)
T ss_pred             HHHHHHhCC-CCHHHHHHHHHHHHHHhhHHHHHHHHHHHH-HcCC-CCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            666665432 244455566666666666666666666665 4443 2222221 111111   22222222223333333


Q ss_pred             hhhccC--CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhH-HHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 011236          271 DIVSKS--KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDY-ITMLGSLVKIGELEEAEKMLEEWELSCYCY  347 (490)
Q Consensus       271 ~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  347 (490)
                      ...+..  .+...+..+...+...|+.++|.+++++.....+......+ ..........++.+.+.+.++...+. .+-
T Consensus       253 ~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~-~p~  331 (409)
T TIGR00540       253 KNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKN-VDD  331 (409)
T ss_pred             HHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHh-CCC
Confidence            222210  24455555555666666666666666655554431111110 11111112234455555555554443 111


Q ss_pred             Cc--hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          348 DF--RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       348 ~~--~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      |.  ....++...+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|.++|++.+.
T Consensus       332 ~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l~  398 (409)
T TIGR00540       332 KPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSLG  398 (409)
T ss_pred             ChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            22  333445555555555555555555333322344555555555555555555555555555443

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.

>TIGR00540 hemY_coli hemY protein

Probab=99.68  E-value=1.2e-13  Score=129.38  Aligned_cols=299  Identities=11%  Similarity=0.006  Sum_probs=219.8

Q ss_pred             HHHHHHHH--HhcCChhHHHHHHHHHHhCCCCCChhh-HHHHHHHHHhhcCHHHHHHHHHHccccCCChh--HHHHHHHH
Q 011236           72 LQRVIRQL--RSRKRFKHALQVSEWMSGQGLAFSVHD-HAVQLDLIGKVRGLESAETYFNSLNDEDKVDK--LYGALLNC  146 (490)
Q Consensus        72 ~~~ll~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~--~~~~li~~  146 (490)
                      ...+.+++  ...|+++.|.+.+....+..  |++.. +..........|+.+.|.+.+....+..|+..  +.-.....
T Consensus        85 ~~~~~~glla~~~g~~~~A~~~l~~~~~~~--~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l  162 (409)
T TIGR00540        85 QKQTEEALLKLAEGDYAKAEKLIAKNADHA--AEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRI  162 (409)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHH
Confidence            33444444  35799999999999887764  34333 34456778889999999999999877666543  44446888


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHH-HHHHHH---hccCC
Q 011236          147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYR-ICINSY---GARSE  222 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~-~li~~~---~~~g~  222 (490)
                      +...|+++.|...++.+.+..+. +...+..+...+...|++++|.+.+..+.+.++. +...+. .-..++   ...+.
T Consensus       163 ~l~~~~~~~Al~~l~~l~~~~P~-~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~-~~~~~~~l~~~a~~~~l~~~~  240 (409)
T TIGR00540       163 LLAQNELHAARHGVDKLLEMAPR-HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLF-DDEEFADLEQKAEIGLLDEAM  240 (409)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999998755 7778899999999999999999999999998764 333332 111221   22233


Q ss_pred             hHHHHHHHHHHHhCCC---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhh-HHHHHHHHHhcCChhHH
Q 011236          223 LSSMENVLQEMESQSH---ISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALG-YNHLISHYASLGNKDEM  298 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~---~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~~~~~~a  298 (490)
                      .+++.+.+..+. +..   .+.+...+..+...+...|+.++|.+++++..+..+. ..... ...........++.+.+
T Consensus       241 ~~~~~~~L~~~~-~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd-~~~~~~~~l~~~~~l~~~~~~~~  318 (409)
T TIGR00540       241 ADEGIDGLLNWW-KNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGD-DRAISLPLCLPIPRLKPEDNEKL  318 (409)
T ss_pred             HhcCHHHHHHHH-HHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCC-cccchhHHHHHhhhcCCCChHHH
Confidence            333334555544 222   1237788888999999999999999999999886653 21111 12222223345788889


Q ss_pred             HHHHHHHHHhcCCCCh--hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          299 MKFWGLQKIKCKKQLN--RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       299 ~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      .+.++...+..+ .++  ....++...+.+.|++++|.+.|+........|+...+..+...+.+.|+.++|.+++++..
T Consensus       319 ~~~~e~~lk~~p-~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l  397 (409)
T TIGR00540       319 EKLIEKQAKNVD-DKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSL  397 (409)
T ss_pred             HHHHHHHHHhCC-CChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999987777655 344  56778999999999999999999964444457888888999999999999999999999865


Q ss_pred             H
Q 011236          377 K  377 (490)
Q Consensus       377 ~  377 (490)
                      .
T Consensus       398 ~  398 (409)
T TIGR00540       398 G  398 (409)
T ss_pred             H
Confidence            4

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.

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

Probab=99.67  E-value=6.8e-12  Score=110.36  Aligned_cols=298  Identities=15%  Similarity=0.126  Sum_probs=220.2

Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCC--CCCHHHHHHHHHHHhccCC
Q 011236          145 NCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGV--PPDNFSYRICINSYGARSE  222 (490)
Q Consensus       145 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~--~p~~~~~~~li~~~~~~g~  222 (490)
                      .++-...+.+++..-.+.....|++-+...-+....+.-...++++|+.+|+++.+.+.  --|..+|+.++-.--....
T Consensus       235 ~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~sk  314 (559)
T KOG1155|consen  235 KAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSK  314 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHH
Confidence            44555567777777777777777764444444445555567789999999999887632  1255677776654333222


Q ss_pred             hH-HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHH
Q 011236          223 LS-SMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKF  301 (490)
Q Consensus       223 ~~-~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  301 (490)
                      +. .|..+++-=    .  --+.|...+.+-|+-.++.++|..+|++..+.++  .....|+.+..-|....+...|.+-
T Consensus       315 Ls~LA~~v~~id----K--yR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp--~~~~aWTLmGHEyvEmKNt~AAi~s  386 (559)
T KOG1155|consen  315 LSYLAQNVSNID----K--YRPETCCIIANYYSLRSEHEKAVMYFKRALKLNP--KYLSAWTLMGHEYVEMKNTHAAIES  386 (559)
T ss_pred             HHHHHHHHHHhc----c--CCccceeeehhHHHHHHhHHHHHHHHHHHHhcCc--chhHHHHHhhHHHHHhcccHHHHHH
Confidence            22 233332211    1  3345666788888999999999999999988776  5778899999999999999999999


Q ss_pred             HHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          302 WGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       302 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      |+..+.-++ .|-..|-.+.++|.-.+...-|.-.|++..+. -+.|...|.+|..+|.+.++.++|++.|......|-.
T Consensus       387 YRrAvdi~p-~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~-kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dt  464 (559)
T KOG1155|consen  387 YRRAVDINP-RDYRAWYGLGQAYEIMKMHFYALYYFQKALEL-KPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDT  464 (559)
T ss_pred             HHHHHhcCc-hhHHHHhhhhHHHHHhcchHHHHHHHHHHHhc-CCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhcccc
Confidence            998888776 78889999999999999999999999999886 3457889999999999999999999999999987754


Q ss_pred             CCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          382 PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       382 p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                       +...+..|...|-+.++.++|.+.|++-++.......+.|.. ....-|...+.+.+++++|..........
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             668899999999999999999999988877331111233322 23334556677788888887665554443

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

Probab=99.66  E-value=6.4e-14  Score=122.53  Aligned_cols=403  Identities=14%  Similarity=0.101  Sum_probs=269.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhH-HHHHHHHHhhcCHHHHHHHHHHccccCCC------hhHHH
Q 011236           69 ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDH-AVQLDLIGKVRGLESAETYFNSLNDEDKV------DKLYG  141 (490)
Q Consensus        69 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~A~~~~~~~~~~~p~------~~~~~  141 (490)
                      ...+..|...|..+..+.+|+..|+-+.+...-|+.-.. ..+...+.+.+.+..|+.+++.....-|+      ....+
T Consensus       201 fsvl~nlaqqy~~ndm~~ealntyeiivknkmf~nag~lkmnigni~~kkr~fskaikfyrmaldqvpsink~~rikil~  280 (840)
T KOG2003|consen  201 FSVLFNLAQQYEANDMTAEALNTYEIIVKNKMFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILN  280 (840)
T ss_pred             HHHHHHHHHHhhhhHHHHHHhhhhhhhhcccccCCCceeeeeecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHh
Confidence            334455556666667788889888888877654443332 22445677888899999998876655432      23455


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCC------------CHHH
Q 011236          142 ALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPP------------DNFS  209 (490)
Q Consensus       142 ~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p------------~~~~  209 (490)
                      .+.-.+.+.|+++.|+.-|+...+.  .|+..+--.|+-++..-|+.++..+.|..|+.-...|            +...
T Consensus       281 nigvtfiq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~l  358 (840)
T KOG2003|consen  281 NIGVTFIQAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNL  358 (840)
T ss_pred             hcCeeEEecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHH
Confidence            5666788999999999999998776  4676655455555666789999999999998643333            3333


Q ss_pred             HHHHHH-----HHhccC--ChHHHHHHHHHHHhCCCCCCCHH---------------------HHHHHHHHHHHcCCHHH
Q 011236          210 YRICIN-----SYGARS--ELSSMENVLQEMESQSHISMDWG---------------------TYSTVANYYIIAGLKEK  261 (490)
Q Consensus       210 ~~~li~-----~~~~~g--~~~~a~~~~~~~~~~~~~~~~~~---------------------~~~~li~~~~~~~~~~~  261 (490)
                      .+..|.     -.-+.+  +.++++-.--++. ..-+.|+-.                     .--.-..-|.+.|+++.
T Consensus       359 l~eai~nd~lk~~ek~~ka~aek~i~ta~kii-apvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~  437 (840)
T KOG2003|consen  359 LNEAIKNDHLKNMEKENKADAEKAIITAAKII-APVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEG  437 (840)
T ss_pred             HHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHh-ccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHH
Confidence            332221     111111  2222222222222 222222210                     00112356899999999


Q ss_pred             HHHHHHHHhhhhccCCChhhHHHHH-H----------------------------------HHHhcCChhHHHHHHHHHH
Q 011236          262 AIIYLKKCEDIVSKSKDALGYNHLI-S----------------------------------HYASLGNKDEMMKFWGLQK  306 (490)
Q Consensus       262 a~~~~~~~~~~~~~~~~~~~~~~l~-~----------------------------------~~~~~~~~~~a~~~~~~~~  306 (490)
                      |+++++-..+......+...-|..+ .                                  .....|++++|.+.|++.+
T Consensus       438 aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~ngd~dka~~~ykeal  517 (840)
T KOG2003|consen  438 AIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFANGDLDKAAEFYKEAL  517 (840)
T ss_pred             HHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeeecCcHHHHHHHHHHHH
Confidence            9999988765433211111111100 0                                  0113678888888888776


Q ss_pred             HhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH
Q 011236          307 IKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNS  386 (490)
Q Consensus       307 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~  386 (490)
                      .... .-......+.-.+...|++++|.+.|-++... +..+..+...+...|-...+...|++++-+.... ++.|+..
T Consensus       518 ~nda-sc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~~q~~sl-ip~dp~i  594 (840)
T KOG2003|consen  518 NNDA-SCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELLMQANSL-IPNDPAI  594 (840)
T ss_pred             cCch-HHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CCCCHHH
Confidence            6543 22333334444567788999999988877654 4446667777888888888999999988777665 3448889


Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccchhhhHHHHHH
Q 011236          387 WSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEA  466 (490)
Q Consensus       387 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~  466 (490)
                      ...|...|-+.|+-..|.++.-+-.+      -++-|..+...|...|....-++.+..+|++..-..|...-|..++..
T Consensus       595 lskl~dlydqegdksqafq~~ydsyr------yfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmias  668 (840)
T KOG2003|consen  595 LSKLADLYDQEGDKSQAFQCHYDSYR------YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIAS  668 (840)
T ss_pred             HHHHHHHhhcccchhhhhhhhhhccc------ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHH
Confidence            99999999999999999988766544      466778999999999999999999999999998888887888888777


Q ss_pred             HHh-cC--CcHHHHHHHHHh
Q 011236          467 HIR-SG--QEVDGLLESMKA  483 (490)
Q Consensus       467 ~~~-~g--~~a~~~~~~m~~  483 (490)
                      |.+ .|  ++|+++++....
T Consensus       669 c~rrsgnyqka~d~yk~~hr  688 (840)
T KOG2003|consen  669 CFRRSGNYQKAFDLYKDIHR  688 (840)
T ss_pred             HHHhcccHHHHHHHHHHHHH
Confidence            655 55  999999988754

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

Probab=99.66  E-value=1.4e-11  Score=112.83  Aligned_cols=401  Identities=10%  Similarity=-0.001  Sum_probs=318.6

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQL  111 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  111 (490)
                      ++.++.+++..+...|.-++.               -..+|..-...|.+.+.++-|..+|...++-. +-....+....
T Consensus       494 sv~TcQAIi~avigigvEeed---------------~~~tw~~da~~~~k~~~~~carAVya~alqvf-p~k~slWlra~  557 (913)
T KOG0495|consen  494 SVITCQAIIRAVIGIGVEEED---------------RKSTWLDDAQSCEKRPAIECARAVYAHALQVF-PCKKSLWLRAA  557 (913)
T ss_pred             ChhhHHHHHHHHHhhccccch---------------hHhHHhhhHHHHHhcchHHHHHHHHHHHHhhc-cchhHHHHHHH
Confidence            555566666665555442222               23466677788888899999999999988875 45667777777


Q ss_pred             HHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCc
Q 011236          112 DLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEK  190 (490)
Q Consensus       112 ~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  190 (490)
                      ..--..|..++-..+|++....-| ....|-.....+...|++..|..++....+.... +...|-..+..-..+..++.
T Consensus       558 ~~ek~hgt~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-seeiwlaavKle~en~e~er  636 (913)
T KOG0495|consen  558 MFEKSHGTRESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVKLEFENDELER  636 (913)
T ss_pred             HHHHhcCcHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHHHhhccccHHH
Confidence            777788999999999999887766 4566777788888899999999999999888655 77788888888889999999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Q 011236          191 IPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCE  270 (490)
Q Consensus       191 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  270 (490)
                      |..+|.+...  ..|+...|..-++..--.++.++|.+++++.. + .++.-...|-.+...+-+.++++.|...|..=.
T Consensus       637 aR~llakar~--~sgTeRv~mKs~~~er~ld~~eeA~rllEe~l-k-~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~  712 (913)
T KOG0495|consen  637 ARDLLAKARS--ISGTERVWMKSANLERYLDNVEEALRLLEEAL-K-SFPDFHKLWLMLGQIEEQMENIEMAREAYLQGT  712 (913)
T ss_pred             HHHHHHHHhc--cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHH-H-hCCchHHHHHHHhHHHHHHHHHHHHHHHHHhcc
Confidence            9999998876  45777777777777777899999999999887 2 231334567778888899999999999998866


Q ss_pred             hhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCch
Q 011236          271 DIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFR  350 (490)
Q Consensus       271 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  350 (490)
                      +..+  ..+..|..+...--+.|.+-.|..++++....++ .+...|...|+.=.+.|..++|..++.+.++. ++.+..
T Consensus       713 k~cP--~~ipLWllLakleEk~~~~~rAR~ildrarlkNP-k~~~lwle~Ir~ElR~gn~~~a~~lmakALQe-cp~sg~  788 (913)
T KOG0495|consen  713 KKCP--NSIPLWLLLAKLEEKDGQLVRARSILDRARLKNP-KNALLWLESIRMELRAGNKEQAELLMAKALQE-CPSSGL  788 (913)
T ss_pred             ccCC--CCchHHHHHHHHHHHhcchhhHHHHHHHHHhcCC-CcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCccch
Confidence            6554  4667788888888889999999999998888776 78889999999999999999999999999887 566777


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSS  429 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~  429 (490)
                      .|..-|....+.++-.+....+++     +.-|+.+.-.+...|....++++|.+.|.+++.       +.||. .+|..
T Consensus       789 LWaEaI~le~~~~rkTks~DALkk-----ce~dphVllaia~lfw~e~k~~kar~Wf~Ravk-------~d~d~GD~wa~  856 (913)
T KOG0495|consen  789 LWAEAIWLEPRPQRKTKSIDALKK-----CEHDPHVLLAIAKLFWSEKKIEKAREWFERAVK-------KDPDNGDAWAW  856 (913)
T ss_pred             hHHHHHHhccCcccchHHHHHHHh-----ccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHc-------cCCccchHHHH
Confidence            888888777777774444443333     334788888889999999999999999999998       44665 78999


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHh
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIR  469 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~  469 (490)
                      +...+...|.-++-.+++.+.....|. -..|.++-..-..
T Consensus       857 fykfel~hG~eed~kev~~~c~~~EP~hG~~W~avSK~i~n  897 (913)
T KOG0495|consen  857 FYKFELRHGTEEDQKEVLKKCETAEPTHGELWQAVSKDIKN  897 (913)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhccCCCCCcHHHHHhhhHHh
Confidence            999999999999999999999888888 7777666554433

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

Probab=99.66  E-value=2.7e-14  Score=130.93  Aligned_cols=284  Identities=14%  Similarity=0.069  Sum_probs=200.4

Q ss_pred             ChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC----ChhHHHHHHHHHHhcCChhHHHHH
Q 011236           84 RFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK----VDKLYGALLNCYVREGLVDESLSL  159 (490)
Q Consensus        84 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p----~~~~~~~li~~~~~~g~~~~a~~~  159 (490)
                      +..+|+..|.++...- .-+......+..+|...+++++|..+|+.+.+..|    +...|.+.+.-+-+.    -++..
T Consensus       334 ~~~~A~~~~~klp~h~-~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~----v~Ls~  408 (638)
T KOG1126|consen  334 NCREALNLFEKLPSHH-YNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDE----VALSY  408 (638)
T ss_pred             HHHHHHHHHHhhHHhc-CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhh----HHHHH
Confidence            4677888888854443 44557777778888888888888888888887764    566777776554321    12222


Q ss_pred             -HHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCC-CHHHHHHHHHHHhccCChHHHHHHHHHHHhCC
Q 011236          160 -MQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPP-DNFSYRICINSYGARSELSSMENVLQEMESQS  237 (490)
Q Consensus       160 -~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  237 (490)
                       -+++.... +-.+.+|-++.++|.-+++.+.|++.|++.++.  .| ..++|+.+.+-+.....+|.|...|+... . 
T Consensus       409 Laq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQl--dp~faYayTLlGhE~~~~ee~d~a~~~fr~Al-~-  483 (638)
T KOG1126|consen  409 LAQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQL--DPRFAYAYTLLGHESIATEEFDKAMKSFRKAL-G-  483 (638)
T ss_pred             HHHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhcc--CCccchhhhhcCChhhhhHHHHhHHHHHHhhh-c-
Confidence             22233332 226778888888888888888888888888774  34 66778877777888888888888887776 3 


Q ss_pred             CCCCCHHHHH---HHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCCh
Q 011236          238 HISMDWGTYS---TVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLN  314 (490)
Q Consensus       238 ~~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  314 (490)
                         .+...|+   -+...|.+.++++.|+-.|++..+..+  .+.+....+...+-+.|+.++|++++++.....+ .++
T Consensus       484 ---~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP--~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~-kn~  557 (638)
T KOG1126|consen  484 ---VDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINP--SNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDP-KNP  557 (638)
T ss_pred             ---CCchhhHHHHhhhhheeccchhhHHHHHHHhhhcCCc--cchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCC-CCc
Confidence               3334444   466678888888888888888877666  5667777777777888888888888887776665 444


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH
Q 011236          315 RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTP  384 (490)
Q Consensus       315 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~  384 (490)
                      ..-...+..+...+++++|.+.++++++. ++-+..++..+...|.+.|+.+.|+.-|.-+.+.++++..
T Consensus       558 l~~~~~~~il~~~~~~~eal~~LEeLk~~-vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~~  626 (638)
T KOG1126|consen  558 LCKYHRASILFSLGRYVEALQELEELKEL-VPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGAQ  626 (638)
T ss_pred             hhHHHHHHHHHhhcchHHHHHHHHHHHHh-CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccch
Confidence            44445556666778888888888888775 4445566777778888888888888888777776655433

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

Probab=99.65  E-value=2.4e-12  Score=108.06  Aligned_cols=287  Identities=14%  Similarity=0.119  Sum_probs=163.0

Q ss_pred             cCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCH------HHHHHHHHHHhccCCh
Q 011236          150 EGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDN------FSYRICINSYGARSEL  223 (490)
Q Consensus       150 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~------~~~~~li~~~~~~g~~  223 (490)
                      ..+.++|.++|-+|.+.... +..+.-+|.+.|.+.|..+.|+++.+.+.++   ||.      .....|..-|...|-+
T Consensus        48 s~Q~dKAvdlF~e~l~~d~~-t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~qr~lAl~qL~~Dym~aGl~  123 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDPE-TFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQRLLALQQLGRDYMAAGLL  123 (389)
T ss_pred             hcCcchHHHHHHHHHhcCch-hhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHHHHHHHHHHHHHHHHhhhh
Confidence            35667777777777765322 4444556666777777777777777776654   332      1233445556666777


Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh----hhHHHHHHHHHhcCChhHHH
Q 011236          224 SSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA----LGYNHLISHYASLGNKDEMM  299 (490)
Q Consensus       224 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~  299 (490)
                      |.|+.+|..+. +.+. .-......|+..|-...+|++|+++-+++.+.+.. +..    ..|-.+...+....+.+.|.
T Consensus       124 DRAE~~f~~L~-de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q-~~~~eIAqfyCELAq~~~~~~~~d~A~  200 (389)
T COG2956         124 DRAEDIFNQLV-DEGE-FAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQ-TYRVEIAQFYCELAQQALASSDVDRAR  200 (389)
T ss_pred             hHHHHHHHHHh-cchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCc-cchhHHHHHHHHHHHHHhhhhhHHHHH
Confidence            77777777666 3222 33445555677777777777777776666655543 221    22334444444556666666


Q ss_pred             HHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011236          300 KFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG  379 (490)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  379 (490)
                      .++.+.....+ ..+..-..+.+.....|+++.|.+.++.+.+.+...-..+...|..+|.+.|+.++....+..+.+..
T Consensus       201 ~~l~kAlqa~~-~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~  279 (389)
T COG2956         201 ELLKKALQADK-KCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETN  279 (389)
T ss_pred             HHHHHHHhhCc-cceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHcc
Confidence            66666666554 44444455566666667777777777666666544444556666666666777766666666666543


Q ss_pred             CCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc---CCCHHHHHHHHHHHHhc
Q 011236          380 KTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD---NRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       380 ~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~  453 (490)
                      .  ....-..+...-....-.+.|..++.+-+.       -+|+...+..++..-..   .|...+....++.|...
T Consensus       280 ~--g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~-------r~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge  347 (389)
T COG2956         280 T--GADAELMLADLIELQEGIDAAQAYLTRQLR-------RKPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGE  347 (389)
T ss_pred             C--CccHHHHHHHHHHHhhChHHHHHHHHHHHh-------hCCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHH
Confidence            2  222233333333334444555555555444       34666666666665432   23344444455555443

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

Probab=99.64  E-value=4.6e-14  Score=129.46  Aligned_cols=285  Identities=12%  Similarity=0.014  Sum_probs=166.0

Q ss_pred             hhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCC--CCCCHHHHHHHHHHHhccCChHHHHHHH
Q 011236          153 VDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENG--VPPDNFSYRICINSYGARSELSSMENVL  230 (490)
Q Consensus       153 ~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~--~~p~~~~~~~li~~~~~~g~~~~a~~~~  230 (490)
                      ..+|+..|..+.+.- .-+......+..+|...+++++|.++|+.+.+..  ..-+..+|.+.+-.+-+.-    ++..+
T Consensus       335 ~~~A~~~~~klp~h~-~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v----~Ls~L  409 (638)
T KOG1126|consen  335 CREALNLFEKLPSHH-YNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEV----ALSYL  409 (638)
T ss_pred             HHHHHHHHHhhHHhc-CCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhH----HHHHH
Confidence            456666666644442 2233455566666777777777777777665532  0124455655554432211    11111


Q ss_pred             -HHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhc
Q 011236          231 -QEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKC  309 (490)
Q Consensus       231 -~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  309 (490)
                       +.+. +.+. -.+++|-++.++|.-.++.+.|++.|++..+..+  ...++|+.+..-+.....+|.|...|+..+...
T Consensus       410 aq~Li-~~~~-~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp--~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~  485 (638)
T KOG1126|consen  410 AQDLI-DTDP-NSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDP--RFAYAYTLLGHESIATEEFDKAMKSFRKALGVD  485 (638)
T ss_pred             HHHHH-hhCC-CCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCC--ccchhhhhcCChhhhhHHHHhHHHHHHhhhcCC
Confidence             1122 2221 4456666677777777777777777777666444  356666666666666667777777776554432


Q ss_pred             CCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 011236          310 KKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSI  389 (490)
Q Consensus       310 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~  389 (490)
                      + .+-..|.-+...|.+.++++.|+-.|+++.+-++. +.+....+...+.+.|+.|+|+.+++++...+++ |+..--.
T Consensus       486 ~-rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~-nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~k-n~l~~~~  562 (638)
T KOG1126|consen  486 P-RHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPS-NSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPK-NPLCKYH  562 (638)
T ss_pred             c-hhhHHHHhhhhheeccchhhHHHHHHHhhhcCCcc-chhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCC-CchhHHH
Confidence            2 22233444566666777777777777766664222 4444555556666667777777777777666555 5555555


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          390 IAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       390 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+..+...+++++|++.+++.++       +.|+. ..|..+...|.+.|+.+.|..-|.-+.+.+|.
T Consensus       563 ~~~il~~~~~~~eal~~LEeLk~-------~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpk  623 (638)
T KOG1126|consen  563 RASILFSLGRYVEALQELEELKE-------LVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPK  623 (638)
T ss_pred             HHHHHHhhcchHHHHHHHHHHHH-------hCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCc
Confidence            55566666677777777777665       44544 45556666677777777777777666666665

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

Probab=99.62  E-value=5.9e-12  Score=108.99  Aligned_cols=286  Identities=16%  Similarity=0.127  Sum_probs=207.3

Q ss_pred             cCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHH
Q 011236          150 EGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENV  229 (490)
Q Consensus       150 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~  229 (490)
                      .|+|.+|+++..+-.+.+-. ....|..-..+.-..|+.+.+-.++.+..+..-.++...+-+........|+++.|..-
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 EGDFQQAEKLLRRNAEHGEQ-PVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcc-hHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            67788888888777766544 23345555566667778888888887777653344555566666677777888888877


Q ss_pred             HHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh-------hhHHHHHHHHHhcCChhHHHHHH
Q 011236          230 LQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA-------LGYNHLISHYASLGNKDEMMKFW  302 (490)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~  302 (490)
                      ++++. +.+. -..........+|.+.|++.....++.++.+.+.. .+.       .+|..+++-....+..+.-...|
T Consensus       176 v~~ll-~~~p-r~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l-~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W  252 (400)
T COG3071         176 VDQLL-EMTP-RHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLL-SDEEAARLEQQAWEGLLQQARDDNGSEGLKTWW  252 (400)
T ss_pred             HHHHH-HhCc-CChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCC-ChHHHHHHHHHHHHHHHHHHhccccchHHHHHH
Confidence            77776 5554 45666777778888888888888888888776654 332       45777777776666666666666


Q ss_pred             HHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 011236          303 GLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTP  382 (490)
Q Consensus       303 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p  382 (490)
                      +..-.. .+.++..-.+++.-+.+.|+.++|.++..+..+.+..|+.    ...-.+.+-++.+.-++..++-.+..+. 
T Consensus       253 ~~~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L----~~~~~~l~~~d~~~l~k~~e~~l~~h~~-  326 (400)
T COG3071         253 KNQPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRL----CRLIPRLRPGDPEPLIKAAEKWLKQHPE-  326 (400)
T ss_pred             HhccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhH----HHHHhhcCCCCchHHHHHHHHHHHhCCC-
Confidence            644333 3466677778888888899999999999888888776651    2223455667777777777777665443 


Q ss_pred             CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          383 TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       383 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      ++..+.+|...|.+.+.|.+|...|+.++.       ..|+..+|..+..++.+.|+.+.|.++.++...
T Consensus       327 ~p~L~~tLG~L~~k~~~w~kA~~~leaAl~-------~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~  389 (400)
T COG3071         327 DPLLLSTLGRLALKNKLWGKASEALEAALK-------LRPSASDYAELADALDQLGEPEEAEQVRREALL  389 (400)
T ss_pred             ChhHHHHHHHHHHHhhHHHHHHHHHHHHHh-------cCCChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            567888889999999999999999998877       668889999999999999999999888887653

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

Probab=99.62  E-value=2e-11  Score=110.16  Aligned_cols=414  Identities=10%  Similarity=0.019  Sum_probs=283.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHc----cccC--C-C
Q 011236           64 GQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSL----NDED--K-V  136 (490)
Q Consensus        64 ~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~----~~~~--p-~  136 (490)
                      ++..|+...--+...+.-.|++..|..+...-.-.+  .+.........++.+..++++|..++...    ....  + +
T Consensus        44 ~l~~dp~d~~~~aq~l~~~~~y~ra~~lit~~~le~--~d~~cryL~~~~l~~lk~~~~al~vl~~~~~~~~~f~yy~~~  121 (611)
T KOG1173|consen   44 GLTNDPADIYWLAQVLYLGRQYERAAHLITTYKLEK--RDIACRYLAAKCLVKLKEWDQALLVLGRGHVETNPFSYYEKD  121 (611)
T ss_pred             hccCChHHHHHHHHHHHhhhHHHHHHHHHHHhhhhh--hhHHHHHHHHHHHHHHHHHHHHHHHhcccchhhcchhhcchh
Confidence            444566666667777777777777777766553333  36667777777888888888888887722    1100  0 1


Q ss_pred             h-------hHH-----HHH-------HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcC-----------
Q 011236          137 D-------KLY-----GAL-------LNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTG-----------  186 (490)
Q Consensus       137 ~-------~~~-----~~l-------i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-----------  186 (490)
                      .       ..+     +.-       ...|....+.++|...|.+.....+. .-..+..++....-.-           
T Consensus       122 ~~~~l~~n~~~~~~~~~~essic~lRgk~y~al~n~~~ar~~Y~~Al~~D~~-c~Ea~~~lvs~~mlt~~Ee~~ll~~l~  200 (611)
T KOG1173|consen  122 AANTLELNSAGEDLMINLESSICYLRGKVYVALDNREEARDKYKEALLADAK-CFEAFEKLVSAHMLTAQEEFELLESLD  200 (611)
T ss_pred             hhceeccCcccccccccchhceeeeeeehhhhhccHHHHHHHHHHHHhcchh-hHHHHHHHHHHHhcchhHHHHHHhccc
Confidence            0       001     000       12344556677777777777665322 2222222222221111           


Q ss_pred             -------CcCcHHHHHHHH----HH------------CCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCH
Q 011236          187 -------QHEKIPDVLLDM----KE------------NGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDW  243 (490)
Q Consensus       187 -------~~~~a~~~~~~m----~~------------~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~  243 (490)
                             +.+....+|+--    ..            .+..-+.........-|...+++.+..++++... +..+ +..
T Consensus       201 ~a~~~~ed~e~l~~lyel~~~k~~n~~~~~r~~~~sl~~l~~~~dll~~~ad~~y~~c~f~~c~kit~~ll-e~dp-fh~  278 (611)
T KOG1173|consen  201 LAMLTKEDVERLEILYELKLCKNRNEESLTRNEDESLIGLAENLDLLAEKADRLYYGCRFKECLKITEELL-EKDP-FHL  278 (611)
T ss_pred             HHhhhhhHHHHHHHHHHhhhhhhccccccccCchhhhhhhhhcHHHHHHHHHHHHHcChHHHHHHHhHHHH-hhCC-CCc
Confidence                   001111111100    00            0122334444455566677889999999999988 5544 555


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHH
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGS  323 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  323 (490)
                      ..+..-|.++...|+..+-..+=.++.+..|  ....+|-++...|...|+..+|.++|.+.....+ .-...|..+..+
T Consensus       279 ~~~~~~ia~l~el~~~n~Lf~lsh~LV~~yP--~~a~sW~aVg~YYl~i~k~seARry~SKat~lD~-~fgpaWl~fghs  355 (611)
T KOG1173|consen  279 PCLPLHIACLYELGKSNKLFLLSHKLVDLYP--SKALSWFAVGCYYLMIGKYSEARRYFSKATTLDP-TFGPAWLAFGHS  355 (611)
T ss_pred             chHHHHHHHHHHhcccchHHHHHHHHHHhCC--CCCcchhhHHHHHHHhcCcHHHHHHHHHHhhcCc-cccHHHHHHhHH
Confidence            6666677799999998888877788887676  5778999999999999999999999997766554 555789999999


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHH
Q 011236          324 LVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKA  403 (490)
Q Consensus       324 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  403 (490)
                      |+-.|.-++|...+...-+. ++-...-+--+..-|.+.+.++.|.+.|.+.....+. |+..++-+.-.....+.+.+|
T Consensus       356 fa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~A~ai~P~-Dplv~~Elgvvay~~~~y~~A  433 (611)
T KOG1173|consen  356 FAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKLAEKFFKQALAIAPS-DPLVLHELGVVAYTYEEYPEA  433 (611)
T ss_pred             hhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHHHHHHHHHHHhcCCC-cchhhhhhhheeehHhhhHHH
Confidence            99999999999998887664 1111111223445588899999999999998887544 888888888888889999999


Q ss_pred             HHHHHHHHHhhhcCcCCC-cchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHH
Q 011236          404 FECMKEALAVHEENKFWR-PKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLE  479 (490)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~-p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~  479 (490)
                      ..+|+..+..-.....-. -...+++.|..+|.+.+.+++|...+++.....|. ..++.+++-.|...|  +.|++.|.
T Consensus       434 ~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fh  513 (611)
T KOG1173|consen  434 LKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFH  513 (611)
T ss_pred             HHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHH
Confidence            999999985222111111 24567889999999999999999999999999999 999999999999999  99999998


Q ss_pred             HHHhCCCCCC
Q 011236          480 SMKADDIDED  489 (490)
Q Consensus       480 ~m~~~~~~pd  489 (490)
                      +-..  +.||
T Consensus       514 KaL~--l~p~  521 (611)
T KOG1173|consen  514 KALA--LKPD  521 (611)
T ss_pred             HHHh--cCCc
Confidence            7664  4454

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

Probab=99.61  E-value=3.1e-12  Score=107.40  Aligned_cols=285  Identities=14%  Similarity=0.093  Sum_probs=170.5

Q ss_pred             hcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcc------hHHHHHHHHHhcCCcC
Q 011236          117 VRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSAL------NYNGIMCLYTNTGQHE  189 (490)
Q Consensus       117 ~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~------~~~~l~~~~~~~~~~~  189 (490)
                      ..+.+.|..+|-+|.+.+| +..+--+|.+.|-+.|.++.|+++-+.+.++   ||..      ..-.|..-|...|-++
T Consensus        48 s~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~qr~lAl~qL~~Dym~aGl~D  124 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQRLLALQQLGRDYMAAGLLD  124 (389)
T ss_pred             hcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHHHHHHHHHHHHHHHHhhhhh
Confidence            4566777777777776655 4555566667777777777777777776665   3321      2234555566677777


Q ss_pred             cHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHHcCCHHHHHHH
Q 011236          190 KIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMD----WGTYSTVANYYIIAGLKEKAIIY  265 (490)
Q Consensus       190 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~  265 (490)
                      .|+.+|..+.+.|. .-......|+..|-...+|++|+++-+++. +.+..+.    ...|--+...+....+++.|...
T Consensus       125 RAE~~f~~L~de~e-fa~~AlqqLl~IYQ~treW~KAId~A~~L~-k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~  202 (389)
T COG2956         125 RAEDIFNQLVDEGE-FAEGALQQLLNIYQATREWEKAIDVAERLV-KLGGQTYRVEIAQFYCELAQQALASSDVDRAREL  202 (389)
T ss_pred             HHHHHHHHHhcchh-hhHHHHHHHHHHHHHhhHHHHHHHHHHHHH-HcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence            77777777766432 234456666777777777777777766665 3333222    22334444455556667777777


Q ss_pred             HHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 011236          266 LKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY  345 (490)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  345 (490)
                      +.+..+..+  ..+..-..+.+.+...|+++.|.+.|+...+.++..-..+...|..+|.+.|+.++....+..+.+...
T Consensus       203 l~kAlqa~~--~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~  280 (389)
T COG2956         203 LKKALQADK--KCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNT  280 (389)
T ss_pred             HHHHHhhCc--cceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccC
Confidence            777666554  355555566666677777777777777666666555555666777777777777777777776666422


Q ss_pred             CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc---cCCHHHHHHHHHHHHH
Q 011236          346 CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD---KNNMEKAFECMKEALA  412 (490)
Q Consensus       346 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~  412 (490)
                        ....-..+...-....-.+.|...+.+-+..  +|+...+..++..-..   .|...+.+.+++.|+.
T Consensus       281 --g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r--~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvg  346 (389)
T COG2956         281 --GADAELMLADLIELQEGIDAAQAYLTRQLRR--KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVG  346 (389)
T ss_pred             --CccHHHHHHHHHHHhhChHHHHHHHHHHHhh--CCcHHHHHHHHHhhhccccccchhhhHHHHHHHHH
Confidence              3333333334333344455555555444443  4666666666665432   2345555666666665

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

Probab=99.61  E-value=9.2e-12  Score=107.79  Aligned_cols=291  Identities=14%  Similarity=0.092  Sum_probs=137.1

Q ss_pred             cCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHcccc--CCChhHHHHHHHHHHhcCChhHHHHH
Q 011236           82 RKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDE--DKVDKLYGALLNCYVREGLVDESLSL  159 (490)
Q Consensus        82 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~  159 (490)
                      .|+|.+|.++..+-.+.+ +-..-.|....++.-..|+.+.+-.++.+..+.  +++..++-+........|+...|..-
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 EGDFQQAEKLLRRNAEHG-EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             cCcHHHHHHHHHHhhhcC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            366666666666555554 222333334445555556666666666665555  23444555555555666666666666


Q ss_pred             HHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCC
Q 011236          160 MQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHI  239 (490)
Q Consensus       160 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  239 (490)
                      ++++.+.+.. ++.......++|.+.|++..+..++..+.+.|.-.|...-..                           
T Consensus       176 v~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~l---------------------------  227 (400)
T COG3071         176 VDQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARL---------------------------  227 (400)
T ss_pred             HHHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHH---------------------------
Confidence            6665555443 455555556666666666666666666655554333211000                           


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHH
Q 011236          240 SMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYIT  319 (490)
Q Consensus       240 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (490)
                        ...+|+.+++-....+..+.-...++.....-.  .++..-.+++.-+.+.|+.++|.++..+..+....|.    -.
T Consensus       228 --e~~a~~glL~q~~~~~~~~gL~~~W~~~pr~lr--~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~----L~  299 (400)
T COG3071         228 --EQQAWEGLLQQARDDNGSEGLKTWWKNQPRKLR--NDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR----LC  299 (400)
T ss_pred             --HHHHHHHHHHHHhccccchHHHHHHHhccHHhh--cChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh----HH
Confidence              012233333333333333332233333222211  2333334444444455555555555444444433222    11


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          320 MLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       320 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      ..-.+.+.++.+.-.+..++..+. .+-++..+.+|...|.+.+.+.+|...|+...+.  .|+..+|+.+..++.+.|+
T Consensus       300 ~~~~~l~~~d~~~l~k~~e~~l~~-h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~--~~s~~~~~~la~~~~~~g~  376 (400)
T COG3071         300 RLIPRLRPGDPEPLIKAAEKWLKQ-HPEDPLLLSTLGRLALKNKLWGKASEALEAALKL--RPSASDYAELADALDQLGE  376 (400)
T ss_pred             HHHhhcCCCCchHHHHHHHHHHHh-CCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhc--CCChhhHHHHHHHHHHcCC
Confidence            111233344444444444443332 2223344455555555555555555555544443  3455555555555555555


Q ss_pred             HHHHHHHHHHHHH
Q 011236          400 MEKAFECMKEALA  412 (490)
Q Consensus       400 ~~~a~~~~~~~~~  412 (490)
                      ..+|.+..++.+.
T Consensus       377 ~~~A~~~r~e~L~  389 (400)
T COG3071         377 PEEAEQVRREALL  389 (400)
T ss_pred             hHHHHHHHHHHHH
Confidence            5555555555543

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

Probab=99.60  E-value=2.9e-10  Score=100.60  Aligned_cols=353  Identities=12%  Similarity=0.083  Sum_probs=182.3

Q ss_pred             hhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHH
Q 011236          116 KVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVL  195 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~  195 (490)
                      ..|++..|.++|+.-..-.|+..+|.+.|+.=.+.+.++.|..++++..-.  .|++.+|--....=.+.|+...+..+|
T Consensus       153 ~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~~~~aR~Vy  230 (677)
T KOG1915|consen  153 MLGNIAGARQIFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGNVALARSVY  230 (677)
T ss_pred             HhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            345555555555555555555555555555555555555555555554432  245555555555555555555555555


Q ss_pred             HHHHHC-CC-CCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHHcCC---HHHHHH----
Q 011236          196 LDMKEN-GV-PPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMD--WGTYSTVANYYIIAGL---KEKAII----  264 (490)
Q Consensus       196 ~~m~~~-~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~~~---~~~a~~----  264 (490)
                      ....+. |- .-+...+.+....-.++..++.|.-+|+-.. +. ++.+  ...|.....-=-+-|+   +++++-    
T Consensus       231 erAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAl-d~-~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk  308 (677)
T KOG1915|consen  231 ERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYAL-DH-IPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRK  308 (677)
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hh-cCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhh
Confidence            554432 00 0011122222222223344444444444443 11 1111  1222222222122233   222221    


Q ss_pred             -HHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCCh------hhHHHHHHHH---HhcCCHHHHH
Q 011236          265 -YLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLN------RDYITMLGSL---VKIGELEEAE  334 (490)
Q Consensus       265 -~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~------~~~~~l~~~~---~~~~~~~~a~  334 (490)
                       -|+.+...++  .|-.+|--.+..-...|+.+...++|++.+...++...      ..|.-+=.+|   ....+.+.+.
T Consensus       309 ~qYE~~v~~np--~nYDsWfdylrL~e~~g~~~~Ire~yErAIanvpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr  386 (677)
T KOG1915|consen  309 FQYEKEVSKNP--YNYDSWFDYLRLEESVGDKDRIRETYERAIANVPPASEKRYWRRYIYLWINYALYEELEAEDVERTR  386 (677)
T ss_pred             hHHHHHHHhCC--CCchHHHHHHHHHHhcCCHHHHHHHHHHHHccCCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence             1222233233  35556666666666677777777777776665542111      1111111111   2356777777


Q ss_pred             HHHHHHHhcCCCCCchhHHHHHHHH----HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHH
Q 011236          335 KMLEEWELSCYCYDFRVPNIILLGY----SQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEA  410 (490)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~l~~~~----~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~  410 (490)
                      ++++..++. ++....||..+--.|    .++.++..|.+++...+.  .-|-..+|...|..-.+.++++....++++.
T Consensus       387 ~vyq~~l~l-IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG--~cPK~KlFk~YIelElqL~efDRcRkLYEkf  463 (677)
T KOG1915|consen  387 QVYQACLDL-IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIG--KCPKDKLFKGYIELELQLREFDRCRKLYEKF  463 (677)
T ss_pred             HHHHHHHhh-cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhc--cCCchhHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            777777664 444555555444443    345666777777666554  3455666666666666777777777777777


Q ss_pred             HHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc---hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          411 LAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK---RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       411 ~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~---~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      ++       ..|.. .+|......-...|+++.|..+|+-+.+....   ...|-+.|+.=...|  +.|..+++++.+.
T Consensus       464 le-------~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  464 LE-------FSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             Hh-------cChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHh
Confidence            66       33443 56666666666667777777777766665432   455666666666666  6777777766653

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

Probab=99.57  E-value=1.4e-10  Score=102.30  Aligned_cols=321  Identities=13%  Similarity=0.072  Sum_probs=229.1

Q ss_pred             HHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchH--HHHHHHHHhcCC
Q 011236          110 QLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNY--NGIMCLYTNTGQ  187 (490)
Q Consensus       110 l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~--~~l~~~~~~~~~  187 (490)
                      ....+.+.|....|+..|......-|  ..|.+.+....-.-+.+.+.    ..... ...|..-.  -.+..++.....
T Consensus       170 ~Gvv~k~~~~~s~A~~sfv~~v~~~P--~~W~AWleL~~lit~~e~~~----~l~~~-l~~~~h~M~~~F~~~a~~el~q  242 (559)
T KOG1155|consen  170 YGVVLKELGLLSLAIDSFVEVVNRYP--WFWSAWLELSELITDIEILS----ILVVG-LPSDMHWMKKFFLKKAYQELHQ  242 (559)
T ss_pred             HHHHHHhhchHHHHHHHHHHHHhcCC--cchHHHHHHHHhhchHHHHH----HHHhc-CcccchHHHHHHHHHHHHHHHH
Confidence            33445567777788888777766544  22333333222222222222    22111 11121111  123344555567


Q ss_pred             cCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCC--CCCHHHHHHHHHHHHHcCCHHHHHHH
Q 011236          188 HEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHI--SMDWGTYSTVANYYIIAGLKEKAIIY  265 (490)
Q Consensus       188 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~  265 (490)
                      .+++.+-.......|++-+...-+....+.-...|+++|+.+|+++. +.++  --|..+|+.++-.  +..+-  .+.+
T Consensus       243 ~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~-knDPYRl~dmdlySN~LYv--~~~~s--kLs~  317 (559)
T KOG1155|consen  243 HEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIR-KNDPYRLDDMDLYSNVLYV--KNDKS--KLSY  317 (559)
T ss_pred             HHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHH-hcCCCcchhHHHHhHHHHH--HhhhH--HHHH
Confidence            77888888888888886666555555666667889999999999998 4432  1356777766533  32221  1222


Q ss_pred             HHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 011236          266 LKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY  345 (490)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  345 (490)
                      +-+-...... --+.|+..+.+-|.-.++.++|..+|++....++ .....|+.+..-|....+...|.+-++..++- .
T Consensus       318 LA~~v~~idK-yR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp-~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi-~  394 (559)
T KOG1155|consen  318 LAQNVSNIDK-YRPETCCIIANYYSLRSEHEKAVMYFKRALKLNP-KYLSAWTLMGHEYVEMKNTHAAIESYRRAVDI-N  394 (559)
T ss_pred             HHHHHHHhcc-CCccceeeehhHHHHHHhHHHHHHHHHHHHhcCc-chhHHHHHhhHHHHHhcccHHHHHHHHHHHhc-C
Confidence            2221111222 5667888899999999999999999998888776 66778999999999999999999999999987 4


Q ss_pred             CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchh
Q 011236          346 CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS  425 (490)
Q Consensus       346 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~  425 (490)
                      +.|-..|-.|.++|.-.+...-|+-.|++..+..+. |...|.+|..+|.+.++.++|+..|+.+..      .-..+..
T Consensus       395 p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPn-DsRlw~aLG~CY~kl~~~~eAiKCykrai~------~~dte~~  467 (559)
T KOG1155|consen  395 PRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPN-DSRLWVALGECYEKLNRLEEAIKCYKRAIL------LGDTEGS  467 (559)
T ss_pred             chhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHhccHHHHHHHHHHHHh------ccccchH
Confidence            458889999999999999999999999999997655 889999999999999999999999999988      2234668


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          426 LVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       426 ~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      .+..|...+.+.++.++|.+.+++-.+
T Consensus       468 ~l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  468 ALVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            899999999999999999998887666

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

Probab=99.56  E-value=6.3e-10  Score=98.51  Aligned_cols=404  Identities=10%  Similarity=0.025  Sum_probs=308.5

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC-hhHHHHHH
Q 011236           66 KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV-DKLYGALL  144 (490)
Q Consensus        66 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~li  144 (490)
                      ..+...|..-...=..++++..|..+|+..+... ..+...+...+.+-.+...+..|..+++.....-|- ...|-..+
T Consensus        70 R~~~~~WikYaqwEesq~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyKY~  148 (677)
T KOG1915|consen   70 RLNMQVWIKYAQWEESQKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYKYI  148 (677)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHHHH
Confidence            3455555555555567788899999999999877 456677777888888999999999999998877663 45677777


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChH
Q 011236          145 NCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELS  224 (490)
Q Consensus       145 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~  224 (490)
                      .+=-..|++..|.++|++-.+.  .|+...|++.|+.=.+-+.++.|..+|+..+-  +.|++.+|-.....--+.|+..
T Consensus       149 ymEE~LgNi~gaRqiferW~~w--~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~  224 (677)
T KOG1915|consen  149 YMEEMLGNIAGARQIFERWMEW--EPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVA  224 (677)
T ss_pred             HHHHHhcccHHHHHHHHHHHcC--CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHH
Confidence            7777789999999999998775  79999999999999999999999999999976  5699999999999989999999


Q ss_pred             HHHHHHHHHHhCCCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHH--
Q 011236          225 SMENVLQEMESQSHIS-MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKF--  301 (490)
Q Consensus       225 ~a~~~~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~--  301 (490)
                      .|..+|+......|-. .+...+.+...-=..+..++.|.-+|+-..+..+.......|..+...--+-|+.....+.  
T Consensus       225 ~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv  304 (677)
T KOG1915|consen  225 LARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIV  304 (677)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHh
Confidence            9999999887333321 2233344444444567789999999999888776422345565555555555665444433  


Q ss_pred             ------HHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCch--hHHHHHHH--------HHhcCCH
Q 011236          302 ------WGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFR--VPNIILLG--------YSQKGMI  365 (490)
Q Consensus       302 ------~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~--------~~~~g~~  365 (490)
                            |+.....++ .|-.+|-..++.-...|+.+...++++..... ++|-..  .|.-.|-.        =....++
T Consensus       305 ~KRk~qYE~~v~~np-~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~  382 (677)
T KOG1915|consen  305 GKRKFQYEKEVSKNP-YNYDSWFDYLRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDV  382 (677)
T ss_pred             hhhhhHHHHHHHhCC-CCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence                  344445444 66678888888888899999999999999886 555321  12222211        1346889


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHH----HHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHH
Q 011236          366 EKADAVLKEIVKKGKTPTPNSWSII----AAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVE  441 (490)
Q Consensus       366 ~~A~~~~~~m~~~~~~p~~~~~~~l----~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  441 (490)
                      +.+.++++..++. ++-...||.-+    ...-.++.+...|.+++..++       |..|-..+|...|..-.+.+.++
T Consensus       383 ertr~vyq~~l~l-IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI-------G~cPK~KlFk~YIelElqL~efD  454 (677)
T KOG1915|consen  383 ERTRQVYQACLDL-IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI-------GKCPKDKLFKGYIELELQLREFD  454 (677)
T ss_pred             HHHHHHHHHHHhh-cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh-------ccCCchhHHHHHHHHHHHHhhHH
Confidence            9999999999984 22244454433    344457889999999999986       46799999999999999999999


Q ss_pred             HHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          442 EVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       442 ~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      .+.+++++..+-+|. ..+|.-....=...|  +.|..+|+-....
T Consensus       455 RcRkLYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~q  500 (677)
T KOG1915|consen  455 RCRKLYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIFELAISQ  500 (677)
T ss_pred             HHHHHHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcC
Confidence            999999999999999 888988888888888  8888888766543

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.51  E-value=2.1e-11  Score=105.99  Aligned_cols=203  Identities=16%  Similarity=0.059  Sum_probs=145.6

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHH
Q 011236          241 MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITM  320 (490)
Q Consensus       241 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (490)
                      .....+..+...+...|++++|...+++.....+  .+...+..+...+...|++++|.+.+++.....+ .+...+..+
T Consensus        29 ~~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p--~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~~  105 (234)
T TIGR02521        29 KAAKIRVQLALGYLEQGDLEVAKENLDKALEHDP--DDYLAYLALALYYQQLGELEKAEDSFRRALTLNP-NNGDVLNNY  105 (234)
T ss_pred             cHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc--ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC-CCHHHHHHH
Confidence            3355666677778888888888888887766544  4566777777778888888888888887776654 455666777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCC-CCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYC-YDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      ...+...|++++|.+.+++....... .....+..+...+...|++++|...+++..+..+. +...+..+...+...|+
T Consensus       106 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~  184 (234)
T TIGR02521       106 GTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQ-RPESLLELAELYYLRGQ  184 (234)
T ss_pred             HHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-ChHHHHHHHHHHHHcCC
Confidence            77777888888888888887764222 22345666777788888888888888888776443 55677778888888888


Q ss_pred             HHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          400 MEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       400 ~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      +++|...++++..     . ...+...+..+...+...|+.+.|..+.+.+...
T Consensus       185 ~~~A~~~~~~~~~-----~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       185 YKDARAYLERYQQ-----T-YNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HHHHHHHHHHHHH-----h-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            8888888888877     2 2234456666677777788888888887776654

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.

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

Probab=99.50  E-value=8.9e-11  Score=104.18  Aligned_cols=385  Identities=11%  Similarity=0.016  Sum_probs=255.7

Q ss_pred             HHhhccCCCCCCChHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhc
Q 011236           40 YSRISPLGDPDVSLTPVLDQWVLEGQKIS-ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVR  118 (490)
Q Consensus        40 ~~~l~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  118 (490)
                      -+.+.+.+++++++. .+..-+  ...|+ +.-|.....+|...|+|++..+-.-+.++.+ +.-...+..-..++-..|
T Consensus       122 GN~~f~~kkY~eAIk-yY~~AI--~l~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~-P~Y~KAl~RRA~A~E~lg  197 (606)
T KOG0547|consen  122 GNKFFRNKKYDEAIK-YYTQAI--ELCPDEPIFYSNRAACYESLGDWEKVIEDCTKALELN-PDYVKALLRRASAHEQLG  197 (606)
T ss_pred             hhhhhhcccHHHHHH-HHHHHH--hcCCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcC-cHHHHHHHHHHHHHHhhc
Confidence            345666778888887 555544  34567 7788999999999999999999888888876 223344444556666778


Q ss_pred             CHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHH---------HHhcC--CCCCcchHH-----------
Q 011236          119 GLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQK---------MKEMG--SFGSALNYN-----------  176 (490)
Q Consensus       119 ~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~---------m~~~~--~~p~~~~~~-----------  176 (490)
                      ++++|+.=..-           .++..++....-.--+.+++++         +.+.+  +-|+....+           
T Consensus       198 ~~~eal~D~tv-----------~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~  266 (606)
T KOG0547|consen  198 KFDEALFDVTV-----------LCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPK  266 (606)
T ss_pred             cHHHHHHhhhH-----------HHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhcccccc
Confidence            88777642221           1111111111111111122111         11111  112222111           


Q ss_pred             ------------HHHHHHH--hcC---CcCcHHHHHHHHHHCC-CCCC-----------HHHHHHHHHHHhccCChHHHH
Q 011236          177 ------------GIMCLYT--NTG---QHEKIPDVLLDMKENG-VPPD-----------NFSYRICINSYGARSELSSME  227 (490)
Q Consensus       177 ------------~l~~~~~--~~~---~~~~a~~~~~~m~~~~-~~p~-----------~~~~~~li~~~~~~g~~~~a~  227 (490)
                                  .+..++.  ..+   .+.++...+.+-.... ..++           ..+.......+.-.|+...|.
T Consensus       267 ~~~~~~~~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~  346 (606)
T KOG0547|consen  267 PLFDNKSDKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQ  346 (606)
T ss_pred             ccccCCCccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhh
Confidence                        1111111  011   1222222222211100 1111           112222223345578999999


Q ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 011236          228 NVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKI  307 (490)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  307 (490)
                      .-|+..+ .....+ ...|--+..+|....+.++.+..|....+..+  .|+.+|..-.+.+.-.+++++|..=|++.+.
T Consensus       347 ~d~~~~I-~l~~~~-~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp--~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~  422 (606)
T KOG0547|consen  347 EDFDAAI-KLDPAF-NSLYIKRAAAYADENQSEKMWKDFNKAEDLDP--ENPDVYYHRGQMRFLLQQYEEAIADFQKAIS  422 (606)
T ss_pred             hhHHHHH-hcCccc-chHHHHHHHHHhhhhccHHHHHHHHHHHhcCC--CCCchhHhHHHHHHHHHHHHHHHHHHHHHhh
Confidence            9999998 655533 33377788899999999999999999998777  5777888888888889999999999998887


Q ss_pred             hcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-----C
Q 011236          308 KCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-----P  382 (490)
Q Consensus       308 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-----p  382 (490)
                      ..+ -+...|..+..+.-+.+.++++...|++.++. ++..+..|+.....+...++++.|.+.|+..++....     .
T Consensus       423 L~p-e~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~~~v  500 (606)
T KOG0547|consen  423 LDP-ENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHLIIV  500 (606)
T ss_pred             cCh-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhccccccccc
Confidence            765 67778888888888999999999999999887 7778899999999999999999999999999875322     1


Q ss_pred             C--HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          383 T--PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       383 ~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      +  +.+.-.++..-. .+++..|..++.++++       +.|.. ..|..|...-...|+.++|.++|++....
T Consensus       501 ~~~plV~Ka~l~~qw-k~d~~~a~~Ll~KA~e-------~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa~l  566 (606)
T KOG0547|consen  501 NAAPLVHKALLVLQW-KEDINQAENLLRKAIE-------LDPKCEQAYETLAQFELQRGKIDEAIELFEKSAQL  566 (606)
T ss_pred             cchhhhhhhHhhhch-hhhHHHHHHHHHHHHc-------cCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            1  122223332222 3899999999999998       44555 67889999999999999999999976543

>PRK12370 invasion protein regulator; Provisional

Probab=99.49  E-value=3.2e-11  Score=117.46  Aligned_cols=265  Identities=14%  Similarity=-0.013  Sum_probs=177.4

Q ss_pred             CHHHHHHHHHHHh-----ccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH---------cCCHHHHHHHHHHHhh
Q 011236          206 DNFSYRICINSYG-----ARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII---------AGLKEKAIIYLKKCED  271 (490)
Q Consensus       206 ~~~~~~~li~~~~-----~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------~~~~~~a~~~~~~~~~  271 (490)
                      +...|...+.+-.     ..+++++|...|++.. +.++ -+...|..+..++..         .+++++|...+++..+
T Consensus       255 ~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al-~ldP-~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~  332 (553)
T PRK12370        255 SIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCV-NMSP-NSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE  332 (553)
T ss_pred             ChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHH-hcCC-ccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh
Confidence            3444555555431     1234678888998887 5554 345566666655542         2347889999998888


Q ss_pred             hhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchh
Q 011236          272 IVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRV  351 (490)
Q Consensus       272 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  351 (490)
                      ..+  .+..++..+...+...|++++|...|++.....+ .+...+..+..++...|++++|...+++..+.... +...
T Consensus       333 ldP--~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P-~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~-~~~~  408 (553)
T PRK12370        333 LDH--NNPQALGLLGLINTIHSEYIVGSLLFKQANLLSP-ISADIKYYYGWNLFMAGQLEEALQTINECLKLDPT-RAAA  408 (553)
T ss_pred             cCC--CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC-Chhh
Confidence            766  5778888888888889999999999998888765 55667888888889999999999999998886332 2223


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchh-hHHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS-LVSSI  430 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~-~~~~l  430 (490)
                      +..++..+...|++++|...++++.+...+-++..+..+..++...|+.++|...++++..       ..|+.. ....+
T Consensus       409 ~~~~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~-------~~~~~~~~~~~l  481 (553)
T PRK12370        409 GITKLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEIST-------QEITGLIAVNLL  481 (553)
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhh-------ccchhHHHHHHH
Confidence            3344555666888999999998887664322455677788888889999999999888765       234443 34455


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC-CcHHHHHHHHHhCC
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG-QEVDGLLESMKADD  485 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g-~~a~~~~~~m~~~~  485 (490)
                      ...+...|  +.|...++.+.+.... ...+..+-..|.-.| .+...+++++.+.|
T Consensus       482 ~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~  536 (553)
T PRK12370        482 YAEYCQNS--ERALPTIREFLESEQRIDNNPGLLPLVLVAHGEAIAEKMWNKFKNED  536 (553)
T ss_pred             HHHHhccH--HHHHHHHHHHHHHhhHhhcCchHHHHHHHHHhhhHHHHHHHHhhccc
Confidence            55666666  4777777776654433 211222333444445 33444447776654

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

Probab=99.49  E-value=5.2e-12  Score=106.17  Aligned_cols=232  Identities=13%  Similarity=0.087  Sum_probs=185.8

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHH
Q 011236          241 MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITM  320 (490)
Q Consensus       241 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (490)
                      .|+.--+.+..+|.+.|.+.+|.+.|+.-....   |-+.||..|-++|.+..++..|+.++.+-....+ .++....-+
T Consensus       221 ~dwwWk~Q~gkCylrLgm~r~AekqlqssL~q~---~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP-~~VT~l~g~  296 (478)
T KOG1129|consen  221 LDWWWKQQMGKCYLRLGMPRRAEKQLQSSLTQF---PHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFP-FDVTYLLGQ  296 (478)
T ss_pred             HhHHHHHHHHHHHHHhcChhhhHHHHHHHhhcC---CchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCC-chhhhhhhh
Confidence            455666778889999999999998888766544   5566788888889999999999999887766543 444444567


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM  400 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  400 (490)
                      .+.+...++.++|.++++...+. .+.++....++..+|.-.++++-|+..++++.+.|+. ++..|+.+.-+|.-.+++
T Consensus       297 ARi~eam~~~~~a~~lYk~vlk~-~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~  374 (478)
T KOG1129|consen  297 ARIHEAMEQQEDALQLYKLVLKL-HPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQI  374 (478)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHhc-CCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcch
Confidence            77788888899999999988876 4556777777778888888999999999999998887 888888888888888999


Q ss_pred             HHHHHHHHHHHHhhhcCcCCCcch--hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHH
Q 011236          401 EKAFECMKEALAVHEENKFWRPKP--SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVD  475 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~~~~p~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~  475 (490)
                      +-++..|++++.     .--.|+.  .+|..+.......||+..|.+.|+-....++. ...++.|.-.-.+.|  +.|.
T Consensus       375 D~~L~sf~RAls-----tat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Ar  449 (478)
T KOG1129|consen  375 DLVLPSFQRALS-----TATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGAR  449 (478)
T ss_pred             hhhHHHHHHHHh-----hccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHH
Confidence            999998888887     3333444  57888888888889999999999988888888 888888888888888  8888


Q ss_pred             HHHHHHHh
Q 011236          476 GLLESMKA  483 (490)
Q Consensus       476 ~~~~~m~~  483 (490)
                      .+++....
T Consensus       450 sll~~A~s  457 (478)
T KOG1129|consen  450 SLLNAAKS  457 (478)
T ss_pred             HHHHHhhh
Confidence            88876654

>PRK12370 invasion protein regulator; Provisional

Probab=99.49  E-value=1.8e-11  Score=119.17  Aligned_cols=217  Identities=13%  Similarity=0.063  Sum_probs=109.3

Q ss_pred             ChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHh---------cCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC
Q 011236          152 LVDESLSLMQKMKEMGSFGSALNYNGIMCLYTN---------TGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSE  222 (490)
Q Consensus       152 ~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~---------~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  222 (490)
                      +.++|..+|++..+..+. +...|..+..++..         .+++++|...+++..+.+. -+...+..+...+...|+
T Consensus       276 ~~~~A~~~~~~Al~ldP~-~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP-~~~~a~~~lg~~~~~~g~  353 (553)
T PRK12370        276 SLQQALKLLTQCVNMSPN-SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDH-NNPQALGLLGLINTIHSE  353 (553)
T ss_pred             HHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHHccC
Confidence            355556666555554322 23334333333221         1234556666666655432 244455555555566666


Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHH
Q 011236          223 LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFW  302 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  302 (490)
                      +++|...|++.. +.++ .+...+..+..++...|++++|+..+++..+..+.  +...+..++..+...|++++|...+
T Consensus       354 ~~~A~~~~~~Al-~l~P-~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~--~~~~~~~~~~~~~~~g~~eeA~~~~  429 (553)
T PRK12370        354 YIVGSLLFKQAN-LLSP-ISADIKYYYGWNLFMAGQLEEALQTINECLKLDPT--RAAAGITKLWITYYHTGIDDAIRLG  429 (553)
T ss_pred             HHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC--ChhhHHHHHHHHHhccCHHHHHHHH
Confidence            666666666665 4433 33445555666666666666666666666554442  2222223333344456666666666


Q ss_pred             HHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011236          303 GLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVK  377 (490)
Q Consensus       303 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  377 (490)
                      ++.....+..+...+..+..++...|+.++|...+.++... .+.+....+.+...|+..|  ++|...++.+.+
T Consensus       430 ~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~  501 (553)
T PRK12370        430 DELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ-EITGLIAVNLLYAEYCQNS--ERALPTIREFLE  501 (553)
T ss_pred             HHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc-cchhHHHHHHHHHHHhccH--HHHHHHHHHHHH
Confidence            65554433123334455555556666666666666665443 1112223344444455555  355555555443

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

Probab=99.48  E-value=3.1e-11  Score=114.39  Aligned_cols=275  Identities=12%  Similarity=0.077  Sum_probs=174.1

Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC
Q 011236           55 PVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED  134 (490)
Q Consensus        55 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  134 (490)
                      .++-.+...|+.|+..+|..+|..||..|+.+.|- +|..|.-...+.+...++.++......++.+.+.         .
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk---------e   80 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK---------E   80 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC---------C
Confidence            36677778899999999999999999999998887 8888888877888888888888877878777665         3


Q ss_pred             CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHH-HCCCCCCHHHHHHH
Q 011236          135 KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMK-ENGVPPDNFSYRIC  213 (490)
Q Consensus       135 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~-~~~~~p~~~~~~~l  213 (490)
                      |.+.+|+.|..+|.+.|+..- ++..++           -.-.+...+...|.......++..+. ..+.-||..+   +
T Consensus        81 p~aDtyt~Ll~ayr~hGDli~-fe~veq-----------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n---~  145 (1088)
T KOG4318|consen   81 PLADTYTNLLKAYRIHGDLIL-FEVVEQ-----------DLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAEN---A  145 (1088)
T ss_pred             CchhHHHHHHHHHHhccchHH-HHHHHH-----------HHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHH---H
Confidence            667788888888888888765 222222           11223344555565555555554432 1223344433   3


Q ss_pred             HHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcC
Q 011236          214 INSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG  293 (490)
Q Consensus       214 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  293 (490)
                      +......|-++.+++++..+.......|...    +++-+...  .....++.......... +++.+|..++.+-...|
T Consensus       146 illlv~eglwaqllkll~~~Pvsa~~~p~~v----fLrqnv~~--ntpvekLl~~cksl~e~-~~s~~l~a~l~~alaag  218 (1088)
T KOG4318|consen  146 ILLLVLEGLWAQLLKLLAKVPVSAWNAPFQV----FLRQNVVD--NTPVEKLLNMCKSLVEA-PTSETLHAVLKRALAAG  218 (1088)
T ss_pred             HHHHHHHHHHHHHHHHHhhCCcccccchHHH----HHHHhccC--CchHHHHHHHHHHhhcC-CChHHHHHHHHHHHhcC
Confidence            3444455677777777766641111112111    12222221  22223333332222222 67777777777777777


Q ss_pred             ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC
Q 011236          294 NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM  364 (490)
Q Consensus       294 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  364 (490)
                      +.+.|..++.+|...+...+..-|-.|+-+   .++...++.+++-|...|+.|+..|+...+..+..+|.
T Consensus       219 ~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~  286 (1088)
T KOG4318|consen  219 DVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQ  286 (1088)
T ss_pred             chhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchh
Confidence            777777777777777775555555555544   66777777777777777777777777766666666554

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

Probab=99.48  E-value=4.9e-09  Score=96.43  Aligned_cols=301  Identities=13%  Similarity=0.085  Sum_probs=159.8

Q ss_pred             CCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC------CCChhhH
Q 011236           34 VARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGL------AFSVHDH  107 (490)
Q Consensus        34 ~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~------~~~~~~~  107 (490)
                      .-|...+.-+...+-|+-++. ++++..    +.++..-+.-|..+++.+++++|.+.+...+....      +-+...+
T Consensus       139 rIW~lyl~Fv~~~~lPets~r-vyrRYL----k~~P~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw  213 (835)
T KOG2047|consen  139 RIWDLYLKFVESHGLPETSIR-VYRRYL----KVAPEAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLW  213 (835)
T ss_pred             cchHHHHHHHHhCCChHHHHH-HHHHHH----hcCHHHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHH
Confidence            347777777777777766666 777774    34566678888889999999999999988775432      3344455


Q ss_pred             HHHHHHHHhhcCHH---HHHHHHHHccccCCC--hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHH
Q 011236          108 AVQLDLIGKVRGLE---SAETYFNSLNDEDKV--DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLY  182 (490)
Q Consensus       108 ~~l~~~~~~~~~~~---~A~~~~~~~~~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~  182 (490)
                      ..+.....+.-+.-   ....+++.+...-+|  ...|.+|.+-|.+.|.+++|.++|++....-  .++.-|..+.++|
T Consensus       214 ~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Y  291 (835)
T KOG2047|consen  214 LELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAY  291 (835)
T ss_pred             HHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHH
Confidence            55555555443322   344455555555555  4568899999999999999999998876641  1333444444443


Q ss_pred             Hhc----------------CC------cCcHHHHHHHHHHCCC-----------CCCHHHHHHHHHHHhccCChHHHHHH
Q 011236          183 TNT----------------GQ------HEKIPDVLLDMKENGV-----------PPDNFSYRICINSYGARSELSSMENV  229 (490)
Q Consensus       183 ~~~----------------~~------~~~a~~~~~~m~~~~~-----------~p~~~~~~~li~~~~~~g~~~~a~~~  229 (490)
                      +.-                ++      ++-.+.-|+.+.....           +.++.+|..-+..  ..|+..+-...
T Consensus       292 a~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~lNsVlLRQn~~nV~eW~kRV~l--~e~~~~~~i~t  369 (835)
T KOG2047|consen  292 AQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLLNSVLLRQNPHNVEEWHKRVKL--YEGNAAEQINT  369 (835)
T ss_pred             HHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHHHHHHHhcCCccHHHHHhhhhh--hcCChHHHHHH
Confidence            321                11      1112223333332210           1122222222222  23445555555


Q ss_pred             HHHHHhCCCCC----CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC--hhhHHHHHHHHHhcCChhHHHHHHH
Q 011236          230 LQEMESQSHIS----MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD--ALGYNHLISHYASLGNKDEMMKFWG  303 (490)
Q Consensus       230 ~~~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~  303 (490)
                      |.+....-++.    .-...|..+.+.|-..|+++.|..+|++......+..+  ..+|..-..+-.+..+++.|+++.+
T Consensus       370 yteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~  449 (835)
T KOG2047|consen  370 YTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMR  449 (835)
T ss_pred             HHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            55554211111    01233445566666666666666666665543331000  1344444455555556666666555


Q ss_pred             HHHHhcCCC-----------------ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 011236          304 LQKIKCKKQ-----------------LNRDYITMLGSLVKIGELEEAEKMLEEWELS  343 (490)
Q Consensus       304 ~~~~~~~~~-----------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  343 (490)
                      ........|                 +...|...++.--..|-++....+++.+.+.
T Consensus       450 ~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidL  506 (835)
T KOG2047|consen  450 RATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDL  506 (835)
T ss_pred             hhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            332211110                 1123444445445555666666666665554

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

Probab=99.47  E-value=2.8e-09  Score=97.10  Aligned_cols=426  Identities=13%  Similarity=0.064  Sum_probs=238.8

Q ss_pred             ccHHHhhccCC---CCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011236           37 NNLYSRISPLG---DPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDL  113 (490)
Q Consensus        37 ~~l~~~l~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  113 (490)
                      ..++..+.+.+   ++++++. ....+... .+-+...+..=+-++.+.++|++|+.+.+.-....  ....-+..-.-+
T Consensus        13 ~~l~t~ln~~~~~~e~e~a~k-~~~Kil~~-~pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~--~~~~~~fEKAYc   88 (652)
T KOG2376|consen   13 EALLTDLNRHGKNGEYEEAVK-TANKILSI-VPDDEDAIRCKVVALIQLDKYEDALKLIKKNGALL--VINSFFFEKAYC   88 (652)
T ss_pred             HHHHHHHHHhccchHHHHHHH-HHHHHHhc-CCCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhh--hcchhhHHHHHH
Confidence            35555554443   4444555 44444433 34555666666667778888888885554422111  011111122233


Q ss_pred             HHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhc-CCcCcHH
Q 011236          114 IGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNT-GQHEKIP  192 (490)
Q Consensus       114 ~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~-~~~~~a~  192 (490)
                      ..+.+..++|+..++.....  +..+...-.+.+.+.|++++|+.+|+.+.+.+    ...+...+++-+.. +....+.
T Consensus        89 ~Yrlnk~Dealk~~~~~~~~--~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~----~dd~d~~~r~nl~a~~a~l~~~  162 (652)
T KOG2376|consen   89 EYRLNKLDEALKTLKGLDRL--DDKLLELRAQVLYRLERYDEALDIYQHLAKNN----SDDQDEERRANLLAVAAALQVQ  162 (652)
T ss_pred             HHHcccHHHHHHHHhccccc--chHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC----CchHHHHHHHHHHHHHHhhhHH
Confidence            34778888888888733322  23344445567778888888888888887763    33333333221111 1111111


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHH---HHhccCChHHHHHHHHHHH----h---CCCC-----CCCHHH-HHHHHHHHHHc
Q 011236          193 DVLLDMKENGVPPDNFSYRICIN---SYGARSELSSMENVLQEME----S---QSHI-----SMDWGT-YSTVANYYIIA  256 (490)
Q Consensus       193 ~~~~~m~~~~~~p~~~~~~~li~---~~~~~g~~~~a~~~~~~~~----~---~~~~-----~~~~~~-~~~li~~~~~~  256 (490)
                          .+......| ..+|..+.+   .+...|++.+|+++++...    +   +.+.     .....+ -..+...+-..
T Consensus       163 ----~~q~v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~  237 (652)
T KOG2376|consen  163 ----LLQSVPEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQ  237 (652)
T ss_pred             ----HHHhccCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHh
Confidence                122222233 234444433   4556889999999988872    0   1111     111111 12355567788


Q ss_pred             CCHHHHHHHHHHHhhhhccCCChhh----HHHHHHHHHhcCChh----------------HHHH----------------
Q 011236          257 GLKEKAIIYLKKCEDIVSKSKDALG----YNHLISHYASLGNKD----------------EMMK----------------  300 (490)
Q Consensus       257 ~~~~~a~~~~~~~~~~~~~~~~~~~----~~~l~~~~~~~~~~~----------------~a~~----------------  300 (490)
                      |+.++|..+|.......+  +|...    -|.++..-....-++                .++.                
T Consensus       238 Gqt~ea~~iy~~~i~~~~--~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~l  315 (652)
T KOG2376|consen  238 GQTAEASSIYVDIIKRNP--ADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNAL  315 (652)
T ss_pred             cchHHHHHHHHHHHHhcC--CCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999988887665  34321    122221111100000                0000                


Q ss_pred             --HH-------HHHHHhcC-CCChhhHHHHHHHHHh--cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 011236          301 --FW-------GLQKIKCK-KQLNRDYITMLGSLVK--IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKA  368 (490)
Q Consensus       301 --~~-------~~~~~~~~-~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  368 (490)
                        +|       ++.....+ ......+.+++..+.+  ......+.+++....+....-...+.-..+......|+++.|
T Consensus       316 L~l~tnk~~q~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~~A  395 (652)
T KOG2376|consen  316 LALFTNKMDQVRELSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPEVA  395 (652)
T ss_pred             HHHHhhhHHHHHHHHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHHHH
Confidence              00       00001111 1122344455554433  224666777777766542222234455566777889999999


Q ss_pred             HHHHH--------HHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCC
Q 011236          369 DAVLK--------EIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRD  439 (490)
Q Consensus       369 ~~~~~--------~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~  439 (490)
                      .+++.        .+.+.+-.|-  +-..+...+.+.++.+.|.+++.+++..+.....-.+.. .++..+...-.+.|+
T Consensus       396 ~~il~~~~~~~~ss~~~~~~~P~--~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~  473 (652)
T KOG2376|consen  396 LEILSLFLESWKSSILEAKHLPG--TVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGN  473 (652)
T ss_pred             HHHHHHHhhhhhhhhhhhccChh--HHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCc
Confidence            99999        5555554444  445566777888888889999998888663222222222 233344444457799


Q ss_pred             HHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC-CcHHHHHHHH
Q 011236          440 VEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG-QEVDGLLESM  481 (490)
Q Consensus       440 ~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g-~~a~~~~~~m  481 (490)
                      -++|..+++++.+..|+ ..+...++.+|++.. +.|..+-+.+
T Consensus       474 ~~ea~s~leel~k~n~~d~~~l~~lV~a~~~~d~eka~~l~k~L  517 (652)
T KOG2376|consen  474 EEEASSLLEELVKFNPNDTDLLVQLVTAYARLDPEKAESLSKKL  517 (652)
T ss_pred             hHHHHHHHHHHHHhCCchHHHHHHHHHHHHhcCHHHHHHHhhcC
Confidence            99999999999998888 999999999999999 8888876554

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

Probab=99.46  E-value=2.6e-10  Score=103.16  Aligned_cols=283  Identities=13%  Similarity=0.028  Sum_probs=223.7

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011236          138 KLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSY  217 (490)
Q Consensus       138 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  217 (490)
                      ........-+...+++.+..++++...+.. +++...+..-|.++...|+..+-..+=.++.+. .+-...+|-++.--|
T Consensus       245 dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~aVg~YY  322 (611)
T KOG1173|consen  245 DLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFAVGCYY  322 (611)
T ss_pred             HHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhhHHHHH
Confidence            334445566777899999999999998874 346777777777888999999888888888875 444667899999888


Q ss_pred             hccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhH
Q 011236          218 GARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE  297 (490)
Q Consensus       218 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  297 (490)
                      ...|+..+|.+.|.+.. ..+. .-...|-.+...|.-.|.-|+|+..+...-+..+.  ....+--+..-|.+.++.+.
T Consensus       323 l~i~k~seARry~SKat-~lD~-~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G--~hlP~LYlgmey~~t~n~kL  398 (611)
T KOG1173|consen  323 LMIGKYSEARRYFSKAT-TLDP-TFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPG--CHLPSLYLGMEYMRTNNLKL  398 (611)
T ss_pred             HHhcCcHHHHHHHHHHh-hcCc-cccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccC--CcchHHHHHHHHHHhccHHH
Confidence            88999999999999886 4443 22345666888999999999999998887765442  33334445566888999999


Q ss_pred             HHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CC----CCchhHHHHHHHHHhcCCHHHHHHH
Q 011236          298 MMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSC--YC----YDFRVPNIILLGYSQKGMIEKADAV  371 (490)
Q Consensus       298 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~----~~~~~~~~l~~~~~~~g~~~~A~~~  371 (490)
                      |.++|.......+ .|+...+-+.-.....+.+.+|..+|+..+..-  ..    .-..+++.|.++|.+.+++++|+..
T Consensus       399 Ae~Ff~~A~ai~P-~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~  477 (611)
T KOG1173|consen  399 AEKFFKQALAIAP-SDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDY  477 (611)
T ss_pred             HHHHHHHHHhcCC-CcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHH
Confidence            9999998887766 777788888877788899999999998876321  11    1234578899999999999999999


Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHH
Q 011236          372 LKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLG  435 (490)
Q Consensus       372 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~  435 (490)
                      +++.+...++ |..++.++.-.|...|+++.|.+.|.+++.       +.|+..+-..++..+.
T Consensus       478 ~q~aL~l~~k-~~~~~asig~iy~llgnld~Aid~fhKaL~-------l~p~n~~~~~lL~~ai  533 (611)
T KOG1173|consen  478 YQKALLLSPK-DASTHASIGYIYHLLGNLDKAIDHFHKALA-------LKPDNIFISELLKLAI  533 (611)
T ss_pred             HHHHHHcCCC-chhHHHHHHHHHHHhcChHHHHHHHHHHHh-------cCCccHHHHHHHHHHH
Confidence            9999988766 899999999999999999999999999987       7788877777766443

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

Probab=99.46  E-value=9.7e-12  Score=104.55  Aligned_cols=233  Identities=10%  Similarity=0.021  Sum_probs=198.8

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHH
Q 011236          210 YRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHY  289 (490)
Q Consensus       210 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  289 (490)
                      -+.+.++|.+.|.+.+|++.|+... +..  |-+.||-.|-..|.+..+.+.|+.++.+-.+..+  .|+.....+.+.+
T Consensus       226 k~Q~gkCylrLgm~r~AekqlqssL-~q~--~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP--~~VT~l~g~ARi~  300 (478)
T KOG1129|consen  226 KQQMGKCYLRLGMPRRAEKQLQSSL-TQF--PHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFP--FDVTYLLGQARIH  300 (478)
T ss_pred             HHHHHHHHHHhcChhhhHHHHHHHh-hcC--CchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCC--chhhhhhhhHHHH
Confidence            3678899999999999999999887 332  5556777799999999999999999999877665  4555556677888


Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHH
Q 011236          290 ASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKAD  369 (490)
Q Consensus       290 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  369 (490)
                      -..++.++|.++|+...+..+ .++....++...|.-.++.+-|..+++.+.+.|+. +...|+.+.-+|.-.+++|-++
T Consensus       301 eam~~~~~a~~lYk~vlk~~~-~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L  378 (478)
T KOG1129|consen  301 EAMEQQEDALQLYKLVLKLHP-INVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVL  378 (478)
T ss_pred             HHHHhHHHHHHHHHHHHhcCC-ccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhH
Confidence            889999999999998887766 78888888888999999999999999999999876 7788999999999999999999


Q ss_pred             HHHHHHHHcCCCCCH--HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHH
Q 011236          370 AVLKEIVKKGKTPTP--NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAF  446 (490)
Q Consensus       370 ~~~~~m~~~~~~p~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~  446 (490)
                      .-|++....--.|+.  ..|-.+.......|++..|.+.|+-++.       -.|+ ...++.|.-.-.+.|+.++|..+
T Consensus       379 ~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~-------~d~~h~ealnNLavL~~r~G~i~~Arsl  451 (478)
T KOG1129|consen  379 PSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALT-------SDAQHGEALNNLAVLAARSGDILGARSL  451 (478)
T ss_pred             HHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhc-------cCcchHHHHHhHHHHHhhcCchHHHHHH
Confidence            999998876444544  5798999999999999999999999987       2244 47899888888899999999999


Q ss_pred             HHHHHhcccc
Q 011236          447 VSSLKIKVQK  456 (490)
Q Consensus       447 ~~~~~~~~~~  456 (490)
                      +....+..|.
T Consensus       452 l~~A~s~~P~  461 (478)
T KOG1129|consen  452 LNAAKSVMPD  461 (478)
T ss_pred             HHHhhhhCcc
Confidence            9999998887

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.45  E-value=9e-11  Score=101.92  Aligned_cols=201  Identities=15%  Similarity=0.032  Sum_probs=144.0

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHH
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHL  285 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  285 (490)
                      ....+..+...+...|++++|...+++.. +... .+...+..+...+...|++++|.+.+++.....+  .+...+..+
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l-~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~--~~~~~~~~~  105 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKAL-EHDP-DDYLAYLALALYYQQLGELEKAEDSFRRALTLNP--NNGDVLNNY  105 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHH-HhCc-ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC--CCHHHHHHH
Confidence            34556667777777888888888887776 4332 4456667777778888888888888887776554  455667777


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCC-CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKCKK-QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM  364 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  364 (490)
                      ...+...|++++|.+.++........ .....+..+...+...|++++|...+.+..+.. +.+...+..+...+...|+
T Consensus       106 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~  184 (234)
T TIGR02521       106 GTFLCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQ  184 (234)
T ss_pred             HHHHHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCC
Confidence            77788888888888888877654321 233456667777788888888888888877752 2345567777788888888


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          365 IEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       365 ~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +++|...+++..+.. +.+...+..+...+...|+.++|..+++.+..
T Consensus       185 ~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       185 YKDARAYLERYQQTY-NQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            888888888887763 33566667777777888888888888777654

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.

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

Probab=99.45  E-value=1.3e-09  Score=102.72  Aligned_cols=128  Identities=20%  Similarity=0.265  Sum_probs=73.3

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc
Q 011236          283 NHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQK  362 (490)
Q Consensus       283 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  362 (490)
                      ..+.+.|-..|++++|++++++.+...+ ..+..|..-.+.+-+.|++.+|.+.++....... -|..+-+..+..+.++
T Consensus       198 ~~lAqhyd~~g~~~~Al~~Id~aI~htP-t~~ely~~KarilKh~G~~~~Aa~~~~~Ar~LD~-~DRyiNsK~aKy~LRa  275 (517)
T PF12569_consen  198 YFLAQHYDYLGDYEKALEYIDKAIEHTP-TLVELYMTKARILKHAGDLKEAAEAMDEARELDL-ADRYINSKCAKYLLRA  275 (517)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHhcCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCh-hhHHHHHHHHHHHHHC
Confidence            4445556666666666666666665543 3345566666666666666666666666665422 2444445555556666


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHH------HH--HHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          363 GMIEKADAVLKEIVKKGKTPTPN------SW--SIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       363 g~~~~A~~~~~~m~~~~~~p~~~------~~--~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      |++++|.+++......+..|-..      .|  .....+|.+.|++..|+..|....+
T Consensus       276 ~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk~~~~v~k  333 (517)
T PF12569_consen  276 GRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALKRFHAVLK  333 (517)
T ss_pred             CCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            66666666666665544322211      11  2334556666776666666655554

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 [], [].

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.43  E-value=6.6e-09  Score=90.65  Aligned_cols=365  Identities=9%  Similarity=0.007  Sum_probs=242.2

Q ss_pred             hhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhc-CCh-hH-------------HHHHHHHHHhcC-
Q 011236          104 VHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVRE-GLV-DE-------------SLSLMQKMKEMG-  167 (490)
Q Consensus       104 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~-g~~-~~-------------a~~~~~~m~~~~-  167 (490)
                      .+.....+.+|...++-+.|...+...+.....+ --|.++..+-+. ++- ++             |+..+.-..+.+ 
T Consensus        97 ~e~~r~~aecy~~~~n~~~Ai~~l~~~p~t~r~p-~inlMla~l~~~g~r~~~~vl~ykevvrecp~aL~~i~~ll~l~v  175 (564)
T KOG1174|consen   97 AEQRRRAAECYRQIGNTDMAIETLLQVPPTLRSP-RINLMLARLQHHGSRHKEAVLAYKEVIRECPMALQVIEALLELGV  175 (564)
T ss_pred             HHHHHHHHHHHHHHccchHHHHHHhcCCccccch-hHHHHHHHHHhccccccHHHHhhhHHHHhcchHHHHHHHHHHHhh
Confidence            3444556777777888888888877776543222 122222222222 221 11             112222222222 


Q ss_pred             --------------CCCCcchHHHHHHHHHh--cCCcCcHHHHHHHHHHC-CCCCCHHHHHHHHHHHhccCChHHHHHHH
Q 011236          168 --------------SFGSALNYNGIMCLYTN--TGQHEKIPDVLLDMKEN-GVPPDNFSYRICINSYGARSELSSMENVL  230 (490)
Q Consensus       168 --------------~~p~~~~~~~l~~~~~~--~~~~~~a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~~~  230 (490)
                                    +.|+..+....+.+++.  .++...+...+-.+... -++-|+.....+.+++...|+.++|+..|
T Consensus       176 ~g~e~~S~~m~~~~~~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~F  255 (564)
T KOG1174|consen  176 NGNEINSLVMHAATVPDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIF  255 (564)
T ss_pred             cchhhhhhhhhheecCCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHH
Confidence                          23333444444554443  34444444444333322 25667788899999999999999999999


Q ss_pred             HHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC
Q 011236          231 QEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK  310 (490)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  310 (490)
                      ++.. -.++ -+........-.+...|+.+....+...+.....  .....|-.-........++..|+.+-++.+...+
T Consensus       256 e~~~-~~dp-y~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~~--~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~  331 (564)
T KOG1174|consen  256 SSTL-CANP-DNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKVK--YTASHWFVHAQLLYDEKKFERALNFVEKCIDSEP  331 (564)
T ss_pred             HHHh-hCCh-hhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhhh--cchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCc
Confidence            9887 4333 2233333334456678888888887777665432  2344455556666678889999999887777655


Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 011236          311 KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSII  390 (490)
Q Consensus       311 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l  390 (490)
                       .+...|..-...+...|+.++|.-.|+..... -+-+..+|.-|+..|...|++.+|..+-+...+. ..-+..+...+
T Consensus       332 -r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~L-ap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~-~~~sA~~LtL~  408 (564)
T KOG1174|consen  332 -RNHEALILKGRLLIALERHTQAVIAFRTAQML-APYRLEIYRGLFHSYLAQKRFKEANALANWTIRL-FQNSARSLTLF  408 (564)
T ss_pred             -ccchHHHhccHHHHhccchHHHHHHHHHHHhc-chhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHH-hhcchhhhhhh
Confidence             56667777778888999999999999998875 2347889999999999999999998887766554 12255555555


Q ss_pred             H-HHHhc-cCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccchhhhHHHHHHH
Q 011236          391 A-AGYAD-KNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAH  467 (490)
Q Consensus       391 ~-~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~~  467 (490)
                      . ..+.. ..--++|..++++.+.       +.|+. .....+...|...|..+++..++++.....++....+.|++.+
T Consensus       409 g~~V~~~dp~~rEKAKkf~ek~L~-------~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~~~D~~LH~~Lgd~~  481 (564)
T KOG1174|consen  409 GTLVLFPDPRMREKAKKFAEKSLK-------INPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLIIFPDVNLHNHLGDIM  481 (564)
T ss_pred             cceeeccCchhHHHHHHHHHhhhc-------cCCccHHHHHHHHHHHHhhCccchHHHHHHHHHhhccccHHHHHHHHHH
Confidence            3 33333 2335789999998877       56776 5677788889999999999999999998888888888888888


Q ss_pred             HhcC--CcHHHHHHHHHh
Q 011236          468 IRSG--QEVDGLLESMKA  483 (490)
Q Consensus       468 ~~~g--~~a~~~~~~m~~  483 (490)
                      ...+  ++|++.|.....
T Consensus       482 ~A~Ne~Q~am~~y~~ALr  499 (564)
T KOG1174|consen  482 RAQNEPQKAMEYYYKALR  499 (564)
T ss_pred             HHhhhHHHHHHHHHHHHh
Confidence            8877  777777766554

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

Probab=99.42  E-value=9e-09  Score=94.94  Aligned_cols=385  Identities=16%  Similarity=0.115  Sum_probs=187.8

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHH
Q 011236           81 SRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSL  159 (490)
Q Consensus        81 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~  159 (490)
                      ..+++...+.+.+.+++. .+-.+++.....-.+...|+-++|..........++ +.+.|..+.-.+-...++++|+..
T Consensus        19 E~kQYkkgLK~~~~iL~k-~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y~eaiKc   97 (700)
T KOG1156|consen   19 ETKQYKKGLKLIKQILKK-FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKYDEAIKC   97 (700)
T ss_pred             HHHHHHhHHHHHHHHHHh-CCccchhHHhccchhhcccchHHHHHHHHHHhccCcccchhHHHHHHHHhhhhhHHHHHHH
Confidence            445555566666655552 233444444444444455666666666655555443 455565555555555666666666


Q ss_pred             HHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCC
Q 011236          160 MQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHI  239 (490)
Q Consensus       160 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  239 (490)
                      |......+.. |...|.-|.-.-.+.|+++.....-.+..+.. +.....|..+..++--.|+...|..++++......-
T Consensus        98 y~nAl~~~~d-N~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~  175 (700)
T KOG1156|consen   98 YRNALKIEKD-NLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNT  175 (700)
T ss_pred             HHHHHhcCCC-cHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            6666555433 44444444444445555555555555554431 112334445555555556666666666555522222


Q ss_pred             CCCHHHHHHHH------HHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC
Q 011236          240 SMDWGTYSTVA------NYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL  313 (490)
Q Consensus       240 ~~~~~~~~~li------~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  313 (490)
                      .|+...|.-..      ....+.|..++|.+.+..-.....  .....-..-...+.+.+++++|..+|..++...  ||
T Consensus       176 ~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~--Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rn--Pd  251 (700)
T KOG1156|consen  176 SPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIV--DKLAFEETKADLLMKLGQLEEAVKVYRRLLERN--PD  251 (700)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHH--HHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhC--ch
Confidence            34444443221      223344555555555544333221  111112223344455556666666665554443  33


Q ss_pred             hhhHH-HHHHHHHhcCCHHHHH-HHHH----------------------------------HHHhcCCCCCchhHHHHHH
Q 011236          314 NRDYI-TMLGSLVKIGELEEAE-KMLE----------------------------------EWELSCYCYDFRVPNIILL  357 (490)
Q Consensus       314 ~~~~~-~l~~~~~~~~~~~~a~-~~~~----------------------------------~~~~~~~~~~~~~~~~l~~  357 (490)
                      ...|. .+..++.+..+.-++. .+|.                                  .+.+.|+++   ++..+..
T Consensus       252 n~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~---vf~dl~S  328 (700)
T KOG1156|consen  252 NLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPS---VFKDLRS  328 (700)
T ss_pred             hHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCc---hhhhhHH
Confidence            33332 2222222222222222 3333                                  333333322   2233333


Q ss_pred             HHHhcCCHHHHHHHHHHHHH---c---CC------------CCCHHHH--HHHHHHHhccCCHHHHHHHHHHHHHhhhcC
Q 011236          358 GYSQKGMIEKADAVLKEIVK---K---GK------------TPTPNSW--SIIAAGYADKNNMEKAFECMKEALAVHEEN  417 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~---~---~~------------~p~~~~~--~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  417 (490)
                      .|-.-...+    +++++..   .   |-            +|....|  -.++..|-+.|+++.|..+++.+++     
T Consensus       329 Lyk~p~k~~----~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AId-----  399 (700)
T KOG1156|consen  329 LYKDPEKVA----FLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAID-----  399 (700)
T ss_pred             HHhchhHhH----HHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc-----
Confidence            332222111    2222211   1   11            2333333  3455667777778888887777776     


Q ss_pred             cCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccchhhhH-HHHHHHHhcC--CcHHHHHHHHHhCCC
Q 011236          418 KFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYH-ALTEAHIRSG--QEVDGLLESMKADDI  486 (490)
Q Consensus       418 ~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~-~l~~~~~~~g--~~a~~~~~~m~~~~~  486 (490)
                        -.|+. ..|..=.+.+...|+.++|..++++..+.+......| --..-..+++  ++|.+++....+.|.
T Consensus       400 --HTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  400 --HTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDTADRAINSKCAKYMLRANEIEEAEEVLSKFTREGF  470 (700)
T ss_pred             --cCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccchhHHHHHHHHHHHHHccccHHHHHHHHHhhhccc
Confidence              33554 3444445667777788888877777777665533333 4455555666  777777766665553

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

Probab=99.40  E-value=3.3e-10  Score=107.62  Aligned_cols=272  Identities=12%  Similarity=0.091  Sum_probs=173.9

Q ss_pred             HHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC-C-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 011236           90 QVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED-K-VDKLYGALLNCYVREGLVDESLSLMQKMKEMG  167 (490)
Q Consensus        90 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  167 (490)
                      .++-.+...|+.|+..+|..+|..||..|+++.|- +|.-|.-.+ | +..+++.++.+..+.++.+.+.          
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk----------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK----------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC----------
Confidence            35556677777777788888888888888888777 776665554 3 5667888888777777776665          


Q ss_pred             CCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHH
Q 011236          168 SFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYS  247 (490)
Q Consensus       168 ~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  247 (490)
                       .|...||..|..+|...||...    |+...+        -.-.+...+...|....-..++..+.-..+.-||...  
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~----fe~veq--------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n--  144 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLIL----FEVVEQ--------DLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAEN--  144 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHH----HHHHHH--------HHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHH--
Confidence             5677788888888888887655    222221        1122334455555555555555554324444466555  


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  327 (490)
                       .+......|-++.+++++..+......  .+  +..+++-+...  +.-..++..........|++.+|..++.+-.-.
T Consensus       145 -~illlv~eglwaqllkll~~~Pvsa~~--~p--~~vfLrqnv~~--ntpvekLl~~cksl~e~~~s~~l~a~l~~alaa  217 (1088)
T KOG4318|consen  145 -AILLLVLEGLWAQLLKLLAKVPVSAWN--AP--FQVFLRQNVVD--NTPVEKLLNMCKSLVEAPTSETLHAVLKRALAA  217 (1088)
T ss_pred             -HHHHHHHHHHHHHHHHHHhhCCccccc--ch--HHHHHHHhccC--CchHHHHHHHHHHhhcCCChHHHHHHHHHHHhc
Confidence             566666677777777777665332221  11  11123333322  233334444232222247788888888888888


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc
Q 011236          328 GELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK  397 (490)
Q Consensus       328 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  397 (490)
                      |+.+.|..++.+|.+.|++.+..-|-.|+-+   .+...-+..+++-|.+.|+.|+..|+...+..+...
T Consensus       218 g~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N  284 (1088)
T KOG4318|consen  218 GDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSN  284 (1088)
T ss_pred             CchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcc
Confidence            8888888888888888887777766666655   677777778888888888888888777666655553

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

Probab=99.40  E-value=1.6e-08  Score=93.21  Aligned_cols=428  Identities=11%  Similarity=0.085  Sum_probs=257.7

Q ss_pred             cccHHHhhccCCCCCCChHHHHHHHHH-cCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHH
Q 011236           36 RNNLYSRISPLGDPDVSLTPVLDQWVL-EGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLI  114 (490)
Q Consensus        36 ~~~l~~~l~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  114 (490)
                      |-..+..+.+.|+....- ..++.-.. ..+.-....|...+......+-++-++.+++..++.    +|....-.+..+
T Consensus       105 wl~Ylq~l~~Q~~iT~tR-~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk~----~P~~~eeyie~L  179 (835)
T KOG2047|consen  105 WLDYLQFLIKQGLITRTR-RTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLKV----APEAREEYIEYL  179 (835)
T ss_pred             HHHHHHHHHhcchHHHHH-HHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHhc----CHHHHHHHHHHH
Confidence            555555555555533221 13333222 234445556777777777888888888888888876    455577778888


Q ss_pred             HhhcCHHHHHHHHHHccccC-------C-ChhHHHHHHHHHHhcCChhH---HHHHHHHHHhcCCCCC--cchHHHHHHH
Q 011236          115 GKVRGLESAETYFNSLNDED-------K-VDKLYGALLNCYVREGLVDE---SLSLMQKMKEMGSFGS--ALNYNGIMCL  181 (490)
Q Consensus       115 ~~~~~~~~A~~~~~~~~~~~-------p-~~~~~~~li~~~~~~g~~~~---a~~~~~~m~~~~~~p~--~~~~~~l~~~  181 (490)
                      ++.+++++|.+.+......+       + +...|.-+-+..++.-+.-.   ...+++.+..+  -+|  ...|.+|.+.
T Consensus       180 ~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~r--ftDq~g~Lw~SLAdY  257 (835)
T KOG2047|consen  180 AKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRR--FTDQLGFLWCSLADY  257 (835)
T ss_pred             HhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhccc--CcHHHHHHHHHHHHH
Confidence            99999999999888876542       3 45677777777666544332   33344444433  223  3468999999


Q ss_pred             HHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc----------------C------ChHHHHHHHHHHHhCCCC
Q 011236          182 YTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGAR----------------S------ELSSMENVLQEMESQSHI  239 (490)
Q Consensus       182 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~----------------g------~~~~a~~~~~~~~~~~~~  239 (490)
                      |.+.|.+++|..+|++..+.-  .++.-|..+.++|+.-                +      +++-...-|+.+.....+
T Consensus       258 YIr~g~~ekarDvyeeai~~v--~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~  335 (835)
T KOG2047|consen  258 YIRSGLFEKARDVYEEAIQTV--MTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPL  335 (835)
T ss_pred             HHHhhhhHHHHHHHHHHHHhh--eehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccch
Confidence            999999999999999987742  2333444444444321                1      122333444444422111


Q ss_pred             C----------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC----CChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 011236          240 S----------MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS----KDALGYNHLISHYASLGNKDEMMKFWGLQ  305 (490)
Q Consensus       240 ~----------~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  305 (490)
                      -          .++..|..  ..-+..|+..+-...|.+..+...+.    .-...|..+...|-..|+++.|..+|++.
T Consensus       336 ~lNsVlLRQn~~nV~eW~k--RV~l~e~~~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka  413 (835)
T KOG2047|consen  336 LLNSVLLRQNPHNVEEWHK--RVKLYEGNAAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKA  413 (835)
T ss_pred             HHHHHHHhcCCccHHHHHh--hhhhhcCChHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHh
Confidence            1          11222211  12233566777777787776543321    22356888999999999999999999977


Q ss_pred             HHhcCCCCh----hhHHHHHHHHHhcCCHHHHHHHHHHHHhcC-----------CC------CCchhHHHHHHHHHhcCC
Q 011236          306 KIKCKKQLN----RDYITMLGSLVKIGELEEAEKMLEEWELSC-----------YC------YDFRVPNIILLGYSQKGM  364 (490)
Q Consensus       306 ~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----------~~------~~~~~~~~l~~~~~~~g~  364 (490)
                      ..... +..    .+|..-...=.+..+++.|.++++.....-           .+      -+...|...++.--..|-
T Consensus       414 ~~V~y-~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gt  492 (835)
T KOG2047|consen  414 TKVPY-KTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGT  492 (835)
T ss_pred             hcCCc-cchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhcc
Confidence            65443 222    344444555556778888888887765321           11      123455566666667788


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHc---CCCH
Q 011236          365 IEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGD---NRDV  440 (490)
Q Consensus       365 ~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~---~g~~  440 (490)
                      ++....+++++++..+. ++.........+-.+.-++++.+.+++-+.+.     -.|+. ..|+..+.-+.+   ....
T Consensus       493 festk~vYdriidLria-TPqii~NyAmfLEeh~yfeesFk~YErgI~LF-----k~p~v~diW~tYLtkfi~rygg~kl  566 (835)
T KOG2047|consen  493 FESTKAVYDRIIDLRIA-TPQIIINYAMFLEEHKYFEESFKAYERGISLF-----KWPNVYDIWNTYLTKFIKRYGGTKL  566 (835)
T ss_pred             HHHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhhHHHHHHHHHHHcCCccC-----CCccHHHHHHHHHHHHHHHhcCCCH
Confidence            99999999999887665 44443334444555666777777777766522     22444 455555544432   2357


Q ss_pred             HHHHHHHHHHHhcccc--h-hhhHHHHHHHHhcC--CcHHHHHHHH
Q 011236          441 EEVEAFVSSLKIKVQK--R-NMYHALTEAHIRSG--QEVDGLLESM  481 (490)
Q Consensus       441 ~~a~~~~~~~~~~~~~--~-~~~~~l~~~~~~~g--~~a~~~~~~m  481 (490)
                      +.|..+|++..+..|+  . ..|-.....=-+.|  ..|++++++.
T Consensus       567 EraRdLFEqaL~~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyera  612 (835)
T KOG2047|consen  567 ERARDLFEQALDGCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERA  612 (835)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            7788888887776665  1 22222222223345  6677777664

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

Probab=99.39  E-value=1.2e-08  Score=96.06  Aligned_cols=374  Identities=13%  Similarity=0.011  Sum_probs=246.7

Q ss_pred             CCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC-CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcch-H
Q 011236           98 QGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED-KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALN-Y  175 (490)
Q Consensus        98 ~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~-~  175 (490)
                      ..+..++..|..+.-++...|+++.+.+.|++....- .....|+.+...|...|.-..|+.++++-......|+..+ +
T Consensus       317 ~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~  396 (799)
T KOG4162|consen  317 KKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVL  396 (799)
T ss_pred             hhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHH
Confidence            3345678888888888888899999999998876543 3466788888888888988888888887665543343333 3


Q ss_pred             HHHHHHHH-hcCCcCcHHHHHHHHHHC--CC--CCCHHHHHHHHHHHhcc----C-------ChHHHHHHHHHHHhCCCC
Q 011236          176 NGIMCLYT-NTGQHEKIPDVLLDMKEN--GV--PPDNFSYRICINSYGAR----S-------ELSSMENVLQEMESQSHI  239 (490)
Q Consensus       176 ~~l~~~~~-~~~~~~~a~~~~~~m~~~--~~--~p~~~~~~~li~~~~~~----g-------~~~~a~~~~~~~~~~~~~  239 (490)
                      -..-..|. +.+..+++.++-.+....  +.  ......|..+.-+|...    .       ...++.+.+++.. +.+.
T Consensus       397 Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av-~~d~  475 (799)
T KOG4162|consen  397 LMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAV-QFDP  475 (799)
T ss_pred             HHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHH-hcCC
Confidence            33333333 346677777766666551  11  11233444444444321    1       1235677777776 4333


Q ss_pred             -CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCC------
Q 011236          240 -SMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQ------  312 (490)
Q Consensus       240 -~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~------  312 (490)
                       .|++..|  +.--|+..++++.|.+..++....+.. .+...|..+.-.+...+++.+|+.+.+......+..      
T Consensus       476 ~dp~~if~--lalq~A~~R~l~sAl~~~~eaL~l~~~-~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~  552 (799)
T KOG4162|consen  476 TDPLVIFY--LALQYAEQRQLTSALDYAREALALNRG-DSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDG  552 (799)
T ss_pred             CCchHHHH--HHHHHHHHHhHHHHHHHHHHHHHhcCC-ccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchh
Confidence             3444444  555677788899999988888887555 788888888888888889999998888666654320      


Q ss_pred             ---------C----hhhHHHHHHHHHh------cC-----------------CHHHHHHHHHHH----H----hcC----
Q 011236          313 ---------L----NRDYITMLGSLVK------IG-----------------ELEEAEKMLEEW----E----LSC----  344 (490)
Q Consensus       313 ---------~----~~~~~~l~~~~~~------~~-----------------~~~~a~~~~~~~----~----~~~----  344 (490)
                               +    ..|...++..+-.      .+                 +..++......+    .    ..|    
T Consensus       553 ~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~  632 (799)
T KOG4162|consen  553 KIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELK  632 (799)
T ss_pred             hhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccc
Confidence                     0    0111111111110      00                 111111111100    0    001    


Q ss_pred             -----C--CCCc------hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHH
Q 011236          345 -----Y--CYDF------RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEAL  411 (490)
Q Consensus       345 -----~--~~~~------~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  411 (490)
                           .  .|+.      ..|......+.+.+..++|...+.+.....+. ....|......+...|.+++|.+.|..++
T Consensus       633 Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l-~~~~~~~~G~~~~~~~~~~EA~~af~~Al  711 (799)
T KOG4162|consen  633 LPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKIDPL-SASVYYLRGLLLEVKGQLEEAKEAFLVAL  711 (799)
T ss_pred             cCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcchh-hHHHHHHhhHHHHHHHhhHHHHHHHHHHH
Confidence                 0  1111      13344556677788888888888777765432 55677777788889999999999999998


Q ss_pred             HhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHH--HHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHh
Q 011236          412 AVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEA--FVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       412 ~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~--~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~  483 (490)
                      .       +.|+. ....++...+.+.|+..-|..  ++..+.+.+|. +..|..++..+.+.|  ++|.+.|+.-.+
T Consensus       712 ~-------ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~q  782 (799)
T KOG4162|consen  712 A-------LDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQ  782 (799)
T ss_pred             h-------cCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHh
Confidence            8       56776 688899999999999888888  99999999999 999999999999999  888888876543

>PF13041 PPR_2: PPR repeat family

Probab=99.38  E-value=1e-12  Score=82.09  Aligned_cols=49  Identities=24%  Similarity=0.373  Sum_probs=25.9

Q ss_pred             CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHH
Q 011236          135 KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYT  183 (490)
Q Consensus       135 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~  183 (490)
                      ||..+||++|++|++.|++++|.++|++|.+.|+.||..||+.+|++|+
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~   49 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLC   49 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHc
Confidence            4445555555555555555555555555555555555555555555544

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.38  E-value=2.9e-09  Score=90.98  Aligned_cols=194  Identities=9%  Similarity=-0.043  Sum_probs=94.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcC-CCChhhHHHHHHHH-----HhcCCHHHHHHHHHHHHhcCCCCCchh-HHHHHH
Q 011236          285 LISHYASLGNKDEMMKFWGLQKIKCK-KQLNRDYITMLGSL-----VKIGELEEAEKMLEEWELSCYCYDFRV-PNIILL  357 (490)
Q Consensus       285 l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~-----~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~l~~  357 (490)
                      |+-.|.+.+++.+|..+.+..   .+ .|.......++.+.     .......-|.+.|+..-.++..-|+.. -.++..
T Consensus       291 L~iYyL~q~dVqeA~~L~Kdl---~PttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs  367 (557)
T KOG3785|consen  291 LIIYYLNQNDVQEAISLCKDL---DPTTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMAS  367 (557)
T ss_pred             heeeecccccHHHHHHHHhhc---CCCChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHH
Confidence            444456677777777665532   22 12222222222211     111234445555555544444333221 233444


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHH-HHHHHHHc
Q 011236          358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVS-SILDWLGD  436 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~-~l~~~~~~  436 (490)
                      .+.-..++++.+..++.+...=...|... -.+.++++..|++.+|.++|-....     ..+ -|..+|. .|.++|.+
T Consensus       368 ~fFL~~qFddVl~YlnSi~sYF~NdD~Fn-~N~AQAk~atgny~eaEelf~~is~-----~~i-kn~~~Y~s~LArCyi~  440 (557)
T KOG3785|consen  368 YFFLSFQFDDVLTYLNSIESYFTNDDDFN-LNLAQAKLATGNYVEAEELFIRISG-----PEI-KNKILYKSMLARCYIR  440 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcchhh-hHHHHHHHHhcChHHHHHHHhhhcC-----hhh-hhhHHHHHHHHHHHHh
Confidence            44555566666666666655433323333 3456667777777777777766543     222 2234444 34456667


Q ss_pred             CCCHHHHHHHHHHHHhcccchhhhHHHHHHHHhcC--CcHHHHHHHHHhCCCCC
Q 011236          437 NRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSG--QEVDGLLESMKADDIDE  488 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~~~p  488 (490)
                      .|..+.|+.++-++...+..-.....+.+-|.+++  =-|...|+.+...+..|
T Consensus       441 nkkP~lAW~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~p  494 (557)
T KOG3785|consen  441 NKKPQLAWDMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTP  494 (557)
T ss_pred             cCCchHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCc
Confidence            77777776655443322211333444555566666  34444555554444444

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.38  E-value=6.2e-10  Score=103.60  Aligned_cols=244  Identities=15%  Similarity=0.108  Sum_probs=172.8

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHhC----CCC-CCCHHH-HHHHHHHHHHcCCHHHHHHHHHHHhhhhc-----cC
Q 011236          208 FSYRICINSYGARSELSSMENVLQEMESQ----SHI-SMDWGT-YSTVANYYIIAGLKEKAIIYLKKCEDIVS-----KS  276 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~~~-~~~li~~~~~~~~~~~a~~~~~~~~~~~~-----~~  276 (490)
                      .+...+...|...|+++.|+.+++.....    .|. .|...+ .+.+...|...+++++|..+|+++.....     ..
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h  279 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH  279 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC
Confidence            45555777777788888777777766521    121 133333 33477788888999999888888764321     11


Q ss_pred             CC-hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC------CCCh-hhHHHHHHHHHhcCCHHHHHHHHHHHHhc---CC
Q 011236          277 KD-ALGYNHLISHYASLGNKDEMMKFWGLQKIKCK------KQLN-RDYITMLGSLVKIGELEEAEKMLEEWELS---CY  345 (490)
Q Consensus       277 ~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~------~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~  345 (490)
                      |. ..+++.|..+|.+.|++++|..+++....-..      .|.. ..++.+...|+..+++++|..+++...+.   -+
T Consensus       280 ~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~  359 (508)
T KOG1840|consen  280 PAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAP  359 (508)
T ss_pred             HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhc
Confidence            21 25677778889999999888888776554321      1222 23667778888999999999998876543   12


Q ss_pred             CCC----chhHHHHHHHHHhcCCHHHHHHHHHHHHHcC----C--CC-CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhh
Q 011236          346 CYD----FRVPNIILLGYSQKGMIEKADAVLKEIVKKG----K--TP-TPNSWSIIAAGYADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       346 ~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~----~--~p-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  414 (490)
                      .++    ..+++.|...|...|++++|.+++++.+...    -  .+ ....++.|...|.+.+++++|.++|.+...+.
T Consensus       360 g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~  439 (508)
T KOG1840|consen  360 GEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIM  439 (508)
T ss_pred             cccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHH
Confidence            222    3478899999999999999999999887531    1  11 23468889999999999999999999988866


Q ss_pred             hcCcC-CCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          415 EENKF-WRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       415 ~~~~~-~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                       ...| -.|+. .+|..|...|...|+++.|.++.+....
T Consensus       440 -~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  440 -KLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             -HHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence             2233 33444 6889999999999999999999887653

>PF13041 PPR_2: PPR repeat family

Probab=99.38  E-value=1.5e-12  Score=81.24  Aligned_cols=50  Identities=28%  Similarity=0.509  Sum_probs=35.9

Q ss_pred             CCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          347 YDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       347 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      ||..+||++|++|++.|++++|.++|++|.+.|+.||..||+.++.+|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            56677777777777777777777777777777777777777777777653

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

Probab=99.37  E-value=2.7e-09  Score=100.66  Aligned_cols=294  Identities=17%  Similarity=0.076  Sum_probs=209.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHH-HHHHHHHHhc---
Q 011236           75 VIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLY-GALLNCYVRE---  150 (490)
Q Consensus        75 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~-~~li~~~~~~---  150 (490)
                      ....+...|++++|++.++.-...- .............+.+.|+.++|..++..+...+|+...| ..+..+..-.   
T Consensus        10 ~~~il~e~g~~~~AL~~L~~~~~~I-~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~   88 (517)
T PF12569_consen   10 KNSILEEAGDYEEALEHLEKNEKQI-LDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQL   88 (517)
T ss_pred             HHHHHHHCCCHHHHHHHHHhhhhhC-CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhccc
Confidence            3455678899999999998765553 4556677778899999999999999999999999965555 4455554222   


Q ss_pred             --CChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCc-CcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHH
Q 011236          151 --GLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQH-EKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSME  227 (490)
Q Consensus       151 --g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~-~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~  227 (490)
                        .+.+...++++++...-  |.......+.-.+.....+ ..+...+..+...|++   .+|+.|-..|....+..-..
T Consensus        89 ~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP---slF~~lk~Ly~d~~K~~~i~  163 (517)
T PF12569_consen   89 SDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP---SLFSNLKPLYKDPEKAAIIE  163 (517)
T ss_pred             ccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc---hHHHHHHHHHcChhHHHHHH
Confidence              25677788898887764  3333333332222222233 2345566777788874   34566666666555555555


Q ss_pred             HHHHHHHhC---C----------CCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhc
Q 011236          228 NVLQEMESQ---S----------HISMDW--GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASL  292 (490)
Q Consensus       228 ~~~~~~~~~---~----------~~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  292 (490)
                      +++......   .          .-+|+.  .++..+...|...|++++|++++++.....+  ..+..|..-...+-+.
T Consensus       164 ~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htP--t~~ely~~KarilKh~  241 (517)
T PF12569_consen  164 SLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTP--TLVELYMTKARILKHA  241 (517)
T ss_pred             HHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCC--CcHHHHHHHHHHHHHC
Confidence            555554311   1          112443  3456678889999999999999999988765  4578899999999999


Q ss_pred             CChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhH--------HHHHHHHHhcCC
Q 011236          293 GNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVP--------NIILLGYSQKGM  364 (490)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--------~~l~~~~~~~g~  364 (490)
                      |++.+|.+.++.....+. -|...-+-.+..+.+.|++++|.+++....+.+..|-...+        .-...+|.+.|+
T Consensus       242 G~~~~Aa~~~~~Ar~LD~-~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~  320 (517)
T PF12569_consen  242 GDLKEAAEAMDEARELDL-ADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGD  320 (517)
T ss_pred             CCHHHHHHHHHHHHhCCh-hhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999998777665 77778888889999999999999999999887654433222        345567889999


Q ss_pred             HHHHHHHHHHHHH
Q 011236          365 IEKADAVLKEIVK  377 (490)
Q Consensus       365 ~~~A~~~~~~m~~  377 (490)
                      +..|++.|..+.+
T Consensus       321 ~~~ALk~~~~v~k  333 (517)
T PF12569_consen  321 YGLALKRFHAVLK  333 (517)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999887766554

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 [], [].

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

Probab=99.34  E-value=7.5e-08  Score=89.04  Aligned_cols=374  Identities=13%  Similarity=0.080  Sum_probs=202.6

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNC  146 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~  146 (490)
                      ...+.....-.+...|+-++|......-.+.+ .-+...+..+.-.+....++++|+..|......+| |...|.-+.-.
T Consensus        40 HgeslAmkGL~L~~lg~~~ea~~~vr~glr~d-~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlslL  118 (700)
T KOG1156|consen   40 HGESLAMKGLTLNCLGKKEEAYELVRLGLRND-LKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKIEKDNLQILRDLSLL  118 (700)
T ss_pred             cchhHHhccchhhcccchHHHHHHHHHHhccC-cccchhHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHH
Confidence            33344444444455566666666666655544 24455555555555556666777777766666665 45556555555


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCC-CCCCHHHHHHHH------HHHhc
Q 011236          147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENG-VPPDNFSYRICI------NSYGA  219 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~~li------~~~~~  219 (490)
                      -++.|+++........+.+..+. ....|..+..++.-.|+...|..+.++..+.. -.|+...|.-..      ....+
T Consensus       119 Q~QmRd~~~~~~tr~~LLql~~~-~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E  197 (700)
T KOG1156|consen  119 QIQMRDYEGYLETRNQLLQLRPS-QRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIE  197 (700)
T ss_pred             HHHHHhhhhHHHHHHHHHHhhhh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHH
Confidence            55666666666665555554222 34455666666666666666666666665543 234444433221      22344


Q ss_pred             cCChHHHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHH
Q 011236          220 RSELSSMENVLQEMESQSHISMDWGTY-STVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEM  298 (490)
Q Consensus       220 ~g~~~~a~~~~~~~~~~~~~~~~~~~~-~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  298 (490)
                      .|.++.|.+.+..-+  ..+ .|-..+ -.-...+.+.+++++|..++..+....+  .+...|-.+..++.+-.+.-++
T Consensus       198 ~g~~q~ale~L~~~e--~~i-~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rnP--dn~~Yy~~l~~~lgk~~d~~~~  272 (700)
T KOG1156|consen  198 AGSLQKALEHLLDNE--KQI-VDKLAFEETKADLLMKLGQLEEAVKVYRRLLERNP--DNLDYYEGLEKALGKIKDMLEA  272 (700)
T ss_pred             cccHHHHHHHHHhhh--hHH-HHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhCc--hhHHHHHHHHHHHHHHhhhHHH
Confidence            556666665555442  222 222222 2344556666666777666666665443  2223233333333222222222


Q ss_pred             H-HHHHHHHHhcC-------------------------------CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc--C
Q 011236          299 M-KFWGLQKIKCK-------------------------------KQLNRDYITMLGSLVKIGELEEAEKMLEEWELS--C  344 (490)
Q Consensus       299 ~-~~~~~~~~~~~-------------------------------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~  344 (490)
                      + .+|.......+                               ..-+.++..+...|-.....+-.+++.-.+...  |
T Consensus       273 lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~  352 (700)
T KOG1156|consen  273 LKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPSVFKDLRSLYKDPEKVAFLEKLVTSYQHSLSG  352 (700)
T ss_pred             HHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCchhhhhHHHHhchhHhHHHHHHHHHHHhhccc
Confidence            2 33332222111                               011122333333332222222112222222211  1


Q ss_pred             C------------CCCchhH--HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHhccCCHHHHHHHHHH
Q 011236          345 Y------------CYDFRVP--NIILLGYSQKGMIEKADAVLKEIVKKGKTPTPN-SWSIIAAGYADKNNMEKAFECMKE  409 (490)
Q Consensus       345 ~------------~~~~~~~--~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~-~~~~l~~~~~~~~~~~~a~~~~~~  409 (490)
                      .            +|....|  -.++..|-+.|+++.|..+++..++  -.|+.. .|..=.+.+...|++++|..++++
T Consensus       353 ~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AId--HTPTliEly~~KaRI~kH~G~l~eAa~~l~e  430 (700)
T KOG1156|consen  353 TGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAID--HTPTLIELYLVKARIFKHAGLLDEAAAWLDE  430 (700)
T ss_pred             ccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc--cCchHHHHHHHHHHHHHhcCChHHHHHHHHH
Confidence            1            3444444  4567778899999999999998875  555543 344445788999999999999999


Q ss_pred             HHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          410 ALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       410 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      +.++.      .||...=.--.....++...++|.++.....+.+..
T Consensus       431 a~elD------~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~~  471 (700)
T KOG1156|consen  431 AQELD------TADRAINSKCAKYMLRANEIEEAEEVLSKFTREGFG  471 (700)
T ss_pred             HHhcc------chhHHHHHHHHHHHHHccccHHHHHHHHHhhhcccc
Confidence            98822      244433335556667889999999999998887754

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

Probab=99.30  E-value=8.2e-08  Score=90.56  Aligned_cols=388  Identities=12%  Similarity=0.005  Sum_probs=265.1

Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC--
Q 011236           57 LDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED--  134 (490)
Q Consensus        57 ~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--  134 (490)
                      ++++.......+...|..+.-++...|+++.+.+.|++....-+ -..+.+..+...+...|.-..|..+++......  
T Consensus       311 ~~k~r~~~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~-~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~  389 (799)
T KOG4162|consen  311 LRKLRLKKFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSF-GEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQ  389 (799)
T ss_pred             HHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhh-hhHHHHHHHHHHHHHhccchHHHHHHHhhcccccC
Confidence            44444556777899999999999999999999999999877653 456777888888889999999999999876665  


Q ss_pred             C-ChhHHHHHHHHHH-hcCChhHHHHHHHHHHhc--CC--CCCcchHHHHHHHHHhcC-----------CcCcHHHHHHH
Q 011236          135 K-VDKLYGALLNCYV-REGLVDESLSLMQKMKEM--GS--FGSALNYNGIMCLYTNTG-----------QHEKIPDVLLD  197 (490)
Q Consensus       135 p-~~~~~~~li~~~~-~~g~~~~a~~~~~~m~~~--~~--~p~~~~~~~l~~~~~~~~-----------~~~~a~~~~~~  197 (490)
                      | +...+-..-..|. +.+.+++++++-.+....  +.  ......|..+.-+|...-           ...++.+.+++
T Consensus       390 ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~  469 (799)
T KOG4162|consen  390 PSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEE  469 (799)
T ss_pred             CCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHH
Confidence            4 3334433334443 356677777766666551  11  113445555555554321           13466777888


Q ss_pred             HHHCCC-CCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC
Q 011236          198 MKENGV-PPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS  276 (490)
Q Consensus       198 m~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~  276 (490)
                      ..+.+. .|++..|  +.--|+..++++.|.+..++.. ..+...+...|..+.-.+...+++.+|+.+.+......+..
T Consensus       470 av~~d~~dp~~if~--lalq~A~~R~l~sAl~~~~eaL-~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N  546 (799)
T KOG4162|consen  470 AVQFDPTDPLVIFY--LALQYAEQRQLTSALDYAREAL-ALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDN  546 (799)
T ss_pred             HHhcCCCCchHHHH--HHHHHHHHHhHHHHHHHHHHHH-HhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhh
Confidence            877543 3433333  3444667789999999999998 77666888899999999999999999999998876543310


Q ss_pred             ------------------CChhhHHHHHHHHHh-----------------------cCChhHHHHHHHHH--------HH
Q 011236          277 ------------------KDALGYNHLISHYAS-----------------------LGNKDEMMKFWGLQ--------KI  307 (490)
Q Consensus       277 ------------------~~~~~~~~l~~~~~~-----------------------~~~~~~a~~~~~~~--------~~  307 (490)
                                        .-..|...++...-.                       ..+..++....+..        ..
T Consensus       547 ~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~  626 (799)
T KOG4162|consen  547 HVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKS  626 (799)
T ss_pred             hhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhh
Confidence                              001122222222210                       00111111111100        00


Q ss_pred             hc-----C------CCCh------hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHH
Q 011236          308 KC-----K------KQLN------RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADA  370 (490)
Q Consensus       308 ~~-----~------~~~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  370 (490)
                      .+     +      .|+.      ..|......+.+.+..++|...+.+..+. .+.....|......+...|..++|.+
T Consensus       627 ~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~-~~l~~~~~~~~G~~~~~~~~~~EA~~  705 (799)
T KOG4162|consen  627 AGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKI-DPLSASVYYLRGLLLEVKGQLEEAKE  705 (799)
T ss_pred             cccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhc-chhhHHHHHHhhHHHHHHHhhHHHHH
Confidence            00     0      1111      12445666777888888888888887765 45566677777788888999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHH--HHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHH
Q 011236          371 VLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFE--CMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVS  448 (490)
Q Consensus       371 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~--~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  448 (490)
                      .|......++. ++....++...+.+.|+...|..  ++.++++..|      -++..|..+...+.+.|+.++|...|.
T Consensus       706 af~~Al~ldP~-hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp------~n~eaW~~LG~v~k~~Gd~~~Aaecf~  778 (799)
T KOG4162|consen  706 AFLVALALDPD-HVPSMTALAELLLELGSPRLAEKRSLLSDALRLDP------LNHEAWYYLGEVFKKLGDSKQAAECFQ  778 (799)
T ss_pred             HHHHHHhcCCC-CcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCC------CCHHHHHHHHHHHHHccchHHHHHHHH
Confidence            99999887655 67788999999999999888877  9999998332      455899999999999999999999999


Q ss_pred             HHHhcccc
Q 011236          449 SLKIKVQK  456 (490)
Q Consensus       449 ~~~~~~~~  456 (490)
                      ......+.
T Consensus       779 aa~qLe~S  786 (799)
T KOG4162|consen  779 AALQLEES  786 (799)
T ss_pred             HHHhhccC
Confidence            87766544

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.28  E-value=6.3e-09  Score=92.92  Aligned_cols=127  Identities=18%  Similarity=-0.001  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSL  324 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  324 (490)
                      .|..+...|...|+.++|...|++..+..+  .+...|+.+...+...|++++|...|+......+ .+..++..+..++
T Consensus        66 ~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P--~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P-~~~~a~~~lg~~l  142 (296)
T PRK11189         66 LHYERGVLYDSLGLRALARNDFSQALALRP--DMADAYNYLGIYLTQAGNFDAAYEAFDSVLELDP-TYNYAYLNRGIAL  142 (296)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHcCC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHH
Confidence            344455555555555555555555555443  3455555555555555666666555555554433 3344455555555


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          325 VKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      ...|++++|.+.++...+.  .|+..........+...++.++|...|++..
T Consensus       143 ~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        143 YYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            5555666666555555553  2222111111112233445556655554433

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

Probab=99.26  E-value=7.2e-08  Score=89.54  Aligned_cols=311  Identities=10%  Similarity=-0.033  Sum_probs=155.5

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcch---HHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHH-
Q 011236          137 DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALN---YNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRI-  212 (490)
Q Consensus       137 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~---~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~-  212 (490)
                      ...|..+...+...|+.+.+...+........ ++...   .......+...|++++|.+++++..+.. +.|...+.. 
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~~   83 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALA-ARATERERAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALKLH   83 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHh
Confidence            33455555555556666665555555443321 12111   1122233445667777777776666542 123223331 


Q ss_pred             --HHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHH
Q 011236          213 --CINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYA  290 (490)
Q Consensus       213 --li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  290 (490)
                        ........+..+.+.+.++..  ....+........+...+...|++++|...+++.....+  .+...+..+...+.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~p--~~~~~~~~la~i~~  159 (355)
T cd05804          84 LGAFGLGDFSGMRDHVARVLPLW--APENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELNP--DDAWAVHAVAHVLE  159 (355)
T ss_pred             HHHHHhcccccCchhHHHHHhcc--CcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC--CCcHHHHHHHHHHH
Confidence              111111234444444444432  222223334444556667777777777777777776554  45566677777777


Q ss_pred             hcCChhHHHHHHHHHHHhcCC-CCh--hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC-CCchhH-H--HHHHHHHhcC
Q 011236          291 SLGNKDEMMKFWGLQKIKCKK-QLN--RDYITMLGSLVKIGELEEAEKMLEEWELSCYC-YDFRVP-N--IILLGYSQKG  363 (490)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~-~~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~-~--~l~~~~~~~g  363 (490)
                      ..|++++|...+++.....+. ++.  ..|..+...+...|++++|..++++....... +..... +  .++.-+...|
T Consensus       160 ~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g  239 (355)
T cd05804         160 MQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAG  239 (355)
T ss_pred             HcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcC
Confidence            777777777777766654431 221  23445666777778888887777776543211 111111 1  2223333344


Q ss_pred             CHHHHHHH--H-HHHHHcCC-CCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcC--cCCC-cchhhHHHHHHHHHc
Q 011236          364 MIEKADAV--L-KEIVKKGK-TPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEEN--KFWR-PKPSLVSSILDWLGD  436 (490)
Q Consensus       364 ~~~~A~~~--~-~~m~~~~~-~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~-p~~~~~~~l~~~~~~  436 (490)
                      ..+.+.+.  + ........ ............++...|+.+.|..+++.+.......  .+.. ...........++..
T Consensus       240 ~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~  319 (355)
T cd05804         240 HVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFA  319 (355)
T ss_pred             CCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHH
Confidence            33322222  1 11111100 0111222245566777888888888888776622110  0000 011122222234567


Q ss_pred             CCCHHHHHHHHHHHHhc
Q 011236          437 NRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~  453 (490)
                      .|++++|.+.+......
T Consensus       320 ~g~~~~A~~~L~~al~~  336 (355)
T cd05804         320 EGNYATALELLGPVRDD  336 (355)
T ss_pred             cCCHHHHHHHHHHHHHH
Confidence            88888888888776654

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.

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

Probab=99.26  E-value=1.4e-08  Score=81.90  Aligned_cols=202  Identities=13%  Similarity=-0.022  Sum_probs=152.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSL  324 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  324 (490)
                      +...|.-.|...|+...|..-+++..+..+  .+..+|..+...|.+.|+.+.|.+.|++.++..+ .+....|....-+
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~DP--s~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p-~~GdVLNNYG~FL  113 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHDP--SYYLAHLVRAHYYQKLGENDLADESYRKALSLAP-NNGDVLNNYGAFL  113 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCc--ccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCC-CccchhhhhhHHH
Confidence            344566778888888888888888887665  5677788888888888888888888887777765 5667777777778


Q ss_pred             HhcCCHHHHHHHHHHHHhcCC-CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHH
Q 011236          325 VKIGELEEAEKMLEEWELSCY-CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKA  403 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  403 (490)
                      |..|++++|.+.|++....-. ..-..+|..+.-+..+.|+.+.|...|++.++..+. ...+...+.....+.|++-.|
T Consensus       114 C~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~-~~~~~l~~a~~~~~~~~y~~A  192 (250)
T COG3063         114 CAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQ-FPPALLELARLHYKAGDYAPA  192 (250)
T ss_pred             HhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcC-CChHHHHHHHHHHhcccchHH
Confidence            888888888888888776522 122346777777777888888888888888887654 455677777888888888888


Q ss_pred             HHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          404 FECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..+++....      +..++..+....|+.-.+.|+.+.+-++=..+.+..|.
T Consensus       193 r~~~~~~~~------~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~  239 (250)
T COG3063         193 RLYLERYQQ------RGGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPY  239 (250)
T ss_pred             HHHHHHHHh------cccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            888888766      33377777777777777888888888777777777766

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.26  E-value=4.3e-08  Score=88.72  Aligned_cols=397  Identities=12%  Similarity=0.058  Sum_probs=206.9

Q ss_pred             hccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHH
Q 011236           43 ISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLES  122 (490)
Q Consensus        43 l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  122 (490)
                      ....|+.+.++....+.+ .-. ++|-..|..=..++.+.|++++|++=-.+-.+.. |.-+..|.....++...|++++
T Consensus        12 a~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   12 AFSSGDFETAIRLFTEAI-MLS-PTNHVLYSNRSAAYASLGSYEKALKDATKTRRLN-PDWAKGYSRKGAALFGLGDYEE   88 (539)
T ss_pred             hcccccHHHHHHHHHHHH-ccC-CCccchhcchHHHHHHHhhHHHHHHHHHHHHhcC-CchhhHHHHhHHHHHhcccHHH
Confidence            344566666666333332 121 2255556666666777777777766666655555 3455666666666667777777


Q ss_pred             HHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHH---HHHHHHHHhc---CCCCCcchHHHHHHHHHhcC-------Cc
Q 011236          123 AETYFNSLNDEDK-VDKLYGALLNCYVREGLVDES---LSLMQKMKEM---GSFGSALNYNGIMCLYTNTG-------QH  188 (490)
Q Consensus       123 A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a---~~~~~~m~~~---~~~p~~~~~~~l~~~~~~~~-------~~  188 (490)
                      |+.-|.+-.+.+| |...++-+..++.......+.   -.++......   ........|..++..+-+.-       +.
T Consensus        89 A~~ay~~GL~~d~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~~l~d  168 (539)
T KOG0548|consen   89 AILAYSEGLEKDPSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKLYLND  168 (539)
T ss_pred             HHHHHHHHhhcCCchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhccccc
Confidence            7777777666666 455566666655111000000   0000000000   00000111222221111100       00


Q ss_pred             CcHHHHHHHHH--------HCC-------CCC------------C----------HHHHHHHHHHHhccCChHHHHHHHH
Q 011236          189 EKIPDVLLDMK--------ENG-------VPP------------D----------NFSYRICINSYGARSELSSMENVLQ  231 (490)
Q Consensus       189 ~~a~~~~~~m~--------~~~-------~~p------------~----------~~~~~~li~~~~~~g~~~~a~~~~~  231 (490)
                      +...+..-.+.        ..|       ..|            |          ..-...+.++..+..+++.|++-+.
T Consensus       169 ~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~q~y~  248 (539)
T KOG0548|consen  169 PRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAIQHYA  248 (539)
T ss_pred             HHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHH
Confidence            00000000000        000       001            0          0113345555556666777777766


Q ss_pred             HHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHH-------HHHHHhcCChhHHHHHHHH
Q 011236          232 EMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHL-------ISHYASLGNKDEMMKFWGL  304 (490)
Q Consensus       232 ~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~~~~~~a~~~~~~  304 (490)
                      ... +..  .+..-++....+|...|.+.++...-+...+.|.  ....-|+.+       ..+|.+.++++.+...|.+
T Consensus       249 ~a~-el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gr--e~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~k  323 (539)
T KOG0548|consen  249 KAL-ELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGR--ELRADYKLIAKALARLGNAYTKREDYEGAIKYYQK  323 (539)
T ss_pred             HHH-hHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhH--HHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHH
Confidence            665 333  4444555566667777776666665555444443  122223222       2344445666677777766


Q ss_pred             HHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCch-hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011236          305 QKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFR-VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT  383 (490)
Q Consensus       305 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~  383 (490)
                      .......|+..         .+....+++........-.  .|... -...-...+.+.|++..|...|.++++..+. |
T Consensus       324 aLte~Rt~~~l---------s~lk~~Ek~~k~~e~~a~~--~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~P~-D  391 (539)
T KOG0548|consen  324 ALTEHRTPDLL---------SKLKEAEKALKEAERKAYI--NPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRDPE-D  391 (539)
T ss_pred             HhhhhcCHHHH---------HHHHHHHHHHHHHHHHHhh--ChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCc-h
Confidence            55554443321         1223333333333332222  22211 1112245577888999999999999888755 8


Q ss_pred             HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhH
Q 011236          384 PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYH  461 (490)
Q Consensus       384 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~  461 (490)
                      ...|....-+|.+.|.+..|+.-.+..+++       .|+. ..|.-=..++....+++.|.+.|.+..+..|. ...-.
T Consensus       392 a~lYsNRAac~~kL~~~~~aL~Da~~~ieL-------~p~~~kgy~RKg~al~~mk~ydkAleay~eale~dp~~~e~~~  464 (539)
T KOG0548|consen  392 ARLYSNRAACYLKLGEYPEALKDAKKCIEL-------DPNFIKAYLRKGAALRAMKEYDKALEAYQEALELDPSNAEAID  464 (539)
T ss_pred             hHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-------CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchhHHHHH
Confidence            888999999999999999999888888872       3443 44544455566667888999999998888887 43333


Q ss_pred             HHHHH
Q 011236          462 ALTEA  466 (490)
Q Consensus       462 ~l~~~  466 (490)
                      .+.++
T Consensus       465 ~~~rc  469 (539)
T KOG0548|consen  465 GYRRC  469 (539)
T ss_pred             HHHHH
Confidence            33333

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.25  E-value=5.4e-09  Score=97.43  Aligned_cols=241  Identities=18%  Similarity=0.115  Sum_probs=179.5

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhh-----ccCCChhh-HHHHHHHHHhcCChhHHHHHHHHHHHhcC-----
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIV-----SKSKDALG-YNHLISHYASLGNKDEMMKFWGLQKIKCK-----  310 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~-~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----  310 (490)
                      -..+...+...|...|++++|+.+++...+..     ...|...+ .+.+...|...+++++|..+|+++.....     
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            35666679999999999999999999877651     11134333 34477788999999999999998875422     


Q ss_pred             -CCC-hhhHHHHHHHHHhcCCHHHHHHHHHHHHhc-----C-CCCCch-hHHHHHHHHHhcCCHHHHHHHHHHHHHc---
Q 011236          311 -KQL-NRDYITMLGSLVKIGELEEAEKMLEEWELS-----C-YCYDFR-VPNIILLGYSQKGMIEKADAVLKEIVKK---  378 (490)
Q Consensus       311 -~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~m~~~---  378 (490)
                       .|. ..+++.|..+|.+.|++++|...++...+-     | ..|.+. .++.+...|+..+++++|..++++..+.   
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             222 245778888999999999999988876542     1 122222 3566777789999999999999877542   


Q ss_pred             CCCCC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCC-Ccc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          379 GKTPT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFW-RPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       379 ~~~p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      -+.++    ..+++.|...|...|++++|.+++++++....+..|- .+. ...++.+...|.+.++.++|.++|.+...
T Consensus       358 ~~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~  437 (508)
T KOG1840|consen  358 APGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKD  437 (508)
T ss_pred             hccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHH
Confidence            12222    3579999999999999999999999999865433332 233 35678888899999999999988875433


Q ss_pred             ----cccc----hhhhHHHHHHHHhcC--CcHHHHHHHHH
Q 011236          453 ----KVQK----RNMYHALTEAHIRSG--QEVDGLLESMK  482 (490)
Q Consensus       453 ----~~~~----~~~~~~l~~~~~~~g--~~a~~~~~~m~  482 (490)
                          .||.    ..+|..|...|.+.|  +.|.++.+...
T Consensus       438 i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  438 IMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence                3444    678999999999999  88888877664

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.25  E-value=4.1e-08  Score=85.84  Aligned_cols=311  Identities=13%  Similarity=0.011  Sum_probs=216.8

Q ss_pred             HHHhCCCCCChhhHHHHHHHHHhh--cCHHHHHHHHH--HccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCC
Q 011236           94 WMSGQGLAFSVHDHAVQLDLIGKV--RGLESAETYFN--SLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGS  168 (490)
Q Consensus        94 ~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~A~~~~~--~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~  168 (490)
                      .|-....++...+....+.+++.+  ++...|...+-  +....-| |+.....+...+...|+.++|+..|+.....++
T Consensus       184 ~m~~~~~~~~~dwls~wika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dp  263 (564)
T KOG1174|consen  184 VMHAATVPDHFDWLSKWIKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCANP  263 (564)
T ss_pred             hhhheecCCCccHHHHHHHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhCCh
Confidence            344444455555555555555543  44444444443  3333335 688888999999999999999999998877632


Q ss_pred             CCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHH
Q 011236          169 FGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYST  248 (490)
Q Consensus       169 ~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~  248 (490)
                      - ++.....-.-.+.+.|+.+....+...+.... .-+...|-.-+......+++..|+.+-++.+ +.+. -+...|-.
T Consensus       264 y-~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I-~~~~-r~~~alil  339 (564)
T KOG1174|consen  264 D-NVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCI-DSEP-RNHEALIL  339 (564)
T ss_pred             h-hhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHh-ccCc-ccchHHHh
Confidence            1 22222222333457788888888877776532 1223333333444556788999999988887 6554 55666655


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH-HHHH-h
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML-GSLV-K  326 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~-~~~~-~  326 (490)
                      -...+...++.++|.=.|+......+  .+...|..|+.+|...|++.+|.-.-+.....-+ .+..+...+. ..|. .
T Consensus       340 KG~lL~~~~R~~~A~IaFR~Aq~Lap--~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~~-~sA~~LtL~g~~V~~~d  416 (564)
T KOG1174|consen  340 KGRLLIALERHTQAVIAFRTAQMLAP--YRLEIYRGLFHSYLAQKRFKEANALANWTIRLFQ-NSARSLTLFGTLVLFPD  416 (564)
T ss_pred             ccHHHHhccchHHHHHHHHHHHhcch--hhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHhh-cchhhhhhhcceeeccC
Confidence            66778889999999999998877665  5788899999999999999999888776666544 5566666553 3333 2


Q ss_pred             cCCHHHHHHHHHHHHhcCCCCC-chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHH
Q 011236          327 IGELEEAEKMLEEWELSCYCYD-FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       327 ~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      ..--++|..+++...+.  .|+ ....+.+...+...|+.+.+..++++-...  .||....+.|.+.+...+.+++|++
T Consensus       417 p~~rEKAKkf~ek~L~~--~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~L~~--~~D~~LH~~Lgd~~~A~Ne~Q~am~  492 (564)
T KOG1174|consen  417 PRMREKAKKFAEKSLKI--NPIYTPAVNLIAELCQVEGPTKDIIKLLEKHLII--FPDVNLHNHLGDIMRAQNEPQKAME  492 (564)
T ss_pred             chhHHHHHHHHHhhhcc--CCccHHHHHHHHHHHHhhCccchHHHHHHHHHhh--ccccHHHHHHHHHHHHhhhHHHHHH
Confidence            33457788888887764  444 335567777888899999999999888764  5789999999999999999999999


Q ss_pred             HHHHHHHhhh
Q 011236          406 CMKEALAVHE  415 (490)
Q Consensus       406 ~~~~~~~~~~  415 (490)
                      .|..++..+|
T Consensus       493 ~y~~ALr~dP  502 (564)
T KOG1174|consen  493 YYYKALRQDP  502 (564)
T ss_pred             HHHHHHhcCc
Confidence            9988888665

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.25  E-value=8.3e-09  Score=92.17  Aligned_cols=219  Identities=13%  Similarity=0.050  Sum_probs=116.6

Q ss_pred             CChhHHHHHHHHHHhCCC---CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHH
Q 011236           83 KRFKHALQVSEWMSGQGL---AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLS  158 (490)
Q Consensus        83 ~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~  158 (490)
                      +..+.++.-+.+++....   ......+......+...|+.++|...|+......| +..+|+.+...+...|++++|..
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~  119 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYE  119 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            344555666666654331   11123355555566666777777777777666666 46667777777777777777777


Q ss_pred             HHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCC
Q 011236          159 LMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSH  238 (490)
Q Consensus       159 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  238 (490)
                      .|++..+..+. +..+|..+..++...|++++|.+.|+...+..  |+..........+...+++++|...|++.. ...
T Consensus       120 ~~~~Al~l~P~-~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~~--P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~-~~~  195 (296)
T PRK11189        120 AFDSVLELDPT-YNYAYLNRGIALYYGGRYELAQDDLLAFYQDD--PNDPYRALWLYLAESKLDPKQAKENLKQRY-EKL  195 (296)
T ss_pred             HHHHHHHhCCC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHccCCHHHHHHHHHHHH-hhC
Confidence            77777665433 45566666666666777777777777766542  332211112222334556777777775543 221


Q ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC-----CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC
Q 011236          239 ISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS-----KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK  310 (490)
Q Consensus       239 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  310 (490)
                      . ++...+   .......|+.+.+ ..+..+.......     ....+|..+...+.+.|++++|...|++.....+
T Consensus       196 ~-~~~~~~---~~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~  267 (296)
T PRK11189        196 D-KEQWGW---NIVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNV  267 (296)
T ss_pred             C-ccccHH---HHHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            1 221111   1222234444333 2333332211000     1234566666666677777777777766665543

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

Probab=99.24  E-value=1.3e-08  Score=82.08  Aligned_cols=200  Identities=10%  Similarity=0.010  Sum_probs=154.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHh
Q 011236          139 LYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYG  218 (490)
Q Consensus       139 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  218 (490)
                      +..-|.-.|.+.|+...|..-+++..+..+. +..+|..+...|.+.|+.+.|.+-|+...+... -+..+.|.....+|
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~DPs-~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p-~~GdVLNNYG~FLC  114 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHDPS-YYLAHLVRAHYYQKLGENDLADESYRKALSLAP-NNGDVLNNYGAFLC  114 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCC-CccchhhhhhHHHH
Confidence            3556677788888888888888888887554 666788888888888888888888888877532 25567777777788


Q ss_pred             ccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHH
Q 011236          219 ARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEM  298 (490)
Q Consensus       219 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  298 (490)
                      ..|++++|...|++.........-..+|..+.-|..+.|+.+.|...|++..+..+  ....+...+.....+.|++-.|
T Consensus       115 ~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp--~~~~~~l~~a~~~~~~~~y~~A  192 (250)
T COG3063         115 AQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDP--QFPPALLELARLHYKAGDYAPA  192 (250)
T ss_pred             hCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCc--CCChHHHHHHHHHHhcccchHH
Confidence            88888888888888775555545566777788888888888888888888877665  4556677888888888888888


Q ss_pred             HHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 011236          299 MKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELS  343 (490)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  343 (490)
                      ..+++.....++ ++..+.-..|+.-...|+.+.+.+.=..+.+.
T Consensus       193 r~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~  236 (250)
T COG3063         193 RLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL  236 (250)
T ss_pred             HHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence            888887777666 77788877888888888888777776666654

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

Probab=99.22  E-value=1.1e-07  Score=88.20  Aligned_cols=199  Identities=13%  Similarity=0.080  Sum_probs=95.8

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh--hhHHHHHHHH
Q 011236          212 ICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA--LGYNHLISHY  289 (490)
Q Consensus       212 ~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--~~~~~l~~~~  289 (490)
                      .+...+...|++++|...+++.. +... .+...+..+..++...|++++|...+++.....+..++.  ..|..+...+
T Consensus       119 ~~a~~~~~~G~~~~A~~~~~~al-~~~p-~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~  196 (355)
T cd05804         119 MLAFGLEEAGQYDRAEEAARRAL-ELNP-DDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFY  196 (355)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHH-hhCC-CCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHH
Confidence            34445555666666666666665 4332 334455555666666666666666666555433210111  2233455556


Q ss_pred             HhcCChhHHHHHHHHHHHhcCC-CChhhH-H--HHHHHHHhcCCHHHHHHH--HHHHHhcCCCCCchhH--HHHHHHHHh
Q 011236          290 ASLGNKDEMMKFWGLQKIKCKK-QLNRDY-I--TMLGSLVKIGELEEAEKM--LEEWELSCYCYDFRVP--NIILLGYSQ  361 (490)
Q Consensus       290 ~~~~~~~~a~~~~~~~~~~~~~-~~~~~~-~--~l~~~~~~~~~~~~a~~~--~~~~~~~~~~~~~~~~--~~l~~~~~~  361 (490)
                      ...|++++|..++++.....+. +..... +  .++.-+...|....+.+.  +........+.....+  .....++..
T Consensus       197 ~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~  276 (355)
T cd05804         197 LERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAG  276 (355)
T ss_pred             HHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhc
Confidence            6666666666666654322210 111111 1  122222223322222222  1111111011111112  245556677


Q ss_pred             cCCHHHHHHHHHHHHHcCCCC--------CHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          362 KGMIEKADAVLKEIVKKGKTP--------TPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~~~~p--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .|+.+.|..+++.+......+        .....-....++...|+.++|.+.+..++.
T Consensus       277 ~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~  335 (355)
T cd05804         277 AGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRD  335 (355)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            788888888887776532110        111222223345678899999998888877

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.

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.21  E-value=5.4e-08  Score=83.40  Aligned_cols=364  Identities=11%  Similarity=0.006  Sum_probs=211.2

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC-------------CChhH----
Q 011236           77 RQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED-------------KVDKL----  139 (490)
Q Consensus        77 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-------------p~~~~----  139 (490)
                      ..+-..|++++|+..+..+.... .++......+..+..-.|.+.+|..+-...++..             -|..-    
T Consensus        65 ~C~fhLgdY~~Al~~Y~~~~~~~-~~~~el~vnLAcc~FyLg~Y~eA~~~~~ka~k~pL~~RLlfhlahklndEk~~~~f  143 (557)
T KOG3785|consen   65 HCYFHLGDYEEALNVYTFLMNKD-DAPAELGVNLACCKFYLGQYIEAKSIAEKAPKTPLCIRLLFHLAHKLNDEKRILTF  143 (557)
T ss_pred             HHHHhhccHHHHHHHHHHHhccC-CCCcccchhHHHHHHHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCcHHHHHHH
Confidence            44457799999999999888765 4555666666666667788888888766654321             01110    


Q ss_pred             ----------HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHH-HHHHhcCCcCcHHHHHHHHHHCCCCCCHH
Q 011236          140 ----------YGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIM-CLYTNTGQHEKIPDVLLDMKENGVPPDNF  208 (490)
Q Consensus       140 ----------~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~-~~~~~~~~~~~a~~~~~~m~~~~~~p~~~  208 (490)
                                --+|.....-.-.+.+|++++.+....+  |+-...|.-+ -+|.+..-++-+.+++.-..+. ++.++.
T Consensus       144 h~~LqD~~EdqLSLAsvhYmR~HYQeAIdvYkrvL~dn--~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q-~pdSti  220 (557)
T KOG3785|consen  144 HSSLQDTLEDQLSLASVHYMRMHYQEAIDVYKRVLQDN--PEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ-FPDSTI  220 (557)
T ss_pred             HHHHhhhHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcC--hhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh-CCCcHH
Confidence                      1112222222334667777777776653  3444444433 3456667777777777776653 333334


Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHh-------------CCCC------------CCC-----HHHHHHHHHHHHHcCC
Q 011236          209 SYRICINSYGARSELSSMENVLQEMES-------------QSHI------------SMD-----WGTYSTVANYYIIAGL  258 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~-------------~~~~------------~~~-----~~~~~~li~~~~~~~~  258 (490)
                      ..|.......+.=+-..|+.-...+..             +.++            -|.     +.+--.|+-.|.+.++
T Consensus       221 A~NLkacn~fRl~ngr~ae~E~k~ladN~~~~~~f~~~l~rHNLVvFrngEgALqVLP~L~~~IPEARlNL~iYyL~q~d  300 (557)
T KOG3785|consen  221 AKNLKACNLFRLINGRTAEDEKKELADNIDQEYPFIEYLCRHNLVVFRNGEGALQVLPSLMKHIPEARLNLIIYYLNQND  300 (557)
T ss_pred             HHHHHHHHHhhhhccchhHHHHHHHHhcccccchhHHHHHHcCeEEEeCCccHHHhchHHHhhChHhhhhheeeeccccc
Confidence            444433332221111111111111110             1110            011     1222235566888999


Q ss_pred             HHHHHHHHHHHhhhhccCCChhhHHHH-----HHHHHhcCChhHHHHHHHHHHHhcC-CCChhhHHHHHHHHHhcCCHHH
Q 011236          259 KEKAIIYLKKCEDIVSKSKDALGYNHL-----ISHYASLGNKDEMMKFWGLQKIKCK-KQLNRDYITMLGSLVKIGELEE  332 (490)
Q Consensus       259 ~~~a~~~~~~~~~~~~~~~~~~~~~~l-----~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  332 (490)
                      +.+|..+.+++..   ..|-......+     .+-........-|.+.|...-.... ..+...-.++..++.-..++++
T Consensus       301 VqeA~~L~Kdl~P---ttP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFdd  377 (557)
T KOG3785|consen  301 VQEAISLCKDLDP---TTPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDD  377 (557)
T ss_pred             HHHHHHHHhhcCC---CChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHH
Confidence            9999998887532   11222222222     2212222345567777763322222 2222334566677777788899


Q ss_pred             HHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH-HHHHHhccCCHHHHHHHHHHHH
Q 011236          333 AEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSI-IAAGYADKNNMEKAFECMKEAL  411 (490)
Q Consensus       333 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~-l~~~~~~~~~~~~a~~~~~~~~  411 (490)
                      +...+..+..-=...|...+| +..+++..|.+.+|.++|-.+....++ |..+|.+ |.++|.+.+.++.|+.++-++-
T Consensus       378 Vl~YlnSi~sYF~NdD~Fn~N-~AQAk~atgny~eaEelf~~is~~~ik-n~~~Y~s~LArCyi~nkkP~lAW~~~lk~~  455 (557)
T KOG3785|consen  378 VLTYLNSIESYFTNDDDFNLN-LAQAKLATGNYVEAEELFIRISGPEIK-NKILYKSMLARCYIRNKKPQLAWDMMLKTN  455 (557)
T ss_pred             HHHHHHHHHHHhcCcchhhhH-HHHHHHHhcChHHHHHHHhhhcChhhh-hhHHHHHHHHHHHHhcCCchHHHHHHHhcC
Confidence            998888887763344444444 789999999999999999887766555 6666654 5578889999999988776643


Q ss_pred             HhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccch
Q 011236          412 AVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKR  457 (490)
Q Consensus       412 ~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  457 (490)
                      .        ..+. .....+...|.+.+.+=-|-+.|+.+...+|.+
T Consensus       456 t--------~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~p  494 (557)
T KOG3785|consen  456 T--------PSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTP  494 (557)
T ss_pred             C--------chhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCc
Confidence            3        1222 334455567888888888888888888777663

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.18  E-value=8.2e-08  Score=80.37  Aligned_cols=394  Identities=14%  Similarity=0.030  Sum_probs=213.7

Q ss_pred             cccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHH-HHHHH
Q 011236           36 RNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAV-QLDLI  114 (490)
Q Consensus        36 ~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~~  114 (490)
                      +.+.+-.+.+..+..+++. ++....++ .+.+...++.|...|-...++..|-+.++++...-  |...-|.. -...+
T Consensus        13 ftaviy~lI~d~ry~DaI~-~l~s~~Er-~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~--P~~~qYrlY~AQSL   88 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQ-LLGSELER-SPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLH--PELEQYRLYQAQSL   88 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHH-HHHHHHhc-CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--hHHHHHHHHHHHHH
Confidence            4455555555555555444 33222222 12255555666666666666666666666665543  22222222 23445


Q ss_pred             HhhcCHHHHHHHHHHccccCCChhHHHHH--HH--HHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCc
Q 011236          115 GKVRGLESAETYFNSLNDEDKVDKLYGAL--LN--CYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEK  190 (490)
Q Consensus       115 ~~~~~~~~A~~~~~~~~~~~p~~~~~~~l--i~--~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  190 (490)
                      .+.+.+.+|+++...|... ++  ..+..  +.  .....+++..+..++++....|   +..+.+.......+.|+++.
T Consensus        89 Y~A~i~ADALrV~~~~~D~-~~--L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegqyEa  162 (459)
T KOG4340|consen   89 YKACIYADALRVAFLLLDN-PA--LHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQYEA  162 (459)
T ss_pred             HHhcccHHHHHHHHHhcCC-HH--HHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccccHHH
Confidence            5566666666666655542 11  11111  11  1223555666666666555322   44455555555568889999


Q ss_pred             HHHHHHHHHHC-CCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCC-------------CCH-------------
Q 011236          191 IPDVLLDMKEN-GVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHIS-------------MDW-------------  243 (490)
Q Consensus       191 a~~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-------------~~~-------------  243 (490)
                      |.+-|+...+- |.. ....|+..+ ++.+.|+.+.|++...++. ++|++             ||+             
T Consensus       163 AvqkFqaAlqvsGyq-pllAYniAL-aHy~~~qyasALk~iSEIi-eRG~r~HPElgIGm~tegiDvrsvgNt~~lh~Sa  239 (459)
T KOG4340|consen  163 AVQKFQAALQVSGYQ-PLLAYNLAL-AHYSSRQYASALKHISEII-ERGIRQHPELGIGMTTEGIDVRSVGNTLVLHQSA  239 (459)
T ss_pred             HHHHHHHHHhhcCCC-chhHHHHHH-HHHhhhhHHHHHHHHHHHH-HhhhhcCCccCccceeccCchhcccchHHHHHHH
Confidence            99999988774 454 445676544 4556788999998888887 44432             121             


Q ss_pred             --HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          244 --GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       244 --~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                        ..+|.-...+.+.++++.|.+.+..|........|++|...+.-.- ..+++.+..+-+.-+....+ -...||..++
T Consensus       240 l~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~nP-fP~ETFANlL  317 (459)
T KOG4340|consen  240 LVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQNP-FPPETFANLL  317 (459)
T ss_pred             HHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcCC-CChHHHHHHH
Confidence              1222223345677889999988888865444336777776654432 24555566666665666555 5667888899


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCC-CCchhHHHHHHHHH-hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYC-YDFRVPNIILLGYS-QKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~-~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      -.||+..-++.|-.++.+-...... .+...|+ |++++. ..-..++|.+-++.+...- .-......+-++--...++
T Consensus       318 llyCKNeyf~lAADvLAEn~~lTyk~L~~Yly~-LLdaLIt~qT~pEea~KKL~~La~~l-~~kLRklAi~vQe~r~~~d  395 (459)
T KOG4340|consen  318 LLYCKNEYFDLAADVLAENAHLTYKFLTPYLYD-LLDALITCQTAPEEAFKKLDGLAGML-TEKLRKLAIQVQEARHNRD  395 (459)
T ss_pred             HHHhhhHHHhHHHHHHhhCcchhHHHhhHHHHH-HHHHHHhCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhccc
Confidence            9999998888888887763322111 1233343 334433 3445677776665554320 0000111111111111222


Q ss_pred             ---HHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          400 ---MEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       400 ---~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                         ...+++-+++.++         .-..+...-.+.+++..|+..++++|+.-.+-..
T Consensus       396 d~a~R~ai~~Yd~~LE---------~YLPVlMa~AkiyW~~~Dy~~vEk~Fr~SvefC~  445 (459)
T KOG4340|consen  396 DEAIRKAVNEYDETLE---------KYLPVLMAQAKIYWNLEDYPMVEKIFRKSVEFCN  445 (459)
T ss_pred             HHHHHHHHHHHHHHHH---------HHHHHHHHHHHhhccccccHHHHHHHHHHHhhhc
Confidence               2223333333333         1112233334566788899999999987665443

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

Probab=99.11  E-value=2.5e-09  Score=94.00  Aligned_cols=253  Identities=18%  Similarity=0.102  Sum_probs=135.1

Q ss_pred             HHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHH
Q 011236          182 YTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEK  261 (490)
Q Consensus       182 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~  261 (490)
                      +.-.|++..++.-.+ ........+......+.+++...|+.+.   ++.++. ... .|.......+...+...++-+.
T Consensus        11 ~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~---vl~ei~-~~~-~~~l~av~~la~y~~~~~~~e~   84 (290)
T PF04733_consen   11 QFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDS---VLSEIK-KSS-SPELQAVRLLAEYLSSPSDKES   84 (290)
T ss_dssp             HHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHH---HHHHS--TTS-SCCCHHHHHHHHHHCTSTTHHC
T ss_pred             HHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhH---HHHHhc-cCC-ChhHHHHHHHHHHHhCccchHH
Confidence            334566666664444 2221111223344455666777776654   334443 222 4555555444444433344455


Q ss_pred             HHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          262 AIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWE  341 (490)
Q Consensus       262 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  341 (490)
                      ++.-+++.........+..........+...|++++|++++...      .+.......+..|.+.++++.|.+.++.|.
T Consensus        85 ~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~  158 (290)
T PF04733_consen   85 ALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNMQ  158 (290)
T ss_dssp             HHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            55555443332221022222233334455667777777776521      344556666777777777777777777776


Q ss_pred             hcCCCCCchhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcC
Q 011236          342 LSCYCYDFRVPNIILLGYSQ----KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEEN  417 (490)
Q Consensus       342 ~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  417 (490)
                      +.  ..| .+...+..++..    .+.+.+|..+|+++.+. ..+++.+.+.+..++...|++++|.+++++++...   
T Consensus       159 ~~--~eD-~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~---  231 (290)
T PF04733_consen  159 QI--DED-SILTQLAEAWVNLATGGEKYQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKD---  231 (290)
T ss_dssp             CC--SCC-HHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC----
T ss_pred             hc--CCc-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhc---
Confidence            64  223 233334444332    23577777777776654 34567777777777777777777777777776511   


Q ss_pred             cCCCcchhhHHHHHHHHHcCCCH-HHHHHHHHHHHhcccc
Q 011236          418 KFWRPKPSLVSSILDWLGDNRDV-EEVEAFVSSLKIKVQK  456 (490)
Q Consensus       418 ~~~~p~~~~~~~l~~~~~~~g~~-~~a~~~~~~~~~~~~~  456 (490)
                         .-++.+...++-+....|+. +.+.+++.++....|.
T Consensus       232 ---~~~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~~p~  268 (290)
T PF04733_consen  232 ---PNDPDTLANLIVCSLHLGKPTEAAERYLSQLKQSNPN  268 (290)
T ss_dssp             ---CCHHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHHTTT
T ss_pred             ---cCCHHHHHHHHHHHHHhCCChhHHHHHHHHHHHhCCC
Confidence               12345666666666666666 5666777777766654

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.09  E-value=1.3e-06  Score=91.80  Aligned_cols=343  Identities=11%  Similarity=-0.023  Sum_probs=218.1

Q ss_pred             HHHhhcCHHHHHHHHHHccccC--CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCC------CCCc--chHHHHHHHH
Q 011236          113 LIGKVRGLESAETYFNSLNDED--KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGS------FGSA--LNYNGIMCLY  182 (490)
Q Consensus       113 ~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~------~p~~--~~~~~l~~~~  182 (490)
                      .....|+++.+..+++.++...  .+..........+...|++++|..++......--      .|..  .....+...+
T Consensus       383 ~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~  462 (903)
T PRK04841        383 SLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVA  462 (903)
T ss_pred             HHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHH
Confidence            3445677787778877764321  1222233445555678999999999988754311      1111  1122233455


Q ss_pred             HhcCCcCcHHHHHHHHHHCCCCCCH----HHHHHHHHHHhccCChHHHHHHHHHHHh---CCCC-CCCHHHHHHHHHHHH
Q 011236          183 TNTGQHEKIPDVLLDMKENGVPPDN----FSYRICINSYGARSELSSMENVLQEMES---QSHI-SMDWGTYSTVANYYI  254 (490)
Q Consensus       183 ~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~-~~~~~~~~~li~~~~  254 (490)
                      ...|++++|...+++..+.-...+.    ...+.+...+...|++++|...+++...   ..+. .....++..+...+.
T Consensus       463 ~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~  542 (903)
T PRK04841        463 INDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILF  542 (903)
T ss_pred             HhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHH
Confidence            6789999999999988763111121    2345566677889999999999888762   1121 111234556777889


Q ss_pred             HcCCHHHHHHHHHHHhhhhccC--C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC--CC--ChhhHHHHHHHH
Q 011236          255 IAGLKEKAIIYLKKCEDIVSKS--K----DALGYNHLISHYASLGNKDEMMKFWGLQKIKCK--KQ--LNRDYITMLGSL  324 (490)
Q Consensus       255 ~~~~~~~a~~~~~~~~~~~~~~--~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~--~~~~~~~l~~~~  324 (490)
                      ..|++++|...+++........  +    ....+..+...+...|++++|...+.+......  .+  ....+..+...+
T Consensus       543 ~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~  622 (903)
T PRK04841        543 AQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKIS  622 (903)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHH
Confidence            9999999999988865532110  1    123344556667778999999999887655322  11  223445566777


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCC-chhH-----HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHh
Q 011236          325 VKIGELEEAEKMLEEWELSCYCYD-FRVP-----NIILLGYSQKGMIEKADAVLKEIVKKGKTPTP---NSWSIIAAGYA  395 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~~~~~-~~~~-----~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~---~~~~~l~~~~~  395 (490)
                      ...|+.++|.+.+........... ...+     ...+..+...|+.+.|...+............   ..+..+..++.
T Consensus       623 ~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~  702 (903)
T PRK04841        623 LARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQI  702 (903)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHH
Confidence            889999999999988755311111 1111     11224455689999999988775542211111   12456677888


Q ss_pred             ccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          396 DKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       396 ~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..|++++|...++++..... ..|..++. .+...+..++.+.|+.++|...+.++.+....
T Consensus       703 ~~g~~~~A~~~l~~al~~~~-~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la~~  763 (903)
T PRK04841        703 LLGQFDEAEIILEELNENAR-SLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLANR  763 (903)
T ss_pred             HcCCHHHHHHHHHHHHHHHH-HhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCc
Confidence            99999999999999887432 12333322 45667777889999999999999998876544

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.09  E-value=1.2e-06  Score=75.16  Aligned_cols=316  Identities=10%  Similarity=0.022  Sum_probs=184.9

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhH-HHHHHHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKL-YGALLNC  146 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~-~~~li~~  146 (490)
                      ++.-.-.+-+.+...|.+..|+.-|...++.+ +.+-.++..-...|...|+-.-|+.=|+...+..||-.. --.-...
T Consensus        37 dvekhlElGk~lla~~Q~sDALt~yHaAve~d-p~~Y~aifrRaT~yLAmGksk~al~Dl~rVlelKpDF~~ARiQRg~v  115 (504)
T KOG0624|consen   37 DVEKHLELGKELLARGQLSDALTHYHAAVEGD-PNNYQAIFRRATVYLAMGKSKAALQDLSRVLELKPDFMAARIQRGVV  115 (504)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCC-chhHHHHHHHHHHHhhhcCCccchhhHHHHHhcCccHHHHHHHhchh
Confidence            33334445555666666666666666665543 112222222234555556666666666666655555211 1112234


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHH
Q 011236          147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSM  226 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  226 (490)
                      +.+.|.+++|..=|+.......  +..+   ...+..+.-       ..+++         ......+..+...|+...|
T Consensus       116 llK~Gele~A~~DF~~vl~~~~--s~~~---~~eaqskl~-------~~~e~---------~~l~~ql~s~~~~GD~~~a  174 (504)
T KOG0624|consen  116 LLKQGELEQAEADFDQVLQHEP--SNGL---VLEAQSKLA-------LIQEH---------WVLVQQLKSASGSGDCQNA  174 (504)
T ss_pred             hhhcccHHHHHHHHHHHHhcCC--Ccch---hHHHHHHHH-------hHHHH---------HHHHHHHHHHhcCCchhhH
Confidence            5566666666666666655422  1111   000100000       00000         1112233445567777788


Q ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 011236          227 ENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQK  306 (490)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  306 (490)
                      +.....+. +..+ -|...|..-..+|...|++..|+.=++...+...  .+..++--+-..+...|+.+.++...++.+
T Consensus       175 i~~i~~ll-Ei~~-Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs~--DnTe~~ykis~L~Y~vgd~~~sL~~iRECL  250 (504)
T KOG0624|consen  175 IEMITHLL-EIQP-WDASLRQARAKCYIAEGEPKKAIHDLKQASKLSQ--DNTEGHYKISQLLYTVGDAENSLKEIRECL  250 (504)
T ss_pred             HHHHHHHH-hcCc-chhHHHHHHHHHHHhcCcHHHHHHHHHHHHhccc--cchHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            88777777 4444 5666777777788888888888777766655443  456666666777777787777777777666


Q ss_pred             HhcCCCChhh----HHH---H------HHHHHhcCCHHHHHHHHHHHHhcCCCCCc---hhHHHHHHHHHhcCCHHHHHH
Q 011236          307 IKCKKQLNRD----YIT---M------LGSLVKIGELEEAEKMLEEWELSCYCYDF---RVPNIILLGYSQKGMIEKADA  370 (490)
Q Consensus       307 ~~~~~~~~~~----~~~---l------~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~  370 (490)
                      ...+  +...    |..   +      +......++|.++.+-.+...+.......   ..+..+..+|...|++.+|++
T Consensus       251 Kldp--dHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiq  328 (504)
T KOG0624|consen  251 KLDP--DHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQ  328 (504)
T ss_pred             ccCc--chhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHH
Confidence            5443  3221    111   1      12234456777777777777765433222   234456677778899999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          371 VLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       371 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...+.++..+. |+.++.--..+|.-...++.|+.-|+.+.+
T Consensus       329 qC~evL~~d~~-dv~~l~dRAeA~l~dE~YD~AI~dye~A~e  369 (504)
T KOG0624|consen  329 QCKEVLDIDPD-DVQVLCDRAEAYLGDEMYDDAIHDYEKALE  369 (504)
T ss_pred             HHHHHHhcCch-HHHHHHHHHHHHhhhHHHHHHHHHHHHHHh
Confidence            99998886433 578888888899989999999999999988

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.06  E-value=2.1e-06  Score=90.38  Aligned_cols=334  Identities=9%  Similarity=-0.049  Sum_probs=210.7

Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCC--C----CCCH--HHHHHHHHH
Q 011236          145 NCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENG--V----PPDN--FSYRICINS  216 (490)
Q Consensus       145 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~--~----~p~~--~~~~~li~~  216 (490)
                      ......|+++.+..+++.+.......+..........+...|+++++..++......-  .    .+..  .....+...
T Consensus       382 ~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~  461 (903)
T PRK04841        382 WSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQV  461 (903)
T ss_pred             HHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHH
Confidence            3445567777777777665322112233333444555667899999999988775431  1    1111  122233345


Q ss_pred             HhccCChHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC--C--ChhhHHHHHHH
Q 011236          217 YGARSELSSMENVLQEMESQSHISMD----WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS--K--DALGYNHLISH  288 (490)
Q Consensus       217 ~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~--~--~~~~~~~l~~~  288 (490)
                      +...|++++|...+++.. ......+    ....+.+...+...|++++|...+++........  +  ...++..+...
T Consensus       462 ~~~~g~~~~A~~~~~~al-~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~  540 (903)
T PRK04841        462 AINDGDPEEAERLAELAL-AELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEI  540 (903)
T ss_pred             HHhCCCHHHHHHHHHHHH-hcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHH
Confidence            667999999999999876 3211122    1344566777888999999999998876432210  1  12345566777


Q ss_pred             HHhcCChhHHHHHHHHHHHhcC---CC----ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CCC--CchhHHHHHH
Q 011236          289 YASLGNKDEMMKFWGLQKIKCK---KQ----LNRDYITMLGSLVKIGELEEAEKMLEEWELSC--YCY--DFRVPNIILL  357 (490)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~---~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~--~~~~~~~l~~  357 (490)
                      +...|++++|...+++......   .+    ....+..+...+...|++++|...+.+.....  ..+  ....+..+..
T Consensus       541 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~  620 (903)
T PRK04841        541 LFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAK  620 (903)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHH
Confidence            8889999999999887655321   11    12234455666777899999999998876531  112  1233445666


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCC-CHHHH-----HHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc---hhhHH
Q 011236          358 GYSQKGMIEKADAVLKEIVKKGKTP-TPNSW-----SIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK---PSLVS  428 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~~~~~p-~~~~~-----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~---~~~~~  428 (490)
                      .+...|+.+.|...+.......... ....+     ...+..+...|+.+.|.+++.....     ......   ...+.
T Consensus       621 ~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~-----~~~~~~~~~~~~~~  695 (903)
T PRK04841        621 ISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPK-----PEFANNHFLQGQWR  695 (903)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCC-----CCCccchhHHHHHH
Confidence            7788999999999998885531111 11111     1122444568899999998877544     111111   11234


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcc----cc---hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          429 SILDWLGDNRDVEEVEAFVSSLKIKV----QK---RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~~~~~~~~~~----~~---~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      .+..++...|++++|...+++.....    ..   ..++..+..++.+.|  ++|...+.+..+.
T Consensus       696 ~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~l  760 (903)
T PRK04841        696 NIARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKL  760 (903)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            56677888999999999999876642    21   456778888889999  7888888877653

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.03  E-value=3.7e-08  Score=89.95  Aligned_cols=223  Identities=17%  Similarity=0.128  Sum_probs=152.8

Q ss_pred             HHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcH
Q 011236          113 LIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKI  191 (490)
Q Consensus       113 ~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  191 (490)
                      -+.+.|++.+|.-.|+.....+| +..+|-.|.......++-..|+..+.+..+..+. |....-.|.-.|...|.-..|
T Consensus       294 ~lm~nG~L~~A~LafEAAVkqdP~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~-NleaLmaLAVSytNeg~q~~A  372 (579)
T KOG1125|consen  294 NLMKNGDLSEAALAFEAAVKQDPQHAEAWQKLGITQAENENEQNAISALRRCLELDPT-NLEALMALAVSYTNEGLQNQA  372 (579)
T ss_pred             HHHhcCCchHHHHHHHHHHhhChHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCc-cHHHHHHHHHHHhhhhhHHHH
Confidence            34567778888888888888777 5778888888888888888888888888887554 666666777777777877788


Q ss_pred             HHHHHHHHHCCCC--------CCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHH
Q 011236          192 PDVLLDMKENGVP--------PDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAI  263 (490)
Q Consensus       192 ~~~~~~m~~~~~~--------p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~  263 (490)
                      ++.++.-+...++        ++...-..  ..+.....+....++|-++....+..+|..++..|.-.|...|++++|+
T Consensus       373 l~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdrai  450 (579)
T KOG1125|consen  373 LKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAV  450 (579)
T ss_pred             HHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHH
Confidence            8877776553211        00000000  1122223344555666666535554567777777877888888888888


Q ss_pred             HHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          264 IYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWE  341 (490)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  341 (490)
                      +.|+......|  .|...||-|...++...+..+|+..|.+.++..+ .-++....|.-+|...|.+.+|...|-..+
T Consensus       451 Dcf~~AL~v~P--nd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP-~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL  525 (579)
T KOG1125|consen  451 DCFEAALQVKP--NDYLLWNRLGATLANGNRSEEAISAYNRALQLQP-GYVRVRYNLGISCMNLGAYKEAVKHLLEAL  525 (579)
T ss_pred             HHHHHHHhcCC--chHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCC-CeeeeehhhhhhhhhhhhHHHHHHHHHHHH
Confidence            88888777665  5777888888888888888888888887777665 344455556666777888888777776554

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

Probab=99.02  E-value=9.9e-06  Score=74.67  Aligned_cols=351  Identities=10%  Similarity=0.042  Sum_probs=204.2

Q ss_pred             HHHHH--hcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-C--hhHHHHHHHHHHhc
Q 011236           76 IRQLR--SRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-V--DKLYGALLNCYVRE  150 (490)
Q Consensus        76 l~~~~--~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~--~~~~~~li~~~~~~  150 (490)
                      =.+||  +.++.++|+..++...    +.+..+...-...+.+.|++++|..+|+.+.+.+. +  ...-..++.+-.. 
T Consensus        84 EKAYc~Yrlnk~Dealk~~~~~~----~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~-  158 (652)
T KOG2376|consen   84 EKAYCEYRLNKLDEALKTLKGLD----RLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAA-  158 (652)
T ss_pred             HHHHHHHHcccHHHHHHHHhccc----ccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHh-
Confidence            34444  6788999999888222    23455777778889999999999999999977652 2  1112222211110 


Q ss_pred             CChhHHHHHHHHHHhcCCCCCcchHHHHHH---HHHhcCCcCcHHHHHHHHHHCC-------------CCCCHHH-HHHH
Q 011236          151 GLVDESLSLMQKMKEMGSFGSALNYNGIMC---LYTNTGQHEKIPDVLLDMKENG-------------VPPDNFS-YRIC  213 (490)
Q Consensus       151 g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~---~~~~~~~~~~a~~~~~~m~~~~-------------~~p~~~~-~~~l  213 (490)
                         -.+ .+.   ......| ..+|..+.+   .+...|++.+|+++++...+.+             +.-+..+ -..+
T Consensus       159 ---l~~-~~~---q~v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQl  230 (652)
T KOG2376|consen  159 ---LQV-QLL---QSVPEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQL  230 (652)
T ss_pred             ---hhH-HHH---HhccCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHH
Confidence               111 122   2222222 345554443   4557799999999988873211             1111111 1234


Q ss_pred             HHHHhccCChHHHHHHHHHHHhCCCCCCCHHHH----HHHHHHHHHcCCHH----------------HHHHHH-------
Q 011236          214 INSYGARSELSSMENVLQEMESQSHISMDWGTY----STVANYYIIAGLKE----------------KAIIYL-------  266 (490)
Q Consensus       214 i~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~----~~li~~~~~~~~~~----------------~a~~~~-------  266 (490)
                      .-++-..|+.++|..+|.... ..+. +|....    |.|+..-....-++                .+...|       
T Consensus       231 ayVlQ~~Gqt~ea~~iy~~~i-~~~~-~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~  308 (652)
T KOG2376|consen  231 AYVLQLQGQTAEASSIYVDII-KRNP-ADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQA  308 (652)
T ss_pred             HHHHHHhcchHHHHHHHHHHH-HhcC-CCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            455667899999999998887 5554 443221    22221110000000                000000       


Q ss_pred             ------------------HHHhhhhccCCChhhHHHHHHHHHh--cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHh
Q 011236          267 ------------------KKCEDIVSKSKDALGYNHLISHYAS--LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVK  326 (490)
Q Consensus       267 ------------------~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  326 (490)
                                        ++.....+.......+.+++..+.+  ......+..++.......+.........++.....
T Consensus       309 i~~N~~lL~l~tnk~~q~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is  388 (652)
T KOG2376|consen  309 IYRNNALLALFTNKMDQVRELSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKIS  388 (652)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHh
Confidence                              0000111110112334444444332  22456666666655555443334566677788889


Q ss_pred             cCCHHHHHHHHH--------HHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCCCHH----HHHHHHH
Q 011236          327 IGELEEAEKMLE--------EWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK--GKTPTPN----SWSIIAA  392 (490)
Q Consensus       327 ~~~~~~a~~~~~--------~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~--~~~p~~~----~~~~l~~  392 (490)
                      .|+++.|.+++.        .+.+.+..|.  +...+...|.+.++-+.|..++.+.+..  .-.+...    ++..+..
T Consensus       389 ~gn~~~A~~il~~~~~~~~ss~~~~~~~P~--~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~  466 (652)
T KOG2376|consen  389 QGNPEVALEILSLFLESWKSSILEAKHLPG--TVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAE  466 (652)
T ss_pred             cCCHHHHHHHHHHHhhhhhhhhhhhccChh--HHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhH
Confidence            999999999999        5555444444  4556777788888877788888776542  1111222    3444444


Q ss_pred             HHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 011236          393 GYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       393 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  450 (490)
                      .-.+.|+-++|..++++.++      -..+|..+...++.+|++. +.+.|..+-+.+
T Consensus       467 f~lr~G~~~ea~s~leel~k------~n~~d~~~l~~lV~a~~~~-d~eka~~l~k~L  517 (652)
T KOG2376|consen  467 FKLRHGNEEEASSLLEELVK------FNPNDTDLLVQLVTAYARL-DPEKAESLSKKL  517 (652)
T ss_pred             HHHhcCchHHHHHHHHHHHH------hCCchHHHHHHHHHHHHhc-CHHHHHHHhhcC
Confidence            55678999999999999998      3346778999999999886 688888776654

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.01  E-value=2.9e-08  Score=90.56  Aligned_cols=242  Identities=14%  Similarity=0.093  Sum_probs=187.3

Q ss_pred             HHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCCh
Q 011236          216 SYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNK  295 (490)
Q Consensus       216 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  295 (490)
                      -+.+.|++.+|.-.|+... ..++ -+...|-.|.......++-..|+..+.+..+..+  .|......|.-.|...|.-
T Consensus       294 ~lm~nG~L~~A~LafEAAV-kqdP-~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP--~NleaLmaLAVSytNeg~q  369 (579)
T KOG1125|consen  294 NLMKNGDLSEAALAFEAAV-KQDP-QHAEAWQKLGITQAENENEQNAISALRRCLELDP--TNLEALMALAVSYTNEGLQ  369 (579)
T ss_pred             HHHhcCCchHHHHHHHHHH-hhCh-HHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCC--ccHHHHHHHHHHHhhhhhH
Confidence            3567899999999999988 6665 6788898899999999999999999999988776  6888899999999999999


Q ss_pred             hHHHHHHHHHHHhcCC--------CChhhHHHHHHHHHhcCCHHHHHHHHHHHH-hcCCCCCchhHHHHHHHHHhcCCHH
Q 011236          296 DEMMKFWGLQKIKCKK--------QLNRDYITMLGSLVKIGELEEAEKMLEEWE-LSCYCYDFRVPNIILLGYSQKGMIE  366 (490)
Q Consensus       296 ~~a~~~~~~~~~~~~~--------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~g~~~  366 (490)
                      ..|+..++.-+...++        ++...-..  ..+..........++|-++. ..+..+|..+...|.-.|--.|+++
T Consensus       370 ~~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efd  447 (579)
T KOG1125|consen  370 NQALKMLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFD  447 (579)
T ss_pred             HHHHHHHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHH
Confidence            9999999887665531        01100000  12222233445555555554 4444578888888998999999999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHH
Q 011236          367 KADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEA  445 (490)
Q Consensus       367 ~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~  445 (490)
                      +|...|+.++...+. |..+||.|...++...+.++|+..|+++++       ++|+. .....|.-.|...|.+++|.+
T Consensus       448 raiDcf~~AL~v~Pn-d~~lWNRLGAtLAN~~~s~EAIsAY~rALq-------LqP~yVR~RyNlgIS~mNlG~ykEA~~  519 (579)
T KOG1125|consen  448 RAVDCFEAALQVKPN-DYLLWNRLGATLANGNRSEEAISAYNRALQ-------LQPGYVRVRYNLGISCMNLGAYKEAVK  519 (579)
T ss_pred             HHHHHHHHHHhcCCc-hHHHHHHhhHHhcCCcccHHHHHHHHHHHh-------cCCCeeeeehhhhhhhhhhhhHHHHHH
Confidence            999999999997665 888999999999999999999999999998       66877 677788889999999999998


Q ss_pred             HHHHHHhcccc-----------hhhhHHHHHHHHhcC
Q 011236          446 FVSSLKIKVQK-----------RNMYHALTEAHIRSG  471 (490)
Q Consensus       446 ~~~~~~~~~~~-----------~~~~~~l~~~~~~~g  471 (490)
                      .|-.+......           ..+|.+|=.++.-.+
T Consensus       520 hlL~AL~mq~ks~~~~~~~~~se~iw~tLR~als~~~  556 (579)
T KOG1125|consen  520 HLLEALSMQRKSRNHNKAPMASENIWQTLRLALSAMN  556 (579)
T ss_pred             HHHHHHHhhhcccccccCCcchHHHHHHHHHHHHHcC
Confidence            88765443211           247777776666666

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

Probab=99.00  E-value=8.6e-09  Score=90.64  Aligned_cols=81  Identities=17%  Similarity=0.170  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH-HHHHHHHH
Q 011236          330 LEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM-EKAFECMK  408 (490)
Q Consensus       330 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~-~~a~~~~~  408 (490)
                      +.+|.-+|+++.+. ..+++.+.+.+..++...|++++|..++.+..+.+.. |+.+...++.+....|+. +.+.+++.
T Consensus       183 ~~~A~y~f~El~~~-~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~-~~d~LaNliv~~~~~gk~~~~~~~~l~  260 (290)
T PF04733_consen  183 YQDAFYIFEELSDK-FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPN-DPDTLANLIVCSLHLGKPTEAAERYLS  260 (290)
T ss_dssp             CCHHHHHHHHHHCC-S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CC-HHHHHHHHHHHHHHTT-TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhCCChhHHHHHHH
Confidence            44555555554333 3344444555555555555555555555555444333 444444455444444444 34444555


Q ss_pred             HHHH
Q 011236          409 EALA  412 (490)
Q Consensus       409 ~~~~  412 (490)
                      ++..
T Consensus       261 qL~~  264 (290)
T PF04733_consen  261 QLKQ  264 (290)
T ss_dssp             HCHH
T ss_pred             HHHH
Confidence            5444

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.

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

Probab=99.00  E-value=1.1e-05  Score=78.81  Aligned_cols=358  Identities=11%  Similarity=0.104  Sum_probs=164.2

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC-C---ChhHH
Q 011236           67 ISELELQRVIRQLRSRKRFKHALQVSEWMSGQGL--AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED-K---VDKLY  140 (490)
Q Consensus        67 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-p---~~~~~  140 (490)
                      .|...|..++.--     -.--.++.++..+.++  .-+|......+.++...+-..+-+++++++.-.. +   +...-
T Consensus       950 ~D~~LW~~VL~e~-----n~~rRqLiDqVv~tal~E~~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQ 1024 (1666)
T KOG0985|consen  950 SDPDLWAKVLNEE-----NPYRRQLIDQVVQTALPETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQ 1024 (1666)
T ss_pred             cChHHHHHHHhcc-----ChHHHHHHHHHHHhcCCccCChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhh
Confidence            3555666555311     1112345555555444  3455566666666666666666666666654432 1   12223


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc
Q 011236          141 GALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGAR  220 (490)
Q Consensus       141 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  220 (490)
                      |.|+-...+. +.....+..+++-..+. |+      +...+..++-+++|+.+|+...     .+....+.|+.-   .
T Consensus      1025 nLLiLtAika-d~trVm~YI~rLdnyDa-~~------ia~iai~~~LyEEAF~ifkkf~-----~n~~A~~VLie~---i 1088 (1666)
T KOG0985|consen 1025 NLLILTAIKA-DRTRVMEYINRLDNYDA-PD------IAEIAIENQLYEEAFAIFKKFD-----MNVSAIQVLIEN---I 1088 (1666)
T ss_pred             hhHHHHHhhc-ChHHHHHHHHHhccCCc-hh------HHHHHhhhhHHHHHHHHHHHhc-----ccHHHHHHHHHH---h
Confidence            3333333332 33344444444433311 11      2233334455555665555432     233334444432   2


Q ss_pred             CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHH
Q 011236          221 SELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMK  300 (490)
Q Consensus       221 g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  300 (490)
                      +.++.|.++-++..       .+..|+.+..+-.+.|.+.+|++-|-+.       .|+..|..++....+.|.|++-.+
T Consensus      1089 ~~ldRA~efAe~~n-------~p~vWsqlakAQL~~~~v~dAieSyika-------dDps~y~eVi~~a~~~~~~edLv~ 1154 (1666)
T KOG0985|consen 1089 GSLDRAYEFAERCN-------EPAVWSQLAKAQLQGGLVKDAIESYIKA-------DDPSNYLEVIDVASRTGKYEDLVK 1154 (1666)
T ss_pred             hhHHHHHHHHHhhC-------ChHHHHHHHHHHHhcCchHHHHHHHHhc-------CCcHHHHHHHHHHHhcCcHHHHHH
Confidence            44555555444442       1233555555555555555555544331       344455555555555555555555


Q ss_pred             HHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHc--
Q 011236          301 FWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK--  378 (490)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~--  378 (490)
                      ++....+....|.  .=+.|+-+|++.++..+.++++       ..|+......+.+-|...|.++.|.-+|.....-  
T Consensus      1155 yL~MaRkk~~E~~--id~eLi~AyAkt~rl~elE~fi-------~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~ 1225 (1666)
T KOG0985|consen 1155 YLLMARKKVREPY--IDSELIFAYAKTNRLTELEEFI-------AGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAK 1225 (1666)
T ss_pred             HHHHHHHhhcCcc--chHHHHHHHHHhchHHHHHHHh-------cCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHH
Confidence            5553333322222  2234555555555554443332       1233333333444444444444443333221100  


Q ss_pred             ------------------CCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCH
Q 011236          379 ------------------GKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDV  440 (490)
Q Consensus       379 ------------------~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  440 (490)
                                        .-..+..||..+-.+|...+.+..|.     |..     ..+-....-...++..|...|-+
T Consensus      1226 La~TLV~LgeyQ~AVD~aRKAns~ktWK~VcfaCvd~~EFrlAQ-----iCG-----L~iivhadeLeeli~~Yq~rGyF 1295 (1666)
T KOG0985|consen 1226 LASTLVYLGEYQGAVDAARKANSTKTWKEVCFACVDKEEFRLAQ-----ICG-----LNIIVHADELEELIEYYQDRGYF 1295 (1666)
T ss_pred             HHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHhchhhhhHHH-----hcC-----ceEEEehHhHHHHHHHHHhcCcH
Confidence                              00013344555555554444433321     211     12233334456667777777777


Q ss_pred             HHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC-CcHHHHH
Q 011236          441 EEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG-QEVDGLL  478 (490)
Q Consensus       441 ~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g-~~a~~~~  478 (490)
                      ++...+++........ ...|+-|.-.|.+-. ++-.+.+
T Consensus      1296 eElIsl~Ea~LGLERAHMgmfTELaiLYskykp~km~EHl 1335 (1666)
T KOG0985|consen 1296 EELISLLEAGLGLERAHMGMFTELAILYSKYKPEKMMEHL 1335 (1666)
T ss_pred             HHHHHHHHhhhchhHHHHHHHHHHHHHHHhcCHHHHHHHH
Confidence            7777776665443333 556666666666665 4444433

>PLN02789 farnesyltranstransferase

Probab=98.93  E-value=3.7e-06  Score=75.15  Aligned_cols=231  Identities=11%  Similarity=0.038  Sum_probs=109.0

Q ss_pred             cCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC-CHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCCh--h
Q 011236          220 RSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAG-LKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNK--D  296 (490)
Q Consensus       220 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~  296 (490)
                      .+..++|+.+++++. +.++ -+..+|+....++...| ++++++..++++....+  .+..+|+.-...+.+.|+.  +
T Consensus        50 ~e~serAL~lt~~aI-~lnP-~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~np--knyqaW~~R~~~l~~l~~~~~~  125 (320)
T PLN02789         50 DERSPRALDLTADVI-RLNP-GNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNP--KNYQIWHHRRWLAEKLGPDAAN  125 (320)
T ss_pred             CCCCHHHHHHHHHHH-HHCc-hhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCC--cchHHhHHHHHHHHHcCchhhH
Confidence            344445555555544 3222 22233333333344444 34555555555554443  3444444443333333332  3


Q ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc---CC----HHHHH
Q 011236          297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQK---GM----IEKAD  369 (490)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---g~----~~~A~  369 (490)
                      +++.+++.+....+ -+..+|+....++...|+++++.+.++++++.++. |...|+.....+.+.   |.    .++++
T Consensus       126 ~el~~~~kal~~dp-kNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~~~~e~el  203 (320)
T PLN02789        126 KELEFTRKILSLDA-KNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSPLLGGLEAMRDSEL  203 (320)
T ss_pred             HHHHHHHHHHHhCc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhccccccccccHHHHH
Confidence            44555554544443 44455555555555555555555555555554322 333444433333322   11    23455


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHhcc----CCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCC------
Q 011236          370 AVLKEIVKKGKTPTPNSWSIIAAGYADK----NNMEKAFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNR------  438 (490)
Q Consensus       370 ~~~~~m~~~~~~p~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g------  438 (490)
                      ....+++...+. |...|+.+...+...    +...+|.+.+.+...       ..| +...+..|+..|+...      
T Consensus       204 ~y~~~aI~~~P~-N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~-------~~~~s~~al~~l~d~~~~~~~~~~~~  275 (320)
T PLN02789        204 KYTIDAILANPR-NESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLS-------KDSNHVFALSDLLDLLCEGLQPTAEF  275 (320)
T ss_pred             HHHHHHHHhCCC-CcCHHHHHHHHHhcCCcccccchhHHHHHHHhhc-------ccCCcHHHHHHHHHHHHhhhccchhh
Confidence            555555555444 555666666655552    223445555555444       123 3345555555555421      


Q ss_pred             ------------CHHHHHHHHHHHHhcccc-hhhhHHHH
Q 011236          439 ------------DVEEVEAFVSSLKIKVQK-RNMYHALT  464 (490)
Q Consensus       439 ------------~~~~a~~~~~~~~~~~~~-~~~~~~l~  464 (490)
                                  ..+.|.++++.+.+.+|. ..-|+...
T Consensus       276 ~~~~~~~~~~~~~~~~a~~~~~~l~~~d~ir~~yw~~~~  314 (320)
T PLN02789        276 RDTVDTLAEELSDSTLAQAVCSELEVADPMRRNYWAWRK  314 (320)
T ss_pred             hhhhhccccccccHHHHHHHHHHHHhhCcHHHHHHHHHH
Confidence                        346677777777555555 44444333

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.93  E-value=1.3e-05  Score=68.96  Aligned_cols=312  Identities=11%  Similarity=0.027  Sum_probs=198.0

Q ss_pred             HHHHHHHhhcCHHHHHHHHHHccccCCC-hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchH-HHHHHHHHhcC
Q 011236          109 VQLDLIGKVRGLESAETYFNSLNDEDKV-DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNY-NGIMCLYTNTG  186 (490)
Q Consensus       109 ~l~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~-~~l~~~~~~~~  186 (490)
                      -+...+...|++.+|+.-|....+.+|+ -.++-.-...|...|+...|+.=|.+..+.  +||...- -.-...+.+.|
T Consensus        43 ElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQRg~vllK~G  120 (504)
T KOG0624|consen   43 ELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQRGVVLLKQG  120 (504)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHHhchhhhhcc
Confidence            3445555556666666666666665553 223333344555566666666555555554  3332211 11122344555


Q ss_pred             CcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011236          187 QHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYL  266 (490)
Q Consensus       187 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  266 (490)
                      .++.|..=|+..++..  |+..+   ...++.+.-..++       +          ......+..+...|+...|+...
T Consensus       121 ele~A~~DF~~vl~~~--~s~~~---~~eaqskl~~~~e-------~----------~~l~~ql~s~~~~GD~~~ai~~i  178 (504)
T KOG0624|consen  121 ELEQAEADFDQVLQHE--PSNGL---VLEAQSKLALIQE-------H----------WVLVQQLKSASGSGDCQNAIEMI  178 (504)
T ss_pred             cHHHHHHHHHHHHhcC--CCcch---hHHHHHHHHhHHH-------H----------HHHHHHHHHHhcCCchhhHHHHH
Confidence            5555555555555432  21110   1111111101111       1          11223455667789999999999


Q ss_pred             HHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 011236          267 KKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYC  346 (490)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  346 (490)
                      ..+.+..+  .|...|..-..+|...|++..|+.=++...... ..+..++.-+-..+-..|+.+.+....++-++  +.
T Consensus       179 ~~llEi~~--Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK--ld  253 (504)
T KOG0624|consen  179 THLLEIQP--WDASLRQARAKCYIAEGEPKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECLK--LD  253 (504)
T ss_pred             HHHHhcCc--chhHHHHHHHHHHHhcCcHHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc--cC
Confidence            99998766  799999999999999999999998887544433 36666777777778889999998888888776  45


Q ss_pred             CCchhH----HHH---------HHHHHhcCCHHHHHHHHHHHHHcCCCCCHH---HHHHHHHHHhccCCHHHHHHHHHHH
Q 011236          347 YDFRVP----NII---------LLGYSQKGMIEKADAVLKEIVKKGKTPTPN---SWSIIAAGYADKNNMEKAFECMKEA  410 (490)
Q Consensus       347 ~~~~~~----~~l---------~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~---~~~~l~~~~~~~~~~~~a~~~~~~~  410 (490)
                      ||...+    -.|         +....+.+++.+++.-.+...+..+.....   .+..+-.++...+++.+|++...+.
T Consensus       254 pdHK~Cf~~YKklkKv~K~les~e~~ie~~~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~ev  333 (504)
T KOG0624|consen  254 PDHKLCFPFYKKLKKVVKSLESAEQAIEEKHWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEV  333 (504)
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHH
Confidence            554321    111         112345677888888888887775542233   3556667788889999999999999


Q ss_pred             HHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          411 LAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       411 ~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ++       +.|+ ..++.--..+|.-...++.|..-|+.+.+.++.
T Consensus       334 L~-------~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A~e~n~s  373 (504)
T KOG0624|consen  334 LD-------IDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKALELNES  373 (504)
T ss_pred             Hh-------cCchHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcc
Confidence            88       5576 578888888888888999999999888877655

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

Probab=98.92  E-value=2.1e-06  Score=86.48  Aligned_cols=250  Identities=12%  Similarity=0.087  Sum_probs=185.1

Q ss_pred             cCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC---HHHHHHHHHHHHHcCCHHHHHH
Q 011236          188 HEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMD---WGTYSTVANYYIIAGLKEKAII  264 (490)
Q Consensus       188 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~~li~~~~~~~~~~~a~~  264 (490)
                      .+.|.++-+..+..  +-....|-..|..+...++.++|.+++++....-++.-.   ...|.++++.-...|.-+...+
T Consensus      1441 pesaeDferlvrss--PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~k 1518 (1710)
T KOG1070|consen 1441 PESAEDFERLVRSS--PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKK 1518 (1710)
T ss_pred             CcCHHHHHHHHhcC--CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHH
Confidence            33444444444432  223456778888888899999999999988744444333   3456667777777788888888


Q ss_pred             HHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 011236          265 YLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSC  344 (490)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  344 (490)
                      +|+++.+...   ....|..|...|.+.+..++|.++++.|..... .....|...+..+.+.++-+.|..++.+..+. 
T Consensus      1519 VFeRAcqycd---~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~-q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~- 1593 (1710)
T KOG1070|consen 1519 VFERACQYCD---AYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG-QTRKVWIMYADFLLRQNEAEAARELLKRALKS- 1593 (1710)
T ss_pred             HHHHHHHhcc---hHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc-chhhHHHHHHHHHhcccHHHHHHHHHHHHHhh-
Confidence            9988876443   245678888899999999999999998888776 67788899999999999999999999988875 


Q ss_pred             CCC--CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc
Q 011236          345 YCY--DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP  422 (490)
Q Consensus       345 ~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p  422 (490)
                      ++-  ........+..-.+.|+.+++..+|+......++ -...|+..++.-.++|+.+.+..+|++++.     .++.|
T Consensus      1594 lPk~eHv~~IskfAqLEFk~GDaeRGRtlfEgll~ayPK-RtDlW~VYid~eik~~~~~~vR~lfeRvi~-----l~l~~ 1667 (1710)
T KOG1070|consen 1594 LPKQEHVEFISKFAQLEFKYGDAERGRTLFEGLLSAYPK-RTDLWSVYIDMEIKHGDIKYVRDLFERVIE-----LKLSI 1667 (1710)
T ss_pred             cchhhhHHHHHHHHHHHhhcCCchhhHHHHHHHHhhCcc-chhHHHHHHHHHHccCCHHHHHHHHHHHHh-----cCCCh
Confidence            222  2334555666677889999999999998887665 677899999999999999999999999988     66666


Q ss_pred             ch--hhHHHHHHHHHcCCCHHHHHHHHHHH
Q 011236          423 KP--SLVSSILDWLGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       423 ~~--~~~~~l~~~~~~~g~~~~a~~~~~~~  450 (490)
                      -.  ..|.-.+..-...|+-+.++.+=.++
T Consensus      1668 kkmKfffKkwLeyEk~~Gde~~vE~VKarA 1697 (1710)
T KOG1070|consen 1668 KKMKFFFKKWLEYEKSHGDEKNVEYVKARA 1697 (1710)
T ss_pred             hHhHHHHHHHHHHHHhcCchhhHHHHHHHH
Confidence            54  56667776666667766665554443

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.91  E-value=4e-06  Score=76.35  Aligned_cols=373  Identities=14%  Similarity=0.029  Sum_probs=226.4

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCC-HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKIS-ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQ  110 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  110 (490)
                      +...|..=...+++.|++.+++..--...   ...|+ ...|+....++.-.|++++|+..|.+-++.. +-+...+.-+
T Consensus        35 nhvlySnrsaa~a~~~~~~~al~da~k~~---~l~p~w~kgy~r~Gaa~~~lg~~~eA~~ay~~GL~~d-~~n~~L~~gl  110 (539)
T KOG0548|consen   35 NHVLYSNRSAAYASLGSYEKALKDATKTR---RLNPDWAKGYSRKGAALFGLGDYEEAILAYSEGLEKD-PSNKQLKTGL  110 (539)
T ss_pred             ccchhcchHHHHHHHhhHHHHHHHHHHHH---hcCCchhhHHHHhHHHHHhcccHHHHHHHHHHHhhcC-CchHHHHHhH
Confidence            44555566677888888777766433322   34444 4589999999999999999999999998887 4566666666


Q ss_pred             HHHHHhhcCHHHHHHHH------HHccccC-----CChhHHHHHHHHHHhc----------CChhHHHHHHHHH-----H
Q 011236          111 LDLIGKVRGLESAETYF------NSLNDED-----KVDKLYGALLNCYVRE----------GLVDESLSLMQKM-----K  164 (490)
Q Consensus       111 ~~~~~~~~~~~~A~~~~------~~~~~~~-----p~~~~~~~li~~~~~~----------g~~~~a~~~~~~m-----~  164 (490)
                      ..++....   .+.+.|      ..+....     .....|..++..+-+.          .++..|.-.+...     .
T Consensus       111 ~~a~~~~~---~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~~l~d~r~m~a~~~l~~~~~~~~~  187 (539)
T KOG0548|consen  111 AQAYLEDY---AADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKLYLNDPRLMKADGQLKGVDELLFY  187 (539)
T ss_pred             HHhhhHHH---HhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhcccccHHHHHHHHHHhcCcccccc
Confidence            66662110   011111      1111100     0112233333322110          1111121111110     0


Q ss_pred             hcC-------CCCC----------------------cchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011236          165 EMG-------SFGS----------------------ALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICIN  215 (490)
Q Consensus       165 ~~~-------~~p~----------------------~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~  215 (490)
                      ..|       ..|.                      ..-...+.++..+..+++.+.+-+.......  -+..-++....
T Consensus       188 ~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA  265 (539)
T KOG0548|consen  188 ASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAA  265 (539)
T ss_pred             ccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHH
Confidence            001       1110                      0123567777778888899999998888754  35555666777


Q ss_pred             HHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHH-------HHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHH
Q 011236          216 SYGARSELSSMENVLQEMESQSHISMDWGTYSTV-------ANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISH  288 (490)
Q Consensus       216 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l-------i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  288 (490)
                      +|...|.+.+....-+... +.|- -...-|+.+       ..+|.+.++++.|+..|.+....... |+..        
T Consensus       266 ~~~e~~~~~~c~~~c~~a~-E~gr-e~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~kaLte~Rt-~~~l--------  334 (539)
T KOG0548|consen  266 VYLERGKYAECIELCEKAV-EVGR-ELRADYKLIAKALARLGNAYTKREDYEGAIKYYQKALTEHRT-PDLL--------  334 (539)
T ss_pred             HHHhccHHHHhhcchHHHH-HHhH-HHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHHHhhhhcC-HHHH--------
Confidence            8888888888777766665 4443 233334333       34666778899999999986554433 3322        


Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 011236          289 YASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKA  368 (490)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  368 (490)
                       .+....+++........-.++.. ..-...-...+.+.|++..|...|.++++.. +-|...|..-.-+|.+.|.+..|
T Consensus       335 -s~lk~~Ek~~k~~e~~a~~~pe~-A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~-P~Da~lYsNRAac~~kL~~~~~a  411 (539)
T KOG0548|consen  335 -SKLKEAEKALKEAERKAYINPEK-AEEEREKGNEAFKKGDYPEAVKHYTEAIKRD-PEDARLYSNRAACYLKLGEYPEA  411 (539)
T ss_pred             -HHHHHHHHHHHHHHHHHhhChhH-HHHHHHHHHHHHhccCHHHHHHHHHHHHhcC-CchhHHHHHHHHHHHHHhhHHHH
Confidence             12233344444444333222211 1222333677888999999999999999884 55788899999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHH
Q 011236          369 DAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLG  435 (490)
Q Consensus       369 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~  435 (490)
                      ++-.+..++.++. ....|..=..++....++++|++.|++.++       ..|+..-+..-+.-|.
T Consensus       412 L~Da~~~ieL~p~-~~kgy~RKg~al~~mk~ydkAleay~eale-------~dp~~~e~~~~~~rc~  470 (539)
T KOG0548|consen  412 LKDAKKCIELDPN-FIKAYLRKGAALRAMKEYDKALEAYQEALE-------LDPSNAEAIDGYRRCV  470 (539)
T ss_pred             HHHHHHHHhcCch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------cCchhHHHHHHHHHHH
Confidence            9998888887533 445566666677777889999999999988       3366544444443333

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.91  E-value=4.8e-05  Score=69.56  Aligned_cols=409  Identities=11%  Similarity=0.058  Sum_probs=221.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHH
Q 011236           64 GQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGAL  143 (490)
Q Consensus        64 ~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~l  143 (490)
                      ..+-|+.+|+.||+-+... ..+++.+.++++...- +.++..+..-+..-.+..+++....+|.+....--+...|...
T Consensus        15 ~nP~di~sw~~lire~qt~-~~~~~R~~YEq~~~~F-P~s~r~W~~yi~~El~skdfe~VEkLF~RCLvkvLnlDLW~lY   92 (656)
T KOG1914|consen   15 ENPYDIDSWSQLIREAQTQ-PIDKVRETYEQLVNVF-PSSPRAWKLYIERELASKDFESVEKLFSRCLVKVLNLDLWKLY   92 (656)
T ss_pred             cCCccHHHHHHHHHHHccC-CHHHHHHHHHHHhccC-CCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHhHHHHH
Confidence            4577999999999988666 8999999999998875 6788889999999999999999999999988766677788877


Q ss_pred             HHHHHh-cCChhH----HHHHHHHH-HhcCCCCC-cchHHHHHHHH---------HhcCCcCcHHHHHHHHHHCCCCCCH
Q 011236          144 LNCYVR-EGLVDE----SLSLMQKM-KEMGSFGS-ALNYNGIMCLY---------TNTGQHEKIPDVLLDMKENGVPPDN  207 (490)
Q Consensus       144 i~~~~~-~g~~~~----a~~~~~~m-~~~~~~p~-~~~~~~l~~~~---------~~~~~~~~a~~~~~~m~~~~~~p~~  207 (490)
                      +.---+ .|+...    ..+.|+-. .+.|+.+- ...|+.-+..+         ....+.+.+.++|+++....+.-=.
T Consensus        93 l~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~nlE  172 (656)
T KOG1914|consen   93 LSYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMHNLE  172 (656)
T ss_pred             HHHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCccccHH
Confidence            764433 233222    22333332 33353322 22344444432         2333455667778877764321111


Q ss_pred             HHHH------HHHHHH-------hccCChHHHHHHHHHHHh-CCCCC------CCHH---------HHHHHHHHHHHcCC
Q 011236          208 FSYR------ICINSY-------GARSELSSMENVLQEMES-QSHIS------MDWG---------TYSTVANYYIIAGL  258 (490)
Q Consensus       208 ~~~~------~li~~~-------~~~g~~~~a~~~~~~~~~-~~~~~------~~~~---------~~~~li~~~~~~~~  258 (490)
                      ..|+      .=|+..       -+...+..|.++++++.. ..|+.      |...         .|-.+|.- -+.+-
T Consensus       173 kLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~w-EksNp  251 (656)
T KOG1914|consen  173 KLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKW-EKSNP  251 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHH-HhcCC
Confidence            1221      112111       123345566777666641 11211      1111         11112211 11110


Q ss_pred             H---------HHHHHHHHHHhhhhccCCChhhH-----HHHHHHHHhcCC-------hhHHHHHHHHHHHhcCCCChhhH
Q 011236          259 K---------EKAIIYLKKCEDIVSKSKDALGY-----NHLISHYASLGN-------KDEMMKFWGLQKIKCKKQLNRDY  317 (490)
Q Consensus       259 ~---------~~a~~~~~~~~~~~~~~~~~~~~-----~~l~~~~~~~~~-------~~~a~~~~~~~~~~~~~~~~~~~  317 (490)
                      .         ....-.+++........|+..-.     ...-+.+...|+       .+++..+++.........+..+|
T Consensus       252 L~t~~~~~~~~Rv~yayeQ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~~~~~Ly  331 (656)
T KOG1914|consen  252 LRTLDGTMLTRRVMYAYEQCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLKENKLLY  331 (656)
T ss_pred             cccccccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            0         11112222222211110221100     001112222333       34455555554444333333444


Q ss_pred             HHHHHHHHhcC---CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHH
Q 011236          318 ITMLGSLVKIG---ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTP-TPNSWSIIAAG  393 (490)
Q Consensus       318 ~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p-~~~~~~~l~~~  393 (490)
                      ..+...=-..-   ..+....+++++...-..--..+|..++..-.+..-+..|..+|.+..+.+..+ ++..+++++..
T Consensus       332 ~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy  411 (656)
T KOG1914|consen  332 FALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEY  411 (656)
T ss_pred             HHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHH
Confidence            44333211111   245555566655543222223356667777777777777888888887776665 66667777775


Q ss_pred             HhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcc--cc--hhhhHHHHHHHHh
Q 011236          394 YADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV--QK--RNMYHALTEAHIR  469 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--~~--~~~~~~l~~~~~~  469 (490)
                      || .++..-|.++|+--+.      .+.-++.-....+..+...++-..+..+|++.....  ++  ..+|..++..=..
T Consensus       412 ~c-skD~~~AfrIFeLGLk------kf~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~  484 (656)
T KOG1914|consen  412 YC-SKDKETAFRIFELGLK------KFGDSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESN  484 (656)
T ss_pred             Hh-cCChhHHHHHHHHHHH------hcCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHh
Confidence            55 4566777777777766      222333444566666777777777888888777762  22  5777777777777


Q ss_pred             cC--CcHHHHHHHHH
Q 011236          470 SG--QEVDGLLESMK  482 (490)
Q Consensus       470 ~g--~~a~~~~~~m~  482 (490)
                      -|  ..+.++-+++.
T Consensus       485 vGdL~si~~lekR~~  499 (656)
T KOG1914|consen  485 VGDLNSILKLEKRRF  499 (656)
T ss_pred             cccHHHHHHHHHHHH
Confidence            77  55555555443

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

Probab=98.89  E-value=1.6e-05  Score=77.78  Aligned_cols=301  Identities=10%  Similarity=0.095  Sum_probs=196.7

Q ss_pred             CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcC--CCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHH
Q 011236          135 KVDKLYGALLNCYVREGLVDESLSLMQKMKEMG--SFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRI  212 (490)
Q Consensus       135 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~--~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  212 (490)
                      .|+..-+..+.++...+-..+-+++++++.-.+  +.-+...-|.|+-...+ -+...+.+..+++-..+. |+      
T Consensus       982 ~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAik-ad~trVm~YI~rLdnyDa-~~------ 1053 (1666)
T KOG0985|consen  982 QDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIK-ADRTRVMEYINRLDNYDA-PD------ 1053 (1666)
T ss_pred             CChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhh-cChHHHHHHHHHhccCCc-hh------
Confidence            456667778899999999999999999986542  11122234555544444 455677777777765432 33      


Q ss_pred             HHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhc
Q 011236          213 CINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASL  292 (490)
Q Consensus       213 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  292 (490)
                      +...+...+-+++|..+|++..      .+..+.+.||.   ..+..|.|.++-++.       ..+..|+.+..+-.+.
T Consensus      1054 ia~iai~~~LyEEAF~ifkkf~------~n~~A~~VLie---~i~~ldRA~efAe~~-------n~p~vWsqlakAQL~~ 1117 (1666)
T KOG0985|consen 1054 IAEIAIENQLYEEAFAIFKKFD------MNVSAIQVLIE---NIGSLDRAYEFAERC-------NEPAVWSQLAKAQLQG 1117 (1666)
T ss_pred             HHHHHhhhhHHHHHHHHHHHhc------ccHHHHHHHHH---HhhhHHHHHHHHHhh-------CChHHHHHHHHHHHhc
Confidence            4456667788999999999885      44455555554   456788888887764       3456799999999999


Q ss_pred             CChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHH
Q 011236          293 GNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVL  372 (490)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  372 (490)
                      |...+|.+-|-+      ..|+..|..+++.+.+.|.+++-.+.+...++..-.|.+.  +.||-+|++.++..+...++
T Consensus      1118 ~~v~dAieSyik------adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt~rl~elE~fi 1189 (1666)
T KOG0985|consen 1118 GLVKDAIESYIK------ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKTNRLTELEEFI 1189 (1666)
T ss_pred             CchHHHHHHHHh------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHhchHHHHHHHh
Confidence            999999988752      2677889999999999999999999999888876666554  57999999999988766554


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhh---------------hcCcCCCcchhhHHHHHHHHHcC
Q 011236          373 KEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVH---------------EENKFWRPKPSLVSSILDWLGDN  437 (490)
Q Consensus       373 ~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---------------~~~~~~~p~~~~~~~l~~~~~~~  437 (490)
                      .       -||..-...+.+-|...+.++.|.-+|.......               .+...-..+..||..+.-+|...
T Consensus      1190 ~-------gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKAns~ktWK~VcfaCvd~ 1262 (1666)
T KOG0985|consen 1190 A-------GPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKANSTKTWKEVCFACVDK 1262 (1666)
T ss_pred             c-------CCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhccchhHHHHHHHHHhch
Confidence            1       2455555555555555555555544433221100               00000113346677776676665


Q ss_pred             CCHHHHHHHHHHHHhcccc--hhhhHHHHHHHHhcC--CcHHHHHH
Q 011236          438 RDVEEVEAFVSSLKIKVQK--RNMYHALTEAHIRSG--QEVDGLLE  479 (490)
Q Consensus       438 g~~~~a~~~~~~~~~~~~~--~~~~~~l~~~~~~~g--~~a~~~~~  479 (490)
                      +.+.-|.     |...+..  .+-..-|+..|-..|  ++-+.+++
T Consensus      1263 ~EFrlAQ-----iCGL~iivhadeLeeli~~Yq~rGyFeElIsl~E 1303 (1666)
T KOG0985|consen 1263 EEFRLAQ-----ICGLNIIVHADELEELIEYYQDRGYFEELISLLE 1303 (1666)
T ss_pred             hhhhHHH-----hcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHH
Confidence            5544432     2222222  455566666666666  55555544

>PLN02789 farnesyltranstransferase

Probab=98.88  E-value=2.9e-06  Score=75.78  Aligned_cols=210  Identities=9%  Similarity=-0.008  Sum_probs=160.3

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcC-ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG-NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  327 (490)
                      +-..+...+..++|+..+.++....+  .+..+|+.-..++...| ++++++..++++....+ .+..+|+.....+.+.
T Consensus        43 ~ra~l~~~e~serAL~lt~~aI~lnP--~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~np-knyqaW~~R~~~l~~l  119 (320)
T PLN02789         43 FRAVYASDERSPRALDLTADVIRLNP--GNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNP-KNYQIWHHRRWLAEKL  119 (320)
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHCc--hhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCC-cchHHhHHHHHHHHHc
Confidence            44445556788999999999988776  46677777777777777 67999999998888776 5556677665556666


Q ss_pred             CCH--HHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc---CC---
Q 011236          328 GEL--EEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK---NN---  399 (490)
Q Consensus       328 ~~~--~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~---~~---  399 (490)
                      |+.  +++..+++++.+.. +-+..+|+.....+...|+++++++.++++++.++. |...|+.....+.+.   |.   
T Consensus       120 ~~~~~~~el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~~  197 (320)
T PLN02789        120 GPDAANKELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSPLLGGLEA  197 (320)
T ss_pred             CchhhHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhccccccccc
Confidence            653  67888898888763 347778988888899999999999999999999877 788888877766554   22   


Q ss_pred             -HHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcC----CCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhc
Q 011236          400 -MEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDN----RDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRS  470 (490)
Q Consensus       400 -~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~----g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~  470 (490)
                       .++.+++..+++.       ..|+. ..|+.+...+...    +...+|..++.+....++. ......|++.|+..
T Consensus       198 ~~e~el~y~~~aI~-------~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~  268 (320)
T PLN02789        198 MRDSELKYTIDAIL-------ANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSNHVFALSDLLDLLCEG  268 (320)
T ss_pred             cHHHHHHHHHHHHH-------hCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCCcHHHHHHHHHHHHhh
Confidence             3567888888887       33444 6777777777663    4456788888888887777 88899999999863

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.88  E-value=2.7e-06  Score=71.55  Aligned_cols=336  Identities=12%  Similarity=0.054  Sum_probs=212.9

Q ss_pred             CCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHH
Q 011236           99 GLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNG  177 (490)
Q Consensus        99 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~  177 (490)
                      |.....-.+...+..+.+..++++|++++..-.+..| +....+.|..+|....++..|...++++...-  |...-|..
T Consensus         5 g~~i~EGeftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~--P~~~qYrl   82 (459)
T KOG4340|consen    5 GAQIPEGEFTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLH--PELEQYRL   82 (459)
T ss_pred             cccCCCCchHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--hHHHHHHH
Confidence            3333444567777778899999999999998888887 67778888899999999999999999987763  34333322


Q ss_pred             -HHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHH--HHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Q 011236          178 -IMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICIN--SYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYI  254 (490)
Q Consensus       178 -l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~--~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  254 (490)
                       -...+-+.+.+..|+++...|...   |+...-..-+.  .....+++..+..++++.. ..   -+..+.+.......
T Consensus        83 Y~AQSLY~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp-~e---n~Ad~~in~gClly  155 (459)
T KOG4340|consen   83 YQAQSLYKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLP-SE---NEADGQINLGCLLY  155 (459)
T ss_pred             HHHHHHHHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhcc-CC---Cccchhccchheee
Confidence             233455778899999999888653   33322222222  2345788888888888775 22   23344444556677


Q ss_pred             HcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC--C-----------Chh------
Q 011236          255 IAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK--Q-----------LNR------  315 (490)
Q Consensus       255 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~-----------~~~------  315 (490)
                      +.|+++.|.+-|+...+-+.. .....|+..+. +.+.|+.+.|+++..+++..+.+  |           |..      
T Consensus       156 kegqyEaAvqkFqaAlqvsGy-qpllAYniALa-Hy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt~  233 (459)
T KOG4340|consen  156 KEGQYEAAVQKFQAALQVSGY-QPLLAYNLALA-HYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNTL  233 (459)
T ss_pred             ccccHHHHHHHHHHHHhhcCC-CchhHHHHHHH-HHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccchH
Confidence            899999999999998887765 56677776654 55778999999999988888762  1           111      


Q ss_pred             --hHHHHHHH-------HHhcCCHHHHHHHHHHHHhcC-CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH
Q 011236          316 --DYITMLGS-------LVKIGELEEAEKMLEEWELSC-YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPN  385 (490)
Q Consensus       316 --~~~~l~~~-------~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~  385 (490)
                        .-+.++.+       +.+.|+++.|.+.+..|.... ...|+.|...+.-.- ..+++-+..+-+.-+.+.++- ...
T Consensus       234 ~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~nPf-P~E  311 (459)
T KOG4340|consen  234 VLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQNPF-PPE  311 (459)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcCCC-ChH
Confidence              12233333       345677777777776664321 233555544332221 134455555555555555543 456


Q ss_pred             HHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCC-CcchhhHHHHHHHHH-cCCCHHHHHHHHHHHHhc
Q 011236          386 SWSIIAAGYADKNNMEKAFECMKEALAVHEENKFW-RPKPSLVSSILDWLG-DNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       386 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~p~~~~~~~l~~~~~-~~g~~~~a~~~~~~~~~~  453 (490)
                      ||..++-.||+..-++.|..++.+-..     ... -.+...|+ ++.++. ..-..++|.+-++.+.+.
T Consensus       312 TFANlLllyCKNeyf~lAADvLAEn~~-----lTyk~L~~Yly~-LLdaLIt~qT~pEea~KKL~~La~~  375 (459)
T KOG4340|consen  312 TFANLLLLYCKNEYFDLAADVLAENAH-----LTYKFLTPYLYD-LLDALITCQTAPEEAFKKLDGLAGM  375 (459)
T ss_pred             HHHHHHHHHhhhHHHhHHHHHHhhCcc-----hhHHHhhHHHHH-HHHHHHhCCCCHHHHHHHHHHHHHH
Confidence            777777778888777777777765322     111 12223333 333333 345566666666655443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.85  E-value=1e-06  Score=76.36  Aligned_cols=192  Identities=11%  Similarity=-0.048  Sum_probs=124.3

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCCh--hhH
Q 011236          241 MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD-ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLN--RDY  317 (490)
Q Consensus       241 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~  317 (490)
                      .....+..+...+...|++++|...|+++....+..+. ..++..+..++...|++++|...++......+....  .++
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~  110 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAY  110 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHH
Confidence            45666777888888999999999999988776553121 246677888888899999999999988877652222  134


Q ss_pred             HHHHHHHHhc--------CCHHHHHHHHHHHHhcCCCCCc-hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 011236          318 ITMLGSLVKI--------GELEEAEKMLEEWELSCYCYDF-RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS  388 (490)
Q Consensus       318 ~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~  388 (490)
                      ..+..++...        |+.++|.+.++.+.+.  .|+. ..+..+...    +.....      .        .....
T Consensus       111 ~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~----~~~~~~------~--------~~~~~  170 (235)
T TIGR03302       111 YLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRM----DYLRNR------L--------AGKEL  170 (235)
T ss_pred             HHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHH----HHHHHH------H--------HHHHH
Confidence            4455555543        6677777777777764  2332 122111111    000000      0        00122


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       389 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      .+...+.+.|++++|...++++++..|   +-......+..+..++.+.|++++|..+++.+....|
T Consensus       171 ~~a~~~~~~g~~~~A~~~~~~al~~~p---~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~~  234 (235)
T TIGR03302       171 YVARFYLKRGAYVAAINRFETVVENYP---DTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANYP  234 (235)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHHCC---CCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            455678888999999999998887332   1112346778888888899999999988888877655

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).

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.85  E-value=5.7e-06  Score=80.71  Aligned_cols=368  Identities=12%  Similarity=-0.012  Sum_probs=223.1

Q ss_pred             ChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHH
Q 011236           84 RFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQK  162 (490)
Q Consensus        84 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~  162 (490)
                      +...|+..|-+..+... .-...|..+...|+...+...|.+.|+...+.++ +...+......|++..+++.|..+.-.
T Consensus       473 ~~~~al~ali~alrld~-~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~  551 (1238)
T KOG1127|consen  473 NSALALHALIRALRLDV-SLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLR  551 (1238)
T ss_pred             hHHHHHHHHHHHHhccc-chhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHH
Confidence            35666666666666653 3456788888888888899999999999998886 678899999999999999999988443


Q ss_pred             HHhcCCC-CCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCC
Q 011236          163 MKEMGSF-GSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISM  241 (490)
Q Consensus       163 m~~~~~~-p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  241 (490)
                      ..+.... .-...|....-.|.+.++...+..-|+...+..+ -|...|..+..+|..+|.+..|.++|.+.. ..++ .
T Consensus       552 ~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dP-kD~n~W~gLGeAY~~sGry~~AlKvF~kAs-~LrP-~  628 (1238)
T KOG1127|consen  552 AAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRTDP-KDYNLWLGLGEAYPESGRYSHALKVFTKAS-LLRP-L  628 (1238)
T ss_pred             HhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcCCc-hhHHHHHHHHHHHHhcCceehHHHhhhhhH-hcCc-H
Confidence            3332110 0122233455567788889999999988887544 377789999999999999999999998887 4443 2


Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC-----CChhhHHHHHHHHHhcCChhHHHHHHHHHH-------Hhc
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS-----KDALGYNHLISHYASLGNKDEMMKFWGLQK-------IKC  309 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~-------~~~  309 (490)
                      +...---..-.-+..|.+.+|...+..+.......     .-..++..+...+...|-...+.++++.-+       .+.
T Consensus       629 s~y~~fk~A~~ecd~GkYkeald~l~~ii~~~s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~f~~~l~h~  708 (1238)
T KOG1127|consen  629 SKYGRFKEAVMECDNGKYKEALDALGLIIYAFSLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIESFIVSLIHS  708 (1238)
T ss_pred             hHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHh
Confidence            22222223445677888888888887765432210     111223223333333333333333333222       222


Q ss_pred             CCCChhhHHHHHHHHHhcCCHH------HHHHHH-HHHHhcC--------------------CCCCchhHHHHHHHHHh-
Q 011236          310 KKQLNRDYITMLGSLVKIGELE------EAEKML-EEWELSC--------------------YCYDFRVPNIILLGYSQ-  361 (490)
Q Consensus       310 ~~~~~~~~~~l~~~~~~~~~~~------~a~~~~-~~~~~~~--------------------~~~~~~~~~~l~~~~~~-  361 (490)
                      ...+...|..+.++|.---..+      ....++ .+....+                    ...+..+|..|+..|.+ 
T Consensus       709 ~~~~~~~Wi~asdac~~f~q~e~~~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~~hlsl~~~~~~WyNLGinylr~  788 (1238)
T KOG1127|consen  709 LQSDRLQWIVASDACYIFSQEEPSIVNMHYLIILSKQLEKTGALKKNDLLFLGYECGIAHLSLAIHMYPWYNLGINYLRY  788 (1238)
T ss_pred             hhhhHHHHHHHhHHHHHHHHhcccchHHHHHHHHHHHHHhcccCcchhHHHHHHHHhhHHHHHhhccchHHHHhHHHHHH
Confidence            1122222322222221100000      000011 1111111                    11223444445444433 


Q ss_pred             ---c----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHH
Q 011236          362 ---K----GMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWL  434 (490)
Q Consensus       362 ---~----g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~  434 (490)
                         .    .+...|...+.+.++..-. +..+|+.|.-. ...|++.-|...|-+.+..      .+-+..+|..+.-.+
T Consensus       789 f~~l~et~~~~~~Ai~c~KkaV~L~an-n~~~WnaLGVl-sg~gnva~aQHCfIks~~s------ep~~~~~W~NlgvL~  860 (1238)
T KOG1127|consen  789 FLLLGETMKDACTAIRCCKKAVSLCAN-NEGLWNALGVL-SGIGNVACAQHCFIKSRFS------EPTCHCQWLNLGVLV  860 (1238)
T ss_pred             HHHcCCcchhHHHHHHHHHHHHHHhhc-cHHHHHHHHHh-hccchhhhhhhhhhhhhhc------cccchhheeccceeE
Confidence               1    2334677777777765433 66777777665 6668888888888777662      223446788888888


Q ss_pred             HcCCCHHHHHHHHHHHHhcccc-hhhhHHH
Q 011236          435 GDNRDVEEVEAFVSSLKIKVQK-RNMYHAL  463 (490)
Q Consensus       435 ~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l  463 (490)
                      ....+++.|...|.+.+...|. ...|-..
T Consensus       861 l~n~d~E~A~~af~~~qSLdP~nl~~WlG~  890 (1238)
T KOG1127|consen  861 LENQDFEHAEPAFSSVQSLDPLNLVQWLGE  890 (1238)
T ss_pred             EecccHHHhhHHHHhhhhcCchhhHHHHHH
Confidence            8899999999999999888887 5445433

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

Probab=98.84  E-value=6e-07  Score=90.15  Aligned_cols=218  Identities=13%  Similarity=0.067  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC---CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS---KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                      .|-..|......++.++|.+++++........   .-...|.++++.-..-|.-+...++|+++.+...  .-..|..|.
T Consensus      1460 ~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd--~~~V~~~L~ 1537 (1710)
T KOG1070|consen 1460 LWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCD--AYTVHLKLL 1537 (1710)
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcc--hHHHHHHHH
Confidence            33334444445555555555555544332110   0112344444444444444445555554433321  123344555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHhccCCH
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PTPNSWSIIAAGYADKNNM  400 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~  400 (490)
                      ..|.+.+..++|.++++.|.+. +.-...+|...+..+.+.++-+.|..++.+..+.=++ -......-.++.-.+.|+.
T Consensus      1538 ~iy~k~ek~~~A~ell~~m~KK-F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~GDa 1616 (1710)
T KOG1070|consen 1538 GIYEKSEKNDEADELLRLMLKK-FGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKYGDA 1616 (1710)
T ss_pred             HHHHHhhcchhHHHHHHHHHHH-hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhcCCc
Confidence            5555555555555555555544 3333444555555555555555555555554443111 0122233333334445555


Q ss_pred             HHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc----hhhhHHHHHHHHhcC
Q 011236          401 EKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK----RNMYHALTEAHIRSG  471 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~l~~~~~~~g  471 (490)
                      +++..+|+..+.-+      +-....|+.+++.-.+.|+.+.++.+|+++...+..    -..|.-++..=...|
T Consensus      1617 eRGRtlfEgll~ay------PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~G 1685 (1710)
T KOG1070|consen 1617 ERGRTLFEGLLSAY------PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHG 1685 (1710)
T ss_pred             hhhHHHHHHHHhhC------ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcC
Confidence            55555555554411      112244555555555555555555555555554433    333444444444444

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.83  E-value=6.8e-06  Score=77.60  Aligned_cols=195  Identities=15%  Similarity=0.153  Sum_probs=139.3

Q ss_pred             HHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhc
Q 011236          213 CINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASL  292 (490)
Q Consensus       213 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  292 (490)
                      .+.+......|.+|+.+++.++ +.+.  ...-|..+.+.|...|+++.|.++|.+    +.      .++-.|.+|.+.
T Consensus       738 aieaai~akew~kai~ildniq-dqk~--~s~yy~~iadhyan~~dfe~ae~lf~e----~~------~~~dai~my~k~  804 (1636)
T KOG3616|consen  738 AIEAAIGAKEWKKAISILDNIQ-DQKT--ASGYYGEIADHYANKGDFEIAEELFTE----AD------LFKDAIDMYGKA  804 (1636)
T ss_pred             HHHHHhhhhhhhhhHhHHHHhh-hhcc--ccccchHHHHHhccchhHHHHHHHHHh----cc------hhHHHHHHHhcc
Confidence            3455667788999999999887 4433  334567788899999999999999876    22      266678889999


Q ss_pred             CChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHH
Q 011236          293 GNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVL  372 (490)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  372 (490)
                      |+|..|.++-.+.  .++......|.+-..-+-+.|++.+|++++-.+-    .|+     .-|..|-+.|..+..+++.
T Consensus       805 ~kw~da~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~-----~aiqmydk~~~~ddmirlv  873 (1636)
T KOG3616|consen  805 GKWEDAFKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPD-----KAIQMYDKHGLDDDMIRLV  873 (1636)
T ss_pred             ccHHHHHHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhheeEEcc----Cch-----HHHHHHHhhCcchHHHHHH
Confidence            9999998876533  3334455566666677778899999888876542    233     3577888999988888877


Q ss_pred             HHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHH
Q 011236          373 KEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVS  448 (490)
Q Consensus       373 ~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  448 (490)
                      .+--..   .-..|...+..-|-..|+...|...|-++-+              |.+.++.|...+-|++|-++-+
T Consensus       874 ~k~h~d---~l~dt~~~f~~e~e~~g~lkaae~~flea~d--------------~kaavnmyk~s~lw~dayriak  932 (1636)
T KOG3616|consen  874 EKHHGD---HLHDTHKHFAKELEAEGDLKAAEEHFLEAGD--------------FKAAVNMYKASELWEDAYRIAK  932 (1636)
T ss_pred             HHhChh---hhhHHHHHHHHHHHhccChhHHHHHHHhhhh--------------HHHHHHHhhhhhhHHHHHHHHh
Confidence            654221   1234667777888888999999888877655              5566667777777777766543

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

Probab=98.82  E-value=3.2e-07  Score=86.26  Aligned_cols=219  Identities=11%  Similarity=0.104  Sum_probs=171.0

Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhH
Q 011236          238 HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDY  317 (490)
Q Consensus       238 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  317 (490)
                      +.+|-+..-..+...+...|-...|..+|+++.          .|...+.+|+..|+..+|..+.....+  ..|++..|
T Consensus       393 ~lpp~Wq~q~~laell~slGitksAl~I~Erle----------mw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~ly  460 (777)
T KOG1128|consen  393 HLPPIWQLQRLLAELLLSLGITKSALVIFERLE----------MWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLY  460 (777)
T ss_pred             CCCCcchHHHHHHHHHHHcchHHHHHHHHHhHH----------HHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhH
Confidence            345666777778889999999999999998743          366788899999999999998886665  34888999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK  397 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  397 (490)
                      ..+.+......-+++|.++.+.....       .-..+.....+.++++++.+.|+.-.+.++- -..+|-.+..+..+.
T Consensus       461 c~LGDv~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~npl-q~~~wf~~G~~ALql  532 (777)
T KOG1128|consen  461 CLLGDVLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEINPL-QLGTWFGLGCAALQL  532 (777)
T ss_pred             HHhhhhccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcCcc-chhHHHhccHHHHHH
Confidence            99988877777788888888765432       1122222234478889999988887776543 567888888888888


Q ss_pred             CCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--Cc
Q 011236          398 NNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QE  473 (490)
Q Consensus       398 ~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~  473 (490)
                      ++++.|.+.|...+.       ..|+. ..|+.+-.+|.+.|+-.+|...+.+..+.+.. ..+|...+-...+.|  ++
T Consensus       533 ek~q~av~aF~rcvt-------L~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~ed  605 (777)
T KOG1128|consen  533 EKEQAAVKAFHRCVT-------LEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFED  605 (777)
T ss_pred             hhhHHHHHHHHHHhh-------cCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHH
Confidence            999999999988887       45666 78899999999999999999999988887765 788888888888888  88


Q ss_pred             HHHHHHHHHh
Q 011236          474 VDGLLESMKA  483 (490)
Q Consensus       474 a~~~~~~m~~  483 (490)
                      |++.+.+|..
T Consensus       606 a~~A~~rll~  615 (777)
T KOG1128|consen  606 AIKAYHRLLD  615 (777)
T ss_pred             HHHHHHHHHH
Confidence            8888887764

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.80  E-value=2.7e-05  Score=76.25  Aligned_cols=161  Identities=11%  Similarity=-0.010  Sum_probs=120.7

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-Chh--HHHHHHH
Q 011236           69 ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDK--LYGALLN  145 (490)
Q Consensus        69 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~--~~~~li~  145 (490)
                      ...|..|...|+...+...|.+.|++.-+.+ +.+..........|+...+++.|..+.-...+..| -..  .|-.+.-
T Consensus       492 apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~  570 (1238)
T KOG1127|consen  492 APAFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGP  570 (1238)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccc
Confidence            3467788888888888888999999988876 45677778888999999999999988554444443 122  2333445


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHH--HHHHHhccCCh
Q 011236          146 CYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRI--CINSYGARSEL  223 (490)
Q Consensus       146 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~--li~~~~~~g~~  223 (490)
                      .|.+.++...|+.-|+...+..+. |...|..++.+|...|.+..|.++|.+...  +.|+.. |..  ..-..+..|.+
T Consensus       571 yyLea~n~h~aV~~fQsALR~dPk-D~n~W~gLGeAY~~sGry~~AlKvF~kAs~--LrP~s~-y~~fk~A~~ecd~GkY  646 (1238)
T KOG1127|consen  571 YYLEAHNLHGAVCEFQSALRTDPK-DYNLWLGLGEAYPESGRYSHALKVFTKASL--LRPLSK-YGRFKEAVMECDNGKY  646 (1238)
T ss_pred             cccCccchhhHHHHHHHHhcCCch-hHHHHHHHHHHHHhcCceehHHHhhhhhHh--cCcHhH-HHHHHHHHHHHHhhhH
Confidence            577889999999999999888766 888999999999999999999999988876  345432 222  22234567888


Q ss_pred             HHHHHHHHHHH
Q 011236          224 SSMENVLQEME  234 (490)
Q Consensus       224 ~~a~~~~~~~~  234 (490)
                      .+|...+....
T Consensus       647 keald~l~~ii  657 (1238)
T KOG1127|consen  647 KEALDALGLII  657 (1238)
T ss_pred             HHHHHHHHHHH
Confidence            88887777664

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

Probab=98.78  E-value=4.5e-07  Score=85.25  Aligned_cols=238  Identities=15%  Similarity=0.098  Sum_probs=185.1

Q ss_pred             CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHH
Q 011236          101 AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMC  180 (490)
Q Consensus       101 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~  180 (490)
                      +|-......+...+...|-...|..+|+++.       .|.-+|.+|+..|+..+|..+...-.++  +||...|..+.+
T Consensus       395 pp~Wq~q~~laell~slGitksAl~I~Erle-------mw~~vi~CY~~lg~~~kaeei~~q~lek--~~d~~lyc~LGD  465 (777)
T KOG1128|consen  395 PPIWQLQRLLAELLLSLGITKSALVIFERLE-------MWDPVILCYLLLGQHGKAEEINRQELEK--DPDPRLYCLLGD  465 (777)
T ss_pred             CCcchHHHHHHHHHHHcchHHHHHHHHHhHH-------HHHHHHHHHHHhcccchHHHHHHHHhcC--CCcchhHHHhhh
Confidence            5556666777888899999999999998753       5888899999999999999998888773  678889999988


Q ss_pred             HHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHH
Q 011236          181 LYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKE  260 (490)
Q Consensus       181 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~  260 (490)
                      ......-+++|.++++....+       .-..+.....+.+++.++.+.|+.-. +.+. ....+|-.+..+..+.++++
T Consensus       466 v~~d~s~yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl-~~np-lq~~~wf~~G~~ALqlek~q  536 (777)
T KOG1128|consen  466 VLHDPSLYEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSL-EINP-LQLGTWFGLGCAALQLEKEQ  536 (777)
T ss_pred             hccChHHHHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHh-hcCc-cchhHHHhccHHHHHHhhhH
Confidence            887777788888888775432       22223333445789999999998876 5554 56677877888889999999


Q ss_pred             HHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011236          261 KAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEW  340 (490)
Q Consensus       261 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  340 (490)
                      .|.+.|.......+  .+...||.+-.+|.+.++-.+|...+.+..+-. ..+...|...+....+.|.+++|.+.+.++
T Consensus       537 ~av~aF~rcvtL~P--d~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn-~~~w~iWENymlvsvdvge~eda~~A~~rl  613 (777)
T KOG1128|consen  537 AAVKAFHRCVTLEP--DNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN-YQHWQIWENYMLVSVDVGEFEDAIKAYHRL  613 (777)
T ss_pred             HHHHHHHHHhhcCC--CchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC-CCCCeeeechhhhhhhcccHHHHHHHHHHH
Confidence            99999999887555  577899999999999999999999999888776 466677777888888999999999999887


Q ss_pred             HhcCC-CCCchhHHHHHHHH
Q 011236          341 ELSCY-CYDFRVPNIILLGY  359 (490)
Q Consensus       341 ~~~~~-~~~~~~~~~l~~~~  359 (490)
                      ..... ..|..+...++...
T Consensus       614 l~~~~~~~d~~vl~~iv~~~  633 (777)
T KOG1128|consen  614 LDLRKKYKDDEVLLIIVRTV  633 (777)
T ss_pred             HHhhhhcccchhhHHHHHHH
Confidence            65321 11444444444443

>PF12854 PPR_1: PPR repeat

Probab=98.78  E-value=9.6e-09  Score=57.36  Aligned_cols=32  Identities=25%  Similarity=0.495  Sum_probs=16.4

Q ss_pred             CCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          202 GVPPDNFSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       202 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      |+.||..||++||++|++.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            44455555555555555555555555555544

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

Probab=98.77  E-value=3e-05  Score=74.34  Aligned_cols=176  Identities=16%  Similarity=0.175  Sum_probs=96.5

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHh--
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVK--  326 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--  326 (490)
                      +++..|-.|+.++|-++-++      . .|....-.+.+.|-..|++.+|..+|.+...         |...|+.|-.  
T Consensus       944 ~VrI~C~qGk~~kAa~iA~e------s-gd~AAcYhlaR~YEn~g~v~~Av~FfTrAqa---------fsnAIRlcKEnd 1007 (1416)
T KOG3617|consen  944 MVRIKCIQGKTDKAARIAEE------S-GDKAACYHLARMYENDGDVVKAVKFFTRAQA---------FSNAIRLCKEND 1007 (1416)
T ss_pred             heeeEeeccCchHHHHHHHh------c-ccHHHHHHHHHHhhhhHHHHHHHHHHHHHHH---------HHHHHHHHHhcC
Confidence            33344444444444444333      1 4555666777777777777777777764432         2223332211  


Q ss_pred             -------------cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHH--------HHHH--cCCCCC
Q 011236          327 -------------IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLK--------EIVK--KGKTPT  383 (490)
Q Consensus       327 -------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~--------~m~~--~~~~p~  383 (490)
                                   ..+.-.|-++|++.   |.     -+..-+..|.+.|.+.+|+++--        +++.  .....|
T Consensus      1008 ~~d~L~nlal~s~~~d~v~aArYyEe~---g~-----~~~~AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sD 1079 (1416)
T KOG3617|consen 1008 MKDRLANLALMSGGSDLVSAARYYEEL---GG-----YAHKAVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSD 1079 (1416)
T ss_pred             HHHHHHHHHhhcCchhHHHHHHHHHHc---ch-----hhhHHHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCC
Confidence                         11222333333332   11     11234456888888888876532        1222  233446


Q ss_pred             HHHHHHHHHHHhccCCHHHHHHHHHHHHHhh----------------------hcCcCCCcch----hhHHHHHHHHHcC
Q 011236          384 PNSWSIIAAGYADKNNMEKAFECMKEALAVH----------------------EENKFWRPKP----SLVSSILDWLGDN  437 (490)
Q Consensus       384 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~----------------------~~~~~~~p~~----~~~~~l~~~~~~~  437 (490)
                      +...+.-.+.|+...++++|..++..+.+..                      |.+.+. |+.    .....+...|.++
T Consensus      1080 p~ll~RcadFF~~~~qyekAV~lL~~ar~~~~AlqlC~~~nv~vtee~aE~mTp~Kd~~-~~e~~R~~vLeqvae~c~qQ 1158 (1416)
T KOG3617|consen 1080 PKLLRRCADFFENNQQYEKAVNLLCLAREFSGALQLCKNRNVRVTEEFAELMTPTKDDM-PNEQERKQVLEQVAELCLQQ 1158 (1416)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHhcCcCcCCC-ccHHHHHHHHHHHHHHHHhc
Confidence            7778888888888888998888775554411                      222222 332    3456667788888


Q ss_pred             CCHHHHHHHHHH
Q 011236          438 RDVEEVEAFVSS  449 (490)
Q Consensus       438 g~~~~a~~~~~~  449 (490)
                      |.+..|.+-|.+
T Consensus      1159 G~Yh~AtKKfTQ 1170 (1416)
T KOG3617|consen 1159 GAYHAATKKFTQ 1170 (1416)
T ss_pred             cchHHHHHHHhh
Confidence            888877665543

>PF12854 PPR_1: PPR repeat

Probab=98.76  E-value=1e-08  Score=57.27  Aligned_cols=32  Identities=22%  Similarity=0.332  Sum_probs=17.4

Q ss_pred             CCCCCchhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011236          344 CYCYDFRVPNIILLGYSQKGMIEKADAVLKEI  375 (490)
Q Consensus       344 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m  375 (490)
                      |+.||..+|++||.+||+.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            44555555555555555555555555555554

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.74  E-value=2.6e-06  Score=70.87  Aligned_cols=118  Identities=8%  Similarity=0.010  Sum_probs=81.4

Q ss_pred             cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHH-HHhcCC--HHHH
Q 011236          292 LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLG-YSQKGM--IEKA  368 (490)
Q Consensus       292 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~--~~~A  368 (490)
                      .++.+++...++......+ .+...|..+...|...|++++|...+++..+.. +.+...+..+..+ +...|+  .++|
T Consensus        52 ~~~~~~~i~~l~~~L~~~P-~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A  129 (198)
T PRK10370         52 QQTPEAQLQALQDKIRANP-QNSEQWALLGEYYLWRNDYDNALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQT  129 (198)
T ss_pred             chhHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHH
Confidence            4555666666666666655 666777777777777777777777777777753 2255566666665 355565  4777


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          369 DAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       369 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .+++++..+.++. +...+..+...+.+.|++++|+..|+++++
T Consensus       130 ~~~l~~al~~dP~-~~~al~~LA~~~~~~g~~~~Ai~~~~~aL~  172 (198)
T PRK10370        130 REMIDKALALDAN-EVTALMLLASDAFMQADYAQAIELWQKVLD  172 (198)
T ss_pred             HHHHHHHHHhCCC-ChhHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            7777777777655 666777777777777777777777777776

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.72  E-value=2.1e-06  Score=74.47  Aligned_cols=162  Identities=12%  Similarity=0.118  Sum_probs=96.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc---hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH--HHHHHH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDF---RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTP--NSWSII  390 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~--~~~~~l  390 (490)
                      .+..+...+...|++++|...++++..... .+.   ..+..+..+|.+.|++++|...++++.+..+....  .++..+
T Consensus        35 ~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~  113 (235)
T TIGR03302        35 ELYEEAKEALDSGDYTEAIKYFEALESRYP-FSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLR  113 (235)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHH
Confidence            344444455555555555555555544311 111   23344445555555555555555555554322111  123333


Q ss_pred             HHHHhcc--------CCHHHHHHHHHHHHHhhhcCcCCCcchh-h-----------------HHHHHHHHHcCCCHHHHH
Q 011236          391 AAGYADK--------NNMEKAFECMKEALAVHEENKFWRPKPS-L-----------------VSSILDWLGDNRDVEEVE  444 (490)
Q Consensus       391 ~~~~~~~--------~~~~~a~~~~~~~~~~~~~~~~~~p~~~-~-----------------~~~l~~~~~~~g~~~~a~  444 (490)
                      ..++...        |++++|.+.+++++..+       |+.. .                 ...+...+.+.|++++|.
T Consensus       114 g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-------p~~~~~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~  186 (235)
T TIGR03302       114 GLSNYNQIDRVDRDQTAAREAFEAFQELIRRY-------PNSEYAPDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAI  186 (235)
T ss_pred             HHHHHHhcccccCCHHHHHHHHHHHHHHHHHC-------CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHH
Confidence            3333332        56677777777776633       3221 1                 124556778899999999


Q ss_pred             HHHHHHHhcccc----hhhhHHHHHHHHhcC--CcHHHHHHHHHhCC
Q 011236          445 AFVSSLKIKVQK----RNMYHALTEAHIRSG--QEVDGLLESMKADD  485 (490)
Q Consensus       445 ~~~~~~~~~~~~----~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~  485 (490)
                      ..++.+.+..|.    ...+..++.++.+.|  ++|..+++.+..+.
T Consensus       187 ~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~  233 (235)
T TIGR03302       187 NRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANY  233 (235)
T ss_pred             HHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            999999988664    688999999999999  89999988887653

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).

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

Probab=98.71  E-value=2.1e-06  Score=81.92  Aligned_cols=260  Identities=15%  Similarity=0.140  Sum_probs=141.3

Q ss_pred             ChhhHHHHHH--HHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhc-C--------CCCC
Q 011236          103 SVHDHAVQLD--LIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEM-G--------SFGS  171 (490)
Q Consensus       103 ~~~~~~~l~~--~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-~--------~~p~  171 (490)
                      ++.+-..+++  .|...|+.+.|.+-.+.+.    +..+|..+.+.|.+.++.+-|.-.+-.|... |        -.|+
T Consensus       725 d~~TRkaml~FSfyvtiG~MD~AfksI~~Ik----S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~  800 (1416)
T KOG3617|consen  725 DESTRKAMLDFSFYVTIGSMDAAFKSIQFIK----SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE  800 (1416)
T ss_pred             CHHHHHhhhceeEEEEeccHHHHHHHHHHHh----hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc
Confidence            4444444433  4556677777766665554    3456777777777777777777666666432 1        1111


Q ss_pred             cchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHH
Q 011236          172 ALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVAN  251 (490)
Q Consensus       172 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~  251 (490)
                       .+-..+.-.....|..++|..+|++..+.         ..|=..|-..|.+++|.++-+.-. +-   .-..||.....
T Consensus       801 -e~eakvAvLAieLgMlEeA~~lYr~ckR~---------DLlNKlyQs~g~w~eA~eiAE~~D-Ri---HLr~Tyy~yA~  866 (1416)
T KOG3617|consen  801 -EDEAKVAVLAIELGMLEEALILYRQCKRY---------DLLNKLYQSQGMWSEAFEIAETKD-RI---HLRNTYYNYAK  866 (1416)
T ss_pred             -chhhHHHHHHHHHhhHHHHHHHHHHHHHH---------HHHHHHHHhcccHHHHHHHHhhcc-ce---ehhhhHHHHHH
Confidence             22222222233455566666666555442         123334445566666655543322 11   22234444555


Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHH
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELE  331 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  331 (490)
                      -+-..++.+.|++.|++.        +...++.. +.+  ..++.....+.++      ..|...|.--...+...|+.+
T Consensus       867 ~Lear~Di~~AleyyEK~--------~~hafev~-rmL--~e~p~~~e~Yv~~------~~d~~L~~WWgqYlES~Gemd  929 (1416)
T KOG3617|consen  867 YLEARRDIEAALEYYEKA--------GVHAFEVF-RML--KEYPKQIEQYVRR------KRDESLYSWWGQYLESVGEMD  929 (1416)
T ss_pred             HHHhhccHHHHHHHHHhc--------CChHHHHH-HHH--HhChHHHHHHHHh------ccchHHHHHHHHHHhcccchH
Confidence            555556666666666552        11111110 000  0111111111111      234455666666667788888


Q ss_pred             HHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHH
Q 011236          332 EAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEAL  411 (490)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  411 (490)
                      .|..+|.....         |-++++..|-.|+.++|-++-++--      |......|.+.|-..|++.+|..+|.++.
T Consensus       930 aAl~~Y~~A~D---------~fs~VrI~C~qGk~~kAa~iA~esg------d~AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  930 AALSFYSSAKD---------YFSMVRIKCIQGKTDKAARIAEESG------DKAACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             HHHHHHHHhhh---------hhhheeeEeeccCchHHHHHHHhcc------cHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            88888877654         3456667777888888877765422      55566677888888888888888887765


Q ss_pred             H
Q 011236          412 A  412 (490)
Q Consensus       412 ~  412 (490)
                      .
T Consensus       995 a  995 (1416)
T KOG3617|consen  995 A  995 (1416)
T ss_pred             H
Confidence            4

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

Probab=98.71  E-value=1.1e-05  Score=80.64  Aligned_cols=238  Identities=12%  Similarity=0.058  Sum_probs=117.2

Q ss_pred             CChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC-hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHH
Q 011236          102 FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV-DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMC  180 (490)
Q Consensus       102 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~  180 (490)
                      .....+..++..+...+++++|.++.+......|+ ...|-.+...+.+.++.+.+..+                 .++.
T Consensus        29 ~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv-----------------~~l~   91 (906)
T PRK14720         29 SKFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLL-----------------NLID   91 (906)
T ss_pred             chHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhh-----------------hhhh
Confidence            34444555555555555555555555554444443 22333333344444443333322                 1222


Q ss_pred             HHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHH
Q 011236          181 LYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKE  260 (490)
Q Consensus       181 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~  260 (490)
                      ......++..+..++..|...+  -+...+..+..+|-+.|+.+++..+++++. +.++ -+..+.|.+...|... +++
T Consensus        92 ~~~~~~~~~~ve~~~~~i~~~~--~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L-~~D~-~n~~aLNn~AY~~ae~-dL~  166 (906)
T PRK14720         92 SFSQNLKWAIVEHICDKILLYG--ENKLALRTLAEAYAKLNENKKLKGVWERLV-KADR-DNPEIVKKLATSYEEE-DKE  166 (906)
T ss_pred             hcccccchhHHHHHHHHHHhhh--hhhHHHHHHHHHHHHcCChHHHHHHHHHHH-hcCc-ccHHHHHHHHHHHHHh-hHH
Confidence            2222333333333333333321  233355556666666666666666666666 5553 5556666666666666 666


Q ss_pred             HHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011236          261 KAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEW  340 (490)
Q Consensus       261 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  340 (490)
                      +|.+++.+....                +...+++..+.++|.++....+                 .+.+.-.++.+.+
T Consensus       167 KA~~m~~KAV~~----------------~i~~kq~~~~~e~W~k~~~~~~-----------------~d~d~f~~i~~ki  213 (906)
T PRK14720        167 KAITYLKKAIYR----------------FIKKKQYVGIEEIWSKLVHYNS-----------------DDFDFFLRIERKV  213 (906)
T ss_pred             HHHHHHHHHHHH----------------HHhhhcchHHHHHHHHHHhcCc-----------------ccchHHHHHHHHH
Confidence            666665554332                3333444455555554443322                 1222223333333


Q ss_pred             Hhc-CCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 011236          341 ELS-CYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA  395 (490)
Q Consensus       341 ~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~  395 (490)
                      ..+ |..--..++-.+-..|...++++++..+++.+.+.... |.....-++.+|.
T Consensus       214 ~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~-n~~a~~~l~~~y~  268 (906)
T PRK14720        214 LGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNK-NNKAREELIRFYK  268 (906)
T ss_pred             HhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCc-chhhHHHHHHHHH
Confidence            322 22222334445556677777777888888887776655 5566666666665

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.70  E-value=4.7e-05  Score=72.20  Aligned_cols=149  Identities=13%  Similarity=0.097  Sum_probs=81.8

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCH
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMI  365 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  365 (490)
                      +.+......|.+|+.+++.+....  .-..-|..+.+.|...|+++.|+++|.+.-         .++--|..|.+.|++
T Consensus       739 ieaai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw  807 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKW  807 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccH
Confidence            344445666777777776554432  233446666777777777777777776531         234556777777777


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHH-------------H------HHHHhhhcCcCCCcch--
Q 011236          366 EKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECM-------------K------EALAVHEENKFWRPKP--  424 (490)
Q Consensus       366 ~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~-------------~------~~~~~~~~~~~~~p~~--  424 (490)
                      +.|.++-.+.  .|+......|-.-..-+-++|++.+|.+++             +      .|+++.   ....|+.  
T Consensus       808 ~da~kla~e~--~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~~~ddmirlv---~k~h~d~l~  882 (1636)
T KOG3616|consen  808 EDAFKLAEEC--HGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHGLDDDMIRLV---EKHHGDHLH  882 (1636)
T ss_pred             HHHHHHHHHh--cCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhCcchHHHHHH---HHhChhhhh
Confidence            7777665433  333334444544444444455444444433             1      122111   1122333  


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHH
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~  450 (490)
                      .|...+..-+...|+...|+.-|-+.
T Consensus       883 dt~~~f~~e~e~~g~lkaae~~flea  908 (1636)
T KOG3616|consen  883 DTHKHFAKELEAEGDLKAAEEHFLEA  908 (1636)
T ss_pred             HHHHHHHHHHHhccChhHHHHHHHhh
Confidence            45566666677777777777655443

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.70  E-value=6.7e-06  Score=68.23  Aligned_cols=159  Identities=12%  Similarity=0.047  Sum_probs=106.1

Q ss_pred             HHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Q 011236          176 NGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII  255 (490)
Q Consensus       176 ~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  255 (490)
                      ..+-..+...|+-+....+....... .+-|....+.++....+.|++..|...|++.. .... +|+.+|+.+.-+|.+
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~-~l~p-~d~~~~~~lgaaldq  146 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAA-RLAP-TDWEAWNLLGAALDQ  146 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHh-ccCC-CChhhhhHHHHHHHH
Confidence            44445555666666666666554332 22344455557777777777777777777776 5555 777777777777777


Q ss_pred             cCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011236          256 AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEK  335 (490)
Q Consensus       256 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  335 (490)
                      .|+++.|..-|.+..+..+  .+....+.+...+.-.|+.+.|..++........ -+...-..+..+....|++++|+.
T Consensus       147 ~Gr~~~Ar~ay~qAl~L~~--~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~-ad~~v~~NLAl~~~~~g~~~~A~~  223 (257)
T COG5010         147 LGRFDEARRAYRQALELAP--NEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPA-ADSRVRQNLALVVGLQGDFREAED  223 (257)
T ss_pred             ccChhHHHHHHHHHHHhcc--CCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCC-CchHHHHHHHHHHhhcCChHHHHh
Confidence            7777777777777776555  4566677777777777777777777775555443 456666667777777777777777


Q ss_pred             HHHHH
Q 011236          336 MLEEW  340 (490)
Q Consensus       336 ~~~~~  340 (490)
                      +...-
T Consensus       224 i~~~e  228 (257)
T COG5010         224 IAVQE  228 (257)
T ss_pred             hcccc
Confidence            65543

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.69  E-value=1.6e-06  Score=68.12  Aligned_cols=107  Identities=11%  Similarity=-0.074  Sum_probs=62.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSSI  430 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l  430 (490)
                      +..+...+...|++++|...|+......+. +...|..+..++...|++++|...|+++..       ..| +...+..+
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~-------l~p~~~~a~~~l   98 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQPW-SWRAHIALAGTWMMLKEYTTAINFYGHALM-------LDASHPEPVYQT   98 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-------cCCCCcHHHHHH
Confidence            334455556666666666666666655433 555666666666666666666666666665       223 33555566


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHH
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEA  466 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~  466 (490)
                      ..++...|+.++|...|+...+..|. +..|.....+
T Consensus        99 g~~l~~~g~~~eAi~~~~~Al~~~p~~~~~~~~~~~~  135 (144)
T PRK15359         99 GVCLKMMGEPGLAREAFQTAIKMSYADASWSEIRQNA  135 (144)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHH
Confidence            66666666666666666666666665 5555444433

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.69  E-value=1.6e-05  Score=65.98  Aligned_cols=115  Identities=22%  Similarity=0.171  Sum_probs=53.2

Q ss_pred             HHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh----cC
Q 011236          288 HYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ----KG  363 (490)
Q Consensus       288 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g  363 (490)
                      .|++.|++++|++....    +  .+......=+..+.+..+.+-|.+.+++|.+.  . +..+.+.|..++.+    .+
T Consensus       117 i~~~~~~~deAl~~~~~----~--~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~i--d-ed~tLtQLA~awv~la~gge  187 (299)
T KOG3081|consen  117 IYMHDGDFDEALKALHL----G--ENLEAAALNVQILLKMHRFDLAEKELKKMQQI--D-EDATLTQLAQAWVKLATGGE  187 (299)
T ss_pred             HhhcCCChHHHHHHHhc----c--chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc--c-hHHHHHHHHHHHHHHhccch
Confidence            34555555555555442    0  11122222233334445555555555555442  1 22333444444432    23


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          364 MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       364 ~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .+.+|.-+|++|-++ ..|+..+.+-...++...|++++|..++++++.
T Consensus       188 k~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~  235 (299)
T KOG3081|consen  188 KIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALD  235 (299)
T ss_pred             hhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHh
Confidence            455555555555443 234555555555555555555555555555555

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.69  E-value=0.00027  Score=64.88  Aligned_cols=414  Identities=10%  Similarity=0.049  Sum_probs=255.0

Q ss_pred             hhccCCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhH
Q 011236           28 YRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDH  107 (490)
Q Consensus        28 ~~~~~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  107 (490)
                      ..|.+..+|..|++.+-..  +-+.+....+++... .+.++..|..-|.......+++....+|...+..-  .+.+.+
T Consensus        15 ~nP~di~sw~~lire~qt~--~~~~~R~~YEq~~~~-FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvkv--LnlDLW   89 (656)
T KOG1914|consen   15 ENPYDIDSWSQLIREAQTQ--PIDKVRETYEQLVNV-FPSSPRAWKLYIERELASKDFESVEKLFSRCLVKV--LNLDLW   89 (656)
T ss_pred             cCCccHHHHHHHHHHHccC--CHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH--hhHhHH
Confidence            3455778899999988765  555566678887643 45567788999999999999999999999988775  467777


Q ss_pred             HHHHHHHHhh-cCHHH----HHHHHHHccc-cC--C-ChhHHHHHHHH---------HHhcCChhHHHHHHHHHHhcCCC
Q 011236          108 AVQLDLIGKV-RGLES----AETYFNSLND-ED--K-VDKLYGALLNC---------YVREGLVDESLSLMQKMKEMGSF  169 (490)
Q Consensus       108 ~~l~~~~~~~-~~~~~----A~~~~~~~~~-~~--p-~~~~~~~li~~---------~~~~g~~~~a~~~~~~m~~~~~~  169 (490)
                      ...+..-.+. |+...    ..+.|+-... .+  + +...|+..+..         |....+.+...++++++....+.
T Consensus        90 ~lYl~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~  169 (656)
T KOG1914|consen   90 KLYLSYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMH  169 (656)
T ss_pred             HHHHHHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCccc
Confidence            7777655432 33322    2222332222 22  2 34456655543         33444566777788887765222


Q ss_pred             C------CcchHHHHHHHH-------HhcCCcCcHHHHHHHHHH--CCCCCCHHH---------------HHHHHHHHhc
Q 011236          170 G------SALNYNGIMCLY-------TNTGQHEKIPDVLLDMKE--NGVPPDNFS---------------YRICINSYGA  219 (490)
Q Consensus       170 p------~~~~~~~l~~~~-------~~~~~~~~a~~~~~~m~~--~~~~p~~~~---------------~~~li~~~~~  219 (490)
                      -      |-.+|..=|+-.       -+...+..|.+++++...  +|+.....+               |-.+|.-- +
T Consensus       170 nlEkLW~DY~~fE~~IN~~tarK~i~e~s~~Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~wE-k  248 (656)
T KOG1914|consen  170 NLEKLWKDYEAFEQEINIITARKFIGERSPEYMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKWE-K  248 (656)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHHH-h
Confidence            1      111221111111       123346677777777643  343222211               22222211 1


Q ss_pred             cCChH---------HHHHHHHHHHhCCCCCCCHHH-HHH----HHHHHHHcCC-------HHHHHHHHHHHhhhhccCCC
Q 011236          220 RSELS---------SMENVLQEMESQSHISMDWGT-YST----VANYYIIAGL-------KEKAIIYLKKCEDIVSKSKD  278 (490)
Q Consensus       220 ~g~~~---------~a~~~~~~~~~~~~~~~~~~~-~~~----li~~~~~~~~-------~~~a~~~~~~~~~~~~~~~~  278 (490)
                      .+-+.         ...-++++...-.+..|++.. |..    .-+.+...|+       -+++..+++........ .+
T Consensus       249 sNpL~t~~~~~~~~Rv~yayeQ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~-~~  327 (656)
T KOG1914|consen  249 SNPLRTLDGTMLTRRVMYAYEQCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLK-EN  327 (656)
T ss_pred             cCCcccccccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHH-HH
Confidence            11111         111222322212222233211 111    1122333343       45666777766554443 44


Q ss_pred             hhhHHHHHHHHHhc---CChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-CchhHHH
Q 011236          279 ALGYNHLISHYASL---GNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY-DFRVPNI  354 (490)
Q Consensus       279 ~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~  354 (490)
                      ..+|..+...--..   +..+.....+++...........+|...++.-.+..-+..|..+|.+..+.+..+ ++.++++
T Consensus       328 ~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A  407 (656)
T KOG1914|consen  328 KLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAA  407 (656)
T ss_pred             HHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHH
Confidence            44554444322211   2356667777777766555556788999999899999999999999999988776 7788889


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch--hhHHHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP--SLVSSILD  432 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~--~~~~~l~~  432 (490)
                      ++.-||. ++.+-|.++|+-=.+.- .-++.--...+..+...++-..+..+|++.+.     .++.|+.  ..|..++.
T Consensus       408 ~mEy~cs-kD~~~AfrIFeLGLkkf-~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~-----s~l~~~ks~~Iw~r~l~  480 (656)
T KOG1914|consen  408 LMEYYCS-KDKETAFRIFELGLKKF-GDSPEYVLKYLDFLSHLNDDNNARALFERVLT-----SVLSADKSKEIWDRMLE  480 (656)
T ss_pred             HHHHHhc-CChhHHHHHHHHHHHhc-CCChHHHHHHHHHHHHhCcchhHHHHHHHHHh-----ccCChhhhHHHHHHHHH
Confidence            9988885 67889999998765542 11334445677888889999999999999998     5666665  79999999


Q ss_pred             HHHcCCCHHHHHHHHHHHHhccc
Q 011236          433 WLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       433 ~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      .-+.-|+...+.++-+++....+
T Consensus       481 yES~vGdL~si~~lekR~~~af~  503 (656)
T KOG1914|consen  481 YESNVGDLNSILKLEKRRFTAFP  503 (656)
T ss_pred             HHHhcccHHHHHHHHHHHHHhcc
Confidence            99999999999999888776655

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.68  E-value=7.6e-06  Score=67.90  Aligned_cols=158  Identities=13%  Similarity=0.098  Sum_probs=95.9

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc
Q 011236          283 NHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQK  362 (490)
Q Consensus       283 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  362 (490)
                      ..+-..+...|+-+....+........+ .+.......+....+.|++..|...+.+.... -++|...|+.+.-+|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~~~-~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l-~p~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIAYP-KDRELLAAQGKNQIRNGNFGEAVSVLRKAARL-APTDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhccCc-ccHHHHHHHHHHHHHhcchHHHHHHHHHHhcc-CCCChhhhhHHHHHHHHc
Confidence            4455555556666666666554333322 34444555666666677777777777666654 345666677777777777


Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHH
Q 011236          363 GMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEE  442 (490)
Q Consensus       363 g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  442 (490)
                      |+++.|..-|.+..+..+. +...++.+...+.-.|+.+.|..++..+..      .-.-|...-..+..+....|++++
T Consensus       148 Gr~~~Ar~ay~qAl~L~~~-~p~~~nNlgms~~L~gd~~~A~~lll~a~l------~~~ad~~v~~NLAl~~~~~g~~~~  220 (257)
T COG5010         148 GRFDEARRAYRQALELAPN-EPSIANNLGMSLLLRGDLEDAETLLLPAYL------SPAADSRVRQNLALVVGLQGDFRE  220 (257)
T ss_pred             cChhHHHHHHHHHHHhccC-CchhhhhHHHHHHHcCCHHHHHHHHHHHHh------CCCCchHHHHHHHHHHhhcCChHH
Confidence            7777777777666665443 455566666666666777777777666655      112244555566666666677777


Q ss_pred             HHHHHHH
Q 011236          443 VEAFVSS  449 (490)
Q Consensus       443 a~~~~~~  449 (490)
                      |+++...
T Consensus       221 A~~i~~~  227 (257)
T COG5010         221 AEDIAVQ  227 (257)
T ss_pred             HHhhccc
Confidence            7665543

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.63  E-value=7.2e-06  Score=80.93  Aligned_cols=131  Identities=15%  Similarity=0.083  Sum_probs=61.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNC  146 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~  146 (490)
                      +...+..|.....+.|++++|..+++...+.. |-+......+...+.+.+++++|+..+++....+| +......+..+
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~-Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~  163 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQRF-PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAKS  163 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Confidence            34444444444445555555555555544443 23334444444444455555555555555444444 23334444444


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHH
Q 011236          147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKE  200 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  200 (490)
                      +.+.|++++|..+|+++...+.. +..++..+..++...|+.++|...|+...+
T Consensus       164 l~~~g~~~~A~~~y~~~~~~~p~-~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~  216 (694)
T PRK15179        164 WDEIGQSEQADACFERLSRQHPE-FENGYVGWAQSLTRRGALWRARDVLQAGLD  216 (694)
T ss_pred             HHHhcchHHHHHHHHHHHhcCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44455555555555554442221 244444444444445555555555544443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.63  E-value=2.5e-05  Score=77.23  Aligned_cols=134  Identities=11%  Similarity=-0.041  Sum_probs=87.9

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHH
Q 011236          241 MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITM  320 (490)
Q Consensus       241 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (490)
                      .+...+..|.......|.+++|..+++...+..+  .+......+...+.+.+++++|+..+++.....+ -+......+
T Consensus        84 ~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~P--d~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p-~~~~~~~~~  160 (694)
T PRK15179         84 HTELFQVLVARALEAAHRSDEGLAVWRGIHQRFP--DSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGS-SSAREILLE  160 (694)
T ss_pred             ccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCC--CcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCC-CCHHHHHHH
Confidence            4566666677777777777777777777666554  4556666666777777777777777776666554 445556666


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      ..++.+.|++++|..+|+++... .+-+..++..+...+...|+.++|...|++..+.
T Consensus       161 a~~l~~~g~~~~A~~~y~~~~~~-~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~  217 (694)
T PRK15179        161 AKSWDEIGQSEQADACFERLSRQ-HPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA  217 (694)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhc-CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            66666777777777777777663 2223556666666677777777777777776664

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.63  E-value=5.2e-05  Score=63.06  Aligned_cols=245  Identities=13%  Similarity=0.026  Sum_probs=135.8

Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHH-
Q 011236          149 REGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSME-  227 (490)
Q Consensus       149 ~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~-  227 (490)
                      -.|++..++..-.......  -++..-..+-++|...|.+.....   ++... -.|.......+......-++.+.-. 
T Consensus        20 Y~Gnyq~~ine~~~~~~~~--~~~e~d~y~~raylAlg~~~~~~~---eI~~~-~~~~lqAvr~~a~~~~~e~~~~~~~~   93 (299)
T KOG3081|consen   20 YLGNYQQCINEAEKFSSSK--TDVELDVYMYRAYLALGQYQIVIS---EIKEG-KATPLQAVRLLAEYLELESNKKSILA   93 (299)
T ss_pred             HhhHHHHHHHHHHhhcccc--chhHHHHHHHHHHHHccccccccc---ccccc-cCChHHHHHHHHHHhhCcchhHHHHH
Confidence            3455555554443332221  233334444555666665544332   22221 1334444444444444444444333 


Q ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 011236          228 NVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKI  307 (490)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  307 (490)
                      ++.+.+. ......+......-...|++.|++++|++..+..       .+......=+..+.+..+.+-|...++.|.+
T Consensus        94 ~l~E~~a-~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~-------~~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~  165 (299)
T KOG3081|consen   94 SLYELVA-DSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLG-------ENLEAAALNVQILLKMHRFDLAEKELKKMQQ  165 (299)
T ss_pred             HHHHHHH-hhccchhHHHHHHhhHHhhcCCChHHHHHHHhcc-------chHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3334443 4444334333333445677777888877777651       2333333334445566677777777777665


Q ss_pred             hcCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011236          308 KCKKQLNRDYITMLGSLVK----IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT  383 (490)
Q Consensus       308 ~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~  383 (490)
                      .   .+..|.+.|..++.+    .+.+..|.-+|++|-+. .+|+..+.+....++...|++++|..+++....+... +
T Consensus       166 i---ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~-d  240 (299)
T KOG3081|consen  166 I---DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAK-D  240 (299)
T ss_pred             c---chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCC-C
Confidence            4   344555555555543    34577788888888765 6777777777777778888888888888888877655 6


Q ss_pred             HHHHHHHHHHHhccCCHHH-HHHHHHHHHH
Q 011236          384 PNSWSIIAAGYADKNNMEK-AFECMKEALA  412 (490)
Q Consensus       384 ~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~  412 (490)
                      +.+...++.+-...|...+ ..+.+...+.
T Consensus       241 petL~Nliv~a~~~Gkd~~~~~r~l~QLk~  270 (299)
T KOG3081|consen  241 PETLANLIVLALHLGKDAEVTERNLSQLKL  270 (299)
T ss_pred             HHHHHHHHHHHHHhCCChHHHHHHHHHHHh
Confidence            6666666655555554433 3455555544

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.61  E-value=8.5e-06  Score=67.78  Aligned_cols=151  Identities=8%  Similarity=-0.041  Sum_probs=116.5

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC
Q 011236          285 LISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM  364 (490)
Q Consensus       285 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  364 (490)
                      .+..|...|+++.+....+....    |. .       .+...++.+++...++...+. -+.|...|..+...|...|+
T Consensus        22 ~~~~Y~~~g~~~~v~~~~~~~~~----~~-~-------~~~~~~~~~~~i~~l~~~L~~-~P~~~~~w~~Lg~~~~~~g~   88 (198)
T PRK10370         22 CVGSYLLSPKWQAVRAEYQRLAD----PL-H-------QFASQQTPEAQLQALQDKIRA-NPQNSEQWALLGEYYLWRND   88 (198)
T ss_pred             HHHHHHHcchHHHHHHHHHHHhC----cc-c-------cccCchhHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHCCC
Confidence            34567889998886544322111    11 0       122366778888888887776 34577889999999999999


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-hccCC--HHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCH
Q 011236          365 IEKADAVLKEIVKKGKTPTPNSWSIIAAGY-ADKNN--MEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDV  440 (490)
Q Consensus       365 ~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~-~~~~~--~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~  440 (490)
                      +++|...|++..+..+. +...+..+..++ ...|+  .++|.++++++++       ..|+ ...+..+...+...|++
T Consensus        89 ~~~A~~a~~~Al~l~P~-~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~-------~dP~~~~al~~LA~~~~~~g~~  160 (198)
T PRK10370         89 YDNALLAYRQALQLRGE-NAELYAALATVLYYQAGQHMTPQTREMIDKALA-------LDANEVTALMLLASDAFMQADY  160 (198)
T ss_pred             HHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHH-------hCCCChhHHHHHHHHHHHcCCH
Confidence            99999999999998765 788888888864 67777  5999999999998       3354 47788888899999999


Q ss_pred             HHHHHHHHHHHhcccc
Q 011236          441 EEVEAFVSSLKIKVQK  456 (490)
Q Consensus       441 ~~a~~~~~~~~~~~~~  456 (490)
                      ++|...|+++.+..|+
T Consensus       161 ~~Ai~~~~~aL~l~~~  176 (198)
T PRK10370        161 AQAIELWQKVLDLNSP  176 (198)
T ss_pred             HHHHHHHHHHHhhCCC
Confidence            9999999999998888

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.60  E-value=0.00015  Score=65.76  Aligned_cols=201  Identities=15%  Similarity=0.063  Sum_probs=132.2

Q ss_pred             ChHHHHHHHHHHHhCCC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHH
Q 011236          222 ELSSMENVLQEMESQSH--ISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMM  299 (490)
Q Consensus       222 ~~~~a~~~~~~~~~~~~--~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  299 (490)
                      ++..+...-+.+. ..+  -.|+...+...+.+......-..+-.++..-.+  +  ......-.....+...|++++|+
T Consensus       252 RIa~lr~ra~q~p-~~~~~d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~--~--~~~aa~YG~A~~~~~~~~~d~A~  326 (484)
T COG4783         252 RIADLRNRAEQSP-PYNKLDSPDFQLARARIRAKYEALPNQQAADLLAKRSK--R--GGLAAQYGRALQTYLAGQYDEAL  326 (484)
T ss_pred             HHHHHHHHHHhCC-CCCCCCCccHHHHHHHHHHHhccccccchHHHHHHHhC--c--cchHHHHHHHHHHHHhcccchHH
Confidence            4445555555554 222  124455555555544444333333333333222  1  12222333333455778888999


Q ss_pred             HHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC-chhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011236          300 KFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD-FRVPNIILLGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       300 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      ..++.+....+ .|+.........+.+.++..+|.+.++.+...  .|+ ....-.+..+|.+.|++.+|..+++.....
T Consensus       327 ~~l~~L~~~~P-~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~  403 (484)
T COG4783         327 KLLQPLIAAQP-DNPYYLELAGDILLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN  403 (484)
T ss_pred             HHHHHHHHhCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc
Confidence            98888777655 66666777788888889999999999988885  444 556667888888899999999888888877


Q ss_pred             CCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Q 011236          379 GKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV  454 (490)
Q Consensus       379 ~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  454 (490)
                      .+. |+..|..|.++|...|+..++.....++                       +...|+++.|...+....+..
T Consensus       404 ~p~-dp~~w~~LAqay~~~g~~~~a~~A~AE~-----------------------~~~~G~~~~A~~~l~~A~~~~  455 (484)
T COG4783         404 DPE-DPNGWDLLAQAYAELGNRAEALLARAEG-----------------------YALAGRLEQAIIFLMRASQQV  455 (484)
T ss_pred             CCC-CchHHHHHHHHHHHhCchHHHHHHHHHH-----------------------HHhCCCHHHHHHHHHHHHHhc
Confidence            655 8888999999999888888777665554                       344577777777777666654

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

Probab=98.57  E-value=2.9e-05  Score=77.60  Aligned_cols=148  Identities=11%  Similarity=0.038  Sum_probs=79.0

Q ss_pred             CcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHH-HHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHH
Q 011236          171 SALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNF-SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTV  249 (490)
Q Consensus       171 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  249 (490)
                      +...+..|+..+...+++++|.++.+...+.  .|+.. .|-.+...+...++.+.+..+  .                +
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv--~----------------~   89 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLL--N----------------L   89 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhh--h----------------h
Confidence            3445666777777777777777777755553  23332 222233344455554443333  1                2


Q ss_pred             HHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCC
Q 011236          250 ANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGE  329 (490)
Q Consensus       250 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  329 (490)
                      +.......++.-...+...|...+   .+..++..+..+|-+.|+.+++..+|++.....+ -++...+.+...|... +
T Consensus        90 l~~~~~~~~~~~ve~~~~~i~~~~---~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~-~n~~aLNn~AY~~ae~-d  164 (906)
T PRK14720         90 IDSFSQNLKWAIVEHICDKILLYG---ENKLALRTLAEAYAKLNENKKLKGVWERLVKADR-DNPEIVKKLATSYEEE-D  164 (906)
T ss_pred             hhhcccccchhHHHHHHHHHHhhh---hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHh-h
Confidence            222222333322233333333322   2344566666666666777777777766666653 5566666666666666 6


Q ss_pred             HHHHHHHHHHHHhc
Q 011236          330 LEEAEKMLEEWELS  343 (490)
Q Consensus       330 ~~~a~~~~~~~~~~  343 (490)
                      .++|.+++.+....
T Consensus       165 L~KA~~m~~KAV~~  178 (906)
T PRK14720        165 KEKAITYLKKAIYR  178 (906)
T ss_pred             HHHHHHHHHHHHHH
Confidence            66666666665543

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.57  E-value=9.5e-05  Score=61.11  Aligned_cols=187  Identities=18%  Similarity=0.113  Sum_probs=119.4

Q ss_pred             CChHHHHHHHHHHHh--CCC-CCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChh
Q 011236          221 SELSSMENVLQEMES--QSH-ISMD-WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKD  296 (490)
Q Consensus       221 g~~~~a~~~~~~~~~--~~~-~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  296 (490)
                      .+.++..+++.++..  ..+ ..++ +..|-.++-+....|+.+.|...++++....+.  +...-..-...+-..|+++
T Consensus        26 rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~--S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   26 RNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPG--SKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             cCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCC--ChhHHHHHHHHHHHhhchh
Confidence            355566666655542  122 3333 334555666667777777777777777766543  2222222222344567788


Q ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      +|.++|+.....++ .|..++.--+...-..|+.-+|++-+.+..+. +..|...|.-+...|...|++++|.-.+++++
T Consensus       104 ~A~e~y~~lL~ddp-t~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~l  181 (289)
T KOG3060|consen  104 EAIEYYESLLEDDP-TDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELL  181 (289)
T ss_pred             hHHHHHHHHhccCc-chhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHH
Confidence            88888887776664 56666666566666667766777777777766 66788888888888888888888888888887


Q ss_pred             HcCCCCCHHHHHHHHHHHhcc---CCHHHHHHHHHHHHH
Q 011236          377 KKGKTPTPNSWSIIAAGYADK---NNMEKAFECMKEALA  412 (490)
Q Consensus       377 ~~~~~p~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~  412 (490)
                      -..+. ++..+..+...+.-.   .+.+.+..+|.++++
T Consensus       182 l~~P~-n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alk  219 (289)
T KOG3060|consen  182 LIQPF-NPLYFQRLAEVLYTQGGAENLELARKYYERALK  219 (289)
T ss_pred             HcCCC-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence            76543 555555555554433   346677788888877

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.56  E-value=3.5e-06  Score=66.24  Aligned_cols=94  Identities=11%  Similarity=0.014  Sum_probs=55.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhc
Q 011236           72 LQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVRE  150 (490)
Q Consensus        72 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~  150 (490)
                      +......+...|++++|...|+...... +.+...+..+..++...|++++|...|+.....+| +..++..+..++.+.
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~~  105 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKMM  105 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHc
Confidence            4444555556666666666666665554 34555555555566666666666666666655554 455555556666666


Q ss_pred             CChhHHHHHHHHHHhc
Q 011236          151 GLVDESLSLMQKMKEM  166 (490)
Q Consensus       151 g~~~~a~~~~~~m~~~  166 (490)
                      |+.++|+..|+.....
T Consensus       106 g~~~eAi~~~~~Al~~  121 (144)
T PRK15359        106 GEPGLAREAFQTAIKM  121 (144)
T ss_pred             CCHHHHHHHHHHHHHh
Confidence            6666666666665554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.54  E-value=0.00018  Score=65.32  Aligned_cols=197  Identities=16%  Similarity=0.094  Sum_probs=111.8

Q ss_pred             HHHHHHHHHHccccC----CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHH
Q 011236          120 LESAETYFNSLNDED----KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVL  195 (490)
Q Consensus       120 ~~~A~~~~~~~~~~~----p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~  195 (490)
                      +.++...-+.++..+    |+...+...+.+......-..+..++.+-.+.  .-...-|..-+. +...|++++|+..+
T Consensus       253 Ia~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~--~~~aa~YG~A~~-~~~~~~~d~A~~~l  329 (484)
T COG4783         253 IADLRNRAEQSPPYNKLDSPDFQLARARIRAKYEALPNQQAADLLAKRSKR--GGLAAQYGRALQ-TYLAGQYDEALKLL  329 (484)
T ss_pred             HHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhccccccchHHHHHHHhCc--cchHHHHHHHHH-HHHhcccchHHHHH
Confidence            344444445554432    44555555555444433333333333222221  112223333333 33567777777777


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhc
Q 011236          196 LDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMD-WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVS  274 (490)
Q Consensus       196 ~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~  274 (490)
                      +.+... .+-|..........+.+.++.++|.+.++++. ...  |+ ....-.+..+|.+.|++.+|+.+++......+
T Consensus       330 ~~L~~~-~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal-~l~--P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~p  405 (484)
T COG4783         330 QPLIAA-QPDNPYYLELAGDILLEANKAKEAIERLKKAL-ALD--PNSPLLQLNLAQALLKGGKPQEAIRILNRYLFNDP  405 (484)
T ss_pred             HHHHHh-CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHH-hcC--CCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcCC
Confidence            776664 22344444555567777777777777777776 333  33 33444566777777777777777777666555


Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 011236          275 KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELS  343 (490)
Q Consensus       275 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  343 (490)
                        .|+..|..|.++|...|+..++.....+.                  +...|++++|...+....+.
T Consensus       406 --~dp~~w~~LAqay~~~g~~~~a~~A~AE~------------------~~~~G~~~~A~~~l~~A~~~  454 (484)
T COG4783         406 --EDPNGWDLLAQAYAELGNRAEALLARAEG------------------YALAGRLEQAIIFLMRASQQ  454 (484)
T ss_pred             --CCchHHHHHHHHHHHhCchHHHHHHHHHH------------------HHhCCCHHHHHHHHHHHHHh
Confidence              56677777777777777766666555432                  34456777777776666655

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.46  E-value=9.1e-05  Score=61.20  Aligned_cols=192  Identities=16%  Similarity=0.092  Sum_probs=138.6

Q ss_pred             HcCCHHHHHHHHHHHhhhhccC---CCh-hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCH
Q 011236          255 IAGLKEKAIIYLKKCEDIVSKS---KDA-LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGEL  330 (490)
Q Consensus       255 ~~~~~~~a~~~~~~~~~~~~~~---~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  330 (490)
                      ...+.++..+++.++......+   ++. ..|..++-+....|+.+.|...++.+....+ .+...-..-..-+-..|++
T Consensus        24 ~~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp-~S~RV~~lkam~lEa~~~~  102 (289)
T KOG3060|consen   24 TVRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFP-GSKRVGKLKAMLLEATGNY  102 (289)
T ss_pred             cccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCC-CChhHHHHHHHHHHHhhch
Confidence            3457888888888887543321   333 3455566677788999999999998777764 3333333333334567899


Q ss_pred             HHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHH
Q 011236          331 EEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEA  410 (490)
Q Consensus       331 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~  410 (490)
                      ++|.++++.+.+.. +.|..++--=+-..-..|+--+|++-+.+..+. +..|...|.-+...|...|++++|.-+++++
T Consensus       103 ~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~  180 (289)
T KOG3060|consen  103 KEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEEL  180 (289)
T ss_pred             hhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHH
Confidence            99999999998874 446666666666666778888888888888776 3449999999999999999999999999999


Q ss_pred             HHhhhcCcCCCcch-hhHHHHHHHHHcCC---CHHHHHHHHHHHHhcccc
Q 011236          411 LAVHEENKFWRPKP-SLVSSILDWLGDNR---DVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       411 ~~~~~~~~~~~p~~-~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~~~  456 (490)
                      +-       +.|-. ..+..+...+.-.|   +.+.+.+++.+..+..+.
T Consensus       181 ll-------~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~~  223 (289)
T KOG3060|consen  181 LL-------IQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNPK  223 (289)
T ss_pred             HH-------cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhChH
Confidence            87       44544 44556666554444   456788899998888774

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

Probab=98.45  E-value=9.6e-06  Score=63.38  Aligned_cols=95  Identities=15%  Similarity=0.053  Sum_probs=50.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA  395 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~  395 (490)
                      ....+...+...|++++|.+.++.+...+ +.+...+..+...|...|++++|...++...+.++. +...+..+...+.
T Consensus        19 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~la~~~~   96 (135)
T TIGR02552        19 QIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPD-DPRPYFHAAECLL   96 (135)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-ChHHHHHHHHHHH
Confidence            34444455555555555555555555532 224445555555555555566665555555554322 4445555555555


Q ss_pred             ccCCHHHHHHHHHHHHH
Q 011236          396 DKNNMEKAFECMKEALA  412 (490)
Q Consensus       396 ~~~~~~~a~~~~~~~~~  412 (490)
                      ..|++++|...|+.+++
T Consensus        97 ~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        97 ALGEPESALKALDLAIE  113 (135)
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            55666666666655555

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

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

Probab=98.37  E-value=2.2e-05  Score=61.35  Aligned_cols=112  Identities=13%  Similarity=0.011  Sum_probs=91.8

Q ss_pred             HHHHHHhcCCCC-CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhh
Q 011236          336 MLEEWELSCYCY-DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       336 ~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  414 (490)
                      .++.....  .| +......+...+...|++++|...|+.+...++. +...|..+...+...|++++|..+++.+... 
T Consensus         5 ~~~~~l~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-   80 (135)
T TIGR02552         5 TLKDLLGL--DSEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPY-NSRYWLGLAACCQMLKEYEEAIDAYALAAAL-   80 (135)
T ss_pred             hHHHHHcC--ChhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-
Confidence            44555553  33 3445667778889999999999999999887654 7888999999999999999999999999871 


Q ss_pred             hcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          415 EENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       415 ~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                           ...+...+..+...+...|++++|...|+...+..|.
T Consensus        81 -----~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~  117 (135)
T TIGR02552        81 -----DPDDPRPYFHAAECLLALGEPESALKALDLAIEICGE  117 (135)
T ss_pred             -----CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccc
Confidence                 2234577888888999999999999999999998887

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

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.36  E-value=0.0034  Score=61.56  Aligned_cols=225  Identities=9%  Similarity=-0.001  Sum_probs=135.5

Q ss_pred             CCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHH
Q 011236           46 LGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAET  125 (490)
Q Consensus        46 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  125 (490)
                      .++...|+..+-.-+.+.+..+....+..+.  +.+.|+.++|..+++.....+. .+..+...+-.+|...++.++|..
T Consensus        22 ~~qfkkal~~~~kllkk~Pn~~~a~vLkaLs--l~r~gk~~ea~~~Le~~~~~~~-~D~~tLq~l~~~y~d~~~~d~~~~   98 (932)
T KOG2053|consen   22 SSQFKKALAKLGKLLKKHPNALYAKVLKALS--LFRLGKGDEALKLLEALYGLKG-TDDLTLQFLQNVYRDLGKLDEAVH   98 (932)
T ss_pred             hHHHHHHHHHHHHHHHHCCCcHHHHHHHHHH--HHHhcCchhHHHHHhhhccCCC-CchHHHHHHHHHHHHHhhhhHHHH
Confidence            3455556653333333333333333333332  3477888888888887776663 477788888888888999999999


Q ss_pred             HHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcC-Cc---------CcHHHHH
Q 011236          126 YFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTG-QH---------EKIPDVL  195 (490)
Q Consensus       126 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-~~---------~~a~~~~  195 (490)
                      +|++..+..|+......+..+|++.+++.+-.++=-+|... .+-+...+=++++.....- ..         .-|.+.+
T Consensus        99 ~Ye~~~~~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~  177 (932)
T KOG2053|consen   99 LYERANQKYPSEELLYHLFMAYVREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMV  177 (932)
T ss_pred             HHHHHHhhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHH
Confidence            99999888888777777888888888776544433333332 2224444444444444332 11         2244556


Q ss_pred             HHHHHCC-CCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhc
Q 011236          196 LDMKENG-VPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVS  274 (490)
Q Consensus       196 ~~m~~~~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~  274 (490)
                      +.+.+.+ .--+..-.......+...|++++|..++..=..+.-...+...-+.-+..+...+++.+..++-.++...+.
T Consensus       178 ~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~~  257 (932)
T KOG2053|consen  178 QKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKGN  257 (932)
T ss_pred             HHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhCC
Confidence            6665543 111222233334455567888888888843321333333444445567778888888888888888877665

>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=98.31  E-value=3.7e-05  Score=70.28  Aligned_cols=120  Identities=17%  Similarity=0.117  Sum_probs=53.6

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC
Q 011236          284 HLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG  363 (490)
Q Consensus       284 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  363 (490)
                      .|+..+...++++.|.++++++....  |+  ....+++.+...++-.+|.+++.+..+. .+-+..........+.+.+
T Consensus       174 ~Ll~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~-~p~d~~LL~~Qa~fLl~k~  248 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcC
Confidence            33334444445555555555444432  22  2223444444444444555555544433 1223333333334444555


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHH
Q 011236          364 MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKE  409 (490)
Q Consensus       364 ~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~  409 (490)
                      +++.|+.+.+++.+..+. +..+|..|..+|.+.|+++.|+..++.
T Consensus       249 ~~~lAL~iAk~av~lsP~-~f~~W~~La~~Yi~~~d~e~ALlaLNs  293 (395)
T PF09295_consen  249 KYELALEIAKKAVELSPS-EFETWYQLAECYIQLGDFENALLALNS  293 (395)
T ss_pred             CHHHHHHHHHHHHHhCch-hHHHHHHHHHHHHhcCCHHHHHHHHhc
Confidence            555555555555544222 333455555555555555555544443

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

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.27  E-value=1.7e-06  Score=49.22  Aligned_cols=33  Identities=30%  Similarity=0.494  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCC
Q 011236          139 LYGALLNCYVREGLVDESLSLMQKMKEMGSFGS  171 (490)
Q Consensus       139 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~  171 (490)
                      +||++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            567777777777777777777777777776665

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.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.23  E-value=2.8e-06  Score=48.24  Aligned_cols=33  Identities=27%  Similarity=0.521  Sum_probs=21.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT  383 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~  383 (490)
                      +||+++.+|++.|++++|.++|++|.+.|+.||
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            466666666666666666666666666666665

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.

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

Probab=98.21  E-value=0.00012  Score=57.87  Aligned_cols=125  Identities=13%  Similarity=0.094  Sum_probs=60.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC---hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc--hhHHHHH
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQL---NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDF--RVPNIIL  356 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~  356 (490)
                      |..++..+ ..++...+...++.+....+ .+   ......+...+...|++++|...|+.+......|+.  ...-.|.
T Consensus        15 y~~~~~~~-~~~~~~~~~~~~~~l~~~~~-~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA   92 (145)
T PF09976_consen   15 YEQALQAL-QAGDPAKAEAAAEQLAKDYP-SSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLA   92 (145)
T ss_pred             HHHHHHHH-HCCCHHHHHHHHHHHHHHCC-CChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHH
Confidence            33344333 25555555555555555443 11   122233445555566666666666666554322221  1222344


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHH
Q 011236          357 LGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEA  410 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~  410 (490)
                      ..+...|++++|+..++......  .....+......|.+.|+.++|...|+.+
T Consensus        93 ~~~~~~~~~d~Al~~L~~~~~~~--~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   93 RILLQQGQYDEALATLQQIPDEA--FKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHcCCHHHHHHHHHhccCcc--hHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            55555666666666664432221  22334455555666666666666665543

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.20  E-value=3.1e-06  Score=47.65  Aligned_cols=33  Identities=36%  Similarity=0.509  Sum_probs=20.6

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCC
Q 011236          138 KLYGALLNCYVREGLVDESLSLMQKMKEMGSFG  170 (490)
Q Consensus       138 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p  170 (490)
                      .+|+.++.+|++.|+++.|.++|++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            356666666666666666666666666666555

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

Probab=98.16  E-value=3.8e-05  Score=70.52  Aligned_cols=120  Identities=16%  Similarity=0.176  Sum_probs=82.3

Q ss_pred             CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC----CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHH
Q 011236          101 AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED----KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYN  176 (490)
Q Consensus       101 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~----p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  176 (490)
                      +.++.....+++.+....+++.+..++-......    .-..+..++++.|.+.|..++++.+++.=...|+-||..++|
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            4455556666666666666666666666555432    112344577777888888888888887777778888888888


Q ss_pred             HHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc
Q 011236          177 GIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGAR  220 (490)
Q Consensus       177 ~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  220 (490)
                      .||+.+.+.|++..|.++..+|...+...+..|+...+.+|.+.
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            88888888888888888777776666656666776666666655

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 [].

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.16  E-value=4.8e-06  Score=46.87  Aligned_cols=32  Identities=22%  Similarity=0.337  Sum_probs=17.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTP  382 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p  382 (490)
                      +|+.++.+|++.|+++.|..+|+.|.+.|++|
T Consensus         3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    3 TYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            45555555555555555555555555555544

>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=98.14  E-value=0.00012  Score=67.00  Aligned_cols=122  Identities=16%  Similarity=0.040  Sum_probs=79.7

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  327 (490)
                      .|+..+...++++.|+.+|+++.+..   |+  ....++..+...++-.+|.+++.+.....+ .+......-...|.+.
T Consensus       174 ~Ll~~l~~t~~~~~ai~lle~L~~~~---pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p-~d~~LL~~Qa~fLl~k  247 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAIELLEKLRERD---PE--VAVLLARVYLLMNEEVEAIRLLNEALKENP-QDSELLNLQAEFLLSK  247 (395)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHhcC---Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhc
Confidence            45555556677777777777766533   22  344466666666677777777776665544 4455555556667777


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          328 GELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       328 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      ++++.|..+.+++.+. .+-+..+|..|..+|.+.|+++.|+..++.+.
T Consensus       248 ~~~~lAL~iAk~av~l-sP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  248 KKYELALEIAKKAVEL-SPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CCHHHHHHHHHHHHHh-CchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            7777777777777775 23344577777777888888887777776654

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

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

Probab=98.14  E-value=0.00017  Score=56.88  Aligned_cols=126  Identities=15%  Similarity=0.101  Sum_probs=92.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC---chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH--HHHHHH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYD---FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTP--NSWSII  390 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~--~~~~~l  390 (490)
                      .|..++..+ ..++...+...++.+.+... .+   ....-.+...+...|++++|...|+.+.+....|+.  .....+
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~-~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDYP-SSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHCC-CChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            455555555 47888999999999988632 22   122333556788899999999999999997643332  245567


Q ss_pred             HHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 011236          391 AAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       391 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  450 (490)
                      ...+...|++++|+..++....     ..  .....+......+.+.|++++|...|+..
T Consensus        92 A~~~~~~~~~d~Al~~L~~~~~-----~~--~~~~~~~~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   92 ARILLQQGQYDEALATLQQIPD-----EA--FKALAAELLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHcCCHHHHHHHHHhccC-----cc--hHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence            7888999999999999976433     22  34456777888999999999999999864

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.11  E-value=0.00016  Score=54.91  Aligned_cols=102  Identities=14%  Similarity=0.050  Sum_probs=50.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKT--PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~--p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                      +..+...+.+.|++++|...|+.+.+..+.  .....+..+...+.+.|+++.|...|+.+....|   +.......+..
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p---~~~~~~~~~~~   81 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYP---KSPKAPDALLK   81 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCC---CCCcccHHHHH
Confidence            334445555555555555555555543221  0123344455555555666666666655554221   11111234444


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      +..++.+.|+.++|.+.++.+.+..|.
T Consensus        82 ~~~~~~~~~~~~~A~~~~~~~~~~~p~  108 (119)
T TIGR02795        82 LGMSLQELGDKEKAKATLQQVIKRYPG  108 (119)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHHHCcC
Confidence            555555556666666666655555554

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.

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.10  E-value=0.013  Score=57.76  Aligned_cols=211  Identities=10%  Similarity=0.065  Sum_probs=131.1

Q ss_pred             chhhhhhhhhccCCCCcccHHHhh--ccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 011236           20 NLEIFTRAYRAVKPVARNNLYSRI--SPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSG   97 (490)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~l~~~l--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~   97 (490)
                      ++......-+..+...+..++.++  .+.|+.+++.. +++.....+.. |..+...+-..|...++.++|..+|++...
T Consensus        28 al~~~~kllkk~Pn~~~a~vLkaLsl~r~gk~~ea~~-~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~  105 (932)
T KOG2053|consen   28 ALAKLGKLLKKHPNALYAKVLKALSLFRLGKGDEALK-LLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQ  105 (932)
T ss_pred             HHHHHHHHHHHCCCcHHHHHHHHHHHHHhcCchhHHH-HHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHh
Confidence            333333444444555566666664  46889999985 88877665555 888999999999999999999999999998


Q ss_pred             CCCCCChhhHHHHHHHHHhhcCHHH----HHHHHHHccccCCChhHHHHHHHHHHhcC-C---------hhHHHHHHHHH
Q 011236           98 QGLAFSVHDHAVQLDLIGKVRGLES----AETYFNSLNDEDKVDKLYGALLNCYVREG-L---------VDESLSLMQKM  163 (490)
Q Consensus        98 ~~~~~~~~~~~~l~~~~~~~~~~~~----A~~~~~~~~~~~p~~~~~~~li~~~~~~g-~---------~~~a~~~~~~m  163 (490)
                      ..  |+......+..+|.+.+++..    |.+++...++   +...+=++++...+.- .         ..-|.+.++.+
T Consensus       106 ~~--P~eell~~lFmayvR~~~yk~qQkaa~~LyK~~pk---~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~  180 (932)
T KOG2053|consen  106 KY--PSEELLYHLFMAYVREKSYKKQQKAALQLYKNFPK---RAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKL  180 (932)
T ss_pred             hC--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCc---ccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHH
Confidence            86  568888888899999888764    5566654433   2322223333333321 1         12355566666


Q ss_pred             HhcC-CCCCcchHHHHHHHHHhcCCcCcHHHHHH-HHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCC
Q 011236          164 KEMG-SFGSALNYNGIMCLYTNTGQHEKIPDVLL-DMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSH  238 (490)
Q Consensus       164 ~~~~-~~p~~~~~~~l~~~~~~~~~~~~a~~~~~-~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  238 (490)
                      .+.+ ..-+..-...-...+-..|++++|++++. ...+.-..-+...-+.-+..+...+++.+..++-.++. ..+
T Consensus       181 l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll-~k~  256 (932)
T KOG2053|consen  181 LEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLL-EKG  256 (932)
T ss_pred             hccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHH-HhC
Confidence            6553 11111111222233446678888888873 33333233344444556666777777777777666666 444

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=98.10  E-value=0.00046  Score=61.36  Aligned_cols=134  Identities=19%  Similarity=0.129  Sum_probs=67.9

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc-CCHHHHHHHHHHHHHc----CCCCC--HHHHHHHHHHH
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQK-GMIEKADAVLKEIVKK----GKTPT--PNSWSIIAAGY  394 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~m~~~----~~~p~--~~~~~~l~~~~  394 (490)
                      ..|...|++..|-+.+..+               ...|... |++++|++.|++..+.    | .+.  ..++..+...+
T Consensus       102 ~~y~~~G~~~~aA~~~~~l---------------A~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~  165 (282)
T PF14938_consen  102 EIYREAGRFSQAAKCLKEL---------------AEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLY  165 (282)
T ss_dssp             HHHHHCT-HHHHHHHHHHH---------------HHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHH
T ss_pred             HHHHhcCcHHHHHHHHHHH---------------HHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHH
Confidence            3445555555555444443               2334444 6666666666665442    1 111  22455666667


Q ss_pred             hccCCHHHHHHHHHHHHHhhhcCcCCCcchh-hHHHHHHHHHcCCCHHHHHHHHHHHHhcccc------hhhhHHHHHHH
Q 011236          395 ADKNNMEKAFECMKEALAVHEENKFWRPKPS-LVSSILDWLGDNRDVEEVEAFVSSLKIKVQK------RNMYHALTEAH  467 (490)
Q Consensus       395 ~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~------~~~~~~l~~~~  467 (490)
                      .+.|++++|.++|++......+....+.+.. .+...+-.+...||...|.+.+++.....|.      ......|+.++
T Consensus       166 ~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~  245 (282)
T PF14938_consen  166 ARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAY  245 (282)
T ss_dssp             HHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHH
Confidence            7777777777777776652211112223332 2233333455567777777777777766543      34455566666


Q ss_pred             HhcC
Q 011236          468 IRSG  471 (490)
Q Consensus       468 ~~~g  471 (490)
                      -...
T Consensus       246 ~~~D  249 (282)
T PF14938_consen  246 EEGD  249 (282)
T ss_dssp             HTT-
T ss_pred             HhCC
Confidence            6555

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

Probab=98.08  E-value=8e-05  Score=68.41  Aligned_cols=119  Identities=13%  Similarity=0.120  Sum_probs=64.4

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC--CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHH
Q 011236          278 DALGYNHLISHYASLGNKDEMMKFWGLQKIKCK--KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNII  355 (490)
Q Consensus       278 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  355 (490)
                      +......++..+....+.+.+..++-+......  ..-+.|..++++.|.+.|..+.+..+++.=...|+-||..++|.|
T Consensus        65 S~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n~L  144 (429)
T PF10037_consen   65 SSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFNLL  144 (429)
T ss_pred             cHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHHHH
Confidence            444455555555555555555555554443321  122334456666666666666666666655555666666666666


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          356 LLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       356 ~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      ++.+.+.|++..|.++...|...+...+..|+..-+.+|.+
T Consensus       145 md~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~  185 (429)
T PF10037_consen  145 MDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYK  185 (429)
T ss_pred             HHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHH
Confidence            66666666666666666555555444455554444444443

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 [].

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=98.04  E-value=0.0083  Score=53.24  Aligned_cols=120  Identities=16%  Similarity=0.024  Sum_probs=53.3

Q ss_pred             HHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHh--cCCCChhhHHHHHHHHHhc
Q 011236          250 ANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIK--CKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       250 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~  327 (490)
                      ..++.+.|+..++-.+++.+.+..+. |++.    .+..+.+.|+  .++.-+++....  -...+..+...+..+....
T Consensus       270 Aralf~d~~~rKg~~ilE~aWK~ePH-P~ia----~lY~~ar~gd--ta~dRlkRa~~L~slk~nnaes~~~va~aAlda  342 (531)
T COG3898         270 ARALFRDGNLRKGSKILETAWKAEPH-PDIA----LLYVRARSGD--TALDRLKRAKKLESLKPNNAESSLAVAEAALDA  342 (531)
T ss_pred             HHHHHhccchhhhhhHHHHHHhcCCC-hHHH----HHHHHhcCCC--cHHHHHHHHHHHHhcCccchHHHHHHHHHHHhc
Confidence            34555556666666666655554443 4321    1111222332  222222222111  1112334444555555555


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh-cCCHHHHHHHHHHHHHc
Q 011236          328 GELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ-KGMIEKADAVLKEIVKK  378 (490)
Q Consensus       328 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~A~~~~~~m~~~  378 (490)
                      |++..|..--+....  ..|....|-.|.+.-.. .|+-.++...+.+..+.
T Consensus       343 ~e~~~ARa~Aeaa~r--~~pres~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         343 GEFSAARAKAEAAAR--EAPRESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             cchHHHHHHHHHHhh--hCchhhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence            655555554444443  24444455444444322 35666666555555543

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.02  E-value=0.00018  Score=54.63  Aligned_cols=97  Identities=8%  Similarity=-0.058  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC----hhHHHHHH
Q 011236           71 ELQRVIRQLRSRKRFKHALQVSEWMSGQGL--AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV----DKLYGALL  144 (490)
Q Consensus        71 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~----~~~~~~li  144 (490)
                      ++..+...+.+.|++++|.+.|+.+.+...  +..+.....+..++.+.|+++.|...|+.+....|+    ..++..+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            444555556666666666666666665432  111334445556666666666666666665554332    33455555


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcC
Q 011236          145 NCYVREGLVDESLSLMQKMKEMG  167 (490)
Q Consensus       145 ~~~~~~g~~~~a~~~~~~m~~~~  167 (490)
                      .++.+.|+.++|...++++.+..
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~~  106 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKRY  106 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHHC
Confidence            56666666666666666666553

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.

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.01  E-value=0.00056  Score=60.78  Aligned_cols=87  Identities=16%  Similarity=-0.010  Sum_probs=46.9

Q ss_pred             HhcCCHHHHHHHHHHHHhcC---CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHH
Q 011236          325 VKIGELEEAEKMLEEWELSC---YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNME  401 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  401 (490)
                      .+.|++..|.+.+.+.+...   ..|+...|........+.|+.++|+.-.+...+.+.. -...|..-..++...++|+
T Consensus       260 fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~s-yikall~ra~c~l~le~~e  338 (486)
T KOG0550|consen  260 FKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSS-YIKALLRRANCHLALEKWE  338 (486)
T ss_pred             hhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHH-HHHHHHHHHHHHHHHHHHH
Confidence            45666777777776666532   2333344444555556667777777666666554211 1112222233444556666


Q ss_pred             HHHHHHHHHHH
Q 011236          402 KAFECMKEALA  412 (490)
Q Consensus       402 ~a~~~~~~~~~  412 (490)
                      +|.+-++.+.+
T Consensus       339 ~AV~d~~~a~q  349 (486)
T KOG0550|consen  339 EAVEDYEKAMQ  349 (486)
T ss_pred             HHHHHHHHHHh
Confidence            66666666665

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=98.01  E-value=0.00011  Score=52.94  Aligned_cols=93  Identities=14%  Similarity=0.034  Sum_probs=44.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDW  433 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~  433 (490)
                      .+...+...|++++|...++++.+.... +...+..+...+...+++++|.+.++......      ..+..++..+...
T Consensus         5 ~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~~~~   77 (100)
T cd00189           5 NLGNLYYKLGDYDEALEYYEKALELDPD-NADAYYNLAAAYYKLGKYEEALEDYEKALELD------PDNAKAYYNLGLA   77 (100)
T ss_pred             HHHHHHHHHhcHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC------CcchhHHHHHHHH
Confidence            3444445555555555555555444322 23444445555555555555555555554411      1122344444455


Q ss_pred             HHcCCCHHHHHHHHHHHHhc
Q 011236          434 LGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       434 ~~~~g~~~~a~~~~~~~~~~  453 (490)
                      +...|+++.|...+....+.
T Consensus        78 ~~~~~~~~~a~~~~~~~~~~   97 (100)
T cd00189          78 YYKLGKYEEALEAYEKALEL   97 (100)
T ss_pred             HHHHHhHHHHHHHHHHHHcc
Confidence            55555555555555554443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.99  E-value=0.0079  Score=51.88  Aligned_cols=179  Identities=11%  Similarity=0.024  Sum_probs=98.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhH---HHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHH
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGY---NHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLV  325 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  325 (490)
                      ....+...|++++|.+.|+++....+.  +....   -.++.++.+.+++++|...+++.....+.-....+...+.+.+
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~--s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~  115 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPF--GPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLT  115 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCC--ChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHh
Confidence            444455566777777777776665443  22222   3345556667777777777776666655333333333333332


Q ss_pred             h--c---------------CC---HHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH
Q 011236          326 K--I---------------GE---LEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPN  385 (490)
Q Consensus       326 ~--~---------------~~---~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~  385 (490)
                      .  .               .|   ...|...|+.+++.               |-...-..+|...+..+.+.    =..
T Consensus       116 ~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~---------------yP~S~ya~~A~~rl~~l~~~----la~  176 (243)
T PRK10866        116 NMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRG---------------YPNSQYTTDATKRLVFLKDR----LAK  176 (243)
T ss_pred             hhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHH---------------CcCChhHHHHHHHHHHHHHH----HHH
Confidence            1  1               11   12333444444443               22223344454444443321    001


Q ss_pred             HHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHH
Q 011236          386 SWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLK  451 (490)
Q Consensus       386 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  451 (490)
                      ---.+..-|.+.|.+..|..-++.+++.+   .+..........++.+|...|..++|..+...+.
T Consensus       177 ~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Y---p~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        177 YELSVAEYYTKRGAYVAVVNRVEQMLRDY---PDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHHHHHcCchHHHHHHHHHHHHHC---CCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            11244566788888888888888888855   2444445667777788888888888887766553

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.99  E-value=0.00016  Score=61.46  Aligned_cols=102  Identities=20%  Similarity=0.107  Sum_probs=80.9

Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHH
Q 011236          323 SLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEK  402 (490)
Q Consensus       323 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  402 (490)
                      -+.+.+++++|...|.+.++. .+-|.+.|..=..+|++.|.++.|++-.+..+..++. -..+|..|..+|...|++++
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l-~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~-yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIEL-DPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPH-YSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhc-CCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChH-HHHHHHHHHHHHHccCcHHH
Confidence            456778899999999998886 3346677777888899999999999888888886544 45688899999999999999


Q ss_pred             HHHHHHHHHHhhhcCcCCCcchhhHHHHHHH
Q 011236          403 AFECMKEALAVHEENKFWRPKPSLVSSILDW  433 (490)
Q Consensus       403 a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~  433 (490)
                      |++.|+++++       +.|+-.+|..=+..
T Consensus       168 A~~aykKaLe-------ldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  168 AIEAYKKALE-------LDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHhhhc-------cCCCcHHHHHHHHH
Confidence            9999999887       66877777655443

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

Probab=97.98  E-value=0.00013  Score=52.20  Aligned_cols=79  Identities=10%  Similarity=0.173  Sum_probs=56.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCC-CCCchhHHHHHHHHHhcC--------CHHHHHHHHHHHHHcCCCCCHHHHH
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSCY-CYDFRVPNIILLGYSQKG--------MIEKADAVLKEIVKKGKTPTPNSWS  388 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g--------~~~~A~~~~~~m~~~~~~p~~~~~~  388 (490)
                      ...|..|...+++.....+|+.+++.|+ -|+..+|+.++.+.++..        ++-..+.+++.|+..+++|+..+|+
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            4455556666788888888888888887 778888888877766542        2445667777787777888888888


Q ss_pred             HHHHHHhc
Q 011236          389 IIAAGYAD  396 (490)
Q Consensus       389 ~l~~~~~~  396 (490)
                      .++..+.+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            87776654

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 [, , ].

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=97.93  E-value=0.015  Score=52.64  Aligned_cols=133  Identities=11%  Similarity=0.081  Sum_probs=105.2

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhcC-CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH-HHHHH
Q 011236          315 RDYITMLGSLVKIGELEEAEKMLEEWELSC-YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSW-SIIAA  392 (490)
Q Consensus       315 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~-~~l~~  392 (490)
                      ..|...+.+-.+..-++.|..+|-+..+.| +.+++.++++++..++. |+..-|..+|+--...  -||...| +-.+.
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~~-~d~~ta~~ifelGl~~--f~d~~~y~~kyl~  474 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYAT-GDRATAYNIFELGLLK--FPDSTLYKEKYLL  474 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHhc-CCcchHHHHHHHHHHh--CCCchHHHHHHHH
Confidence            456777888788888999999999999988 67888899999988774 6777888888765544  2455443 45566


Q ss_pred             HHhccCCHHHHHHHHHHHHHhhhcCcCCCcc--hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          393 GYADKNNMEKAFECMKEALAVHEENKFWRPK--PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       393 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+...++-..|..+|+..+.      .+..+  ...|..+|..-..-|+...+..+-+++....|.
T Consensus       475 fLi~inde~naraLFetsv~------r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~~pQ  534 (660)
T COG5107         475 FLIRINDEENARALFETSVE------RLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRELVPQ  534 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHH------HHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHHcCc
Confidence            67788999999999998876      33344  478999999989999999999888888888776

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

Probab=97.92  E-value=0.00011  Score=52.73  Aligned_cols=79  Identities=19%  Similarity=0.186  Sum_probs=57.4

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCC-CCCcchHHHHHHHHHhcCC--------cCcHHHHHHHHHHCCCCCCHHHHH
Q 011236          141 GALLNCYVREGLVDESLSLMQKMKEMGS-FGSALNYNGIMCLYTNTGQ--------HEKIPDVLLDMKENGVPPDNFSYR  211 (490)
Q Consensus       141 ~~li~~~~~~g~~~~a~~~~~~m~~~~~-~p~~~~~~~l~~~~~~~~~--------~~~a~~~~~~m~~~~~~p~~~~~~  211 (490)
                      ...|..+...+++.....+|+.+++.|+ .|++.+|+.++.+.++..-        .-..+.+|++|+..+++|+..||+
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            3445556666888888888888888888 8888888888887765432        234566777777777888888888


Q ss_pred             HHHHHHhc
Q 011236          212 ICINSYGA  219 (490)
Q Consensus       212 ~li~~~~~  219 (490)
                      .++..+.+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            77776543

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 [, , ].

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.92  E-value=0.00015  Score=64.10  Aligned_cols=50  Identities=12%  Similarity=0.095  Sum_probs=32.9

Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCcc----hHHHHHHHHHhcCCcCcHHHHH
Q 011236          145 NCYVREGLVDESLSLMQKMKEMGSFGSAL----NYNGIMCLYTNTGQHEKIPDVL  195 (490)
Q Consensus       145 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~~----~~~~l~~~~~~~~~~~~a~~~~  195 (490)
                      .-+|+.|+....+.+|+...+.|.. |..    .|..|.++|.-.+++++|+++.
T Consensus        25 ERLck~gdcraGv~ff~aA~qvGTe-Dl~tLSAIYsQLGNAyfyL~DY~kAl~yH   78 (639)
T KOG1130|consen   25 ERLCKMGDCRAGVDFFKAALQVGTE-DLSTLSAIYSQLGNAYFYLKDYEKALKYH   78 (639)
T ss_pred             HHHHhccchhhhHHHHHHHHHhcch-HHHHHHHHHHHhcchhhhHhhHHHHHhhh
Confidence            3467778888888888888777654 433    3555566666666777776653

>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=97.91  E-value=0.00021  Score=51.45  Aligned_cols=94  Identities=16%  Similarity=0.153  Sum_probs=57.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      +..+...+...|++++|...++.+.+.. +.+...+..+...+...|++++|.+.++...+.... +..++..+...+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPD-NAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc-chhHHHHHHHHHHH
Confidence            3445555566666666766666666542 222345555666666667777777777766665433 44566666666777


Q ss_pred             cCCHHHHHHHHHHHHH
Q 011236          397 KNNMEKAFECMKEALA  412 (490)
Q Consensus       397 ~~~~~~a~~~~~~~~~  412 (490)
                      .|+++.|...+....+
T Consensus        81 ~~~~~~a~~~~~~~~~   96 (100)
T cd00189          81 LGKYEEALEAYEKALE   96 (100)
T ss_pred             HHhHHHHHHHHHHHHc
Confidence            7777777777766654

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

Probab=97.88  E-value=1.7e-05  Score=43.40  Aligned_cols=29  Identities=31%  Similarity=0.689  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 011236          139 LYGALLNCYVREGLVDESLSLMQKMKEMG  167 (490)
Q Consensus       139 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~  167 (490)
                      +|++++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            46666666666666666666666666654

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.

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.88  E-value=0.00036  Score=64.09  Aligned_cols=90  Identities=6%  Similarity=-0.073  Sum_probs=53.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM  400 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  400 (490)
                      ...+...|++++|.+.|+++++.. +.+...|..+..+|.+.|++++|+..++++++..+. +...|..+..+|...|++
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~-~~~a~~~lg~~~~~lg~~   86 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDPS-LAKAYLRKGTACMKLEEY   86 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHhCCH
Confidence            344455566666666666666542 223445555566666666666666666666665433 455566666666666666


Q ss_pred             HHHHHHHHHHHH
Q 011236          401 EKAFECMKEALA  412 (490)
Q Consensus       401 ~~a~~~~~~~~~  412 (490)
                      ++|+..|+++++
T Consensus        87 ~eA~~~~~~al~   98 (356)
T PLN03088         87 QTAKAALEKGAS   98 (356)
T ss_pred             HHHHHHHHHHHH
Confidence            666666666665

>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=97.88  E-value=0.00024  Score=57.77  Aligned_cols=61  Identities=16%  Similarity=0.297  Sum_probs=43.5

Q ss_pred             HHHHHHccccCCChhHHHHHHHHHHh-----cCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 011236          124 ETYFNSLNDEDKVDKLYGALLNCYVR-----EGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTN  184 (490)
Q Consensus       124 ~~~~~~~~~~~p~~~~~~~li~~~~~-----~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  184 (490)
                      ...|+.......+-.+|..++..|.+     .|.++=....+..|.+-|+.-|..+|+.|++.+=+
T Consensus        34 ~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPK   99 (228)
T PF06239_consen   34 EELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPK   99 (228)
T ss_pred             HHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCC
Confidence            34455554444566777777777765     36677777788888888888888888888887654

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

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.87  E-value=0.00063  Score=52.79  Aligned_cols=90  Identities=11%  Similarity=-0.008  Sum_probs=63.2

Q ss_pred             HHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCc
Q 011236          110 QLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQH  188 (490)
Q Consensus       110 l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  188 (490)
                      +...+...|++++|..+|+.+...+| +..-|-.|.-++-..|++++|+..|......++. |+..+-.+..++...|+.
T Consensus        41 ~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~d-dp~~~~~ag~c~L~lG~~  119 (157)
T PRK15363         41 YAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKID-APQAPWAAAECYLACDNV  119 (157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHHHHHHcCCH
Confidence            34445567777777777777777776 4555666777777777777777777777777654 667777777777777777


Q ss_pred             CcHHHHHHHHHH
Q 011236          189 EKIPDVLLDMKE  200 (490)
Q Consensus       189 ~~a~~~~~~m~~  200 (490)
                      +.|.+.|+..+.
T Consensus       120 ~~A~~aF~~Ai~  131 (157)
T PRK15363        120 CYAIKALKAVVR  131 (157)
T ss_pred             HHHHHHHHHHHH
Confidence            777777776655

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.86  E-value=0.00085  Score=54.73  Aligned_cols=62  Identities=11%  Similarity=-0.113  Sum_probs=26.8

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC--hhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          281 GYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL--NRDYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       281 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      .+..+...+...|++++|...|++.....+.+.  ...+..+...+.+.|++++|...+++..+
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  100 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALE  100 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            344444444445555555555554443322111  12344444444444444444444444443

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

Probab=97.86  E-value=2.4e-05  Score=42.85  Aligned_cols=29  Identities=31%  Similarity=0.544  Sum_probs=15.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKG  379 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  379 (490)
                      +|+.++++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            45555555555555555555555555544

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.

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.86  E-value=0.00049  Score=63.21  Aligned_cols=92  Identities=9%  Similarity=-0.153  Sum_probs=61.3

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCH
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMI  365 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  365 (490)
                      ...+...|++++|+..|++.+...+ .+...|..+..+|.+.|++++|...++.+.+.. +.+...|..+..+|...|++
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P-~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~   86 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDP-NNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEY   86 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCH
Confidence            3445566777777777777766655 455666667777777777777777777776642 22445566666677777777


Q ss_pred             HHHHHHHHHHHHcC
Q 011236          366 EKADAVLKEIVKKG  379 (490)
Q Consensus       366 ~~A~~~~~~m~~~~  379 (490)
                      ++|...|++.++.+
T Consensus        87 ~eA~~~~~~al~l~  100 (356)
T PLN03088         87 QTAKAALEKGASLA  100 (356)
T ss_pred             HHHHHHHHHHHHhC
Confidence            77777777777654

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.81  E-value=4.2e-05  Score=53.81  Aligned_cols=20  Identities=30%  Similarity=0.395  Sum_probs=9.0

Q ss_pred             HHHHHHhcCCHHHHHHHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKE  374 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~  374 (490)
                      +..+|.+.|++++|..++++
T Consensus        31 la~~~~~~~~y~~A~~~~~~   50 (84)
T PF12895_consen   31 LAQCYFQQGKYEEAIELLQK   50 (84)
T ss_dssp             HHHHHHHTTHHHHHHHHHHC
T ss_pred             HHHHHHHCCCHHHHHHHHHH
Confidence            34444444444444444444

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.81  E-value=0.00055  Score=60.60  Aligned_cols=132  Identities=14%  Similarity=0.143  Sum_probs=59.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLG-YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~  394 (490)
                      +|..+++..-+.+..+.|..+|.+..+.+ ..+..+|-..... |...++.+.|.++|+...+.- ..+...|...++.+
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f-~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKF-PSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHH-TT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHH
Confidence            34445555555555555555555555321 1122233333333 222344444555555555442 22444555555555


Q ss_pred             hccCCHHHHHHHHHHHHHhhhcCcCCCcch---hhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          395 ADKNNMEKAFECMKEALAVHEENKFWRPKP---SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       395 ~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~---~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      .+.++.+.|..+|++++.      .+.++.   ..|...+..-.+.|+.+.+.++.+++.+..+
T Consensus        81 ~~~~d~~~aR~lfer~i~------~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~  138 (280)
T PF05843_consen   81 IKLNDINNARALFERAIS------SLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFP  138 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCC------TSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTT
T ss_pred             HHhCcHHHHHHHHHHHHH------hcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhh
Confidence            555555555555555554      121211   3555555555555555555555555554433

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.

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.80  E-value=0.00065  Score=52.72  Aligned_cols=90  Identities=7%  Similarity=-0.015  Sum_probs=49.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDW  433 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~  433 (490)
                      +...+...|++++|.++|+.+...++. +..-|-.|..++-..|++++|+..|..+..       +.|| +..+-.+..+
T Consensus        41 ~A~~ly~~G~l~~A~~~f~~L~~~Dp~-~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~-------L~~ddp~~~~~ag~c  112 (157)
T PRK15363         41 YAMQLMEVKEFAGAARLFQLLTIYDAW-SFDYWFRLGECCQAQKHWGEAIYAYGRAAQ-------IKIDAPQAPWAAAEC  112 (157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHh-------cCCCCchHHHHHHHH
Confidence            334445556666666666665554433 445555555556666666666666666655       2232 2455555555


Q ss_pred             HHcCCCHHHHHHHHHHHHh
Q 011236          434 LGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       434 ~~~~g~~~~a~~~~~~~~~  452 (490)
                      +...|+.+.|++.|+....
T Consensus       113 ~L~lG~~~~A~~aF~~Ai~  131 (157)
T PRK15363        113 YLACDNVCYAIKALKAVVR  131 (157)
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            6666666666666655544

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.80  E-value=0.00013  Score=51.27  Aligned_cols=80  Identities=24%  Similarity=0.225  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011236          257 GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM  336 (490)
Q Consensus       257 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  336 (490)
                      |+++.|+.+++++....+..++...+..+..+|.+.|++++|..+++. ....+ .+......+..+|.+.|++++|.++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            444444444444444333101222333344444444444444444443 11111 1122222334444444444444444


Q ss_pred             HH
Q 011236          337 LE  338 (490)
Q Consensus       337 ~~  338 (490)
                      ++
T Consensus        81 l~   82 (84)
T PF12895_consen   81 LE   82 (84)
T ss_dssp             HH
T ss_pred             Hh
Confidence            43

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.79  E-value=0.02  Score=54.73  Aligned_cols=54  Identities=4%  Similarity=-0.010  Sum_probs=31.6

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011236          205 PDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK  268 (490)
Q Consensus       205 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  268 (490)
                      -|....-.+..++.+.|.-++|.+.|-+..    . |-     ..+..|...++|.+|.++-+.
T Consensus       850 e~s~llp~~a~mf~svGMC~qAV~a~Lr~s----~-pk-----aAv~tCv~LnQW~~avelaq~  903 (1189)
T KOG2041|consen  850 EDSELLPVMADMFTSVGMCDQAVEAYLRRS----L-PK-----AAVHTCVELNQWGEAVELAQR  903 (1189)
T ss_pred             cccchHHHHHHHHHhhchHHHHHHHHHhcc----C-cH-----HHHHHHHHHHHHHHHHHHHHh
Confidence            344455566667777777777766654432    1 11     144556666777777766655

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.78  E-value=0.0021  Score=57.23  Aligned_cols=106  Identities=14%  Similarity=-0.013  Sum_probs=75.9

Q ss_pred             HHhcCCHHHHHHHHHHHHHcC---CCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHH
Q 011236          359 YSQKGMIEKADAVLKEIVKKG---KTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWL  434 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~---~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~  434 (490)
                      ..+.|++.+|.+.+.+.+..+   ..|+...|.....+..+.|+.++|+.-.++++.       +.|.. ..+..-..++
T Consensus       259 ~fk~G~y~~A~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~-------iD~syikall~ra~c~  331 (486)
T KOG0550|consen  259 AFKNGNYRKAYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALK-------IDSSYIKALLRRANCH  331 (486)
T ss_pred             HhhccchhHHHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhh-------cCHHHHHHHHHHHHHH
Confidence            567899999999999998754   456777888888889999999999999999987       22322 2233333455


Q ss_pred             HcCCCHHHHHHHHHHHHhcccc---hhhhHHHHHHHHhcC
Q 011236          435 GDNRDVEEVEAFVSSLKIKVQK---RNMYHALTEAHIRSG  471 (490)
Q Consensus       435 ~~~g~~~~a~~~~~~~~~~~~~---~~~~~~l~~~~~~~g  471 (490)
                      ...++|++|.+-+++..+....   ..++.-...++.+..
T Consensus       332 l~le~~e~AV~d~~~a~q~~~s~e~r~~l~~A~~aLkkSk  371 (486)
T KOG0550|consen  332 LALEKWEEAVEDYEKAMQLEKDCEIRRTLREAQLALKKSK  371 (486)
T ss_pred             HHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHhh
Confidence            6678999999999887765544   444544444554444

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.78  E-value=0.00042  Score=59.09  Aligned_cols=98  Identities=17%  Similarity=0.044  Sum_probs=82.0

Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-CchhHHHHHHHHHhcCCHHH
Q 011236          289 YASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY-DFRVPNIILLGYSQKGMIEK  367 (490)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~  367 (490)
                      +.+.+++.+|+..|.+.+...+ .|...|..-..+|++.|.++.|.+-.+..+..  .| ...+|..|..+|...|++++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~P-~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~i--Dp~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELDP-TNAVYYCNRAAAYSKLGEYEDAVKDCESALSI--DPHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCC-CcchHHHHHHHHHHHhcchHHHHHHHHHHHhc--ChHHHHHHHHHHHHHHccCcHHH
Confidence            6778999999999999988776 78888899999999999999999988888774  33 35689999999999999999


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHH
Q 011236          368 ADAVLKEIVKKGKTPTPNSWSIIA  391 (490)
Q Consensus       368 A~~~~~~m~~~~~~p~~~~~~~l~  391 (490)
                      |.+.|++.++.  .|+-.+|..=+
T Consensus       168 A~~aykKaLel--dP~Ne~~K~nL  189 (304)
T KOG0553|consen  168 AIEAYKKALEL--DPDNESYKSNL  189 (304)
T ss_pred             HHHHHHhhhcc--CCCcHHHHHHH
Confidence            99999999886  45555554333

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.75  E-value=0.00093  Score=54.31  Aligned_cols=96  Identities=18%  Similarity=-0.013  Sum_probs=53.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCY--DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG  393 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~  393 (490)
                      .+..+...+...|++++|...++........+  ...++..+...|...|++++|+..+++....... ...++..+...
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~-~~~~~~~la~i  115 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPF-LPQALNNMAVI  115 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHH
Confidence            34455555555666666666666665442221  1235556666666667777777776666654322 33445555555


Q ss_pred             Hh-------ccCCHHHHHHHHHHHHH
Q 011236          394 YA-------DKNNMEKAFECMKEALA  412 (490)
Q Consensus       394 ~~-------~~~~~~~a~~~~~~~~~  412 (490)
                      +.       ..|+++.|...++++..
T Consensus       116 ~~~~~~~~~~~g~~~~A~~~~~~a~~  141 (168)
T CHL00033        116 CHYRGEQAIEQGDSEIAEAWFDQAAE  141 (168)
T ss_pred             HHHhhHHHHHcccHHHHHHHHHHHHH
Confidence            54       66777766555555544

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.74  E-value=0.00028  Score=62.54  Aligned_cols=285  Identities=14%  Similarity=0.001  Sum_probs=130.3

Q ss_pred             HHHhcCCcCcHHHHHHHHHHCCCCCCH----HHHHHHHHHHhccCChHHHHHHHHHHH---h--CCCCCCCHHHHHHHHH
Q 011236          181 LYTNTGQHEKIPDVLLDMKENGVPPDN----FSYRICINSYGARSELSSMENVLQEME---S--QSHISMDWGTYSTVAN  251 (490)
Q Consensus       181 ~~~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~---~--~~~~~~~~~~~~~li~  251 (490)
                      -+++.|+......+|+..++-|.. |.    .+|..|.++|.-.+++++|+++...=.   .  .... -.......|.+
T Consensus        26 RLck~gdcraGv~ff~aA~qvGTe-Dl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdkl-GEAKssgNLGN  103 (639)
T KOG1130|consen   26 RLCKMGDCRAGVDFFKAALQVGTE-DLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKL-GEAKSSGNLGN  103 (639)
T ss_pred             HHHhccchhhhHHHHHHHHHhcch-HHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchh-ccccccccccc
Confidence            367777888888888877776642 32    345666667777777777776532111   0  0001 11222333455


Q ss_pred             HHHHcCCHHHHHHHHHH----HhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc
Q 011236          252 YYIIAGLKEKAIIYLKK----CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~----~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  327 (490)
                      .+--.|.+++|+-.-.+    ..+.+........+-.+...|...|+.-....-    ...+..+...+           
T Consensus       104 tlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~p----ee~g~f~~ev~-----------  168 (639)
T KOG1130|consen  104 TLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAP----EEKGAFNAEVT-----------  168 (639)
T ss_pred             hhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCCh----hhcccccHHHH-----------
Confidence            55555666665543322    222222212223444444555443321100000    00000000000           


Q ss_pred             CCHHHHHHHHHHHH----hcCCC-CCchhHHHHHHHHHhcCCHHHHHHHHHHHH----HcCCC-CCHHHHHHHHHHHhcc
Q 011236          328 GELEEAEKMLEEWE----LSCYC-YDFRVPNIILLGYSQKGMIEKADAVLKEIV----KKGKT-PTPNSWSIIAAGYADK  397 (490)
Q Consensus       328 ~~~~~a~~~~~~~~----~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~----~~~~~-p~~~~~~~l~~~~~~~  397 (490)
                      ..++.|.++|.+-.    +.|-. .--..|..|...|.-.|+++.|+...+.-.    +.|-+ .....+..+..++.-.
T Consensus       169 ~al~~Av~fy~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hifl  248 (639)
T KOG1130|consen  169 SALENAVKFYMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFL  248 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhh
Confidence            01122222222211    11100 011234445555555666766665443321    22211 1223566666777777


Q ss_pred             CCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHh----ccc--c-hhhhHHHHHHHHhc
Q 011236          398 NNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKI----KVQ--K-RNMYHALTEAHIRS  470 (490)
Q Consensus       398 ~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~~~--~-~~~~~~l~~~~~~~  470 (490)
                      |+++.|.+.|+..+.+..+-..-.....+..+|...|.-..+++.|+.++.+-..    .+-  . ...+.+|..+|...
T Consensus       249 g~fe~A~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~al  328 (639)
T KOG1130|consen  249 GNFELAIEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNAL  328 (639)
T ss_pred             cccHhHHHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhh
Confidence            7777777777665442221111222334455666666666666666665543222    111  1 56666777777776


Q ss_pred             C--CcHHHHHHHHH
Q 011236          471 G--QEVDGLLESMK  482 (490)
Q Consensus       471 g--~~a~~~~~~m~  482 (490)
                      |  ++|+.+.+.-.
T Consensus       329 g~h~kAl~fae~hl  342 (639)
T KOG1130|consen  329 GEHRKALYFAELHL  342 (639)
T ss_pred             hhHHHHHHHHHHHH
Confidence            6  66665555443

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.74  E-value=0.012  Score=49.31  Aligned_cols=173  Identities=14%  Similarity=0.051  Sum_probs=76.4

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSK-DALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  327 (490)
                      ....+...|++++|...|+.+....+.++ -....-.++.++.+.|+++.|...++..+...+......+...+.+.+..
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~   90 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYY   90 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHH
Confidence            44455566666666666666665544211 12334455566666666666666666666655522222222222222211


Q ss_pred             C-------------CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011236          328 G-------------ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       328 ~-------------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~  394 (490)
                      .             ...+|...|               ..++.-|-...-..+|...+..+.+.    =..---.+...|
T Consensus        91 ~~~~~~~~~~~D~~~~~~A~~~~---------------~~li~~yP~S~y~~~A~~~l~~l~~~----la~~e~~ia~~Y  151 (203)
T PF13525_consen   91 KQIPGILRSDRDQTSTRKAIEEF---------------EELIKRYPNSEYAEEAKKRLAELRNR----LAEHELYIARFY  151 (203)
T ss_dssp             HHHHHHH-TT---HHHHHHHHHH---------------HHHHHH-TTSTTHHHHHHHHHHHHHH----HHHHHHHHHHHH
T ss_pred             HhCccchhcccChHHHHHHHHHH---------------HHHHHHCcCchHHHHHHHHHHHHHHH----HHHHHHHHHHHH
Confidence            1             111222222               22333333334444444444433321    001112234556


Q ss_pred             hccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHH
Q 011236          395 ADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEV  443 (490)
Q Consensus       395 ~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a  443 (490)
                      .+.|.+..|..-++.+++.+|   +..........++.++.+.|..+.+
T Consensus       152 ~~~~~y~aA~~r~~~v~~~yp---~t~~~~~al~~l~~~y~~l~~~~~a  197 (203)
T PF13525_consen  152 YKRGKYKAAIIRFQYVIENYP---DTPAAEEALARLAEAYYKLGLKQAA  197 (203)
T ss_dssp             HCTT-HHHHHHHHHHHHHHST---TSHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred             HHcccHHHHHHHHHHHHHHCC---CCchHHHHHHHHHHHHHHhCChHHH
Confidence            666666666666666666331   1111223445556666666665533

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.74  E-value=0.0024  Score=61.40  Aligned_cols=133  Identities=9%  Similarity=-0.003  Sum_probs=68.7

Q ss_pred             CChhhHHHHHHHHHhcC-----ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc--------CCHHHHHHHHHHHHhc
Q 011236          277 KDALGYNHLISHYASLG-----NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI--------GELEEAEKMLEEWELS  343 (490)
Q Consensus       277 ~~~~~~~~l~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------~~~~~a~~~~~~~~~~  343 (490)
                      .|...|...+++.....     +...|..+|++.....+ .....+..+..++...        .++..+.+...+....
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP-~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~al  413 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEP-DFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVAL  413 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhhc
Confidence            45566666665543321     24466666666666554 3333343333322211        1122233333332221


Q ss_pred             -CCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          344 -CYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       344 -~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                       ....+...|..+.-.+...|++++|...+++.++.+  |+...|..+...+...|+.++|.+.++++..
T Consensus       414 ~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~--ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~  481 (517)
T PRK10153        414 PELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLE--MSWLNYVLLGKVYELKGDNRLAADAYSTAFN  481 (517)
T ss_pred             ccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence             122233455555555555667777777777766654  4566666666667777777777777776665

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.70  E-value=0.0025  Score=52.03  Aligned_cols=95  Identities=14%  Similarity=0.042  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          243 WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD-ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       243 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                      ...+..+...+...|++++|...|++.....+..++ ...+..+...+.+.|++++|...+.+.....+ .+...+..+.
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg  113 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNP-KQPSALNNIA  113 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHHHH
Confidence            455677778888889999999999888765443122 46788888888889999999999888877654 4456666777


Q ss_pred             HHHHhcCCHHHHHHHHH
Q 011236          322 GSLVKIGELEEAEKMLE  338 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~  338 (490)
                      ..+...|+...+..-++
T Consensus       114 ~~~~~~g~~~~a~~~~~  130 (172)
T PRK02603        114 VIYHKRGEKAEEAGDQD  130 (172)
T ss_pred             HHHHHcCChHhHhhCHH
Confidence            77777777655544333

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.70  E-value=0.017  Score=48.53  Aligned_cols=176  Identities=13%  Similarity=0.047  Sum_probs=104.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCC--CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHH
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKK--QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGY  359 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  359 (490)
                      .-.....+...|++.+|...|+.+....+.  --......++.++.+.|+++.|...++.+.+.-+.....-+...+.+.
T Consensus         8 lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~   87 (203)
T PF13525_consen    8 LYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGL   87 (203)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHH
Confidence            334455667788999999999988877652  222445677788888999999999999888752222222233333333


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCC---CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc
Q 011236          360 SQKGMIEKADAVLKEIVKKGKTP---TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD  436 (490)
Q Consensus       360 ~~~g~~~~A~~~~~~m~~~~~~p---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~  436 (490)
                      +.........     ....+...   -...+..++.-|=......+|...+..+.+..         ...-..+...|.+
T Consensus        88 ~~~~~~~~~~-----~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~l---------a~~e~~ia~~Y~~  153 (203)
T PF13525_consen   88 SYYKQIPGIL-----RSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNRL---------AEHELYIARFYYK  153 (203)
T ss_dssp             HHHHHHHHHH------TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHH---------HHHHHHHHHHHHC
T ss_pred             HHHHhCccch-----hcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHH
Confidence            2211111110     00000000   01235555555666666666666555554411         1112246678999


Q ss_pred             CCCHHHHHHHHHHHHhcccc----hhhhHHHHHHHHhcC
Q 011236          437 NRDVEEVEAFVSSLKIKVQK----RNMYHALTEAHIRSG  471 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~----~~~~~~l~~~~~~~g  471 (490)
                      .|.+..|..-++.+.+..|.    ......++.+|.+.|
T Consensus       154 ~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~  192 (203)
T PF13525_consen  154 RGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLG  192 (203)
T ss_dssp             TT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT
T ss_pred             cccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhC
Confidence            99999999999999999887    678889999999999

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.69  E-value=0.0013  Score=58.23  Aligned_cols=130  Identities=10%  Similarity=0.077  Sum_probs=60.1

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH-cCCHHHHHHHHHHHhhhhccCCChhhHHHHHH
Q 011236          209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII-AGLKEKAIIYLKKCEDIVSKSKDALGYNHLIS  287 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  287 (490)
                      +|..+++..-+.+..+.|..+|.+.. +.+. .+...|......-.. .++.+.|..+|+...+..+  .+...|...+.
T Consensus         3 v~i~~m~~~~r~~g~~~aR~vF~~a~-~~~~-~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~--~~~~~~~~Y~~   78 (280)
T PF05843_consen    3 VWIQYMRFMRRTEGIEAARKVFKRAR-KDKR-CTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFP--SDPDFWLEYLD   78 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH-CCCC-S-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHT--T-HHHHHHHHH
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHH-cCCC-CCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCC--CCHHHHHHHHH
Confidence            45555555555555555555555555 3222 233334333333222 3444445555555555443  34455555555


Q ss_pred             HHHhcCChhHHHHHHHHHHHhcCC-C-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          288 HYASLGNKDEMMKFWGLQKIKCKK-Q-LNRDYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       288 ~~~~~~~~~~a~~~~~~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      .+...|+.+.|..+|++....-.. . ....|...+.-=.+.|+++.+..+.+.+.+
T Consensus        79 ~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   79 FLIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            555555555555555544443210 0 112445555544555555555555555544

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.

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.67  E-value=0.0057  Score=54.45  Aligned_cols=60  Identities=8%  Similarity=0.003  Sum_probs=24.6

Q ss_pred             HHhccCCHHHHHHHHHHHHHhhhcCcCCCcc--hhhHHHHHHHHHc--CCCHHHHHHHHHHHHhccc
Q 011236          393 GYADKNNMEKAFECMKEALAVHEENKFWRPK--PSLVSSILDWLGD--NRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       393 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~--~g~~~~a~~~~~~~~~~~~  455 (490)
                      ++...||...|...+++.....   .++..+  ......|+.++-.  ...+..+..-|+.+.+..+
T Consensus       205 ~~L~~~D~v~A~~~~~~~~~~~---~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~~~ld~  268 (282)
T PF14938_consen  205 CHLAMGDYVAARKALERYCSQD---PSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSISRLDN  268 (282)
T ss_dssp             HHHHTT-HHHHHHHHHHHGTTS---TTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTSS---H
T ss_pred             HHHHcCCHHHHHHHHHHHHhhC---CCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHcccCccHH
Confidence            3334455555555555544422   122222  2344455555543  3445555555554444433

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.67  E-value=0.0035  Score=53.94  Aligned_cols=99  Identities=11%  Similarity=0.028  Sum_probs=55.4

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCCCHHHHH
Q 011236          312 QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG---MIEKADAVLKEIVKKGKTPTPNSWS  388 (490)
Q Consensus       312 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~m~~~~~~p~~~~~~  388 (490)
                      .|...|..|..+|...|+.+.|..-|.+..+. .+++...+..+..++....   ...++..+|+++...+.. |+.+..
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL-~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~-~iral~  231 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRL-AGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPA-NIRALS  231 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCc-cHHHHH
Confidence            55556666666666666666666666665554 2334444444444433221   234556666666665544 555555


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHH
Q 011236          389 IIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       389 ~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .|...+...|++.+|...|+.|++
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~  255 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLD  255 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHh
Confidence            556666666666666666666665

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.66  E-value=0.0016  Score=52.90  Aligned_cols=64  Identities=9%  Similarity=-0.017  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCC-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSK-DALGYNHLISHYASLGNKDEMMKFWGLQKIK  308 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  308 (490)
                      .|..+...+...|++++|+..|++.....+..+ ...++..+...+...|++++|...++.....
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~  101 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER  101 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            334444445555555555555555443322101 1234455555555555555555555544443

>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=97.65  E-value=0.00025  Score=47.48  Aligned_cols=62  Identities=13%  Similarity=0.096  Sum_probs=40.7

Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHH
Q 011236           80 RSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGA  142 (490)
Q Consensus        80 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~  142 (490)
                      .+.|++++|+++|+.+.... |-+......+..++.+.|++++|..+++.+....|+...|..
T Consensus         2 l~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~   63 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQ   63 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHH
Confidence            35677777777777776665 346666666777777777777777777777776666434433

...

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.64  E-value=0.018  Score=49.64  Aligned_cols=174  Identities=10%  Similarity=0.021  Sum_probs=103.7

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCChhh---HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHH
Q 011236          284 HLISHYASLGNKDEMMKFWGLQKIKCKKQLNRD---YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYS  360 (490)
Q Consensus       284 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  360 (490)
                      .....+...|++++|.+.|+......+.+ ...   .-.++.++.+.+++++|...+++..+.-+.....-+...+.+.+
T Consensus        37 ~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~  115 (243)
T PRK10866         37 ATAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLT  115 (243)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHh
Confidence            34445566788888888888777766522 222   23556677778888888888888777532222223333333332


Q ss_pred             h--cC---------------C---HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCC
Q 011236          361 Q--KG---------------M---IEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFW  420 (490)
Q Consensus       361 ~--~g---------------~---~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  420 (490)
                      .  .+               +   ..+|...|+.+++               -|=...-..+|...+..+....      
T Consensus       116 ~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~---------------~yP~S~ya~~A~~rl~~l~~~l------  174 (243)
T PRK10866        116 NMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVR---------------GYPNSQYTTDATKRLVFLKDRL------  174 (243)
T ss_pred             hhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHH---------------HCcCChhHHHHHHHHHHHHHHH------
Confidence            1  10               1   1223333333333               3333333444444333332200      


Q ss_pred             CcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc----hhhhHHHHHHHHhcC--CcHHHHHHHHH
Q 011236          421 RPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK----RNMYHALTEAHIRSG--QEVDGLLESMK  482 (490)
Q Consensus       421 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~l~~~~~~~g--~~a~~~~~~m~  482 (490)
                         ...-..+.+-|.+.|.+..|..=++.+.+.-|.    ......++.+|.+.|  ++|......+.
T Consensus       175 ---a~~e~~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        175 ---AKYELSVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             ---HHHHHHHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence               011125567788999999999999999998887    778889999999999  77777665543

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.64  E-value=0.0088  Score=47.34  Aligned_cols=101  Identities=12%  Similarity=-0.062  Sum_probs=47.5

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC-CCChhhHHH
Q 011236          241 MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK-KQLNRDYIT  319 (490)
Q Consensus       241 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~  319 (490)
                      |++..-..|..+....|+..+|...|.+....... .|......+.++....+++..|...++.+.+..+ ..++.+...
T Consensus        87 pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA-~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll  165 (251)
T COG4700          87 PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFA-HDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLL  165 (251)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccC-CCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHH
Confidence            44444444555555555555555555554443222 4444444455555555555555555554444332 112223334


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHh
Q 011236          320 MLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       320 l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      +.+.+...|..++|+.-|+....
T Consensus       166 ~aR~laa~g~~a~Aesafe~a~~  188 (251)
T COG4700         166 FARTLAAQGKYADAESAFEVAIS  188 (251)
T ss_pred             HHHHHHhcCCchhHHHHHHHHHH
Confidence            44445555555555555555544

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.62  E-value=0.018  Score=48.37  Aligned_cols=130  Identities=12%  Similarity=0.038  Sum_probs=62.9

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHH----
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILL----  357 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~----  357 (490)
                      .+.++.++...|.+.-....+.+.+...+..++.....+++.-.+.||.+.|...|+...+..-..|..+++.++.    
T Consensus       180 my~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~a  259 (366)
T KOG2796|consen  180 MYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNSA  259 (366)
T ss_pred             HHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhhh
Confidence            3444444444555555555555555554444445555555555555555555555555444332333333332222    


Q ss_pred             -HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          358 -GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       358 -~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                       .|.-.+++.+|...+.+....+.. |+..-|.-.-+..-.|+..+|++.++.|++
T Consensus       260 ~i~lg~nn~a~a~r~~~~i~~~D~~-~~~a~NnKALcllYlg~l~DAiK~~e~~~~  314 (366)
T KOG2796|consen  260 FLHLGQNNFAEAHRFFTEILRMDPR-NAVANNNKALCLLYLGKLKDALKQLEAMVQ  314 (366)
T ss_pred             hheecccchHHHHHHHhhccccCCC-chhhhchHHHHHHHHHHHHHHHHHHHHHhc
Confidence             233345555555555555554433 333333333333334555556666655555

>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=97.60  E-value=0.001  Score=54.20  Aligned_cols=88  Identities=14%  Similarity=0.157  Sum_probs=60.2

Q ss_pred             CChhhHHHHHHHHHh-----cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc----------------CCHHHHHH
Q 011236          312 QLNRDYITMLGSLVK-----IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQK----------------GMIEKADA  370 (490)
Q Consensus       312 ~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------------g~~~~A~~  370 (490)
                      .+..+|..+++.+.+     .|.++=....+..|.+-|+.-|..+|+.|++.+=+.                .+.+-|++
T Consensus        45 k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~  124 (228)
T PF06239_consen   45 KDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAID  124 (228)
T ss_pred             ccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHH
Confidence            444455555555543     345555555566666666666666666666664331                24577899


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          371 VLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       371 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      ++++|...|+.||..++..+++.|.+.+.
T Consensus       125 lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  125 LLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            99999999999999999999999987765

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

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.58  E-value=0.00034  Score=46.29  Aligned_cols=56  Identities=18%  Similarity=0.341  Sum_probs=35.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          356 LLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       356 ~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...+.+.|++++|...|+++++..+. +...+..+..++...|++++|...|+++++
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~   59 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQDPD-NPEAWYLLGRILYQQGRYDEALAYYERALE   59 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCSTT-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44566666666666666666666533 555666666666666666666666666665

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.57  E-value=0.0064  Score=45.50  Aligned_cols=91  Identities=19%  Similarity=0.092  Sum_probs=41.6

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCC--chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHhcc
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYCYD--FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTP--TPNSWSIIAAGYADK  397 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p--~~~~~~~l~~~~~~~  397 (490)
                      .++-..|+.++|..+|++....|....  ...+-.+...|...|++++|..+|++.....+.+  +......+..++...
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~   88 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALYNL   88 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHC
Confidence            334445555555555555555544332  1233334444555555555555555555432110  111122223344555


Q ss_pred             CCHHHHHHHHHHHHH
Q 011236          398 NNMEKAFECMKEALA  412 (490)
Q Consensus       398 ~~~~~a~~~~~~~~~  412 (490)
                      |+.++|++.+-..+.
T Consensus        89 gr~~eAl~~~l~~la  103 (120)
T PF12688_consen   89 GRPKEALEWLLEALA  103 (120)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            555555555544443

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.56  E-value=0.0069  Score=58.40  Aligned_cols=139  Identities=14%  Similarity=0.030  Sum_probs=101.2

Q ss_pred             cCCCChhhHHHHHHHHHhc-----CCHHHHHHHHHHHHhcCCCCCc-hhHHHHHHHHHhc--------CCHHHHHHHHHH
Q 011236          309 CKKQLNRDYITMLGSLVKI-----GELEEAEKMLEEWELSCYCYDF-RVPNIILLGYSQK--------GMIEKADAVLKE  374 (490)
Q Consensus       309 ~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~--------g~~~~A~~~~~~  374 (490)
                      ....+...|...+++....     ++.+.|..+|++..+.  .|+- ..|..+..+|...        ++...+.+..++
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l--dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS--EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            3446778888888876542     2377899999999985  4553 4455444444332        123344444444


Q ss_pred             HHHc-CCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          375 IVKK-GKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       375 m~~~-~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      .... ....+...|..+.......|++++|...++++++       +.|+...|..+...+...|+.++|...++++...
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~-------L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L  482 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAID-------LEMSWLNYVLLGKVYELKGDNRLAADAYSTAFNL  482 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHH-------cCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            4342 1233567788887777788999999999999998       5588889999999999999999999999999999


Q ss_pred             ccc
Q 011236          454 VQK  456 (490)
Q Consensus       454 ~~~  456 (490)
                      .|.
T Consensus       483 ~P~  485 (517)
T PRK10153        483 RPG  485 (517)
T ss_pred             CCC
Confidence            888

>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=97.55  E-value=0.0069  Score=47.87  Aligned_cols=77  Identities=12%  Similarity=0.110  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVS  428 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~  428 (490)
                      +...++..+...|++++|..+++.+....+- |...|..+|.+|...|+...|.+.|+++.....+..|+.|+..+-.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~~  140 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPY-DEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETRA  140 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHHH
Confidence            3455677788889999999999999888655 7888999999999999999999999888777666678888886643

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>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=97.55  E-value=0.00035  Score=46.91  Aligned_cols=63  Identities=17%  Similarity=0.175  Sum_probs=40.2

Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC-CHHHHHHHHHHHHH
Q 011236          349 FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKN-NMEKAFECMKEALA  412 (490)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~  412 (490)
                      ..+|..+...+...|++++|+..|++.++.++. +...|..+..+|...| ++++|++.++++++
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~-~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPN-NAEAYYNLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence            345556666666666666666666666666543 5556666666666666 56666666666665

...

>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=97.54  E-value=0.00038  Score=46.53  Aligned_cols=51  Identities=18%  Similarity=0.358  Sum_probs=26.6

Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          361 QKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       361 ~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ..|++++|..+|+++.+..+. +...+..+..+|.+.|++++|.++++++..
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~-~~~~~~~la~~~~~~g~~~~A~~~l~~~~~   53 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPD-NPEARLLLAQCYLKQGQYDEAEELLERLLK   53 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTT-SHHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred             hccCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            345555555555555554433 444455555555555555555555555544

...

>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=97.54  E-value=0.00051  Score=46.09  Aligned_cols=66  Identities=15%  Similarity=0.115  Sum_probs=56.8

Q ss_pred             CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCC-CHHHHHHHHHHHHhccc
Q 011236          383 TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNR-DVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       383 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~~  455 (490)
                      ++.+|..+...+...|++++|+..|+++++       +.|+. ..|..+..++...| ++++|.+.+++..+..|
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~-------~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P   69 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIE-------LDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP   69 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHH-------HSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------cCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence            567899999999999999999999999998       33544 78888889999999 79999999999887665

...

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.53  E-value=0.018  Score=55.07  Aligned_cols=202  Identities=10%  Similarity=0.085  Sum_probs=114.4

Q ss_pred             CCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHC-CCCC--------CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCC
Q 011236          169 FGSALNYNGIMCLYTNTGQHEKIPDVLLDMKEN-GVPP--------DNFSYRICINSYGARSELSSMENVLQEMESQSHI  239 (490)
Q Consensus       169 ~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~~p--------~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  239 (490)
                      .|.+..|..|.......-.++-|...|-+.... |++.        +...-.+=+.+|  -|.+++|+++|-+|. +.++
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~--~g~feeaek~yld~d-rrDL  765 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEFEEAEKLYLDAD-RRDL  765 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcchhHhhhhhhccc-hhhh
Confidence            356666666666555555555555555444321 2210        111111122222  478888888888886 5554


Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCC----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChh
Q 011236          240 SMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSK----DALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNR  315 (490)
Q Consensus       240 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  315 (490)
                               .|..+.+.|++-...++++.    |....    -..+|+.+...++....|++|.++|..-..        
T Consensus       766 ---------Aielr~klgDwfrV~qL~r~----g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~~~~--------  824 (1189)
T KOG2041|consen  766 ---------AIELRKKLGDWFRVYQLIRN----GGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSYCGD--------  824 (1189)
T ss_pred             ---------hHHHHHhhhhHHHHHHHHHc----cCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc--------
Confidence                     67778888888887777765    22101    125678888888888888888887763211        


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA  395 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~  395 (490)
                       ....+.++-+..++++-+.+...     ++-+....-.+.+++.+.|.-++|.+.+-+-.   . |     ...+..|.
T Consensus       825 -~e~~~ecly~le~f~~LE~la~~-----Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s---~-p-----kaAv~tCv  889 (1189)
T KOG2041|consen  825 -TENQIECLYRLELFGELEVLART-----LPEDSELLPVMADMFTSVGMCDQAVEAYLRRS---L-P-----KAAVHTCV  889 (1189)
T ss_pred             -hHhHHHHHHHHHhhhhHHHHHHh-----cCcccchHHHHHHHHHhhchHHHHHHHHHhcc---C-c-----HHHHHHHH
Confidence             12244455555555554444333     34455566667777777777777766553321   1 1     12345566


Q ss_pred             ccCCHHHHHHHHHH
Q 011236          396 DKNNMEKAFECMKE  409 (490)
Q Consensus       396 ~~~~~~~a~~~~~~  409 (490)
                      ..++|.+|.++-++
T Consensus       890 ~LnQW~~avelaq~  903 (1189)
T KOG2041|consen  890 ELNQWGEAVELAQR  903 (1189)
T ss_pred             HHHHHHHHHHHHHh
Confidence            66666666666554

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

Probab=97.46  E-value=0.077  Score=47.72  Aligned_cols=105  Identities=13%  Similarity=0.056  Sum_probs=50.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ  361 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (490)
                      .+..+.-+...|+...|.++-.    ....|+...|-..+.+++..++|++-.++-..      +-++.-|-.++.+|.+
T Consensus       180 l~~Ti~~li~~~~~k~A~kl~k----~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~~  249 (319)
T PF04840_consen  180 LNDTIRKLIEMGQEKQAEKLKK----EFKVPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACLK  249 (319)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHH----HcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHHH
Confidence            3333444445555544444422    22235555555556666666665554443221      1133445555555555


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHH
Q 011236          362 KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFEC  406 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~  406 (490)
                      .|+..+|..+..+     ++     +..-+..|.+.|++.+|.+.
T Consensus       250 ~~~~~eA~~yI~k-----~~-----~~~rv~~y~~~~~~~~A~~~  284 (319)
T PF04840_consen  250 YGNKKEASKYIPK-----IP-----DEERVEMYLKCGDYKEAAQE  284 (319)
T ss_pred             CCCHHHHHHHHHh-----CC-----hHHHHHHHHHCCCHHHHHHH
Confidence            6655555555544     11     23334455555555555443

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

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.43  E-value=0.0043  Score=53.94  Aligned_cols=102  Identities=15%  Similarity=0.045  Sum_probs=58.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKTPT--PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                      |..-+..+.+.|++++|...|+.+++..+...  ...+..+...|...|++++|...|+.++..+|   +-......+..
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP---~s~~~~dAl~k  222 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYP---KSPKAADAMFK  222 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC---CCcchhHHHHH
Confidence            33333334455667777777777766543211  23556666667777777777777777766332   11112234444


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      +...+...|+.+.|..+++.+.+..|.
T Consensus       223 lg~~~~~~g~~~~A~~~~~~vi~~yP~  249 (263)
T PRK10803        223 VGVIMQDKGDTAKAKAVYQQVIKKYPG  249 (263)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence            555566667777777777777666665

>PRK11906 transcriptional regulator; Provisional

Probab=97.40  E-value=0.01  Score=54.63  Aligned_cols=145  Identities=8%  Similarity=-0.078  Sum_probs=105.9

Q ss_pred             CHHHHHHHHHHHHhc-CCCCC-chhHHHHHHHHHh---------cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc
Q 011236          329 ELEEAEKMLEEWELS-CYCYD-FRVPNIILLGYSQ---------KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK  397 (490)
Q Consensus       329 ~~~~a~~~~~~~~~~-~~~~~-~~~~~~l~~~~~~---------~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  397 (490)
                      ..+.|..+|.+.... ...|+ ...|..+..++..         .....+|.++.++..+.+.. |+.....+..+..-.
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld~~-Da~a~~~~g~~~~~~  351 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDITTV-DGKILAIMGLITGLS  351 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHhh
Confidence            345667777777621 23443 3334444443322         23456778888888888766 888888888888888


Q ss_pred             CCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc---hhhhHHHHHHHHhcC-C
Q 011236          398 NNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK---RNMYHALTEAHIRSG-Q  472 (490)
Q Consensus       398 ~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~---~~~~~~l~~~~~~~g-~  472 (490)
                      ++++.|...|+++..       +.||. .+|......+.-.|+.++|.+.+++..+..|.   ..+....++.|+..+ +
T Consensus       352 ~~~~~a~~~f~rA~~-------L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~~~~~~  424 (458)
T PRK11906        352 GQAKVSHILFEQAKI-------HSTDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRRRKAVVIKECVDMYVPNPLK  424 (458)
T ss_pred             cchhhHHHHHHHHhh-------cCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchhhHHHHHHHHHHHHcCCchh
Confidence            889999999999987       55777 56666666777789999999999999998888   566666777999999 8


Q ss_pred             cHHHHHHHH
Q 011236          473 EVDGLLESM  481 (490)
Q Consensus       473 ~a~~~~~~m  481 (490)
                      +|+.++-+-
T Consensus       425 ~~~~~~~~~  433 (458)
T PRK11906        425 NNIKLYYKE  433 (458)
T ss_pred             hhHHHHhhc
Confidence            888887553

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.40  E-value=0.09  Score=47.03  Aligned_cols=294  Identities=14%  Similarity=0.008  Sum_probs=182.2

Q ss_pred             HHHHHHHHHH--hcCChhHHHHHHHHHHhcCCCCCcchHHHHHHH--HHhcCCcCcHHHHHHHHHHCCCCCCHHH--HHH
Q 011236          139 LYGALLNCYV--REGLVDESLSLMQKMKEMGSFGSALNYNGIMCL--YTNTGQHEKIPDVLLDMKENGVPPDNFS--YRI  212 (490)
Q Consensus       139 ~~~~li~~~~--~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~--~~~~~~~~~a~~~~~~m~~~~~~p~~~~--~~~  212 (490)
                      -|.+|-.++.  ..|+-..|.++-.+.... +.-|....-.|+.+  -.-.|+++.|.+-|+.|...   |....  ...
T Consensus        84 gyqALStGliAagAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLRg  159 (531)
T COG3898          84 GYQALSTGLIAAGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLRG  159 (531)
T ss_pred             HHHHHhhhhhhhccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHHH
Confidence            3555544443  357777777766654422 22244444445443  34568999999999999863   33322  233


Q ss_pred             HHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChh--hHHHHHHHHH
Q 011236          213 CINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDAL--GYNHLISHYA  290 (490)
Q Consensus       213 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~~l~~~~~  290 (490)
                      |.-..-+.|+.+.|..+-+..- ..-. .-.......+...|..|+|+.|+++++.-.......++..  .-..|+.+-.
T Consensus       160 LyleAqr~GareaAr~yAe~Aa-~~Ap-~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA  237 (531)
T COG3898         160 LYLEAQRLGAREAARHYAERAA-EKAP-QLPWAARATLEARCAAGDWDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKA  237 (531)
T ss_pred             HHHHHHhcccHHHHHHHHHHHH-hhcc-CCchHHHHHHHHHHhcCChHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHH
Confidence            3334456888888888888776 3333 2244566788899999999999999988765544324432  2222333221


Q ss_pred             h---cCChhHHHHHHHHHHHhcCCCCh-hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHH
Q 011236          291 S---LGNKDEMMKFWGLQKIKCKKQLN-RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIE  366 (490)
Q Consensus       291 ~---~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  366 (490)
                      .   ..+...|...-.+..+.  .|+. ..-.....++.+.|+..++-.+++.+-+....|+.  +  ++..+.+.|+. 
T Consensus       238 ~s~ldadp~~Ar~~A~~a~KL--~pdlvPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP~i--a--~lY~~ar~gdt-  310 (531)
T COG3898         238 MSLLDADPASARDDALEANKL--APDLVPAAVVAARALFRDGNLRKGSKILETAWKAEPHPDI--A--LLYVRARSGDT-  310 (531)
T ss_pred             HHHhcCChHHHHHHHHHHhhc--CCccchHHHHHHHHHHhccchhhhhhHHHHHHhcCCChHH--H--HHHHHhcCCCc-
Confidence            1   23444555544333332  2333 33455567888999999999999999887555553  2  23334555553 


Q ss_pred             HHHHHHHHHHHc-CCCC-CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc-CCCHHHH
Q 011236          367 KADAVLKEIVKK-GKTP-TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD-NRDVEEV  443 (490)
Q Consensus       367 ~A~~~~~~m~~~-~~~p-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~-~g~~~~a  443 (490)
                       ++.-+++.... .++| +..+...+..+-...|++..|..--+.+..       ..|....|..|.+.-.. .||..++
T Consensus       311 -a~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r-------~~pres~~lLlAdIeeAetGDqg~v  382 (531)
T COG3898         311 -ALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAAR-------EAPRESAYLLLADIEEAETGDQGKV  382 (531)
T ss_pred             -HHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhh-------hCchhhHHHHHHHHHhhccCchHHH
Confidence             33333333221 1233 456677777888889999888877777665       56888888888876554 4999999


Q ss_pred             HHHHHHHHhc
Q 011236          444 EAFVSSLKIK  453 (490)
Q Consensus       444 ~~~~~~~~~~  453 (490)
                      ...+.+..+.
T Consensus       383 R~wlAqav~A  392 (531)
T COG3898         383 RQWLAQAVKA  392 (531)
T ss_pred             HHHHHHHhcC
Confidence            9998887764

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.37  E-value=0.013  Score=50.49  Aligned_cols=121  Identities=12%  Similarity=0.079  Sum_probs=87.1

Q ss_pred             HHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc---CCHHHHHHHHHHHHh
Q 011236          266 LKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI---GELEEAEKMLEEWEL  342 (490)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~  342 (490)
                      ++.-....+  .|...|-.|...|...|+.+.|..-|.......+ ++...+..+..++...   ....++..+|+++..
T Consensus       145 Le~~L~~nP--~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g-~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~  221 (287)
T COG4235         145 LETHLQQNP--GDAEGWDLLGRAYMALGRASDALLAYRNALRLAG-DNPEILLGLAEALYYQAGQQMTAKARALLRQALA  221 (287)
T ss_pred             HHHHHHhCC--CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Confidence            333333354  5888899999999999999999999988877766 6666666666665543   346678888998888


Q ss_pred             cCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011236          343 SCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAA  392 (490)
Q Consensus       343 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~  392 (490)
                      . -+-|+.....|...+...|++.+|...|+.|.+..+.  ...+..+|.
T Consensus       222 ~-D~~~iral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~--~~~rr~~ie  268 (287)
T COG4235         222 L-DPANIRALSLLAFAAFEQGDYAEAAAAWQMLLDLLPA--DDPRRSLIE  268 (287)
T ss_pred             c-CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcCCC--CCchHHHHH
Confidence            6 2336667777888888999999999999999887533  333444443

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.35  E-value=0.052  Score=43.18  Aligned_cols=134  Identities=13%  Similarity=0.022  Sum_probs=79.2

Q ss_pred             CCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhH
Q 011236          203 VPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGY  282 (490)
Q Consensus       203 ~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  282 (490)
                      +.|++..--.|..+....|+..+|...|++.. ..-..-|....-.+.++....+++..|...++++.+..+...++.+.
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qal-sG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~  163 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQAL-SGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH  163 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHh-ccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch
Confidence            34565555566677777777777777777765 43344455555566666666777777777777665544433344455


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          283 NHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEE  339 (490)
Q Consensus       283 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  339 (490)
                      ..+...+...|++..|..-|+......+.|....+  ....+.+.|+.+++..-+..
T Consensus       164 Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~ar~~--Y~e~La~qgr~~ea~aq~~~  218 (251)
T COG4700         164 LLFARTLAAQGKYADAESAFEVAISYYPGPQARIY--YAEMLAKQGRLREANAQYVA  218 (251)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHhCCCHHHHHH--HHHHHHHhcchhHHHHHHHH
Confidence            56667777777777777777766665443333332  22334455655554443333

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.29  E-value=0.022  Score=42.63  Aligned_cols=90  Identities=20%  Similarity=0.160  Sum_probs=40.2

Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcCCCC--hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--CchhHHHHHHHHHhc
Q 011236          287 SHYASLGNKDEMMKFWGLQKIKCKKQL--NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY--DFRVPNIILLGYSQK  362 (490)
Q Consensus       287 ~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~  362 (490)
                      .++-..|+.++|+.+|++....+....  ...+..+...+...|++++|..++++....-..+  +......+..++...
T Consensus         9 ~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~   88 (120)
T PF12688_consen    9 WAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALYNL   88 (120)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHC
Confidence            344445555555555555554433211  1234444455555555555555555554431110  111112223344555


Q ss_pred             CCHHHHHHHHHHHH
Q 011236          363 GMIEKADAVLKEIV  376 (490)
Q Consensus       363 g~~~~A~~~~~~m~  376 (490)
                      |+.++|+..+-...
T Consensus        89 gr~~eAl~~~l~~l  102 (120)
T PF12688_consen   89 GRPKEALEWLLEAL  102 (120)
T ss_pred             CCHHHHHHHHHHHH
Confidence            55555555554433

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.28  E-value=0.0015  Score=43.08  Aligned_cols=56  Identities=13%  Similarity=0.065  Sum_probs=26.6

Q ss_pred             HHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 011236          251 NYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIK  308 (490)
Q Consensus       251 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  308 (490)
                      ..+...|++++|+..|+++.+..+  .+...+..+..++...|++++|...|++....
T Consensus         5 ~~~~~~g~~~~A~~~~~~~l~~~P--~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    5 RALYQQGDYDEAIAAFEQALKQDP--DNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHCTHHHHHHHHHHHHHCCST--THHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344445555555555555544443  34444445555555555555555555544433

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.26  E-value=0.046  Score=46.00  Aligned_cols=134  Identities=9%  Similarity=-0.059  Sum_probs=101.1

Q ss_pred             hHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHH-----H
Q 011236          174 NYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYS-----T  248 (490)
Q Consensus       174 ~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~-----~  248 (490)
                      .-+.++.++.-.|.+.-...++++.++...+.++.....|.+.-.+.||.+.|...|++.+ +..-..+..+.+     .
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~ve-k~~~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVE-KVTQKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHH-HHHhhhhccchhHHHHhh
Confidence            4466777777888888889999999888777788888889999899999999999999776 322223333333     3


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK  310 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  310 (490)
                      ....|.-.+++..|...|+++....+  .|+...|.-.-+..-.|+..+|++.++.+....+
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~D~--~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P  317 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRMDP--RNAVANNNKALCLLYLGKLKDALKQLEAMVQQDP  317 (366)
T ss_pred             hhhheecccchHHHHHHHhhccccCC--CchhhhchHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence            34456677888999999988877665  4666666666666668899999999998887765

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.23  E-value=0.0026  Score=43.18  Aligned_cols=55  Identities=25%  Similarity=0.259  Sum_probs=36.1

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          357 LGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ..|.+.+++++|.++++.++..++. +...|......+.+.|++++|.+.|+.+++
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPD-DPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            4456666677777777666666544 555666666666667777777777766666

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=97.21  E-value=0.0017  Score=44.76  Aligned_cols=67  Identities=16%  Similarity=0.201  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcC-CCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKF-WRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      .+|+.+...|...|++++|+..|+++++.. ...| -.|+ ..++..+...+...|++++|++.+++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIE-EQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHH-HHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHH-HHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            457777777777788888887777777642 1122 2232 35667777777778888888877776654

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.19  E-value=0.038  Score=52.51  Aligned_cols=37  Identities=11%  Similarity=0.303  Sum_probs=22.2

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          194 VLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       194 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      -+++++++|-.|+...   +...++-.|++.+|.++|.+-
T Consensus       622 EL~~~k~rge~P~~iL---lA~~~Ay~gKF~EAAklFk~~  658 (1081)
T KOG1538|consen  622 ELEERKKRGETPNDLL---LADVFAYQGKFHEAAKLFKRS  658 (1081)
T ss_pred             HHHHHHhcCCCchHHH---HHHHHHhhhhHHHHHHHHHHc
Confidence            3456666666666543   334455567777777777654

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.18  E-value=0.08  Score=52.06  Aligned_cols=89  Identities=18%  Similarity=0.227  Sum_probs=48.2

Q ss_pred             CHHHHHHHHHH----HHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHH
Q 011236           68 SELELQRVIRQ----LRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGA  142 (490)
Q Consensus        68 ~~~~~~~ll~~----~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~  142 (490)
                      +..+...+...    +-+.|++++|..-|-+-+..- .|     ..++.-+.....+.+-..+++.+.+.+. +..--+.
T Consensus       363 d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~l-e~-----s~Vi~kfLdaq~IknLt~YLe~L~~~gla~~dhttl  436 (933)
T KOG2114|consen  363 DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFL-EP-----SEVIKKFLDAQRIKNLTSYLEALHKKGLANSDHTTL  436 (933)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccC-Ch-----HHHHHHhcCHHHHHHHHHHHHHHHHcccccchhHHH
Confidence            44444444433    345677777766655433321 11     2334444555556666666666666653 4444556


Q ss_pred             HHHHHHhcCChhHHHHHHHH
Q 011236          143 LLNCYVREGLVDESLSLMQK  162 (490)
Q Consensus       143 li~~~~~~g~~~~a~~~~~~  162 (490)
                      |+.+|.+.++.++-.++.+.
T Consensus       437 LLncYiKlkd~~kL~efI~~  456 (933)
T KOG2114|consen  437 LLNCYIKLKDVEKLTEFISK  456 (933)
T ss_pred             HHHHHHHhcchHHHHHHHhc
Confidence            67777777776665554443

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.14  E-value=0.0094  Score=51.88  Aligned_cols=95  Identities=11%  Similarity=0.021  Sum_probs=47.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC----hhHHHHHHH
Q 011236           72 LQRVIRQLRSRKRFKHALQVSEWMSGQGL--AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV----DKLYGALLN  145 (490)
Q Consensus        72 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~----~~~~~~li~  145 (490)
                      |...+..+.+.|++++|+..|+.+.+...  +..+..+..+...+...|++++|...|+.+....|+    ..++-.+..
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~  225 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGV  225 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHH
Confidence            33333333444556666666665555432  111345555555555556666666655555544331    223333444


Q ss_pred             HHHhcCChhHHHHHHHHHHhc
Q 011236          146 CYVREGLVDESLSLMQKMKEM  166 (490)
Q Consensus       146 ~~~~~g~~~~a~~~~~~m~~~  166 (490)
                      .+...|+.++|..+|+++.+.
T Consensus       226 ~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        226 IMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHcCCHHHHHHHHHHHHHH
Confidence            455555555555555555544

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

Probab=97.12  E-value=0.19  Score=45.26  Aligned_cols=113  Identities=15%  Similarity=0.155  Sum_probs=84.9

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011236          315 RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       315 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~  394 (490)
                      .+.+..+.-|...|+...|.++-.+..    -|+...|-.-+.+++..++|++-.++...   .   -.+..|..++.+|
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s---k---KsPIGyepFv~~~  247 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS---K---KSPIGYEPFVEAC  247 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC---C---CCCCChHHHHHHH
Confidence            455666777788899888888877662    36888899999999999999987775432   1   2457899999999


Q ss_pred             hccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          395 ADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       395 ~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      .+.|+..+|..+..++           |    +..-+..|.+.|++.+|.+.-.+..+
T Consensus       248 ~~~~~~~eA~~yI~k~-----------~----~~~rv~~y~~~~~~~~A~~~A~~~kd  290 (319)
T PF04840_consen  248 LKYGNKKEASKYIPKI-----------P----DEERVEMYLKCGDYKEAAQEAFKEKD  290 (319)
T ss_pred             HHCCCHHHHHHHHHhC-----------C----hHHHHHHHHHCCCHHHHHHHHHHcCC
Confidence            9999999998887762           1    14456677888888888776555544

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

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.10  E-value=0.19  Score=45.75  Aligned_cols=28  Identities=14%  Similarity=0.136  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      -.+.+++.++.-.|+.++|.+..++|..
T Consensus       306 Wd~ATl~Ea~vL~~d~~ka~~a~e~~~~  333 (374)
T PF13281_consen  306 WDVATLLEASVLAGDYEKAIQAAEKAFK  333 (374)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhh
Confidence            3445556666666677777777766665

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=96.96  E-value=0.0034  Score=49.64  Aligned_cols=70  Identities=17%  Similarity=0.288  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHH-----CCCCCCHHH
Q 011236          139 LYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKE-----NGVPPDNFS  209 (490)
Q Consensus       139 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~  209 (490)
                      +...++..+...|++++|..+.+.+....+- |...|..+|.++...|+...|.++|+.+.+     .|+.|+..+
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~-~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPY-DEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            3445555556666666666666666665433 555666666666666666666666665532     366666554

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.96  E-value=0.43  Score=46.63  Aligned_cols=324  Identities=16%  Similarity=0.089  Sum_probs=169.1

Q ss_pred             cCCCCCHHHHH-----HHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCH--HHHH-HHHHHccccC
Q 011236           63 EGQKISELELQ-----RVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGL--ESAE-TYFNSLNDED  134 (490)
Q Consensus        63 ~~~~~~~~~~~-----~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--~~A~-~~~~~~~~~~  134 (490)
                      -|++.+..-|.     .+|+.+...+.+..|+++-.++......- ..++......+.+..+.  +++. .+=+++...-
T Consensus       426 ~gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~-~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~~  504 (829)
T KOG2280|consen  426 IGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPESQG-DRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAKL  504 (829)
T ss_pred             cCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCccccc-cHHHHHHHHHHHhccCccchHHHHHHHHHhcccC
Confidence            37777666665     45777888899999999988876543222 56666666666665332  2233 3333333221


Q ss_pred             CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCC----CCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCC--------
Q 011236          135 KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGS----FGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENG--------  202 (490)
Q Consensus       135 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~----~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~--------  202 (490)
                      ....+|..+.+....+|+.+-|..+++.=...+-    -.+..-+...+.-+.+.|+.+-...++-.+.+.-        
T Consensus       505 ~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~~~  584 (829)
T KOG2280|consen  505 TPGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLFMT  584 (829)
T ss_pred             CCceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHH
Confidence            2345688888888899999999988764322210    1133345666677778888888877776665420        


Q ss_pred             ---CCCCHHHHHHHHHH--------HhccCChHHHHHHH--HHH---HhCCCCCCCHHHHHHHHHHHHHcCCHH------
Q 011236          203 ---VPPDNFSYRICINS--------YGARSELSSMENVL--QEM---ESQSHISMDWGTYSTVANYYIIAGLKE------  260 (490)
Q Consensus       203 ---~~p~~~~~~~li~~--------~~~~g~~~~a~~~~--~~~---~~~~~~~~~~~~~~~li~~~~~~~~~~------  260 (490)
                         .+.....|..+++-        +...++..++..-|  +..   ....+..|+..+   ..+.+.+.....      
T Consensus       585 l~~~p~a~~lY~~~~r~~~~~~l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~---~a~~~a~sk~~s~e~ka~  661 (829)
T KOG2280|consen  585 LRNQPLALSLYRQFMRHQDRATLYDFYNQDDNHQALASFHLQASYAAETIEGRIPALKT---AANAFAKSKEKSFEAKAL  661 (829)
T ss_pred             HHhchhhhHHHHHHHHhhchhhhhhhhhcccchhhhhhhhhhhhhhhhhhcccchhHHH---HHHHHhhhhhhhhHHHHH
Confidence               11111222222221        11111111111111  110   000111133222   334444433311      


Q ss_pred             ----HHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011236          261 ----KAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM  336 (490)
Q Consensus       261 ----~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  336 (490)
                          +-+.+.+.+...........+.+--+.-+...|+..+|.++-.+    ...||...|-.-+.+++..+++++-+++
T Consensus       662 ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~----FkipdKr~~wLk~~aLa~~~kweeLekf  737 (829)
T KOG2280|consen  662 EDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSD----FKIPDKRLWWLKLTALADIKKWEELEKF  737 (829)
T ss_pred             HHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHh----cCCcchhhHHHHHHHHHhhhhHHHHHHH
Confidence                11122222222111112233444455555666776776665442    2347777777777777777777765554


Q ss_pred             HHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHH
Q 011236          337 LEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKE  409 (490)
Q Consensus       337 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~  409 (490)
                      -+...      ++.-|..+..+|.+.|+.++|.+++.+...         +.-...+|.+.|++.+|.++--+
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            44322      234456667777777777777777654322         11455667777777776655433

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=96.92  E-value=0.21  Score=42.35  Aligned_cols=183  Identities=15%  Similarity=0.056  Sum_probs=92.9

Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccC-CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc---
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKS-KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI---  327 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---  327 (490)
                      .-.+.|++++|.+.|+.+....+.. -...+.-.++.++.+.++++.|+...++.+...+.-....|..-|.+++.-   
T Consensus        43 ~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs~~~~i  122 (254)
T COG4105          43 TELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKGLSYFFQI  122 (254)
T ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHHHHHhccC
Confidence            3445566666666666666544321 122344445556666677777777766666666533444444444444421   


Q ss_pred             ----CCHH---HHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH
Q 011236          328 ----GELE---EAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM  400 (490)
Q Consensus       328 ----~~~~---~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  400 (490)
                          .|..   .|..-|++++.. . ||.             .=...|......+...    =..-=..+.+-|.+.|.+
T Consensus       123 ~~~~rDq~~~~~A~~~f~~~i~r-y-PnS-------------~Ya~dA~~~i~~~~d~----LA~~Em~IaryY~kr~~~  183 (254)
T COG4105         123 DDVTRDQSAARAAFAAFKELVQR-Y-PNS-------------RYAPDAKARIVKLNDA----LAGHEMAIARYYLKRGAY  183 (254)
T ss_pred             CccccCHHHHHHHHHHHHHHHHH-C-CCC-------------cchhhHHHHHHHHHHH----HHHHHHHHHHHHHHhcCh
Confidence                1222   223333333332 1 221             1112222222222110    000012345667888888


Q ss_pred             HHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          401 EKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..|..-+++|++.++   ...-....+-.+..+|...|-.++|.+.-+-+....|.
T Consensus       184 ~AA~nR~~~v~e~y~---~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~~N~p~  236 (254)
T COG4105         184 VAAINRFEEVLENYP---DTSAVREALARLEEAYYALGLTDEAKKTAKVLGANYPD  236 (254)
T ss_pred             HHHHHHHHHHHhccc---cccchHHHHHHHHHHHHHhCChHHHHHHHHHHHhcCCC
Confidence            888888888887331   11111234555667788888888888777766665554

>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=96.87  E-value=0.015  Score=43.97  Aligned_cols=51  Identities=20%  Similarity=0.214  Sum_probs=29.3

Q ss_pred             cCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc---hhhhHHHHHHHH
Q 011236          418 KFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK---RNMYHALTEAHI  468 (490)
Q Consensus       418 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~---~~~~~~l~~~~~  468 (490)
                      ....|+..+..+++.+|+..|++..|.++++...+..+.   ...|..|++-..
T Consensus        46 spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~~   99 (126)
T PF12921_consen   46 SPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAY   99 (126)
T ss_pred             CCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            345566666666666666666666666666655554433   455555554443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>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=96.83  E-value=0.015  Score=44.01  Aligned_cols=97  Identities=11%  Similarity=0.153  Sum_probs=61.1

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011236          137 DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINS  216 (490)
Q Consensus       137 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  216 (490)
                      ..++.++|.++++.|+.+....+++..-.-  .++...         ..+.         --......|+..+..+++.+
T Consensus         2 e~~~~~ii~al~r~g~~~~i~~~i~~~WgI--~~~~~~---------~~~~---------~~~~spl~Pt~~lL~AIv~s   61 (126)
T PF12921_consen    2 EELLCNIIYALGRSGQLDSIKSYIKSVWGI--DVNGKK---------KEGD---------YPPSSPLYPTSRLLIAIVHS   61 (126)
T ss_pred             hHHHHHHHHHHhhcCCHHHHHHHHHHhcCC--CCCCcc---------ccCc---------cCCCCCCCCCHHHHHHHHHH
Confidence            456677777777777777777766554432  211100         0000         11223466788888888888


Q ss_pred             HhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHH
Q 011236          217 YGARSELSSMENVLQEMESQSHISMDWGTYSTVANYY  253 (490)
Q Consensus       217 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~  253 (490)
                      |+..|++..|.++++......+++.+..+|..|+.-.
T Consensus        62 f~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W~   98 (126)
T PF12921_consen   62 FGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWA   98 (126)
T ss_pred             HHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            8888888888888888776677777777777666543

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.83  E-value=0.14  Score=48.92  Aligned_cols=261  Identities=9%  Similarity=0.041  Sum_probs=135.4

Q ss_pred             CCCcchHHHHHHHHHhcCCcCcHHHHH---------HHHHHCCCCCCHHHHHHHHHHHhccCChH--HHHHHHHHHHhCC
Q 011236          169 FGSALNYNGIMCLYTNTGQHEKIPDVL---------LDMKENGVPPDNFSYRICINSYGARSELS--SMENVLQEMESQS  237 (490)
Q Consensus       169 ~p~~~~~~~l~~~~~~~~~~~~a~~~~---------~~m~~~~~~p~~~~~~~li~~~~~~g~~~--~a~~~~~~~~~~~  237 (490)
                      .|....+.+=+..|...|.+++|.++-         +.+-..  ..+.-.++..=.+|.+..+..  +...-+++++ +.
T Consensus       553 ~~~evp~~~~m~q~Ieag~f~ea~~iaclgVv~~DW~~LA~~--ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k-~r  629 (1081)
T KOG1538|consen  553 SAVEVPQSAPMYQYIERGLFKEAYQIACLGVTDTDWRELAME--ALEALDFETARKAYIRVRDLRYLELISELEERK-KR  629 (1081)
T ss_pred             ecccccccccchhhhhccchhhhhcccccceecchHHHHHHH--HHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHH-hc
Confidence            344455566666777888888776541         111110  012333444455666655543  3444566776 66


Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHH-----HHHHHHHhcCChhHHHHHHHHHHHhcCCC
Q 011236          238 HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYN-----HLISHYASLGNKDEMMKFWGLQKIKCKKQ  312 (490)
Q Consensus       238 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  312 (490)
                      |-.|+...   +...++-.|.+.+|-++|.+--....   -...|+     -..+-+...|..++-..+.++..+-.  .
T Consensus       630 ge~P~~iL---lA~~~Ay~gKF~EAAklFk~~G~enR---AlEmyTDlRMFD~aQE~~~~g~~~eKKmL~RKRA~WA--r  701 (1081)
T KOG1538|consen  630 GETPNDLL---LADVFAYQGKFHEAAKLFKRSGHENR---ALEMYTDLRMFDYAQEFLGSGDPKEKKMLIRKRADWA--R  701 (1081)
T ss_pred             CCCchHHH---HHHHHHhhhhHHHHHHHHHHcCchhh---HHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHh--h
Confidence            66687665   66677778888888888876311110   011111     12233444455444444433221110  0


Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHH------HHhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011236          313 LNRDYITMLGSLVKIGELEEAEKMLEE------WELSCYC---YDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT  383 (490)
Q Consensus       313 ~~~~~~~l~~~~~~~~~~~~a~~~~~~------~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~  383 (490)
                      +..-=.+....+...|+.++|..+..+      +.+-+.+   .+..+...+..-+.+...+.-|-++|.+|-+      
T Consensus       702 ~~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD------  775 (1081)
T KOG1538|consen  702 NIKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGD------  775 (1081)
T ss_pred             hcCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhcc------
Confidence            000011233334455666655544321      1111111   1333444444445556667778888877754      


Q ss_pred             HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhh-----------HHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          384 PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSL-----------VSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       384 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~-----------~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                         ..++++.....++|.+|..+-++.-+       +.|+...           |...-.+|-++|+..+|.++++++..
T Consensus       776 ---~ksiVqlHve~~~W~eAFalAe~hPe-------~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLtn  845 (1081)
T KOG1538|consen  776 ---LKSLVQLHVETQRWDEAFALAEKHPE-------FKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQLTN  845 (1081)
T ss_pred             ---HHHHhhheeecccchHhHhhhhhCcc-------ccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHhhh
Confidence               24567778888999999888777544       4455421           33333566666777777777666655


Q ss_pred             cccc
Q 011236          453 KVQK  456 (490)
Q Consensus       453 ~~~~  456 (490)
                      ....
T Consensus       846 nav~  849 (1081)
T KOG1538|consen  846 NAVA  849 (1081)
T ss_pred             hhhh
Confidence            4443

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.82  E-value=0.0082  Score=40.65  Aligned_cols=57  Identities=11%  Similarity=-0.026  Sum_probs=28.3

Q ss_pred             HHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC
Q 011236           78 QLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK  135 (490)
Q Consensus        78 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p  135 (490)
                      .+.+.++++.|+++++.+...+ |.++..+.....++...|++++|.+.|+...+..|
T Consensus         4 ~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p   60 (73)
T PF13371_consen    4 IYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELSP   60 (73)
T ss_pred             HHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCC
Confidence            3444555555555555555554 23444444444455555555555555555544444

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=96.62  E-value=0.56  Score=43.12  Aligned_cols=138  Identities=14%  Similarity=0.070  Sum_probs=78.0

Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCChhh------HHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHH--HHhc
Q 011236           79 LRSRKRFKHALQVSEWMSGQGLAFSVHD------HAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNC--YVRE  150 (490)
Q Consensus        79 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~------~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~--~~~~  150 (490)
                      +.+.+++++|..+|.++.+..- .++..      -+.++++|. .++++.....+....+..|. ..|-.|..+  +-+.
T Consensus        16 Lqkq~~~~esEkifskI~~e~~-~~~f~lkeEvl~grilnAff-l~nld~Me~~l~~l~~~~~~-s~~l~LF~~L~~Y~~   92 (549)
T PF07079_consen   16 LQKQKKFQESEKIFSKIYDEKE-SSPFLLKEEVLGGRILNAFF-LNNLDLMEKQLMELRQQFGK-SAYLPLFKALVAYKQ   92 (549)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhh-cchHHHHHHHHhhHHHHHHH-HhhHHHHHHHHHHHHHhcCC-chHHHHHHHHHHHHh
Confidence            3467788888888887766532 22222      223444443 35556555555555554442 234444433  2456


Q ss_pred             CChhHHHHHHHHHHhc--CCCC------------CcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCC----CCHHHHHH
Q 011236          151 GLVDESLSLMQKMKEM--GSFG------------SALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVP----PDNFSYRI  212 (490)
Q Consensus       151 g~~~~a~~~~~~m~~~--~~~p------------~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~----p~~~~~~~  212 (490)
                      +.+++|++.+..-.+.  +..|            |...=+..+.++...|.+.++..+++++...=++    -+..+|+.
T Consensus        93 k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~  172 (549)
T PF07079_consen   93 KEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDR  172 (549)
T ss_pred             hhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHH
Confidence            7788888777766554  2221            1111255666777888888888887777654222    46677776


Q ss_pred             HHHHHhc
Q 011236          213 CINSYGA  219 (490)
Q Consensus       213 li~~~~~  219 (490)
                      ++-.+++
T Consensus       173 ~vlmlsr  179 (549)
T PF07079_consen  173 AVLMLSR  179 (549)
T ss_pred             HHHHHhH
Confidence            5555543

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=96.61  E-value=0.7  Score=44.14  Aligned_cols=132  Identities=12%  Similarity=0.059  Sum_probs=84.5

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQL  111 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  111 (490)
                      ....|..|+....+.... .++..+++.+... .|.--.-|......=.+.|..+.+..+|++-+..= +.+...+...+
T Consensus        44 ~f~~wt~li~~~~~~~~~-~~~r~~y~~fL~k-yPl~~gyW~kfA~~E~klg~~~~s~~Vfergv~ai-p~SvdlW~~Y~  120 (577)
T KOG1258|consen   44 DFDAWTTLIQENDSIEDV-DALREVYDIFLSK-YPLCYGYWKKFADYEYKLGNAENSVKVFERGVQAI-PLSVDLWLSYL  120 (577)
T ss_pred             cccchHHHHhccCchhHH-HHHHHHHHHHHhh-CccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhh-hhHHHHHHHHH
Confidence            344565666555544443 4455555555432 22222334555555567788888888888877653 45666665555


Q ss_pred             HHHH-hhcCHHHHHHHHHHcccc-C---CChhHHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 011236          112 DLIG-KVRGLESAETYFNSLNDE-D---KVDKLYGALLNCYVREGLVDESLSLMQKMKEM  166 (490)
Q Consensus       112 ~~~~-~~~~~~~A~~~~~~~~~~-~---p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~  166 (490)
                      ..++ ..|+.+.....|+..... |   .+...|...|.--..++++.....++++.++.
T Consensus       121 ~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRilei  180 (577)
T KOG1258|consen  121 AFLKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILEI  180 (577)
T ss_pred             HHHhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHhh
Confidence            4444 457777788888876653 2   35667888888888888888888888888875

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=96.58  E-value=0.055  Score=40.18  Aligned_cols=94  Identities=10%  Similarity=-0.021  Sum_probs=64.6

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCC--cchhhHHHHHHHHH
Q 011236          358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWR--PKPSLVSSILDWLG  435 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--p~~~~~~~l~~~~~  435 (490)
                      +....|+.+.|++.|.+.+..-++ ....||.-.+++.-+|+.++|++-+++++++.    |-+  --...|..-...|.
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~P~-raSayNNRAQa~RLq~~~e~ALdDLn~AleLa----g~~trtacqa~vQRg~lyR  126 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLAPE-RASAYNNRAQALRLQGDDEEALDDLNKALELA----GDQTRTACQAFVQRGLLYR  126 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhccc-chHhhccHHHHHHHcCChHHHHHHHHHHHHhc----CccchHHHHHHHHHHHHHH
Confidence            356678888888888888776444 67778888888888888888888888887732    211  11123333344566


Q ss_pred             cCCCHHHHHHHHHHHHhcccc
Q 011236          436 DNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       436 ~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..|+-+.|..-|+..-+.|.+
T Consensus       127 l~g~dd~AR~DFe~AA~LGS~  147 (175)
T KOG4555|consen  127 LLGNDDAARADFEAAAQLGSK  147 (175)
T ss_pred             HhCchHHHHHhHHHHHHhCCH
Confidence            678888888888887777765

>PRK15331 chaperone protein SicA; Provisional

Probab=96.57  E-value=0.091  Score=41.29  Aligned_cols=85  Identities=13%  Similarity=-0.096  Sum_probs=55.6

Q ss_pred             HhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHH
Q 011236          115 GKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPD  193 (490)
Q Consensus       115 ~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  193 (490)
                      -..|++++|..+|.-+.-.+| +..-|..|..++-..+++++|+..|......+.. |+..+--...++...|+.+.|..
T Consensus        48 y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~-dp~p~f~agqC~l~l~~~~~A~~  126 (165)
T PRK15331         48 YNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKN-DYRPVFFTGQCQLLMRKAAKARQ  126 (165)
T ss_pred             HHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC-CCCccchHHHHHHHhCCHHHHHH
Confidence            356777777777777666655 5555666666666677777777777766555433 55555556666677777777777


Q ss_pred             HHHHHHH
Q 011236          194 VLLDMKE  200 (490)
Q Consensus       194 ~~~~m~~  200 (490)
                      .|.....
T Consensus       127 ~f~~a~~  133 (165)
T PRK15331        127 CFELVNE  133 (165)
T ss_pred             HHHHHHh
Confidence            7766665

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=96.52  E-value=0.42  Score=40.59  Aligned_cols=53  Identities=13%  Similarity=0.066  Sum_probs=42.1

Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcccc----hhhhHHHHHHHHhcC--CcHHHHHHHH
Q 011236          429 SILDWLGDNRDVEEVEAFVSSLKIKVQK----RNMYHALTEAHIRSG--QEVDGLLESM  481 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~l~~~~~~~g--~~a~~~~~~m  481 (490)
                      .+.+.|.+.|.+..|..-++.|.+.-+.    ...+-.+..+|.+.|  ++|...-+-+
T Consensus       172 ~IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl  230 (254)
T COG4105         172 AIARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVL  230 (254)
T ss_pred             HHHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHHHHH
Confidence            4567889999999999999999998766    667888899999999  5555544433

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.43  E-value=0.028  Score=47.75  Aligned_cols=99  Identities=21%  Similarity=0.273  Sum_probs=61.9

Q ss_pred             HHHHHHccccCCChhHHHHHHHHHHhc-----CChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCC-----------
Q 011236          124 ETYFNSLNDEDKVDKLYGALLNCYVRE-----GLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQ-----------  187 (490)
Q Consensus       124 ~~~~~~~~~~~p~~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~-----------  187 (490)
                      ...|........|-.+|-+.+..+...     +.++-....++.|.+.|+.-|..+|+.|++.+-+..-           
T Consensus        54 e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~  133 (406)
T KOG3941|consen   54 EKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFL  133 (406)
T ss_pred             hhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHh
Confidence            344555554445666677666666543     4566666778888999999999999998887654321           


Q ss_pred             -----cCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC
Q 011236          188 -----HEKIPDVLLDMKENGVPPDNFSYRICINSYGARSE  222 (490)
Q Consensus       188 -----~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  222 (490)
                           -+-+.+++++|...|+.||..+-..|++++++.+-
T Consensus       134 HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  134 HYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             hCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence                 12345555666666666666666666666555443

>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=96.42  E-value=0.016  Score=39.86  Aligned_cols=63  Identities=27%  Similarity=0.399  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhc----cCCC-hhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDIVS----KSKD-ALGYNHLISHYASLGNKDEMMKFWGLQK  306 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~----~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~  306 (490)
                      .+|+.+...|...|++++|+..|++..+...    ..++ ..++..+..++...|++++|++++++..
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            3455566666666666666666665543210    0011 3445555556666666666666665443

...

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.41  E-value=0.54  Score=40.77  Aligned_cols=49  Identities=10%  Similarity=0.192  Sum_probs=22.3

Q ss_pred             hhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHH
Q 011236          116 KVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMK  164 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~  164 (490)
                      ..|++.+|..+|.......| +..+--.++.+|...|+++.|..++..+.
T Consensus       146 ~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP  195 (304)
T COG3118         146 EAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALP  195 (304)
T ss_pred             hccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCc
Confidence            44444444444444444333 23334444444444555555555444443

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.41  E-value=0.32  Score=40.71  Aligned_cols=209  Identities=15%  Similarity=0.131  Sum_probs=106.1

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHh
Q 011236           70 LELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVR  149 (490)
Q Consensus        70 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~  149 (490)
                      ..|..-..+|....++++|...+.+..+.. ..+...|.       ...-++.|.-+.+++....--+..|+.-...|.+
T Consensus        32 s~yekAAvafRnAk~feKakdcLlkA~~~y-Ennrslfh-------AAKayEqaamLake~~klsEvvdl~eKAs~lY~E  103 (308)
T KOG1585|consen   32 SLYEKAAVAFRNAKKFEKAKDCLLKASKGY-ENNRSLFH-------AAKAYEQAAMLAKELSKLSEVVDLYEKASELYVE  103 (308)
T ss_pred             HHHHHHHHHHHhhccHHHHHHHHHHHHHHH-HhcccHHH-------HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence            345555566667777777777666655321 11111111       1123344444444444432223446666677777


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHC---C--CCCCHHHHHHHHHHHhccCChH
Q 011236          150 EGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKEN---G--VPPDNFSYRICINSYGARSELS  224 (490)
Q Consensus       150 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~---~--~~p~~~~~~~li~~~~~~g~~~  224 (490)
                      +|..+.|-..+++.-..                ..+-++++|+++|++...-   +  .+.-...|..+-+.+.+...++
T Consensus       104 ~GspdtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~kf~  167 (308)
T KOG1585|consen  104 CGSPDTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLEKFT  167 (308)
T ss_pred             hCCcchHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhHHhh
Confidence            77777777766665432                1334555666666554321   1  0111223445555666666776


Q ss_pred             HHHHHHHHHHh---CCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhcc--CCChhhHHHHHHHHHhcCChhHH
Q 011236          225 SMENVLQEMES---QSHISMD-WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK--SKDALGYNHLISHYASLGNKDEM  298 (490)
Q Consensus       225 ~a~~~~~~~~~---~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~a  298 (490)
                      +|-..+.+-..   +..--++ -..|...|-.|....++..|...++.--+.+..  ..+..+...|+.+| ..|+.+++
T Consensus       168 Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~E~~  246 (308)
T KOG1585|consen  168 EAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDIEEI  246 (308)
T ss_pred             HHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCHHHH
Confidence            66555443320   0000011 123444555666667777777777764332211  03455666666665 45666666


Q ss_pred             HHHHH
Q 011236          299 MKFWG  303 (490)
Q Consensus       299 ~~~~~  303 (490)
                      ..++.
T Consensus       247 ~kvl~  251 (308)
T KOG1585|consen  247 KKVLS  251 (308)
T ss_pred             HHHHc
Confidence            55543

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=96.38  E-value=1.5  Score=45.46  Aligned_cols=329  Identities=16%  Similarity=0.126  Sum_probs=167.3

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHH-hCCC--CCChhhHHHHHHHHHh-hcCHHHHHHHHHHccccCCChhHHHHHH----H
Q 011236           74 RVIRQLRSRKRFKHALQVSEWMS-GQGL--AFSVHDHAVQLDLIGK-VRGLESAETYFNSLNDEDKVDKLYGALL----N  145 (490)
Q Consensus        74 ~ll~~~~~~~~~~~a~~~~~~~~-~~~~--~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~~~~p~~~~~~~li----~  145 (490)
                      .-+..++..+++.+|..+.++-. ..++  ..++..+..-+.++.+ .++.+--..++..+...+.+...|....    .
T Consensus       682 a~vr~~l~~~~y~~AF~~~RkhRidlnii~d~~~~~Fl~nv~afl~~in~~~~l~lfl~~lk~eDvtk~~y~~~~~s~k~  761 (1265)
T KOG1920|consen  682 AKVRTLLDRLRYKEAFEVMRKHRIDLNIIFDYDPKRFLKNVPAFLKQINRVNHLELFLTELKEEDVTKTMYSSTSGSGKQ  761 (1265)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCccchhhcCHHHHHhhHHHHhccCCcHHHHHHHHhhcccchhhhhhccccccccce
Confidence            34444556666776655544321 1122  3345566655666654 4555666666666665443333332211    1


Q ss_pred             HHHhc----CChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcC--CcCcHHHHHHHHHHCCCCCCHHH----------
Q 011236          146 CYVRE----GLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTG--QHEKIPDVLLDMKENGVPPDNFS----------  209 (490)
Q Consensus       146 ~~~~~----g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~--~~~~a~~~~~~m~~~~~~p~~~~----------  209 (490)
                      .|...    ..++...+.+.....+ ..|+ .-.-.+|..|++.+  ..+.++....+.......++...          
T Consensus       762 ~~~~r~~~d~kv~~vc~~vr~~l~~-~~~~-~~~~~ilTs~vk~~~~~ie~aL~kI~~l~~~~~~~~ad~al~hll~Lvd  839 (1265)
T KOG1920|consen  762 VYMSRDPYDNKVNSVCDAVRNALER-RAPD-KFNLFILTSYVKSNPPEIEEALQKIKELQLAQVAVSADEALKHLLFLVD  839 (1265)
T ss_pred             eEEeccchhhHHHHHHHHHHHHHhh-cCcc-hhhHHHHHHHHhcCcHHHHHHHHHHHHHHhcccchhHHHHHHHHHhhcc
Confidence            11111    2233344444443333 2344 33456777777776  55666666655553211111110          


Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH-------------HcCCHHHHHHHHHHHhhhhccC
Q 011236          210 YRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYI-------------IAGLKEKAIIYLKKCEDIVSKS  276 (490)
Q Consensus       210 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~-------------~~~~~~~a~~~~~~~~~~~~~~  276 (490)
                      -+.+.++..-.-|++.|..+-+.-+      .|+.-|-.+++-+-             ..++++.|+.-+..+       
T Consensus       840 vn~lfn~ALgtYDl~Lal~VAq~Sq------kDPkEyLP~L~el~~m~~~~rkF~ID~~L~ry~~AL~hLs~~-------  906 (1265)
T KOG1920|consen  840 VNELFNSALGTYDLDLALLVAQKSQ------KDPKEYLPFLNELKKMETLLRKFKIDDYLKRYEDALSHLSEC-------  906 (1265)
T ss_pred             HHHHHHhhhcccchHHHHHHHHHhc------cChHHHHHHHHHHhhchhhhhheeHHHHHHHHHHHHHHHHHc-------
Confidence            1122222222224444444433332      11122222222111             124555555555543       


Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHH----HHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhH
Q 011236          277 KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYIT----MLGSLVKIGELEEAEKMLEEWELSCYCYDFRVP  352 (490)
Q Consensus       277 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  352 (490)
                       +...|.-.+..--+.|-+.+|+.++.        |+...+..    ....+...+.+++|--.|+..-+.         
T Consensus       907 -~~~~~~e~~n~I~kh~Ly~~aL~ly~--------~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gkl---------  968 (1265)
T KOG1920|consen  907 -GETYFPECKNYIKKHGLYDEALALYK--------PDSEKQKVIYEAYADHLREELMSDEAALMYERCGKL---------  968 (1265)
T ss_pred             -CccccHHHHHHHHhcccchhhhheec--------cCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccH---------
Confidence             22334455555556777777777776        56655444    444455567777777666654221         


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH--HHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHH
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNS--WSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSI  430 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l  430 (490)
                      .--+.+|..+|++.+|+.+..++...   -|...  -..|+.-+...+++-+|-++..+...         -    ..-.
T Consensus       969 ekAl~a~~~~~dWr~~l~~a~ql~~~---~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~s---------d----~~~a 1032 (1265)
T KOG1920|consen  969 EKALKAYKECGDWREALSLAAQLSEG---KDELVILAEELVSRLVEQRKHYEAAKILLEYLS---------D----PEEA 1032 (1265)
T ss_pred             HHHHHHHHHhccHHHHHHHHHhhcCC---HHHHHHHHHHHHHHHHHcccchhHHHHHHHHhc---------C----HHHH
Confidence            23567788888888888888776532   12222  25677778888998889888888765         1    1123


Q ss_pred             HHHHHcCCCHHHHHHHHHHHH
Q 011236          431 LDWLGDNRDVEEVEAFVSSLK  451 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~  451 (490)
                      +..+++...|++|.++.....
T Consensus      1033 v~ll~ka~~~~eAlrva~~~~ 1053 (1265)
T KOG1920|consen 1033 VALLCKAKEWEEALRVASKAK 1053 (1265)
T ss_pred             HHHHhhHhHHHHHHHHHHhcc
Confidence            334455556777776665544

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.34  E-value=0.091  Score=48.53  Aligned_cols=63  Identities=14%  Similarity=-0.008  Sum_probs=35.8

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc----hhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011236          314 NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDF----RVPNIILLGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       314 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      ...++.+..+|.+.|++++|...|++.++.  .|+.    .+|..+..+|...|+.++|+..+++.++.
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            344556666666666666666666665553  3332    23555666666666666666666666553

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.33  E-value=0.62  Score=40.43  Aligned_cols=161  Identities=12%  Similarity=0.082  Sum_probs=103.9

Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC
Q 011236           57 LDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV  136 (490)
Q Consensus        57 ~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~  136 (490)
                      +++|...-.++....-..-...+...|++.+|..+|....... +-+......+..++...|+.+.|..++..++....+
T Consensus       122 lr~~ld~~~~~~~e~~~~~~~~~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~  200 (304)
T COG3118         122 LRQFLDKVLPAEEEEALAEAKELIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQD  200 (304)
T ss_pred             HHHHHHHhcChHHHHHHHHhhhhhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchh
Confidence            4455544344333333344455678899999999999998886 345778888999999999999999999999876543


Q ss_pred             hhH--HHHHHHHHHhcCChhHHHHHHHHHHhcCCCC-CcchHHHHHHHHHhcCCcCcHHHHHHHHHHC--CCCCCHHHHH
Q 011236          137 DKL--YGALLNCYVREGLVDESLSLMQKMKEMGSFG-SALNYNGIMCLYTNTGQHEKIPDVLLDMKEN--GVPPDNFSYR  211 (490)
Q Consensus       137 ~~~--~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p-~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~~~~  211 (490)
                      ...  ...-|..+.+.....+...+-.+.-..   | |...-..+...+...|+.+.|.+.+-.+.+.  |. -|...-.
T Consensus       201 ~~~~~l~a~i~ll~qaa~~~~~~~l~~~~aad---Pdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~-~d~~~Rk  276 (304)
T COG3118         201 KAAHGLQAQIELLEQAAATPEIQDLQRRLAAD---PDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGF-EDGEARK  276 (304)
T ss_pred             hHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccc-cCcHHHH
Confidence            222  223345555555555555555554443   3 5555556667777788888887766666543  33 2444455


Q ss_pred             HHHHHHhccCC
Q 011236          212 ICINSYGARSE  222 (490)
Q Consensus       212 ~li~~~~~~g~  222 (490)
                      .++..+...|.
T Consensus       277 ~lle~f~~~g~  287 (304)
T COG3118         277 TLLELFEAFGP  287 (304)
T ss_pred             HHHHHHHhcCC
Confidence            55555555553

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=96.33  E-value=0.7  Score=41.03  Aligned_cols=228  Identities=14%  Similarity=0.065  Sum_probs=121.1

Q ss_pred             hccCChHHHHHHHHHHHhCC-CCCCCHHH-----HHHHHHHHHHcC-CHHHHHHHHHHHhhhh----c---cCCCh----
Q 011236          218 GARSELSSMENVLQEMESQS-HISMDWGT-----YSTVANYYIIAG-LKEKAIIYLKKCEDIV----S---KSKDA----  279 (490)
Q Consensus       218 ~~~g~~~~a~~~~~~~~~~~-~~~~~~~~-----~~~li~~~~~~~-~~~~a~~~~~~~~~~~----~---~~~~~----  279 (490)
                      .+.|+.+.|..++.+..... ...|+..-     +-.+.......+ +++.|...+++..+..    .   ..++.    
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr   83 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELR   83 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHH
Confidence            35677777777777766222 12222111     111222333445 7777766666554331    1   00222    


Q ss_pred             -hhHHHHHHHHHhcCChh---HHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHH
Q 011236          280 -LGYNHLISHYASLGNKD---EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNII  355 (490)
Q Consensus       280 -~~~~~l~~~~~~~~~~~---~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  355 (490)
                       .+...++.+|...+..+   +|.++++.+....+ -.+..+..-+..+.+.++.+.+.+++..|... +......+...
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~-~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~-~~~~e~~~~~~  161 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESEYG-NKPEVFLLKLEILLKSFDEEEYEEILMRMIRS-VDHSESNFDSI  161 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCC-CCcHHHHHHHHHHhccCChhHHHHHHHHHHHh-cccccchHHHH
Confidence             45667778887777654   46666665544444 23455556677777789999999999999987 33234455655


Q ss_pred             HHHHHh--cCCHHHHHHHHHHHHHcCCCCCHH-HHHHHH----HHHhccCC------HHHHHHHHHHHHHhhhcCcCCCc
Q 011236          356 LLGYSQ--KGMIEKADAVLKEIVKKGKTPTPN-SWSIIA----AGYADKNN------MEKAFECMKEALAVHEENKFWRP  422 (490)
Q Consensus       356 ~~~~~~--~g~~~~A~~~~~~m~~~~~~p~~~-~~~~l~----~~~~~~~~------~~~a~~~~~~~~~~~~~~~~~~p  422 (490)
                      +..+..  ......|...+..++...+.|... ....++    -...+.++      .+...+++....+    ..+.+.
T Consensus       162 l~~i~~l~~~~~~~a~~~ld~~l~~r~~~~~~~~~e~~vl~~~~~~~~~~~~~~~~~i~~l~~~~~~v~~----~~~~~l  237 (278)
T PF08631_consen  162 LHHIKQLAEKSPELAAFCLDYLLLNRFKSSEDQWLEKLVLTRVLLTTQSKDLSSSEKIESLEELLSIVEH----SLGKQL  237 (278)
T ss_pred             HHHHHHHHhhCcHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHcCCccccchhHHHHHHHHHHHHHH----HhcCCC
Confidence            665522  233456777777776655555443 111111    11122211      3444444543322    122333


Q ss_pred             chhh---HHHHH----HHHHcCCCHHHHHHHHHHHH
Q 011236          423 KPSL---VSSIL----DWLGDNRDVEEVEAFVSSLK  451 (490)
Q Consensus       423 ~~~~---~~~l~----~~~~~~g~~~~a~~~~~~~~  451 (490)
                      +..+   ..+++    ..+.+.++++.|.++|+-..
T Consensus       238 s~~~~~a~~~LLW~~~~~~~~~k~y~~A~~w~~~al  273 (278)
T PF08631_consen  238 SAEAASAIHTLLWNKGKKHYKAKNYDEAIEWYELAL  273 (278)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Confidence            3333   22333    33567899999999988544

It is also involved in sporulation [].

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.33  E-value=0.35  Score=38.16  Aligned_cols=132  Identities=12%  Similarity=0.110  Sum_probs=58.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCCh-hhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHH---
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSV-HDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGAL---  143 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~l---  143 (490)
                      +...|..-++ +.+.+..++|+.-|..+.+.|..--| -............|+...|...|+++....|.+....-+   
T Consensus        58 sgd~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARl  136 (221)
T COG4649          58 SGDAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARL  136 (221)
T ss_pred             chHHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHH
Confidence            4444444444 23445566666666666666542111 111222334445556666666666555443322222111   


Q ss_pred             --HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHH
Q 011236          144 --LNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKE  200 (490)
Q Consensus       144 --i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~  200 (490)
                        .-.+...|.++....-++-+...+-+.-...-..|.-+-.+.|++.+|.+.|..+..
T Consensus       137 raa~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         137 RAAYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HHHHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence              112334455555544444443333222222233444444455555555555555444

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.33  E-value=0.36  Score=37.65  Aligned_cols=85  Identities=15%  Similarity=0.024  Sum_probs=42.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK  397 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  397 (490)
                      ..++..+.+.+.......+++.+...+. .+....+.++..|++.+ ..+....++.      ..+......++..|.+.
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~   82 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKA   82 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHc
Confidence            3444555555556666666666555542 44455566666665543 2223333321      11233344455555556


Q ss_pred             CCHHHHHHHHHHH
Q 011236          398 NNMEKAFECMKEA  410 (490)
Q Consensus       398 ~~~~~a~~~~~~~  410 (490)
                      +.++++..++.++
T Consensus        83 ~l~~~~~~l~~k~   95 (140)
T smart00299       83 KLYEEAVELYKKD   95 (140)
T ss_pred             CcHHHHHHHHHhh
Confidence            6666666655554

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.27  E-value=0.33  Score=46.58  Aligned_cols=164  Identities=12%  Similarity=0.001  Sum_probs=98.6

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHH-----HHHHHHHHHHH----cCCHHHHHHHHHHHhhhhccCCChh
Q 011236          210 YRICINSYGARSELSSMENVLQEMESQSHISMDWG-----TYSTVANYYII----AGLKEKAIIYLKKCEDIVSKSKDAL  280 (490)
Q Consensus       210 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~-----~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~  280 (490)
                      +..++...+-.||-+.+++.+.+.....++.-...     .|...+..++.    ..+.+.|.++++.+....   |+..
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~y---P~s~  267 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRY---PNSA  267 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhC---CCcH
Confidence            34566667778888888888888764444432222     23333333332    446778888888887765   4444


Q ss_pred             hHHH-HHHHHHhcCChhHHHHHHHHHHHhcC---CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHH
Q 011236          281 GYNH-LISHYASLGNKDEMMKFWGLQKIKCK---KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIIL  356 (490)
Q Consensus       281 ~~~~-l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  356 (490)
                      .|.. -.+.+...|++++|++.|+.......   ......+--+...+.-.++|++|.+.|..+.+.. ..+..+|.-+.
T Consensus       268 lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s-~WSka~Y~Y~~  346 (468)
T PF10300_consen  268 LFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKES-KWSKAFYAYLA  346 (468)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcc-ccHHHHHHHHH
Confidence            4433 34556678888888888886553211   2223334556666777888888888888887752 22333443332


Q ss_pred             H-HHHhcCCH-------HHHHHHHHHHHH
Q 011236          357 L-GYSQKGMI-------EKADAVLKEIVK  377 (490)
Q Consensus       357 ~-~~~~~g~~-------~~A~~~~~~m~~  377 (490)
                      - ++...|+.       ++|..+|.+...
T Consensus       347 a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  347 AACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            2 24456666       777777776643

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.

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=96.27  E-value=0.89  Score=41.57  Aligned_cols=35  Identities=11%  Similarity=-0.153  Sum_probs=29.9

Q ss_pred             cchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          422 PKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       422 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+-..+..++.++.-.|+.+.|.+..++|.+..|+
T Consensus       303 ~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~~  337 (374)
T PF13281_consen  303 QDYWDVATLLEASVLAGDYEKAIQAAEKAFKLKPP  337 (374)
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcCCc
Confidence            44456678888999999999999999999998876

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.25  E-value=0.95  Score=41.67  Aligned_cols=405  Identities=13%  Similarity=0.069  Sum_probs=232.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHH
Q 011236           64 GQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGAL  143 (490)
Q Consensus        64 ~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~l  143 (490)
                      ..+.|+.+|-.|+.-+...+..++..+++++|...- +.-+..+...+..-....++.....+|.+......+...|...
T Consensus        37 dNPtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~pf-p~~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~l~ldLW~lY  115 (660)
T COG5107          37 DNPTNILSYFQLIQYLETQESMDAEREMYEQLSSPF-PIMEHAWRLYMSGELARKDFRSVESLFGRCLKKSLNLDLWMLY  115 (660)
T ss_pred             cCchhHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCC-ccccHHHHHHhcchhhhhhHHHHHHHHHHHHhhhccHhHHHHH
Confidence            457799999999999999999999999999998764 5677788888887778899999999999988877778889888


Q ss_pred             HHHHHhcCChh------HHHHHHHHHHh-cCCCCCc-chHHHHHHHH---HhcCCcC------cHHHHHHHHHHCCCCCC
Q 011236          144 LNCYVREGLVD------ESLSLMQKMKE-MGSFGSA-LNYNGIMCLY---TNTGQHE------KIPDVLLDMKENGVPPD  206 (490)
Q Consensus       144 i~~~~~~g~~~------~a~~~~~~m~~-~~~~p~~-~~~~~l~~~~---~~~~~~~------~a~~~~~~m~~~~~~p~  206 (490)
                      +.---+.++.-      ...+.|+-... .++.|-. ..|+..+..+   -..|.|+      .....+.+|+...+..=
T Consensus       116 l~YIRr~n~~~tGq~r~~i~~ayefv~~~~~~e~~s~~~W~ey~~fle~~~~~~kwEeQqrid~iR~~Y~ral~tP~~nl  195 (660)
T COG5107         116 LEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEELGKWEEQQRIDKIRNGYMRALQTPMGNL  195 (660)
T ss_pred             HHHHHhhCcccccchhhhhHHHHHHHHhcccccccccchHHHHHHHHHhccccccHHHHHHHHHHHHHHHHHHcCccccH
Confidence            87655544221      23344544433 3555543 3455555443   2344444      45556777766432211


Q ss_pred             HHHHHH------HHHHH-hc--cC----ChHHHHHHHHHHHh-CCCCC----CCHHHHHH-----------HHHHHHH--
Q 011236          207 NFSYRI------CINSY-GA--RS----ELSSMENVLQEMES-QSHIS----MDWGTYST-----------VANYYII--  255 (490)
Q Consensus       207 ~~~~~~------li~~~-~~--~g----~~~~a~~~~~~~~~-~~~~~----~~~~~~~~-----------li~~~~~--  255 (490)
                      ...|+.      =++-. ++  .|    -+-.|...++++.. ..|+.    .+..+++-           .|.-=..  
T Consensus       196 eklW~dy~~fE~e~N~~TarKfvge~sp~ym~ar~~yqe~~nlt~Gl~v~~~~~~Rt~nK~~r~s~S~WlNwIkwE~en~  275 (660)
T COG5107         196 EKLWKDYENFELELNKITARKFVGETSPIYMSARQRYQEIQNLTRGLSVKNPINLRTANKAARTSDSNWLNWIKWEMENG  275 (660)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHhccccccCchhhhhhccccccccchhhhHhhHhhcCC
Confidence            112221      11111 00  11    13345555555541 11211    12222222           1111000  


Q ss_pred             ---cCC--HHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCH
Q 011236          256 ---AGL--KEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGEL  330 (490)
Q Consensus       256 ---~~~--~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  330 (490)
                         .|+  ....--++++.....+  .....|----..+...++-+.|+..........  |..  -.-+...|.-.++.
T Consensus       276 l~L~~~~~~qRi~y~~~q~~~y~~--~~~evw~dys~Y~~~isd~q~al~tv~rg~~~s--psL--~~~lse~yel~nd~  349 (660)
T COG5107         276 LKLGGRPHEQRIHYIHNQILDYFY--YAEEVWFDYSEYLIGISDKQKALKTVERGIEMS--PSL--TMFLSEYYELVNDE  349 (660)
T ss_pred             cccCCCcHHHHHHHHHHHHHHHhh--hhHHHHHHHHHHHhhccHHHHHHHHHHhcccCC--Cch--heeHHHHHhhcccH
Confidence               011  1112223333333222  233444444444455566666666554332221  110  00111111112222


Q ss_pred             HHHHHHHHHHHh--------------cC---------------CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC-C
Q 011236          331 EEAEKMLEEWEL--------------SC---------------YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG-K  380 (490)
Q Consensus       331 ~~a~~~~~~~~~--------------~~---------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~-~  380 (490)
                      +.....|+...+              ++               ...-..+|..++..-.+..-++.|..+|-+..+.| +
T Consensus       350 e~v~~~fdk~~q~L~r~ys~~~s~~~s~~D~N~e~~~Ell~kr~~k~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~  429 (660)
T COG5107         350 EAVYGCFDKCTQDLKRKYSMGESESASKVDNNFEYSKELLLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIV  429 (660)
T ss_pred             HHHhhhHHHHHHHHHHHHhhhhhhhhccccCCccccHHHHHHHHhhhhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCC
Confidence            222222211100              00               11123456777777788888999999999999988 5


Q ss_pred             CCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhH-HHHHHHHHcCCCHHHHHHHHHHHHhcccc---
Q 011236          381 TPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLV-SSILDWLGDNRDVEEVEAFVSSLKIKVQK---  456 (490)
Q Consensus       381 ~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~-~~l~~~~~~~g~~~~a~~~~~~~~~~~~~---  456 (490)
                      .+++..+++++..++ .|+...|..+|+--+.       .-||...| .-.+..+.+.++-+.|..+|+.....-..   
T Consensus       430 ~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~-------~f~d~~~y~~kyl~fLi~inde~naraLFetsv~r~~~~q~  501 (660)
T COG5107         430 GHHVYIYCAFIEYYA-TGDRATAYNIFELGLL-------KFPDSTLYKEKYLLFLIRINDEENARALFETSVERLEKTQL  501 (660)
T ss_pred             CcceeeeHHHHHHHh-cCCcchHHHHHHHHHH-------hCCCchHHHHHHHHHHHHhCcHHHHHHHHHHhHHHHHHhhh
Confidence            688889999998665 5677889999998776       23565444 45666778889999999999965554333   


Q ss_pred             hhhhHHHHHHHHhcC--CcHHHHHHHHHh
Q 011236          457 RNMYHALTEAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       457 ~~~~~~l~~~~~~~g--~~a~~~~~~m~~  483 (490)
                      ..+|..+|.-=..-|  ..|..+=++|.+
T Consensus       502 k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         502 KRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             hHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            678888888877777  556666566554

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=96.23  E-value=0.067  Score=50.49  Aligned_cols=28  Identities=11%  Similarity=0.060  Sum_probs=13.6

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      +...|..|.....+.|+++-|++.|.+.
T Consensus       346 ~~~~W~~Lg~~AL~~g~~~lAe~c~~k~  373 (443)
T PF04053_consen  346 DPEKWKQLGDEALRQGNIELAEECYQKA  373 (443)
T ss_dssp             THHHHHHHHHHHHHTTBHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHhh
Confidence            3344555555555555555555555444

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.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.20  E-value=0.1  Score=44.56  Aligned_cols=102  Identities=16%  Similarity=0.139  Sum_probs=70.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC--CCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKT--PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVS  428 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~--p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~  428 (490)
                      .|+.-+.. .+.|++..|...|...++..+.  -....+-.|..++...|++++|..+|..+.+.+|+.   .--+..+-
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s---~KApdall  219 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKS---PKAPDALL  219 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCC---CCChHHHH
Confidence            45554443 4466688888888888876543  122346667888888888888888888887744311   11225666


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          429 SILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      -|.....+.|+.++|..+|+++.+..|.
T Consensus       220 Klg~~~~~l~~~d~A~atl~qv~k~YP~  247 (262)
T COG1729         220 KLGVSLGRLGNTDEACATLQQVIKRYPG  247 (262)
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHCCC
Confidence            6777777888888888888888888776

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=96.13  E-value=0.22  Score=38.83  Aligned_cols=125  Identities=12%  Similarity=0.168  Sum_probs=70.7

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc
Q 011236          141 GALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGAR  220 (490)
Q Consensus       141 ~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  220 (490)
                      ..++..+.+.+.......+++.+...+. .+...++.++..|++.+. .+..+.+..      ..+......+++.|.+.
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~~-~~ll~~l~~------~~~~yd~~~~~~~c~~~   82 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYDP-QKEIERLDN------KSNHYDIEKVGKLCEKA   82 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHCH-HHHHHHHHh------ccccCCHHHHHHHHHHc
Confidence            4556666666777777777777766653 466667777777765532 233333331      12334444566667667


Q ss_pred             CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHH
Q 011236          221 SELSSMENVLQEMESQSHISMDWGTYSTVANYYIIA-GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYA  290 (490)
Q Consensus       221 g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  290 (490)
                      +-++++..++.++. .         +...+..+... ++++.|.+++.+-       .+...|..++..+.
T Consensus        83 ~l~~~~~~l~~k~~-~---------~~~Al~~~l~~~~d~~~a~~~~~~~-------~~~~lw~~~~~~~l  136 (140)
T smart00299       83 KLYEEAVELYKKDG-N---------FKDAIVTLIEHLGNYEKAIEYFVKQ-------NNPELWAEVLKALL  136 (140)
T ss_pred             CcHHHHHHHHHhhc-C---------HHHHHHHHHHcccCHHHHHHHHHhC-------CCHHHHHHHHHHHH
Confidence            77777777776653 1         12233334433 6677777766651       34455666665554

>PRK15331 chaperone protein SicA; Provisional

Probab=96.13  E-value=0.098  Score=41.13  Aligned_cols=84  Identities=8%  Similarity=-0.092  Sum_probs=33.3

Q ss_pred             HcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHH
Q 011236          255 IAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAE  334 (490)
Q Consensus       255 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  334 (490)
                      ..|++++|..+|.-+....+  .+..-|..|..++-..+++++|...|........ -|+..+-....++...|+.+.|.
T Consensus        49 ~~Gk~~eA~~~F~~L~~~d~--~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~-~dp~p~f~agqC~l~l~~~~~A~  125 (165)
T PRK15331         49 NQGRLDEAETFFRFLCIYDF--YNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLK-NDYRPVFFTGQCQLLMRKAAKAR  125 (165)
T ss_pred             HCCCHHHHHHHHHHHHHhCc--CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc-CCCCccchHHHHHHHhCCHHHHH
Confidence            34444444444444433222  2333334444444444444444444443222221 22222333333444444444444


Q ss_pred             HHHHHHH
Q 011236          335 KMLEEWE  341 (490)
Q Consensus       335 ~~~~~~~  341 (490)
                      ..|....
T Consensus       126 ~~f~~a~  132 (165)
T PRK15331        126 QCFELVN  132 (165)
T ss_pred             HHHHHHH
Confidence            4444433

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.11  E-value=0.14  Score=43.82  Aligned_cols=95  Identities=12%  Similarity=0.004  Sum_probs=62.7

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC----ChhHHHHHH
Q 011236           71 ELQRVIRQLRSRKRFKHALQVSEWMSGQGL--AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK----VDKLYGALL  144 (490)
Q Consensus        71 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p----~~~~~~~li  144 (490)
                      .|+.-+..+ +.|++..|.+.|...++...  ...+..+-.+..++...|++++|..+|..+.+..|    -+...--|.
T Consensus       144 ~Y~~A~~~~-ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            566666544 45667777777777776654  45566667777777777777777777776665543    234555666


Q ss_pred             HHHHhcCChhHHHHHHHHHHhc
Q 011236          145 NCYVREGLVDESLSLMQKMKEM  166 (490)
Q Consensus       145 ~~~~~~g~~~~a~~~~~~m~~~  166 (490)
                      ....+.|+.++|...|++..++
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHH
Confidence            6667777777777777777665

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=96.07  E-value=0.079  Score=46.00  Aligned_cols=83  Identities=11%  Similarity=0.086  Sum_probs=69.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSI  430 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l  430 (490)
                      ++..++..+...|+++.+...++++....+. |...|..++.+|.+.|+...|+..|+.+.....+..|+.|...+....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~-~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDPY-DEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            5567788888889999999999999888766 788899999999999999999999998888777778899988877776


Q ss_pred             HHHH
Q 011236          431 LDWL  434 (490)
Q Consensus       431 ~~~~  434 (490)
                      ....
T Consensus       234 ~~~~  237 (280)
T COG3629         234 EEIL  237 (280)
T ss_pred             HHHh
Confidence            6663

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.03  E-value=1.7  Score=42.70  Aligned_cols=100  Identities=13%  Similarity=0.136  Sum_probs=68.0

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                      -+.+-.+..+...|+..+|.++-.+.+    -||-..|..=+.+++..+++++-+++-+....           +.-|.-
T Consensus       685 lSl~dTv~~li~~g~~k~a~ql~~~Fk----ipdKr~~wLk~~aLa~~~kweeLekfAkskks-----------PIGy~P  749 (829)
T KOG2280|consen  685 LSLHDTVTTLILIGQNKRAEQLKSDFK----IPDKRLWWLKLTALADIKKWEELEKFAKSKKS-----------PIGYLP  749 (829)
T ss_pred             CcHHHHHHHHHHccchHHHHHHHHhcC----CcchhhHHHHHHHHHhhhhHHHHHHHHhccCC-----------CCCchh
Confidence            344556666777788888877766654    36788888888888888888876666555432           344566


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccchhhhHHHHHHHHhcC
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSG  471 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g  471 (490)
                      .+.+|.+.|+.++|.+++-+....       .-.+.+|.+.|
T Consensus       750 FVe~c~~~~n~~EA~KYiprv~~l-------~ekv~ay~~~~  784 (829)
T KOG2280|consen  750 FVEACLKQGNKDEAKKYIPRVGGL-------QEKVKAYLRVG  784 (829)
T ss_pred             HHHHHHhcccHHHHhhhhhccCCh-------HHHHHHHHHhc
Confidence            778888888888888887664332       24555566665

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.98  E-value=0.1  Score=48.25  Aligned_cols=63  Identities=22%  Similarity=0.277  Sum_probs=50.5

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH----HHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          348 DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPN----SWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       348 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +...++.+..+|.+.|++++|+..|++.++  +.|+..    +|..+..+|...|+.++|++.++++++
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALe--L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALE--LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            445677788888888888888888888776  778753    478888888888888888888888887

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.93  E-value=0.025  Score=33.67  Aligned_cols=39  Identities=10%  Similarity=0.017  Sum_probs=24.3

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHH
Q 011236          426 LVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALT  464 (490)
Q Consensus       426 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~  464 (490)
                      ++..+..+|...|++++|+++++++.+..|. +..|..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La   42 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALA   42 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhh
Confidence            4555666666666666666666666666666 55555543

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.91  E-value=0.24  Score=44.83  Aligned_cols=94  Identities=11%  Similarity=0.009  Sum_probs=71.0

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHH
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHAL  463 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l  463 (490)
                      .++..+..+|.+.+++..|++...+.+...      ++|......=..++...|+++.|+..|+++.+..|. ..+-+-|
T Consensus       258 ~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~------~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el  331 (397)
T KOG0543|consen  258 ACHLNLAACYLKLKEYKEAIESCNKVLELD------PNNVKALYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAEL  331 (397)
T ss_pred             HHhhHHHHHHHhhhhHHHHHHHHHHHHhcC------CCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHH
Confidence            467788888899999999999999888722      245566666677888889999999999999998888 5566666


Q ss_pred             HHHHHhcC---CcHHHHHHHHHhC
Q 011236          464 TEAHIRSG---QEVDGLLESMKAD  484 (490)
Q Consensus       464 ~~~~~~~g---~~a~~~~~~m~~~  484 (490)
                      +..-.+..   +...++|..|-..
T Consensus       332 ~~l~~k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  332 IKLKQKIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhc
Confidence            65555544   6667788888653

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=95.87  E-value=1.2  Score=39.65  Aligned_cols=159  Identities=12%  Similarity=0.066  Sum_probs=88.6

Q ss_pred             HHHHHHHHHHhhhhccCCChhhHHHHHHHHHh--cC----ChhHHHHHHHHHHHhcC---CCChhhHHHHHHHHHhcCC-
Q 011236          260 EKAIIYLKKCEDIVSKSKDALGYNHLISHYAS--LG----NKDEMMKFWGLQKIKCK---KQLNRDYITMLGSLVKIGE-  329 (490)
Q Consensus       260 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~----~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~-  329 (490)
                      ++.+.+++.|.+.+.. .+..+|-+.......  ..    ...++..+|+.|.+.++   .++...+..++..  ..++ 
T Consensus        79 ~~~~~~y~~L~~~gFk-~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   79 KEVLDIYEKLKEAGFK-RSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHhccC-ccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            3455667777776665 555555443222222  22    24567888888888777   4455556666543  3333 


Q ss_pred             ---HHHHHHHHHHHHhcCCCCCchh-HHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHH
Q 011236          330 ---LEEAEKMLEEWELSCYCYDFRV-PNIILLGYSQKG---MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEK  402 (490)
Q Consensus       330 ---~~~a~~~~~~~~~~~~~~~~~~-~~~l~~~~~~~g---~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  402 (490)
                         .+.++.+++.+.+.|+..+-.. +.+-+-++....   .+.++..+++.+.+.|+++....|..+.-...-.+..++
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLall~~~~~~  235 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLALLEDPEEK  235 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHHhcCCchHH
Confidence               3466778888888777655432 222222222211   145778888889998888777776665544333333335


Q ss_pred             HHHHHHHHHHhhhcCcCCC
Q 011236          403 AFECMKEALAVHEENKFWR  421 (490)
Q Consensus       403 a~~~~~~~~~~~~~~~~~~  421 (490)
                      ...-+.++.+...+..++.
T Consensus       236 ~~~~i~ev~~~L~~~k~~~  254 (297)
T PF13170_consen  236 IVEEIKEVIDELKEQKGFG  254 (297)
T ss_pred             HHHHHHHHHHHHhhCcccC
Confidence            5544444444333344544

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.82  E-value=0.17  Score=45.70  Aligned_cols=96  Identities=11%  Similarity=0.048  Sum_probs=70.8

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                      .++..+..+|.+.+++.+|+....+.+..+.. |+...-.-..+|...|+++.|+..|+++++       +.|+......
T Consensus       258 ~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~-N~KALyRrG~A~l~~~e~~~A~~df~ka~k-------~~P~Nka~~~  329 (397)
T KOG0543|consen  258 ACHLNLAACYLKLKEYKEAIESCNKVLELDPN-NVKALYRRGQALLALGEYDLARDDFQKALK-------LEPSNKAARA  329 (397)
T ss_pred             HHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCC-chhHHHHHHHHHHhhccHHHHHHHHHHHHH-------hCCCcHHHHH
Confidence            35667888899999999999999999988755 788877888899999999999999999988       5577655544


Q ss_pred             HHHHHH-cCCCH-HHHHHHHHHHHhc
Q 011236          430 ILDWLG-DNRDV-EEVEAFVSSLKIK  453 (490)
Q Consensus       430 l~~~~~-~~g~~-~~a~~~~~~~~~~  453 (490)
                      =+..|. +.... +...++|..|-..
T Consensus       330 el~~l~~k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  330 ELIKLKQKIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            444333 33333 3346677777554

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.76  E-value=0.26  Score=43.27  Aligned_cols=154  Identities=9%  Similarity=-0.004  Sum_probs=106.8

Q ss_pred             hcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhH----HHHHHHHHhcCCHH
Q 011236          291 SLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVP----NIILLGYSQKGMIE  366 (490)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~g~~~  366 (490)
                      ..|+..+|-..|+++....+ .|...+.-.-++|.-.|+.+.-...++++... ..+|...|    ..+.-++..+|-++
T Consensus       115 ~~g~~h~a~~~wdklL~d~P-tDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y~  192 (491)
T KOG2610|consen  115 GRGKHHEAAIEWDKLLDDYP-TDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIYD  192 (491)
T ss_pred             ccccccHHHHHHHHHHHhCc-hhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccch
Confidence            47788888888888888776 77777888888888999988888888887765 34454333    33444566789999


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHH
Q 011236          367 KADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAF  446 (490)
Q Consensus       367 ~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  446 (490)
                      +|.+.-++..+.+.. |.-.-.++...+--.|++.++.+++.+-.....  .+.-.-...|-...-.+...+.++.|+.+
T Consensus       193 dAEk~A~ralqiN~~-D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr--~s~mlasHNyWH~Al~~iE~aeye~aleI  269 (491)
T KOG2610|consen  193 DAEKQADRALQINRF-DCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWR--QSWMLASHNYWHTALFHIEGAEYEKALEI  269 (491)
T ss_pred             hHHHHHHhhccCCCc-chHHHHHHHHHHHhcchhhhHHHHHHhcccchh--hhhHHHhhhhHHHHHhhhcccchhHHHHH
Confidence            999988888876544 665666777777788889999888877654221  11111122333334445566889999998


Q ss_pred             HHH
Q 011236          447 VSS  449 (490)
Q Consensus       447 ~~~  449 (490)
                      |+.
T Consensus       270 yD~  272 (491)
T KOG2610|consen  270 YDR  272 (491)
T ss_pred             HHH
Confidence            873

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=95.74  E-value=1.1  Score=38.20  Aligned_cols=203  Identities=16%  Similarity=0.060  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhh-hccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHH
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDI-VSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLG  322 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  322 (490)
                      ..+......+...+.+..+...+...... ... .....+......+...++...+...+.........+ .........
T Consensus        60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  137 (291)
T COG0457          60 GLLLLLALALLKLGRLEEALELLEKALELELLP-NLAEALLNLGLLLEALGKYEEALELLEKALALDPDP-DLAEALLAL  137 (291)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhhhhcc-chHHHHHHHHHHHHHHhhHHHHHHHHHHHHcCCCCc-chHHHHHHH
Confidence            33334444444445555544444444331 111 233334444444444444445555544333322211 111111111


Q ss_pred             -HHHhcCCHHHHHHHHHHHHhcCC--CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          323 -SLVKIGELEEAEKMLEEWELSCY--CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       323 -~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                       .+...|+++.+...+.+......  ......+......+...++.+.+...+..............+..+...+...++
T Consensus       138 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  217 (291)
T COG0457         138 GALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGK  217 (291)
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHhhCcccchHHHHHhhHHHHHccc
Confidence             44455555555555555433110  011112222222234445555555555555543211123445555555555555


Q ss_pred             HHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          400 MEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       400 ~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      ++.+...+..+..       ..|+ ...+..+...+...+..+.+...+.+.....+
T Consensus       218 ~~~a~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (291)
T COG0457         218 YEEALEYYEKALE-------LDPDNAEALYNLALLLLELGRYEEALEALEKALELDP  267 (291)
T ss_pred             HHHHHHHHHHHHh-------hCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHhCc
Confidence            5555555555554       1122 22233333333344445555555555544443

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.68  E-value=1  Score=42.23  Aligned_cols=65  Identities=8%  Similarity=0.003  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhh
Q 011236          207 NFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCED  271 (490)
Q Consensus       207 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  271 (490)
                      ..+-..+..++-+.|+.++|.+.+++|.......-.......|+.++...+.+.++..++.+-.+
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdD  323 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDD  323 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhcc
Confidence            33444566666778888888888888762222212344566788888888888888888877654

The molecular function of this protein is uncertain.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=95.61  E-value=1.9  Score=39.91  Aligned_cols=119  Identities=21%  Similarity=0.214  Sum_probs=75.8

Q ss_pred             hcCC-HHHHHHHHHHHHhcCCCCCchhHHHHHH----HHHh---cCCHHHHHHHHHHHHHcCCCCCHH----HHHHHHHH
Q 011236          326 KIGE-LEEAEKMLEEWELSCYCYDFRVPNIILL----GYSQ---KGMIEKADAVLKEIVKKGKTPTPN----SWSIIAAG  393 (490)
Q Consensus       326 ~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~l~~----~~~~---~g~~~~A~~~~~~m~~~~~~p~~~----~~~~l~~~  393 (490)
                      +.|. -++|..+++.+.+- .+.|..+-|.+..    .|.+   ...+.+-..+-+-+.+.|++|-..    .-|.|.++
T Consensus       391 ~~g~~dekalnLLk~il~f-t~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDA  469 (549)
T PF07079_consen  391 EIGQCDEKALNLLKLILQF-TNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLADA  469 (549)
T ss_pred             hcCCccHHHHHHHHHHHHh-ccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHH
Confidence            3444 77888888888764 2234444333322    2322   233445555555566778776433    33333332


Q ss_pred             --HhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          394 --YADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       394 --~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                        +..+|++.++.-.-.-..+       +.|++.+|..+.-.+....++++|..++..+.-
T Consensus       470 EyLysqgey~kc~~ys~WL~~-------iaPS~~~~RLlGl~l~e~k~Y~eA~~~l~~LP~  523 (549)
T PF07079_consen  470 EYLYSQGEYHKCYLYSSWLTK-------IAPSPQAYRLLGLCLMENKRYQEAWEYLQKLPP  523 (549)
T ss_pred             HHHHhcccHHHHHHHHHHHHH-------hCCcHHHHHHHHHHHHHHhhHHHHHHHHHhCCC
Confidence              4567888888766555544       779999999998888889999999999987654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=95.58  E-value=0.061  Score=31.93  Aligned_cols=39  Identities=15%  Similarity=0.361  Sum_probs=25.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSII  390 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l  390 (490)
                      ++..+...|.+.|++++|.++|+++++..+. |...|..+
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~-~~~a~~~L   41 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALALDPD-DPEAWRAL   41 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-CHHHHHHh
Confidence            4556667777777777777777777776544 55555444

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.57  E-value=2.9  Score=41.84  Aligned_cols=179  Identities=12%  Similarity=0.108  Sum_probs=116.0

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHH----HHHHHhhcCHHHHHHHHHHcccc-CCChhHHHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQ----LDLIGKVRGLESAETYFNSLNDE-DKVDKLYGA  142 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l----~~~~~~~~~~~~A~~~~~~~~~~-~p~~~~~~~  142 (490)
                      .......-|+.+.+..-++-|+.+.+.   .+  .++.....+    ...+.+.|++++|...|-+.... +|.     .
T Consensus       333 ~ek~le~kL~iL~kK~ly~~Ai~LAk~---~~--~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~le~s-----~  402 (933)
T KOG2114|consen  333 IEKDLETKLDILFKKNLYKVAINLAKS---QH--LDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGFLEPS-----E  402 (933)
T ss_pred             eeccHHHHHHHHHHhhhHHHHHHHHHh---cC--CCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccCChH-----H
Confidence            344566777888888888888877553   32  244444444    44555789999999887665543 232     3


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC
Q 011236          143 LLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSE  222 (490)
Q Consensus       143 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  222 (490)
                      +|.-|....+...-..+++.+.+.|.. +...-..|+.+|.+.++.++..++.+... .|..  ..-....+..+.+.+-
T Consensus       403 Vi~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~efI~~~~-~g~~--~fd~e~al~Ilr~sny  478 (933)
T KOG2114|consen  403 VIKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTEFISKCD-KGEW--FFDVETALEILRKSNY  478 (933)
T ss_pred             HHHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHHHHhcCC-Ccce--eeeHHHHHHHHHHhCh
Confidence            566667777777888889999999887 77788899999999999888777766544 2221  1113345666666666


Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011236          223 LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKC  269 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  269 (490)
                      .++|..+-.+.. .     ....   +--.+-..+++++|++++..+
T Consensus       479 l~~a~~LA~k~~-~-----he~v---l~ille~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  479 LDEAELLATKFK-K-----HEWV---LDILLEDLHNYEEALRYISSL  516 (933)
T ss_pred             HHHHHHHHHHhc-c-----CHHH---HHHHHHHhcCHHHHHHHHhcC
Confidence            777666655543 1     1112   223344556777777776664

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.54  E-value=0.26  Score=42.14  Aligned_cols=70  Identities=17%  Similarity=0.067  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc----------------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011236          330 LEEAEKMLEEWELSCYCYDFRVPNIILLGYSQK----------------GMIEKADAVLKEIVKKGKTPTPNSWSIIAAG  393 (490)
Q Consensus       330 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----------------g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~  393 (490)
                      ++=....++.|.+-|+.-|..+|+.|+..+-+.                .+-+-+++++++|...|+.||-.+-..|+++
T Consensus        88 veFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~  167 (406)
T KOG3941|consen   88 VEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNA  167 (406)
T ss_pred             HHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHH
Confidence            333334444445555555555555554443221                1334578899999999999999999999999


Q ss_pred             HhccCC
Q 011236          394 YADKNN  399 (490)
Q Consensus       394 ~~~~~~  399 (490)
                      |.+.+.
T Consensus       168 FGr~~~  173 (406)
T KOG3941|consen  168 FGRWNF  173 (406)
T ss_pred             hccccc
Confidence            988776

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.53  E-value=0.63  Score=34.83  Aligned_cols=53  Identities=15%  Similarity=0.107  Sum_probs=24.2

Q ss_pred             HHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 011236          253 YIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKI  307 (490)
Q Consensus       253 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  307 (490)
                      ....|+.+.|++.|.+.....+  .....||.-.+++--.|+.++|++=+++..+
T Consensus        53 laE~g~Ld~AlE~F~qal~l~P--~raSayNNRAQa~RLq~~~e~ALdDLn~Ale  105 (175)
T KOG4555|consen   53 LAEAGDLDGALELFGQALCLAP--ERASAYNNRAQALRLQGDDEEALDDLNKALE  105 (175)
T ss_pred             HHhccchHHHHHHHHHHHHhcc--cchHhhccHHHHHHHcCChHHHHHHHHHHHH
Confidence            3444444444444444444333  2344444444444444444444444444433

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=95.50  E-value=1.7  Score=41.88  Aligned_cols=162  Identities=13%  Similarity=0.027  Sum_probs=106.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChh------hHHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCChhhHH
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDAL------GYNHLISHYAS----LGNKDEMMKFWGLQKIKCKKQLNRDYI  318 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~------~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  318 (490)
                      ++....-.||-+.+++.+.+..+.... ..+.      .|...+..++.    ..+.+.|.+++..+....|  +...|.
T Consensus       194 ll~~vGF~gdR~~GL~~L~~~~~~~~i-~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~yP--~s~lfl  270 (468)
T PF10300_consen  194 LLSFVGFSGDRELGLRLLWEASKSENI-RSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRYP--NSALFL  270 (468)
T ss_pred             HHhhcCcCCcHHHHHHHHHHHhccCCc-chHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhCC--CcHHHH
Confidence            667777789999999999886653332 2222      23444443333    4567889999998887764  444443


Q ss_pred             -HHHHHHHhcCCHHHHHHHHHHHHhcCC---CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-
Q 011236          319 -TMLGSLVKIGELEEAEKMLEEWELSCY---CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG-  393 (490)
Q Consensus       319 -~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~-  393 (490)
                       .-.+.+...|++++|.+.|+.......   ......+--+...+.-.+++++|...|..+.+.+-. ...+|.-+..+ 
T Consensus       271 ~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~W-Ska~Y~Y~~a~c  349 (468)
T PF10300_consen  271 FFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKW-SKAFYAYLAAAC  349 (468)
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhcccc-HHHHHHHHHHHH
Confidence             345666778999999999997654211   112233445666788899999999999999886433 34445444433 


Q ss_pred             HhccCCH-------HHHHHHHHHHHHhh
Q 011236          394 YADKNNM-------EKAFECMKEALAVH  414 (490)
Q Consensus       394 ~~~~~~~-------~~a~~~~~~~~~~~  414 (490)
                      +...++.       ++|.++|.+.-...
T Consensus       350 ~~~l~~~~~~~~~~~~a~~l~~~vp~l~  377 (468)
T PF10300_consen  350 LLMLGREEEAKEHKKEAEELFRKVPKLK  377 (468)
T ss_pred             HHhhccchhhhhhHHHHHHHHHHHHHHH
Confidence            3456666       88888888876644

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.

>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=95.49  E-value=0.28  Score=46.37  Aligned_cols=162  Identities=14%  Similarity=0.045  Sum_probs=95.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcC
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG  328 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  328 (490)
                      ......-.++++++.++...-.-...  -+..-.+.++..+.+.|..+.|+.+-..-         .   .-.....+.|
T Consensus       267 ~fk~av~~~d~~~v~~~i~~~~ll~~--i~~~~~~~i~~fL~~~G~~e~AL~~~~D~---------~---~rFeLAl~lg  332 (443)
T PF04053_consen  267 EFKTAVLRGDFEEVLRMIAASNLLPN--IPKDQGQSIARFLEKKGYPELALQFVTDP---------D---HRFELALQLG  332 (443)
T ss_dssp             HHHHHHHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS-H---------H---HHHHHHHHCT
T ss_pred             HHHHHHHcCChhhhhhhhhhhhhccc--CChhHHHHHHHHHHHCCCHHHHHhhcCCh---------H---HHhHHHHhcC
Confidence            44556677888888777752111111  22445777777788888888887775421         1   1223344678


Q ss_pred             CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHH
Q 011236          329 ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMK  408 (490)
Q Consensus       329 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~  408 (490)
                      +++.|.++.++.      .+...|..|.+...+.|+++-|.+.|++..+         |..|+-.|.-.|+.+.-.++.+
T Consensus       333 ~L~~A~~~a~~~------~~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~  397 (443)
T PF04053_consen  333 NLDIALEIAKEL------DDPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAK  397 (443)
T ss_dssp             -HHHHHHHCCCC------STHHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHH
T ss_pred             CHHHHHHHHHhc------CcHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHH
Confidence            888887765443      2556888888888888888888888877543         5666667777888777777776


Q ss_pred             HHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 011236          409 EALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       409 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  450 (490)
                      .+..     .|      -++....++.-.|+.++..+++.+.
T Consensus       398 ~a~~-----~~------~~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  398 IAEE-----RG------DINIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             HHHH-----TT-------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             HHHH-----cc------CHHHHHHHHHHcCCHHHHHHHHHHc
Confidence            6655     22      1444444555568888887777653

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.

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=95.42  E-value=1.5  Score=37.45  Aligned_cols=63  Identities=17%  Similarity=0.052  Sum_probs=24.9

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011236          315 RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       315 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      ..+..+...+...++++.+...+......... ....+..+...+...+..+.+...+......
T Consensus       203 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         203 EALLNLGLLYLKLGKYEEALEYYEKALELDPD-NAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HHHHHhhHHHHHcccHHHHHHHHHHHHhhCcc-cHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            33334444444444444444444444432111 1122222222333444455555555554443

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.42  E-value=0.94  Score=35.87  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=10.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVK  377 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~  377 (490)
                      |.-+-.+.|++.+|.+.|..+..
T Consensus       173 LglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         173 LGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HhHHHHhccchHHHHHHHHHHHc
Confidence            33333444455555544444443

>PRK11906 transcriptional regulator; Provisional

Probab=95.26  E-value=1.7  Score=40.63  Aligned_cols=117  Identities=15%  Similarity=0.081  Sum_probs=58.3

Q ss_pred             hHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHHc---------CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhc
Q 011236          223 LSSMENVLQEMESQSHISMD-WGTYSTVANYYIIA---------GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASL  292 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~---------~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  292 (490)
                      .+.|..+|.+......+.|+ ...|..+..++...         .+..+|.+..++..+.++  .|......+..+....
T Consensus       274 ~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld~--~Da~a~~~~g~~~~~~  351 (458)
T PRK11906        274 IYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDITT--VDGKILAIMGLITGLS  351 (458)
T ss_pred             HHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcCC--CCHHHHHHHHHHHHhh
Confidence            44677777777633444444 34444444333221         123344444444444444  4555555555555555


Q ss_pred             CChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          293 GNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      ++.+.|...|++.....+ ....+|......+.-.|+.++|.+.+++..+
T Consensus       352 ~~~~~a~~~f~rA~~L~P-n~A~~~~~~~~~~~~~G~~~~a~~~i~~alr  400 (458)
T PRK11906        352 GQAKVSHILFEQAKIHST-DIASLYYYRALVHFHNEKIEEARICIDKSLQ  400 (458)
T ss_pred             cchhhHHHHHHHHhhcCC-ccHHHHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            556666666665555443 3333444444444445666666665555444

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.24  E-value=0.6  Score=41.14  Aligned_cols=156  Identities=15%  Similarity=-0.006  Sum_probs=114.6

Q ss_pred             HHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHH----HHHHHHHhcC
Q 011236          253 YIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYI----TMLGSLVKIG  328 (490)
Q Consensus       253 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----~l~~~~~~~~  328 (490)
                      ....|+..+|-..++++.+..|  .|..++...=.+|...|+.+.-...+++....-. ++...|.    ...-++...|
T Consensus       113 ~~~~g~~h~a~~~wdklL~d~P--tDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn-~dlp~~sYv~GmyaFgL~E~g  189 (491)
T KOG2610|consen  113 LWGRGKHHEAAIEWDKLLDDYP--TDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWN-ADLPCYSYVHGMYAFGLEECG  189 (491)
T ss_pred             hhccccccHHHHHHHHHHHhCc--hhhhhhhhhhhHHHhccchhhhhhHHHHhccccC-CCCcHHHHHHHHHHhhHHHhc
Confidence            3457888888889999998777  6889999999999999999999999987776633 4443333    3334456789


Q ss_pred             CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHhccCCHHHHHH
Q 011236          329 ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK---GKTPTPNSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       329 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~---~~~p~~~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      -+++|++.-++..+.+ +.|...-.++.+.+-..|++.++.+...+-.+.   +...-..-|-...-.+...+.++.|++
T Consensus       190 ~y~dAEk~A~ralqiN-~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~ale  268 (491)
T KOG2610|consen  190 IYDDAEKQADRALQIN-RFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALE  268 (491)
T ss_pred             cchhHHHHHHhhccCC-CcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHH
Confidence            9999999998887753 335556667778888899999999887665432   111112345556666778899999999


Q ss_pred             HHHHHHH
Q 011236          406 CMKEALA  412 (490)
Q Consensus       406 ~~~~~~~  412 (490)
                      +|+.-+-
T Consensus       269 IyD~ei~  275 (491)
T KOG2610|consen  269 IYDREIW  275 (491)
T ss_pred             HHHHHHH
Confidence            9986544

>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=95.06  E-value=1.3  Score=34.85  Aligned_cols=51  Identities=18%  Similarity=0.101  Sum_probs=24.5

Q ss_pred             hhcCHHHHHHHHHHccccCCChh-HHHHHHHHHHhcCChhHHHHHHHHHHhc
Q 011236          116 KVRGLESAETYFNSLNDEDKVDK-LYGALLNCYVREGLVDESLSLMQKMKEM  166 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~~~~p~~~-~~~~li~~~~~~g~~~~a~~~~~~m~~~  166 (490)
                      +.++.+++..+++.+.-..|... .-..-...+.+.|++.+|+++|+++.+.
T Consensus        22 ~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~   73 (160)
T PF09613_consen   22 RLGDPDDAEALLDALRVLRPEFPELDLFDGWLHIVRGDWDDALRLLRELEER   73 (160)
T ss_pred             ccCChHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhcc
Confidence            44555555555555554444211 1111223344556666666666665544

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=95.04  E-value=2.9  Score=38.67  Aligned_cols=70  Identities=19%  Similarity=0.027  Sum_probs=43.4

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          312 QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY---DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       312 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      ....++..+...+.+.|.++.|...+..+...+...   .+.+.-.-+...-..|+..+|...++...+..+.
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            344566777777777788887777777776643211   2233333445556667777777777777764333

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.98  E-value=0.91  Score=34.96  Aligned_cols=74  Identities=12%  Similarity=0.126  Sum_probs=42.1

Q ss_pred             HHHHHhhcCHHHHHHHHHHccccCC----ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 011236          111 LDLIGKVRGLESAETYFNSLNDEDK----VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTN  184 (490)
Q Consensus       111 ~~~~~~~~~~~~A~~~~~~~~~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  184 (490)
                      .....+.|++++|.+.|+.+..+-|    ...+--.|+.+|.+.+++++|...+++.++..+.-.-.-|...+.+++.
T Consensus        17 a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~   94 (142)
T PF13512_consen   17 AQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSY   94 (142)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHH
Confidence            3344455666666666666665542    2344555666666777777777777766666544333445555555443

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=94.83  E-value=3.6  Score=38.77  Aligned_cols=58  Identities=7%  Similarity=0.076  Sum_probs=38.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHhccCCHHHHHHHHHHH
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKGKT-PTPNSWSIIAAGYADKNNMEKAFECMKEA  410 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~~~~~~~l~~~~~~~~~~~~a~~~~~~~  410 (490)
                      ..+..+.-+.|+.++|.+.+++|.+..+. -+......|+.++...+.+.++..++.+-
T Consensus       263 rRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kY  321 (539)
T PF04184_consen  263 RRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKY  321 (539)
T ss_pred             HHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHh
Confidence            34555666677777777777777654322 13346677777777777777777777764

The molecular function of this protein is uncertain.

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.75  E-value=1.3  Score=34.15  Aligned_cols=24  Identities=21%  Similarity=0.221  Sum_probs=9.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          319 TMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       319 ~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      .++.+|.+.++++.|...++..++
T Consensus        52 ~l~yayy~~~~y~~A~a~~~rFir   75 (142)
T PF13512_consen   52 DLAYAYYKQGDYEEAIAAYDRFIR   75 (142)
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHH
Confidence            333444444444444444444443

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=94.69  E-value=0.3  Score=42.55  Aligned_cols=78  Identities=15%  Similarity=0.245  Sum_probs=55.1

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHH-----CCCCCCHHHHHH
Q 011236          138 KLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKE-----NGVPPDNFSYRI  212 (490)
Q Consensus       138 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~~~  212 (490)
                      .++..++..+...|+.+.+...++++....+. +...|..+|.+|.+.|+...|...|+.+.+     .|+.|...+...
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~-~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~  232 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELDPY-DEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRAL  232 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHH
Confidence            45666777777777777777777777776554 667777777777777777777777776644     477777776666


Q ss_pred             HHHH
Q 011236          213 CINS  216 (490)
Q Consensus       213 li~~  216 (490)
                      ....
T Consensus       233 y~~~  236 (280)
T COG3629         233 YEEI  236 (280)
T ss_pred             HHHH
Confidence            6555

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=94.67  E-value=3.1  Score=37.31  Aligned_cols=55  Identities=15%  Similarity=-0.028  Sum_probs=24.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcC-----CCCCchhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          320 MLGSLVKIGELEEAEKMLEEWELSC-----YCYDFRVPNIILLGYSQKGMIEKADAVLKE  374 (490)
Q Consensus       320 l~~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  374 (490)
                      +..++...+.++++.+.|+...+--     ......++..|...|.+..++++|.-+..+
T Consensus       128 ~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~k  187 (518)
T KOG1941|consen  128 MGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFPCK  187 (518)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhhHh
Confidence            4444444445555555555443311     111223444555555555555555544433

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=94.65  E-value=1.2  Score=39.78  Aligned_cols=127  Identities=17%  Similarity=0.054  Sum_probs=59.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccC----CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC---CCh-hhH---
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKS----KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK---QLN-RDY---  317 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~-~~~---  317 (490)
                      +..++...+.++++++.|+...+.-...    .....+-.|...|.+..|+++|.-+..+.......   .|. .-|   
T Consensus       128 ~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~  207 (518)
T KOG1941|consen  128 MGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFPCKAAELVNSYGLKDWSLKYRAM  207 (518)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHH
Confidence            4455555556666666666544321110    12244556666666666666665554433322110   111 111   


Q ss_pred             --HHHHHHHHhcCCHHHHHHHHHHHHh----cCCCC-CchhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011236          318 --ITMLGSLVKIGELEEAEKMLEEWEL----SCYCY-DFRVPNIILLGYSQKGMIEKADAVLKEI  375 (490)
Q Consensus       318 --~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m  375 (490)
                        ..|.-++...|....|.+.-++..+    .|-.+ -......+.+.|...|+.+.|..-|+..
T Consensus       208 ~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~gd~e~af~rYe~A  272 (518)
T KOG1941|consen  208 SLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSRGDLERAFRRYEQA  272 (518)
T ss_pred             HHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhcccHhHHHHHHHHH
Confidence              1233344455555555555554433    22221 1223344556666677776666655543

>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=94.54  E-value=0.0065  Score=47.80  Aligned_cols=135  Identities=13%  Similarity=0.148  Sum_probs=81.2

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQL  111 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  111 (490)
                      ++.....++..+.+.+.+..... .++.+...+...+....+.++..|++.++.+...++++   ..    +......++
T Consensus         6 ~~~~~~~vi~~~~~~~~~~~l~~-yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~---~~----~~yd~~~~~   77 (143)
T PF00637_consen    6 DPLEISEVISAFEERNQPEELIE-YLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK---TS----NNYDLDKAL   77 (143)
T ss_dssp             TTSCSCCCHHHCTTTT-GGGCTC-CHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT---SS----SSS-CTHHH
T ss_pred             CccCHHHHHHHHHhCCCHHHHHH-HHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc---cc----cccCHHHHH
Confidence            34455677788877777776666 78888777666778888889999988887777777766   11    123345566


Q ss_pred             HHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCC
Q 011236          112 DLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQ  187 (490)
Q Consensus       112 ~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  187 (490)
                      ..|-+.|.+++|.-++..+....       ..+..+...++++.|.+...+      .++...|..++..|...+.
T Consensus        78 ~~c~~~~l~~~a~~Ly~~~~~~~-------~al~i~~~~~~~~~a~e~~~~------~~~~~l~~~l~~~~l~~~~  140 (143)
T PF00637_consen   78 RLCEKHGLYEEAVYLYSKLGNHD-------EALEILHKLKDYEEAIEYAKK------VDDPELWEQLLKYCLDSKP  140 (143)
T ss_dssp             HHHHTTTSHHHHHHHHHCCTTHT-------TCSSTSSSTHCSCCCTTTGGG------CSSSHHHHHHHHHHCTSTC
T ss_pred             HHHHhcchHHHHHHHHHHcccHH-------HHHHHHHHHccHHHHHHHHHh------cCcHHHHHHHHHHHHhcCc
Confidence            67777777777777666543321       111112233444444432222      1356677777777665554

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.

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.53  E-value=1.5  Score=33.03  Aligned_cols=136  Identities=10%  Similarity=0.104  Sum_probs=67.5

Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhH---HHHHHHHHHhcCChhHH
Q 011236           80 RSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKL---YGALLNCYVREGLVDES  156 (490)
Q Consensus        80 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~---~~~li~~~~~~g~~~~a  156 (490)
                      .-.|..++..++..+...+.   +..-++.++.-....-+-+-..++++.+-... |...   ...++.+|+..|.    
T Consensus        13 ildG~V~qGveii~k~v~Ss---ni~E~NWvICNiiDaa~C~yvv~~LdsIGkiF-Dis~C~NlKrVi~C~~~~n~----   84 (161)
T PF09205_consen   13 ILDGDVKQGVEIIEKTVNSS---NIKEYNWVICNIIDAADCDYVVETLDSIGKIF-DISKCGNLKRVIECYAKRNK----   84 (161)
T ss_dssp             HHTT-HHHHHHHHHHHHHHS----HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS--GGG-S-THHHHHHHHHTT-----
T ss_pred             HHhchHHHHHHHHHHHcCcC---CccccceeeeecchhhchhHHHHHHHHHhhhc-CchhhcchHHHHHHHHHhcc----
Confidence            34577777788877777664   45566666655555555555555555544321 1111   1223333333332    


Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhC
Q 011236          157 LSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQ  236 (490)
Q Consensus       157 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  236 (490)
                                    +.......+......|+-+...++++++.+. -.+++...-.+..+|.+.|+..++.+++.+.- +
T Consensus        85 --------------~se~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~AC-e  148 (161)
T PF09205_consen   85 --------------LSEYVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEAC-E  148 (161)
T ss_dssp             ----------------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHH-H
T ss_pred             --------------hHHHHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH-H
Confidence                          2223344555566666666666666666542 34566666666667777777777777666665 5


Q ss_pred             CCC
Q 011236          237 SHI  239 (490)
Q Consensus       237 ~~~  239 (490)
                      .|+
T Consensus       149 kG~  151 (161)
T PF09205_consen  149 KGL  151 (161)
T ss_dssp             TT-
T ss_pred             hch
Confidence            554

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=94.15  E-value=8.7  Score=40.35  Aligned_cols=28  Identities=11%  Similarity=-0.058  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHhcC--ChhHHHHHHHHHHh
Q 011236           70 LELQRVIRQLRSRK--RFKHALQVSEWMSG   97 (490)
Q Consensus        70 ~~~~~ll~~~~~~~--~~~~a~~~~~~~~~   97 (490)
                      .-...+|.++.+.+  ..+.|++.......
T Consensus       791 ~~~~~ilTs~vk~~~~~ie~aL~kI~~l~~  820 (1265)
T KOG1920|consen  791 KFNLFILTSYVKSNPPEIEEALQKIKELQL  820 (1265)
T ss_pred             hhhHHHHHHHHhcCcHHHHHHHHHHHHHHh
Confidence            33445556666555  44555555555443

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=94.15  E-value=2.2  Score=33.67  Aligned_cols=72  Identities=10%  Similarity=-0.170  Sum_probs=43.3

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHh
Q 011236           77 RQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVR  149 (490)
Q Consensus        77 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~  149 (490)
                      ..-.+.++.+++..++.-+.-.. |-.+..-..-...+...|++.+|..+|+.+....|....-..|+..|..
T Consensus        18 ~~al~~~~~~D~e~lL~ALrvLR-P~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~CL~   89 (160)
T PF09613_consen   18 SVALRLGDPDDAEALLDALRVLR-PEFPELDLFDGWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALCLY   89 (160)
T ss_pred             HHHHccCChHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHHHH
Confidence            33456677777777777776664 2333333344456667778888888887777666544444444444443

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=93.88  E-value=2.1  Score=32.27  Aligned_cols=54  Identities=26%  Similarity=0.316  Sum_probs=18.9

Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .+...|+-+.-.+++..+.+. -.+++...-.+..+|.+.|+..++.+++.++.+
T Consensus        95 ~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACe  148 (161)
T PF09205_consen   95 ILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACE  148 (161)
T ss_dssp             HHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence            333344444444444433321 123333333444444444444444444444433

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=93.72  E-value=0.0021  Score=50.56  Aligned_cols=53  Identities=11%  Similarity=0.155  Sum_probs=26.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHH
Q 011236          144 LNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLL  196 (490)
Q Consensus       144 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~  196 (490)
                      +..+.+.+.+.....+++.+...+..-+....+.++..|++.++.++..++++
T Consensus        14 i~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   14 ISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             HHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            44444455555555555555544433345555555555555555555555444

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.

>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=93.70  E-value=3  Score=33.36  Aligned_cols=134  Identities=12%  Similarity=0.082  Sum_probs=60.1

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhh
Q 011236          193 DVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDI  272 (490)
Q Consensus       193 ~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  272 (490)
                      +.++.+.+.+++|+...+..+++.+.+.|++..-..++     +.++-+|.......+-.+  .+....+.++--+|...
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~qll-----q~~Vi~DSk~lA~~LLs~--~~~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQLL-----QYHVIPDSKPLACQLLSL--GNQYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHH-----hhcccCCcHHHHHHHHHh--HccChHHHHHHHHHHHH
Confidence            33444455566666666666666666666654433332     444445544433222111  11222233333333222


Q ss_pred             hccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          273 VSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       273 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      -.     ..+..+++.+...|++-+|+++.+....    .+......++.+..+.+|...-..+++-..+
T Consensus        88 L~-----~~~~~iievLL~~g~vl~ALr~ar~~~~----~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   88 LG-----TAYEEIIEVLLSKGQVLEALRYARQYHK----VDSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             hh-----hhHHHHHHHHHhCCCHHHHHHHHHHcCC----cccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            11     0234455555666666666666553211    1222223445555555555444444444433

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=93.50  E-value=1.4  Score=35.85  Aligned_cols=59  Identities=17%  Similarity=0.103  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc--hhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDF--RVPNIILLGYSQKGMIEKADAVLKEI  375 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~g~~~~A~~~~~~m  375 (490)
                      +..+...|++.|+.+.|.+.+.++.+....+..  ..+-.+|+...-.+++..+...+.+.
T Consensus        39 ~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   39 LEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            444555555555555555555555544322221  22334444455555555555554444

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=93.33  E-value=0.2  Score=28.10  Aligned_cols=27  Identities=30%  Similarity=0.415  Sum_probs=17.8

Q ss_pred             HHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          386 SWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       386 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +|..|...|.+.|++++|++++++++.
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~   27 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALA   27 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            356667777777777777777777554

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=93.28  E-value=8.3  Score=37.25  Aligned_cols=407  Identities=11%  Similarity=0.045  Sum_probs=231.5

Q ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHH
Q 011236           67 ISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLN  145 (490)
Q Consensus        67 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~  145 (490)
                      .+...+..+|.--......+.+..++..++..- |.-..-+......=.+.|..+.+..+|++....-| +...|...+.
T Consensus        43 ~~f~~wt~li~~~~~~~~~~~~r~~y~~fL~ky-Pl~~gyW~kfA~~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~~  121 (577)
T KOG1258|consen   43 LDFDAWTTLIQENDSIEDVDALREVYDIFLSKY-PLCYGYWKKFADYEYKLGNAENSVKVFERGVQAIPLSVDLWLSYLA  121 (577)
T ss_pred             hcccchHHHHhccCchhHHHHHHHHHHHHHhhC-ccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence            345556666665544555566777777777654 23333444455556688999999999999877655 5667776665


Q ss_pred             HHH-hcCChhHHHHHHHHHHhc-CCC-CCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHh---c
Q 011236          146 CYV-REGLVDESLSLMQKMKEM-GSF-GSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYG---A  219 (490)
Q Consensus       146 ~~~-~~g~~~~a~~~~~~m~~~-~~~-p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~---~  219 (490)
                      .+. ..|+.+...+.|+..... |.. -....|...|..-...+++.....+++..++..   . ..|+..-.-|.   .
T Consensus       122 f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRileiP---~-~~~~~~f~~f~~~l~  197 (577)
T KOG1258|consen  122 FLKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILEIP---L-HQLNRHFDRFKQLLN  197 (577)
T ss_pred             HHhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHhhh---h-hHhHHHHHHHHHHHh
Confidence            544 467777888888887664 211 145567888887778889999999999988742   1 12222211111   1


Q ss_pred             c------CChHHHHHHHHHHHh-------------------CCCC-CCC-HHHHHHHH-------HHHHHcCCHHHHHHH
Q 011236          220 R------SELSSMENVLQEMES-------------------QSHI-SMD-WGTYSTVA-------NYYIIAGLKEKAIIY  265 (490)
Q Consensus       220 ~------g~~~~a~~~~~~~~~-------------------~~~~-~~~-~~~~~~li-------~~~~~~~~~~~a~~~  265 (490)
                      .      ...+++.++-.....                   ..+- .+. ....+.+-       ..+-...........
T Consensus       198 ~~~~~~l~~~d~~~~l~~~~~~~~~~~~~~~~~e~~~~~v~~~~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~~  277 (577)
T KOG1258|consen  198 QNEEKILLSIDELIQLRSDVAERSKITHSQEPLEELEIGVKDSTDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRWG  277 (577)
T ss_pred             cCChhhhcCHHHHHHHhhhHHhhhhcccccChhHHHHHHHhhccCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHHh
Confidence            1      122222222111110                   0000 000 00111111       111122222223333


Q ss_pred             HHHHhhhhc------cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          266 LKKCEDIVS------KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEE  339 (490)
Q Consensus       266 ~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  339 (490)
                      |+.-.....      ..++..+|..-+..-...|+.+.+.-+|+........-+ ..|--.+.-....|+.+-|..++..
T Consensus       278 fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~cA~Y~-efWiky~~~m~~~~~~~~~~~~~~~  356 (577)
T KOG1258|consen  278 FEEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIPCALYD-EFWIKYARWMESSGDVSLANNVLAR  356 (577)
T ss_pred             hhhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhHHhhhH-HHHHHHHHHHHHcCchhHHHHHHHh
Confidence            333222110      003456788888888899999999999997766554222 3344444444455999988888877


Q ss_pred             HHhcCCCCCchhHHHHHHHHH-hcCCHHHHHHHHHHHHHcCCCCCHHH-HHHHHHHHhccCCHHHHH---HHHHHHHHhh
Q 011236          340 WELSCYCYDFRVPNIILLGYS-QKGMIEKADAVLKEIVKKGKTPTPNS-WSIIAAGYADKNNMEKAF---ECMKEALAVH  414 (490)
Q Consensus       340 ~~~~~~~~~~~~~~~l~~~~~-~~g~~~~A~~~~~~m~~~~~~p~~~~-~~~l~~~~~~~~~~~~a~---~~~~~~~~~~  414 (490)
                      ..+- ..|+......+-..+. ..|+++.|..+++.+.+.-  |+... -..-+....+.|..+.+.   +++.....  
T Consensus       357 ~~~i-~~k~~~~i~L~~a~f~e~~~n~~~A~~~lq~i~~e~--pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~--  431 (577)
T KOG1258|consen  357 ACKI-HVKKTPIIHLLEARFEESNGNFDDAKVILQRIESEY--PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYE--  431 (577)
T ss_pred             hhhh-cCCCCcHHHHHHHHHHHhhccHHHHHHHHHHHHhhC--CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhcc--
Confidence            6654 3333333232323333 3679999999999998763  44322 222233455677777777   44433332  


Q ss_pred             hcCcCCCcchhhHHHHHH-----HHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC-----CcHHHHHHHHHh
Q 011236          415 EENKFWRPKPSLVSSILD-----WLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG-----QEVDGLLESMKA  483 (490)
Q Consensus       415 ~~~~~~~p~~~~~~~l~~-----~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g-----~~a~~~~~~m~~  483 (490)
                          | +-+..+...+.-     .+.-.++.+.|..++.++.+..|+ ...|..++......+     +--.-++..+..
T Consensus       432 ----~-~~~~~i~~~l~~~~~r~~~~i~~d~~~a~~~l~~~~~~~~~~k~~~~~~~~~~~~~~~~~e~d~~e~~~~~~~~  506 (577)
T KOG1258|consen  432 ----G-KENNGILEKLYVKFARLRYKIREDADLARIILLEANDILPDCKVLYLELIRFELIQPSGREYDLLEPIDWKELK  506 (577)
T ss_pred             ----c-ccCcchhHHHHHHHHHHHHHHhcCHHHHHHHHHHhhhcCCccHHHHHHHHHHHHhCCcchhhhhhhhHHHHHHh
Confidence                1 122223332222     223468899999999999999999 889999999988888     223333444444


Q ss_pred             CCCCCC
Q 011236          484 DDIDED  489 (490)
Q Consensus       484 ~~~~pd  489 (490)
                      ..+.+|
T Consensus       507 ~~~~~~  512 (577)
T KOG1258|consen  507 MLIDFD  512 (577)
T ss_pred             hhcccc
Confidence            444444

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=93.16  E-value=6.4  Score=36.83  Aligned_cols=129  Identities=12%  Similarity=-0.017  Sum_probs=76.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcC
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG  328 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  328 (490)
                      -|.--...|++-.|-+-+.......+..|+.....+.|  ....|+++.+...+......-. ....+..++++...+.|
T Consensus       295 si~k~~~~gd~~aas~~~~~~lr~~~~~p~~i~l~~~i--~~~lg~ye~~~~~~s~~~~~~~-s~~~~~~~~~r~~~~l~  371 (831)
T PRK15180        295 SITKQLADGDIIAASQQLFAALRNQQQDPVLIQLRSVI--FSHLGYYEQAYQDISDVEKIIG-TTDSTLRCRLRSLHGLA  371 (831)
T ss_pred             HHHHHhhccCHHHHHHHHHHHHHhCCCCchhhHHHHHH--HHHhhhHHHHHHHhhchhhhhc-CCchHHHHHHHhhhchh
Confidence            34444556776666544444433333215544443333  4567888888887774443333 55567778888888888


Q ss_pred             CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          329 ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       329 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      +++.|...-.-|....+. +..+...-.-.--..|-++++.-.++++...+++
T Consensus       372 r~~~a~s~a~~~l~~eie-~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~~~  423 (831)
T PRK15180        372 RWREALSTAEMMLSNEIE-DEEVLTVAAGSADALQLFDKSYHYWKRVLLLNPE  423 (831)
T ss_pred             hHHHHHHHHHHHhccccC-ChhheeeecccHHHHhHHHHHHHHHHHHhccCCh
Confidence            888888887777766554 2222222222234456678888888877765443

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=93.09  E-value=0.086  Score=29.17  Aligned_cols=30  Identities=20%  Similarity=0.359  Sum_probs=20.1

Q ss_pred             HHccccCC-ChhHHHHHHHHHHhcCChhHHH
Q 011236          128 NSLNDEDK-VDKLYGALLNCYVREGLVDESL  157 (490)
Q Consensus       128 ~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~  157 (490)
                      ++..+.+| +..+|+.+...|...|++++|+
T Consensus         3 ~kAie~~P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    3 KKAIELNPNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence            34444456 5777777777777777777765

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=92.95  E-value=1.7  Score=35.42  Aligned_cols=62  Identities=15%  Similarity=0.085  Sum_probs=32.7

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHhh
Q 011236          209 SYRICINSYGARSELSSMENVLQEMESQSHISMD--WGTYSTVANYYIIAGLKEKAIIYLKKCED  271 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~  271 (490)
                      .+..+...|++.|+.+.|.+.|.++. +....+.  ...+-.+|......+++..+...+.+...
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~-~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~  101 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRAR-DYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAES  101 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHh-hhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            34555566666666666666666655 3332222  22333455555555666665555555443

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.

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=92.92  E-value=0.28  Score=26.91  Aligned_cols=28  Identities=21%  Similarity=0.382  Sum_probs=18.9

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .+|..+...|...|++++|+..|+++++
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            3566667777777777777777777766

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 ....

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=92.89  E-value=8.7  Score=36.41  Aligned_cols=167  Identities=11%  Similarity=0.038  Sum_probs=79.5

Q ss_pred             CChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHH
Q 011236          102 FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCL  181 (490)
Q Consensus       102 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~  181 (490)
                      .+......++..++...++.-...+-.++...+.+-..|..++.+|.+. ..+.-..+++++.+..+. |++.-..|...
T Consensus        64 l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~~ReLa~~  141 (711)
T COG1747          64 LDDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYGESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVIGRELADK  141 (711)
T ss_pred             ccchHHHHHHHHhccchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHHHHHHHHH
Confidence            3444445555555555555555555555555555555555556665555 334555555555555443 33333333333


Q ss_pred             HHhcCCcCcHHHHHHHHHHCCCCC--C---HHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc
Q 011236          182 YTNTGQHEKIPDVLLDMKENGVPP--D---NFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIA  256 (490)
Q Consensus       182 ~~~~~~~~~a~~~~~~m~~~~~~p--~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  256 (490)
                      |-+ ++.+++...|.....+=++.  +   ...|..+...-  ..+.+....+..++....|...-...+.-+-.-|...
T Consensus       142 yEk-ik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~i--~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Ys~~  218 (711)
T COG1747         142 YEK-IKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPELI--GDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKYSEN  218 (711)
T ss_pred             HHH-hchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhc--cccHHHHHHHHHHHHHhhccchHHHHHHHHHHHhccc
Confidence            333 55555555555554432210  0   01233333211  2345555555555543344333344444444555556


Q ss_pred             CCHHHHHHHHHHHhhhh
Q 011236          257 GLKEKAIIYLKKCEDIV  273 (490)
Q Consensus       257 ~~~~~a~~~~~~~~~~~  273 (490)
                      .++++|++++..+.+..
T Consensus       219 eN~~eai~Ilk~il~~d  235 (711)
T COG1747         219 ENWTEAIRILKHILEHD  235 (711)
T ss_pred             cCHHHHHHHHHHHhhhc
Confidence            66666666666554433

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=92.88  E-value=0.18  Score=27.90  Aligned_cols=32  Identities=16%  Similarity=0.340  Sum_probs=20.4

Q ss_pred             HHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHH
Q 011236          372 LKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAF  404 (490)
Q Consensus       372 ~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~  404 (490)
                      |++.++..+. |...|+.+...|...|++++|+
T Consensus         2 y~kAie~~P~-n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    2 YKKAIELNPN-NAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             hHHHHHHCCC-CHHHHHHHHHHHHHCcCHHhhc
Confidence            4455555544 6667777777777777777664

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=92.80  E-value=1.1  Score=31.99  Aligned_cols=61  Identities=11%  Similarity=0.166  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHH
Q 011236          402 KAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAH  467 (490)
Q Consensus       402 ~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~  467 (490)
                      +..+-++.+..     ..+.|++....+.+++|.+..++..|.++|+.++..... ...|..+++-+
T Consensus        28 e~rrglN~l~~-----~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~~~~Y~~~lqEl   89 (108)
T PF02284_consen   28 ELRRGLNNLFG-----YDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNKKEIYPYILQEL   89 (108)
T ss_dssp             HHHHHHHHHTT-----SSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT-TTHHHHHHHHH
T ss_pred             HHHHHHHHHhc-----cccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccChHHHHHHHHHHH
Confidence            44455555555     567788888888888888888888888888877766555 44666666544

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 ....

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=92.79  E-value=10  Score=38.10  Aligned_cols=83  Identities=12%  Similarity=0.200  Sum_probs=32.6

Q ss_pred             HHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHh---
Q 011236          215 NSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYAS---  291 (490)
Q Consensus       215 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---  291 (490)
                      ..+.-.|+++.|.+.+-+..   ....+...+...+.-|.-.+-.+...   ..+.......+...-+..||..|++   
T Consensus       266 ~~LlLtgqFE~AI~~L~~~~---~~~~dAVH~AIaL~~~gLL~~~~~~~---~~lls~~~~~~~~ln~arLI~~Y~~~F~  339 (613)
T PF04097_consen  266 QVLLLTGQFEAAIEFLYRNE---FNRVDAVHFAIALAYYGLLRVSDSSS---APLLSVDPGDPPPLNFARLIGQYTRSFE  339 (613)
T ss_dssp             HHHHHTT-HHHHHHHHHT-----T-HHHHHHHHHHHHHTT---------------------------HHHHHHHHHHTTT
T ss_pred             HHHHHHhhHHHHHHHHHhhc---cCcccHHHHHHHHHHcCCCCCCCccc---cceeeecCCCCCCcCHHHHHHHHHHHHh
Confidence            44455678888887776521   22244444433333222211111111   2222111110222557778888876   


Q ss_pred             cCChhHHHHHHH
Q 011236          292 LGNKDEMMKFWG  303 (490)
Q Consensus       292 ~~~~~~a~~~~~  303 (490)
                      ..++.+|.++|-
T Consensus       340 ~td~~~Al~Y~~  351 (613)
T PF04097_consen  340 ITDPREALQYLY  351 (613)
T ss_dssp             TT-HHHHHHHHH
T ss_pred             ccCHHHHHHHHH
Confidence            456777777776

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.

>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=92.78  E-value=22  Score=40.72  Aligned_cols=315  Identities=13%  Similarity=0.013  Sum_probs=165.8

Q ss_pred             HHHHHHhhcCHHHHHHHHHHcccc----CCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhc
Q 011236          110 QLDLIGKVRGLESAETYFNSLNDE----DKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNT  185 (490)
Q Consensus       110 l~~~~~~~~~~~~A~~~~~~~~~~----~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~  185 (490)
                      +..+-.+++.+.+|...+++-...    ......|-.+...|...+++|...-+...-..     +...++ -|......
T Consensus      1389 La~aSfrc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a-----~~sl~~-qil~~e~~ 1462 (2382)
T KOG0890|consen 1389 LARASFRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFA-----DPSLYQ-QILEHEAS 1462 (2382)
T ss_pred             HHHHHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhc-----CccHHH-HHHHHHhh
Confidence            444566788899999999884221    12334455566689999999888777764111     333333 34455678


Q ss_pred             CCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHHcCCHHHHHH
Q 011236          186 GQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTY-STVANYYIIAGLKEKAII  264 (490)
Q Consensus       186 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~-~~li~~~~~~~~~~~a~~  264 (490)
                      |++..|...|+.+.+.+. +...+++-+++.....|.++.+.-..+-..  .+..+....+ +.=+.+-.+.+++|....
T Consensus      1463 g~~~da~~Cye~~~q~~p-~~~~~~~g~l~sml~~~~l~t~i~~~dg~~--~~~se~~~~~~s~~~eaaW~l~qwD~~e~ 1539 (2382)
T KOG0890|consen 1463 GNWADAAACYERLIQKDP-DKEKHHSGVLKSMLAIQHLSTEILHLDGLI--INRSEEVDELNSLGVEAAWRLSQWDLLES 1539 (2382)
T ss_pred             ccHHHHHHHHHHhhcCCC-ccccchhhHHHhhhcccchhHHHhhhcchh--hccCHHHHHHHHHHHHHHhhhcchhhhhh
Confidence            999999999999987642 236677877777777888888777666554  2222222222 233444577888888777


Q ss_pred             HHHHHhhhhccCCChhhHHHH--HHHHHhcC--ChhHHHHHHHHHHHhcCCC---------ChhhHHHHHHHHHhcCCHH
Q 011236          265 YLKKCEDIVSKSKDALGYNHL--ISHYASLG--NKDEMMKFWGLQKIKCKKQ---------LNRDYITMLGSLVKIGELE  331 (490)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~l--~~~~~~~~--~~~~a~~~~~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~  331 (490)
                      ....        .+..+|...  .....+..  +.-.-.+..+.+......|         -...|..++....-.    
T Consensus      1540 ~l~~--------~n~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l~---- 1607 (2382)
T KOG0890|consen 1540 YLSD--------RNIEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLLL---- 1607 (2382)
T ss_pred             hhhc--------ccccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHHH----
Confidence            6651        233334333  22222211  1111112332222221100         012233333322211    


Q ss_pred             HHHHHHHHHHhcCCCCCchh------HHHHHHHHHhcCCHHH-HHHHHHHHHHcCCCCCHH-----HHHHHHHHHhccCC
Q 011236          332 EAEKMLEEWELSCYCYDFRV------PNIILLGYSQKGMIEK-ADAVLKEIVKKGKTPTPN-----SWSIIAAGYADKNN  399 (490)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~------~~~l~~~~~~~g~~~~-A~~~~~~m~~~~~~p~~~-----~~~~l~~~~~~~~~  399 (490)
                      +-....+...  +..++..+      |-.-+..-....+..+ .+.+-+.+......|+..     +|-...+.....|+
T Consensus      1608 el~~~~~~l~--~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~ 1685 (2382)
T KOG0890|consen 1608 ELENSIEELK--KVSYDEDSANNSDNWKNRLERTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGH 1685 (2382)
T ss_pred             HHHHHHHHhh--ccCccccccccchhHHHHHHHhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhccc
Confidence            1111111111  12222221      1111111111111111 111222222322233332     57777777777899


Q ss_pred             HHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          400 MEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       400 ~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      ++.|...+-++.+     .+ .  +..+.....-+...|+...|..++++..+...
T Consensus      1686 ~q~A~nall~A~e-----~r-~--~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~~~ 1733 (2382)
T KOG0890|consen 1686 LQRAQNALLNAKE-----SR-L--PEIVLERAKLLWQTGDELNALSVLQEILSKNF 1733 (2382)
T ss_pred             HHHHHHHHHhhhh-----cc-c--chHHHHHHHHHHhhccHHHHHHHHHHHHHhhc
Confidence            9999988888877     33 2  34455566777888999999999988776543

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=92.57  E-value=12  Score=37.16  Aligned_cols=277  Identities=11%  Similarity=-0.014  Sum_probs=164.5

Q ss_pred             hhHHHHHHHHHHhcCCCCCcchHHHHHHH-----HHhcCCcCcHHHHHHHHHH-------CCCCCCHHHHHHHHHHHhcc
Q 011236          153 VDESLSLMQKMKEMGSFGSALNYNGIMCL-----YTNTGQHEKIPDVLLDMKE-------NGVPPDNFSYRICINSYGAR  220 (490)
Q Consensus       153 ~~~a~~~~~~m~~~~~~p~~~~~~~l~~~-----~~~~~~~~~a~~~~~~m~~-------~~~~p~~~~~~~li~~~~~~  220 (490)
                      ...|...++.....|   +...-..+..+     +....|.+.|..+|+.+.+       .|   +......+..+|.+.
T Consensus       228 ~~~a~~~~~~~a~~g---~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g  301 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLG---HSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQG  301 (552)
T ss_pred             hhHHHHHHHHHHhhc---chHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcC
Confidence            457888888887776   33333333333     3355688899999988866       44   333455566666653


Q ss_pred             C-----ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc---CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHH--
Q 011236          221 S-----ELSSMENVLQEMESQSHISMDWGTYSTVANYYIIA---GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYA--  290 (490)
Q Consensus       221 g-----~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~--  290 (490)
                      .     +.+.|..++.... ..|. |+...+  +..++...   .+...|.++|...-..|.  ....-+..++-...  
T Consensus       302 ~~~~~~d~~~A~~~~~~aA-~~g~-~~a~~~--lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~--~~A~~~la~~y~~G~g  375 (552)
T KOG1550|consen  302 LGVEKIDYEKALKLYTKAA-ELGN-PDAQYL--LGVLYETGTKERDYRRAFEYYSLAAKAGH--ILAIYRLALCYELGLG  375 (552)
T ss_pred             CCCccccHHHHHHHHHHHH-hcCC-chHHHH--HHHHHHcCCccccHHHHHHHHHHHHHcCC--hHHHHHHHHHHHhCCC
Confidence            2     6677999998887 7776 666654  33344333   357789999999887765  23322222222222  


Q ss_pred             hcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHH---Hh----cC
Q 011236          291 SLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGY---SQ----KG  363 (490)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~---~~----~g  363 (490)
                      ...+...|..++.+....+. |...--...+..+.. ++++.+.-.+..+...|.+.....-..++...   ..    ..
T Consensus       376 v~r~~~~A~~~~k~aA~~g~-~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g~~~~q~~a~~l~~~~~~~~~~~~~~~  453 (552)
T KOG1550|consen  376 VERNLELAFAYYKKAAEKGN-PSAAYLLGAFYEYGV-GRYDTALALYLYLAELGYEVAQSNAAYLLDQSEEDLFSRGVIS  453 (552)
T ss_pred             cCCCHHHHHHHHHHHHHccC-hhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhhhhHHhhHHHHHHHhcccccccccccc
Confidence            23477888999988877763 443333334444444 77777777777777665442221111111111   11    22


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc----CCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHH----H
Q 011236          364 MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK----NNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWL----G  435 (490)
Q Consensus       364 ~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~----~  435 (490)
                      +.+.+..++.+....|   +......+...|...    .+++.|...+..+..     .+    ....-.+...+    .
T Consensus       454 ~~~~~~~~~~~a~~~g---~~~a~~~lgd~y~~g~g~~~d~~~a~~~y~~a~~-----~~----~~~~~nlg~~~e~g~g  521 (552)
T KOG1550|consen  454 TLERAFSLYSRAAAQG---NADAILKLGDYYYYGLGTGRDPEKAAAQYARASE-----QG----AQALFNLGYMHEHGEG  521 (552)
T ss_pred             chhHHHHHHHHHHhcc---CHHHHhhhcceeeecCCCCCChHHHHHHHHHHHH-----hh----hHHHhhhhhHHhcCcC
Confidence            5667777777777665   566666666666544    458888888888876     33    32222333222    2


Q ss_pred             cCCCHHHHHHHHHHHHhcccc
Q 011236          436 DNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       436 ~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..+ +..|.+++++....+..
T Consensus       522 ~~~-~~~a~~~~~~~~~~~~~  541 (552)
T KOG1550|consen  522 IKV-LHLAKRYYDQASEEDSR  541 (552)
T ss_pred             cch-hHHHHHHHHHHHhcCch
Confidence            234 78888888887776554

>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=92.49  E-value=7.4  Score=34.59  Aligned_cols=16  Identities=6%  Similarity=-0.178  Sum_probs=9.2

Q ss_pred             HHhcCCHHHHHHHHHH
Q 011236          359 YSQKGMIEKADAVLKE  374 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~  374 (490)
                      +.+.++++.|...|+-
T Consensus       256 ~~~~k~y~~A~~w~~~  271 (278)
T PF08631_consen  256 HYKAKNYDEAIEWYEL  271 (278)
T ss_pred             HHhhcCHHHHHHHHHH
Confidence            3445666666666653

It is also involved in sporulation [].

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=92.42  E-value=0.34  Score=27.13  Aligned_cols=24  Identities=29%  Similarity=0.398  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Q 011236          246 YSTVANYYIIAGLKEKAIIYLKKC  269 (490)
Q Consensus       246 ~~~li~~~~~~~~~~~a~~~~~~~  269 (490)
                      |..|...|.+.|++++|+++|++.
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            445556666666666666666653

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=92.35  E-value=4.8  Score=32.18  Aligned_cols=135  Identities=13%  Similarity=0.174  Sum_probs=86.1

Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhC
Q 011236          157 LSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQ  236 (490)
Q Consensus       157 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  236 (490)
                      .+.++.+.+.+++|+...|..+++.+.+.|++..    +..+.+.++-+|.......+-.+..  ....+.++--.|..+
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~----L~qllq~~Vi~DSk~lA~~LLs~~~--~~~~~~Ql~lDMLkR   87 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQ----LHQLLQYHVIPDSKPLACQLLSLGN--QYPPAYQLGLDMLKR   87 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHH----HHHHHhhcccCCcHHHHHHHHHhHc--cChHHHHHHHHHHHH
Confidence            3555666778888999999999999999887544    5555666777777766655544433  333444443344312


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 011236          237 SHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKI  307 (490)
Q Consensus       237 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  307 (490)
                      .+     ..+..++..+...|++-+|.++.+....     .+...-..++.+..+.+|...-..+++-...
T Consensus        88 L~-----~~~~~iievLL~~g~vl~ALr~ar~~~~-----~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   88 LG-----TAYEEIIEVLLSKGQVLEALRYARQYHK-----VDSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             hh-----hhHHHHHHHHHhCCCHHHHHHHHHHcCC-----cccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            12     1355688889999999999999887532     2223345677777777776655555553333

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=92.34  E-value=1.2  Score=31.41  Aligned_cols=63  Identities=11%  Similarity=0.134  Sum_probs=41.0

Q ss_pred             CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHH
Q 011236          399 NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEA  466 (490)
Q Consensus       399 ~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~  466 (490)
                      +.-++.+-++.+..     ..+.|++....+.+++|.+.+|+..|.++|+.++..... ...|..+++-
T Consensus        22 D~we~rr~mN~l~~-----~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~~~~y~~~lqe   85 (103)
T cd00923          22 DGWELRRGLNNLFG-----YDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKEIYPYILQE   85 (103)
T ss_pred             cHHHHHHHHHHHhc-----cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCchhhHHHHHHH
Confidence            34455556666655     567777777777777877777787887777776654443 4455555443

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.

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=92.17  E-value=7  Score=33.61  Aligned_cols=211  Identities=14%  Similarity=0.131  Sum_probs=117.9

Q ss_pred             CCCCCCHHHHHHHHHHH-hccCChHHHHHHHHHHHhCCCCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHhhhh----
Q 011236          201 NGVPPDNFSYRICINSY-GARSELSSMENVLQEMESQSHISMDW--GTYSTVANYYIIAGLKEKAIIYLKKCEDIV----  273 (490)
Q Consensus       201 ~~~~p~~~~~~~li~~~-~~~g~~~~a~~~~~~~~~~~~~~~~~--~~~~~li~~~~~~~~~~~a~~~~~~~~~~~----  273 (490)
                      .+-.||+..-|..-++- .+..++++|+.-|++..+-.|-+.++  .+...+|..+.+.|++++....|.++..-.    
T Consensus        20 s~sEpdVDlENQYYnsK~l~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAV   99 (440)
T KOG1464|consen   20 SNSEPDVDLENQYYNSKGLKEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAV   99 (440)
T ss_pred             cCCCCCcchHhhhhccccccccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Confidence            34556665544333221 23457888888888887222322222  234467888888888888888888875421    


Q ss_pred             ccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC-----CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-
Q 011236          274 SKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK-----KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY-  347 (490)
Q Consensus       274 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-  347 (490)
                      ...-+..+.|+++..-....+.+.-.++|+.-...-.     +..-.|-..+...|...+++.....+++++..+.-.. 
T Consensus       100 TrNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~ed  179 (440)
T KOG1464|consen  100 TRNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTED  179 (440)
T ss_pred             hccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhcccc
Confidence            1113445567777766666666666666664333211     1122334566777777777777777777776542111 


Q ss_pred             ----------CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHH-----hccCCHHHHHHHHHHHH
Q 011236          348 ----------DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK-TPTPNSWSIIAAGY-----ADKNNMEKAFECMKEAL  411 (490)
Q Consensus       348 ----------~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~-~p~~~~~~~l~~~~-----~~~~~~~~a~~~~~~~~  411 (490)
                                -..+|..=|..|....+-.+-..++++.+.-.. .|.+... -+|+-|     .+.|++++|..-|-++.
T Consensus       180 GedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlIm-GvIRECGGKMHlreg~fe~AhTDFFEAF  258 (440)
T KOG1464|consen  180 GEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLIM-GVIRECGGKMHLREGEFEKAHTDFFEAF  258 (440)
T ss_pred             CchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHHH-hHHHHcCCccccccchHHHHHhHHHHHH
Confidence                      123455566666666666666666666555432 1333222 223322     34566777765544444


Q ss_pred             H
Q 011236          412 A  412 (490)
Q Consensus       412 ~  412 (490)
                      .
T Consensus       259 K  259 (440)
T KOG1464|consen  259 K  259 (440)
T ss_pred             h
Confidence            4

>PRK09687 putative lyase; Provisional

Probab=92.03  E-value=8.4  Score=34.21  Aligned_cols=233  Identities=12%  Similarity=0.049  Sum_probs=126.9

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCH----HHHHHHHHHHhhhhccCCChh
Q 011236          205 PDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLK----EKAIIYLKKCEDIVSKSKDAL  280 (490)
Q Consensus       205 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~----~~a~~~~~~~~~~~~~~~~~~  280 (490)
                      +|.......+.++...|..+ +...+..+. +.   ++...-...+.++...|+.    +++...+..+....   ++..
T Consensus        35 ~d~~vR~~A~~aL~~~~~~~-~~~~l~~ll-~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~D---~d~~  106 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGGQD-VFRLAIELC-SS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALED---KSAC  106 (280)
T ss_pred             CCHHHHHHHHHHHHhcCcch-HHHHHHHHH-hC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhcC---CCHH
Confidence            56667777777777776543 333333343 21   3445555566777777763    45666666553222   4555


Q ss_pred             hHHHHHHHHHhcCCh-----hHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHH
Q 011236          281 GYNHLISHYASLGNK-----DEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNII  355 (490)
Q Consensus       281 ~~~~l~~~~~~~~~~-----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  355 (490)
                      .-...+.++...+..     ..+...+.   ..-..++..+-...+.++.+.++ ..+...+-.+.+.   +|..+-...
T Consensus       107 VR~~A~~aLG~~~~~~~~~~~~a~~~l~---~~~~D~~~~VR~~a~~aLg~~~~-~~ai~~L~~~L~d---~~~~VR~~A  179 (280)
T PRK09687        107 VRASAINATGHRCKKNPLYSPKIVEQSQ---ITAFDKSTNVRFAVAFALSVIND-EAAIPLLINLLKD---PNGDVRNWA  179 (280)
T ss_pred             HHHHHHHHHhcccccccccchHHHHHHH---HHhhCCCHHHHHHHHHHHhccCC-HHHHHHHHHHhcC---CCHHHHHHH
Confidence            555566665554321     12233332   22222455666677777777776 3455555555543   333344444


Q ss_pred             HHHHHhcC-CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHH
Q 011236          356 LLGYSQKG-MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWL  434 (490)
Q Consensus       356 ~~~~~~~g-~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~  434 (490)
                      +.++.+.+ ....+...+..+..   .+|..+-...+.++.+.++ ..|+..+-+.++     .   ++  .....+.++
T Consensus       180 ~~aLg~~~~~~~~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~-~~av~~Li~~L~-----~---~~--~~~~a~~AL  245 (280)
T PRK09687        180 AFALNSNKYDNPDIREAFVAMLQ---DKNEEIRIEAIIGLALRKD-KRVLSVLIKELK-----K---GT--VGDLIIEAA  245 (280)
T ss_pred             HHHHhcCCCCCHHHHHHHHHHhc---CCChHHHHHHHHHHHccCC-hhHHHHHHHHHc-----C---Cc--hHHHHHHHH
Confidence            44444432 23455555555553   2466677777777777777 456666666655     2   12  234566777


Q ss_pred             HcCCCHHHHHHHHHHHHhcccchhhhHHHHHHH
Q 011236          435 GDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAH  467 (490)
Q Consensus       435 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~~  467 (490)
                      ...|+. +|...+..+.+..++..+-...+.++
T Consensus       246 g~ig~~-~a~p~L~~l~~~~~d~~v~~~a~~a~  277 (280)
T PRK09687        246 GELGDK-TLLPVLDTLLYKFDDNEIITKAIDKL  277 (280)
T ss_pred             HhcCCH-hHHHHHHHHHhhCCChhHHHHHHHHH
Confidence            777774 67777777776555544434444443

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=91.98  E-value=8  Score=33.87  Aligned_cols=113  Identities=11%  Similarity=0.088  Sum_probs=61.8

Q ss_pred             CHHHHHHHHHHccccC---CChhHHHHHHHHHHhcCC--hhHHHHHHHHHH-hcCCCCCcchHHHHHHHHHhcCCcCcHH
Q 011236          119 GLESAETYFNSLNDED---KVDKLYGALLNCYVREGL--VDESLSLMQKMK-EMGSFGSALNYNGIMCLYTNTGQHEKIP  192 (490)
Q Consensus       119 ~~~~A~~~~~~~~~~~---p~~~~~~~li~~~~~~g~--~~~a~~~~~~m~-~~~~~p~~~~~~~l~~~~~~~~~~~~a~  192 (490)
                      .+.+|+.+|+.....+   .|..+...+++......+  ...-.++.+-+. ..|..++..+...++..+++.++|.+.+
T Consensus       143 ~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~kl~  222 (292)
T PF13929_consen  143 IVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWNKLF  222 (292)
T ss_pred             HHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHHHHH
Confidence            3456666666332211   355556666665554111  122222222222 2234556666666777777777777777


Q ss_pred             HHHHHHHHC-CCCCCHHHHHHHHHHHhccCChHHHHHHHH
Q 011236          193 DVLLDMKEN-GVPPDNFSYRICINSYGARSELSSMENVLQ  231 (490)
Q Consensus       193 ~~~~~m~~~-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  231 (490)
                      ++++..... +..-|...|...|+.-...|+..-..++.+
T Consensus       223 ~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~  262 (292)
T PF13929_consen  223 QFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIID  262 (292)
T ss_pred             HHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhh
Confidence            766666544 445566667777777777777665555544

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=91.97  E-value=4.8  Score=31.25  Aligned_cols=19  Identities=16%  Similarity=0.373  Sum_probs=9.4

Q ss_pred             HhcCChhHHHHHHHHHHhc
Q 011236          148 VREGLVDESLSLMQKMKEM  166 (490)
Q Consensus       148 ~~~g~~~~a~~~~~~m~~~  166 (490)
                      ...|++++|+++|++..+.
T Consensus        55 i~rg~w~eA~rvlr~l~~~   73 (153)
T TIGR02561        55 IARGNYDEAARILRELLSS   73 (153)
T ss_pred             HHcCCHHHHHHHHHhhhcc
Confidence            3445555555555554444

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.89  E-value=8.4  Score=37.28  Aligned_cols=26  Identities=12%  Similarity=0.068  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          208 FSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      .-|..|.++....|++..|.+.|.+.
T Consensus       667 ~Kw~~Lg~~al~~~~l~lA~EC~~~a  692 (794)
T KOG0276|consen  667 VKWRQLGDAALSAGELPLASECFLRA  692 (794)
T ss_pred             HHHHHHHHHHhhcccchhHHHHHHhh
Confidence            34555555555555555555555444

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.82  E-value=7.3  Score=33.07  Aligned_cols=148  Identities=10%  Similarity=0.073  Sum_probs=82.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc---C--CCCCchhHHHHH
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELS---C--YCYDFRVPNIIL  356 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~--~~~~~~~~~~l~  356 (490)
                      |+-....|..+|.++.|-..+++....                ...-+++.|.+++++...-   +  ...-...+....
T Consensus        94 ~eKAs~lY~E~GspdtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~s  157 (308)
T KOG1585|consen   94 YEKASELYVECGSPDTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCS  157 (308)
T ss_pred             HHHHHHHHHHhCCcchHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhh
Confidence            444455555555555555555433221                1344566677776655432   0  011122445566


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHH
Q 011236          357 LGYSQKGMIEKADAVLKEIVKK----GKTPTP-NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSIL  431 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~----~~~p~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~  431 (490)
                      +.+.+..++++|-..+.+-...    .--|+. ..|-..|-.+....++..|..+++.-.+.-  ...-.-+..+...|+
T Consensus       158 r~lVrl~kf~Eaa~a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip--~f~~sed~r~lenLL  235 (308)
T KOG1585|consen  158 RVLVRLEKFTEAATAFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIP--AFLKSEDSRSLENLL  235 (308)
T ss_pred             hHhhhhHHhhHHHHHHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCc--cccChHHHHHHHHHH
Confidence            6677778887777666544322    111222 246666667777888888888888876611  011112336777888


Q ss_pred             HHHHcCCCHHHHHHHHH
Q 011236          432 DWLGDNRDVEEVEAFVS  448 (490)
Q Consensus       432 ~~~~~~g~~~~a~~~~~  448 (490)
                      .+|- .||.+++.+++.
T Consensus       236 ~ayd-~gD~E~~~kvl~  251 (308)
T KOG1585|consen  236 TAYD-EGDIEEIKKVLS  251 (308)
T ss_pred             HHhc-cCCHHHHHHHHc
Confidence            7764 578887776665

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=91.75  E-value=6.8  Score=32.58  Aligned_cols=183  Identities=14%  Similarity=0.101  Sum_probs=93.5

Q ss_pred             HHhhcCHHHHHHHHHHccccCCC-hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHH
Q 011236          114 IGKVRGLESAETYFNSLNDEDKV-DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIP  192 (490)
Q Consensus       114 ~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~  192 (490)
                      |-..|-+..|+-=|.+.....|+ +.+||-|.--+...|+++.|.+.|+...+.++.-+-...|.-|. +--.|+++-|.
T Consensus        75 YDSlGL~~LAR~DftQaLai~P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi~-~YY~gR~~LAq  153 (297)
T COG4785          75 YDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIA-LYYGGRYKLAQ  153 (297)
T ss_pred             hhhhhHHHHHhhhhhhhhhcCCCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhcccee-eeecCchHhhH
Confidence            33445556666666666666664 67788888888888999999999988888754433222232222 23457788887


Q ss_pred             HHHHHHHHCCC-CCCHHHHHHHHHHHhccCChHHHHHH-HHHHHhCCCCCCCHHHHHHH-HHHHHHcCCHHHHHHHHHHH
Q 011236          193 DVLLDMKENGV-PPDNFSYRICINSYGARSELSSMENV-LQEMESQSHISMDWGTYSTV-ANYYIIAGLKEKAIIYLKKC  269 (490)
Q Consensus       193 ~~~~~m~~~~~-~p~~~~~~~li~~~~~~g~~~~a~~~-~~~~~~~~~~~~~~~~~~~l-i~~~~~~~~~~~a~~~~~~~  269 (490)
                      +=|...-+.+. .|-...|--+..   ..-++.+|..- .++.. .    .|..-|... +..|...=..+   .+++++
T Consensus       154 ~d~~~fYQ~D~~DPfR~LWLYl~E---~k~dP~~A~tnL~qR~~-~----~d~e~WG~~iV~~yLgkiS~e---~l~~~~  222 (297)
T COG4785         154 DDLLAFYQDDPNDPFRSLWLYLNE---QKLDPKQAKTNLKQRAE-K----SDKEQWGWNIVEFYLGKISEE---TLMERL  222 (297)
T ss_pred             HHHHHHHhcCCCChHHHHHHHHHH---hhCCHHHHHHHHHHHHH-h----ccHhhhhHHHHHHHHhhccHH---HHHHHH
Confidence            76666655432 122222222222   23355555443 33333 2    222222222 22222111111   122222


Q ss_pred             hhhhccC-----CChhhHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 011236          270 EDIVSKS-----KDALGYNHLISHYASLGNKDEMMKFWGLQKIK  308 (490)
Q Consensus       270 ~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  308 (490)
                      .......     .=..||--+.+.+...|+.++|..+|+-.+..
T Consensus       223 ~a~a~~n~~~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLaian  266 (297)
T COG4785         223 KADATDNTSLAEHLTETYFYLGKYYLSLGDLDEATALFKLAVAN  266 (297)
T ss_pred             HhhccchHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence            2111100     11245666666777777777777777755443

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.59  E-value=4.7  Score=32.98  Aligned_cols=53  Identities=19%  Similarity=0.120  Sum_probs=22.4

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +.+.+.++.|+.-..+.++.++. .......-..+|.+...+++|+.-|+..++
T Consensus       144 ~iKl~k~e~aI~dcsKaiel~pt-y~kAl~RRAeayek~ek~eealeDyKki~E  196 (271)
T KOG4234|consen  144 LIKLRKWESAIEDCSKAIELNPT-YEKALERRAEAYEKMEKYEEALEDYKKILE  196 (271)
T ss_pred             HHHhhhHHHHHHHHHhhHhcCch-hHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            34444444444444444444322 222222223344444444444444444444

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=91.46  E-value=1.4  Score=35.92  Aligned_cols=93  Identities=15%  Similarity=0.074  Sum_probs=72.2

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHH
Q 011236          357 LGYSQKGMIEKADAVLKEIVKKGKTPT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSIL  431 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~~~~p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~  431 (490)
                      .-+...|++++|..-|...++.-+...    ...|..-..++.+.+.++.|+.-..++++       +.|+. .....-.
T Consensus       103 N~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaie-------l~pty~kAl~RRA  175 (271)
T KOG4234|consen  103 NELFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIE-------LNPTYEKALERRA  175 (271)
T ss_pred             HHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHh-------cCchhHHHHHHHH
Confidence            347889999999999999998632211    23566666788899999999999999988       33543 3334445


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          432 DWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       432 ~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+|.+...+++|..-++++.+..|.
T Consensus       176 eayek~ek~eealeDyKki~E~dPs  200 (271)
T KOG4234|consen  176 EAYEKMEKYEEALEDYKKILESDPS  200 (271)
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhCcc
Confidence            6788899999999999999999988

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=91.36  E-value=0.55  Score=25.60  Aligned_cols=27  Identities=30%  Similarity=0.573  Sum_probs=16.9

Q ss_pred             HHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          386 SWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       386 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .|..+...+...|++++|++.|+++++
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            455566666666666666666666666

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 ....

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.36  E-value=2.5  Score=34.37  Aligned_cols=130  Identities=13%  Similarity=0.049  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHH--HHHHHHHhhcCHHHHHHHHHHccccCCCh----hHHHH
Q 011236           69 ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHA--VQLDLIGKVRGLESAETYFNSLNDEDKVD----KLYGA  142 (490)
Q Consensus        69 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~A~~~~~~~~~~~p~~----~~~~~  142 (490)
                      +..|..++.... .+.. +.....+.+...+....-..+.  .+...+...|+++.|..-++.......|.    .+--.
T Consensus        54 S~~Y~~~i~~~~-ak~~-~~~~~~ekf~~~n~~t~Ya~laaL~lAk~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lR  131 (207)
T COG2976          54 SAQYQNAIKAVQ-AKKP-KSIAAAEKFVQANGKTIYAVLAALELAKAEVEANNLDKAEAQLKQALAQTKDENLKALAALR  131 (207)
T ss_pred             HHHHHHHHHHHh-cCCc-hhHHHHHHHHhhccccHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHH
Confidence            445566665553 2222 4445555555544222222222  23445556667777766666555432221    11223


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCC
Q 011236          143 LLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENG  202 (490)
Q Consensus       143 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~  202 (490)
                      |.+.....|.+++|+..++...+.+..  ......-.+.+...|+-++|..-|....+.+
T Consensus       132 LArvq~q~~k~D~AL~~L~t~~~~~w~--~~~~elrGDill~kg~k~~Ar~ay~kAl~~~  189 (207)
T COG2976         132 LARVQLQQKKADAALKTLDTIKEESWA--AIVAELRGDILLAKGDKQEARAAYEKALESD  189 (207)
T ss_pred             HHHHHHHhhhHHHHHHHHhccccccHH--HHHHHHhhhHHHHcCchHHHHHHHHHHHHcc
Confidence            445566667777777766655544321  1122333456666677777777777666654

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.33  E-value=7.9  Score=34.17  Aligned_cols=97  Identities=16%  Similarity=0.178  Sum_probs=63.5

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcC---CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 011236          314 NRDYITMLGSLVKIGELEEAEKMLEEWELSC---YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSII  390 (490)
Q Consensus       314 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l  390 (490)
                      ..+...++..-....+++.+...+-+++.+.   ..|+...+ ..++.+. .-++++++.++..=++.|+-||.++++.+
T Consensus        64 ~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~-~~irlll-ky~pq~~i~~l~npIqYGiF~dqf~~c~l  141 (418)
T KOG4570|consen   64 SLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIH-TWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQFTFCLL  141 (418)
T ss_pred             eeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHH-HHHHHHH-ccChHHHHHHHhCcchhccccchhhHHHH
Confidence            3445555555555677777877777766541   12222222 2233332 34566888888887888888888888888


Q ss_pred             HHHHhccCCHHHHHHHHHHHHH
Q 011236          391 AAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       391 ~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ++.+.+.+++.+|.++.-.|..
T Consensus       142 ~D~flk~~n~~~aa~vvt~~~~  163 (418)
T KOG4570|consen  142 MDSFLKKENYKDAASVVTEVMM  163 (418)
T ss_pred             HHHHHhcccHHHHHHHHHHHHH
Confidence            8888888888888877777665

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=91.24  E-value=9.6  Score=33.31  Aligned_cols=76  Identities=12%  Similarity=0.018  Sum_probs=56.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLV  427 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~  427 (490)
                      +++.....|..+|.+.+|.++.++.+..++- +...|-.++..+...|+--.+...++++.+......|+..+...+
T Consensus       281 llgkva~~yle~g~~neAi~l~qr~ltldpL-~e~~nk~lm~~la~~gD~is~~khyerya~vleaelgi~vddsie  356 (361)
T COG3947         281 LLGKVARAYLEAGKPNEAIQLHQRALTLDPL-SEQDNKGLMASLATLGDEISAIKHYERYAEVLEAELGIDVDDSIE  356 (361)
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHhhcChh-hhHHHHHHHHHHHHhccchhhhhHHHHHHHHHHHHhCCCcchhHH
Confidence            3455667788889999999988888887543 777788888888888887788777777766444446666665444

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=91.20  E-value=8.7  Score=33.64  Aligned_cols=59  Identities=14%  Similarity=0.179  Sum_probs=29.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHHh-cCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011236          277 KDALGYNHLISHYASLGNKDEMMKFWGLQKIK-CKKQLNRDYITMLGSLVKIGELEEAEK  335 (490)
Q Consensus       277 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~a~~  335 (490)
                      ++..+...++..++..++|..-.++|+..... .+..|...|..+|+.....|+..-...
T Consensus       200 l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~k  259 (292)
T PF13929_consen  200 LTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRK  259 (292)
T ss_pred             CChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHH
Confidence            44444555555555555555555555543333 233444555555555555555443333

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=91.13  E-value=2  Score=35.51  Aligned_cols=76  Identities=14%  Similarity=0.024  Sum_probs=49.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC--CCCHHHHHHHHHH
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK--TPTPNSWSIIAAG  393 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~--~p~~~~~~~l~~~  393 (490)
                      ...-+..+.+.+.+.+++...++-.+.+ +.|...-..+++.||-.|++++|..-++-.-...+  .+-..+|..+|.+
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            4445566677778888888777766652 33555666677888888888888777766655432  2334556666654

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.09  E-value=2.9  Score=36.72  Aligned_cols=99  Identities=11%  Similarity=0.137  Sum_probs=66.9

Q ss_pred             CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC-----CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchH
Q 011236          101 AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED-----KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNY  175 (490)
Q Consensus       101 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-----p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~  175 (490)
                      +.+..+....+.......+++.+...+-.+....     |+.. -.++++.+. .-+.++++.++..=.+.|+-||.+++
T Consensus        61 ~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~-~~~~irlll-ky~pq~~i~~l~npIqYGiF~dqf~~  138 (418)
T KOG4570|consen   61 PVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWT-IHTWIRLLL-KYDPQKAIYTLVNPIQYGIFPDQFTF  138 (418)
T ss_pred             CcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhcccc-HHHHHHHHH-ccChHHHHHHHhCcchhccccchhhH
Confidence            4455555555555555677888887776665542     2211 112233332 33567888888888888888999999


Q ss_pred             HHHHHHHHhcCCcCcHHHHHHHHHHC
Q 011236          176 NGIMCLYTNTGQHEKIPDVLLDMKEN  201 (490)
Q Consensus       176 ~~l~~~~~~~~~~~~a~~~~~~m~~~  201 (490)
                      +.+|+.+.+.+++..|.++...|...
T Consensus       139 c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  139 CLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            99999999999988888887777654

>KOG2063 consensus Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.81  E-value=22  Score=36.81  Aligned_cols=186  Identities=14%  Similarity=0.105  Sum_probs=100.1

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcC---CCChhhHHHHHHHHHhcCCH--HHHHHHHHHHHhcCCCCCchhHH---
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCK---KQLNRDYITMLGSLVKIGEL--EEAEKMLEEWELSCYCYDFRVPN---  353 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~~~~--~~a~~~~~~~~~~~~~~~~~~~~---  353 (490)
                      |..|+..|...|..++|+++|........   ......+..++..+.+.+..  +-..++-+-..+....-...++.   
T Consensus       507 y~~Li~LY~~kg~h~~AL~ll~~l~d~~~~~d~~~~~~~e~ii~YL~~l~~~~~~Li~~y~~wvl~~~p~~gi~Ift~~~  586 (877)
T KOG2063|consen  507 YRELIELYATKGMHEKALQLLRDLVDEDSDTDSFQLDGLEKIIEYLKKLGAENLDLILEYADWVLNKNPEAGIQIFTSED  586 (877)
T ss_pred             HHHHHHHHHhccchHHHHHHHHHHhccccccccchhhhHHHHHHHHHHhcccchhHHHHHhhhhhccCchhheeeeeccC
Confidence            67777777788888888888776655321   11112233455555555543  44444444333332111111111   


Q ss_pred             ---------HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc--------CCHHHHHHH-----HHHHH
Q 011236          354 ---------IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK--------NNMEKAFEC-----MKEAL  411 (490)
Q Consensus       354 ---------~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~--------~~~~~a~~~-----~~~~~  411 (490)
                               .-+-.|......+-+..+++.+....-.++....+.++..|.+.        ++.+++.+.     +..++
T Consensus       587 ~~~~~sis~~~Vl~~l~~~~~~l~I~YLE~li~~~~~~~~~lht~ll~ly~e~v~~~~~~~~kg~e~~E~~~rekl~~~l  666 (877)
T KOG2063|consen  587 KQEAESISRDDVLNYLKSKEPKLLIPYLEHLISDNRLTSTLLHTVLLKLYLEKVLEQASTDGKGEEAPETTVREKLLDFL  666 (877)
T ss_pred             hhhhccCCHHHHHHHhhhhCcchhHHHHHHHhHhccccchHHHHHHHHHHHHHHhhccCchhccccchhhhHHHHHHHHh
Confidence                     12334666777788888888888765556777777777776542        122233333     22222


Q ss_pred             HhhhcCcCCCcch--------hhHHHHHHHHHcCCCHHHHHHHHHHHHhc--------------ccc-hhhhHHHHHHHH
Q 011236          412 AVHEENKFWRPKP--------SLVSSILDWLGDNRDVEEVEAFVSSLKIK--------------VQK-RNMYHALTEAHI  468 (490)
Q Consensus       412 ~~~~~~~~~~p~~--------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--------------~~~-~~~~~~l~~~~~  468 (490)
                      +   ....+.|..        ..|....-.+.+.|+.++|..++-.....              +.. ...|-.++..|.
T Consensus       667 ~---~s~~Y~p~~~L~~~~~~~l~ee~aill~rl~khe~aL~Iyv~~L~d~~~A~~Yc~~~y~~~~~~~~~y~~lL~~~l  743 (877)
T KOG2063|consen  667 E---SSDLYDPQLLLERLNGDELYEERAILLGRLGKHEEALHIYVHELDDIDAAESYCLPQYESDKTNKEIYLTLLRIYL  743 (877)
T ss_pred             h---hhcccCcchhhhhccchhHHHHHHHHHhhhhhHHHHHHHHHHHhcchhHHHHHHHHhccCCCcccHHHHHHHHHHh
Confidence            2   112333332        23333333445888888888877655442              122 566777777776


Q ss_pred             hc
Q 011236          469 RS  470 (490)
Q Consensus       469 ~~  470 (490)
                      ..
T Consensus       744 ~~  745 (877)
T KOG2063|consen  744 NP  745 (877)
T ss_pred             cc
Confidence            65

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=90.73  E-value=2.5  Score=33.98  Aligned_cols=49  Identities=8%  Similarity=0.048  Sum_probs=24.2

Q ss_pred             CCcch-hhHHHHHHHHHcCC-----------CHHHHHHHHHHHHhcccchhhhHHHHHHHH
Q 011236          420 WRPKP-SLVSSILDWLGDNR-----------DVEEVEAFVSSLKIKVQKRNMYHALTEAHI  468 (490)
Q Consensus       420 ~~p~~-~~~~~l~~~~~~~g-----------~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~  468 (490)
                      +.|+. .++.++..++...+           .+++|...|+++....|....|+.-+....
T Consensus        64 I~P~~hdAlw~lGnA~ts~A~l~~d~~~A~~~F~kA~~~FqkAv~~~P~ne~Y~ksLe~~~  124 (186)
T PF06552_consen   64 INPNKHDALWCLGNAYTSLAFLTPDTAEAEEYFEKATEYFQKAVDEDPNNELYRKSLEMAA  124 (186)
T ss_dssp             H-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHH
T ss_pred             cCCchHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHH
Confidence            55665 56666666554322           144455555555555666555655555543

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>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=90.65  E-value=2.9  Score=34.38  Aligned_cols=82  Identities=17%  Similarity=0.162  Sum_probs=56.2

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCC
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNR  438 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  438 (490)
                      ..+.|+ +.|.+.|-.+...+.--++.....|...|. ..+.+++.+++.++++...  .+-.+|+..+.+|...+.+.|
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~--~~~~~n~eil~sLas~~~~~~  192 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSN--PDDNFNPEILKSLASIYQKLK  192 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcC--CCCCCCHHHHHHHHHHHHHhc
Confidence            455555 567777777776655545555555555555 5677888888888887553  333677788888888888888


Q ss_pred             CHHHHH
Q 011236          439 DVEEVE  444 (490)
Q Consensus       439 ~~~~a~  444 (490)
                      +++.|-
T Consensus       193 ~~e~AY  198 (203)
T PF11207_consen  193 NYEQAY  198 (203)
T ss_pred             chhhhh
Confidence            887764

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=90.40  E-value=0.79  Score=25.04  Aligned_cols=32  Identities=9%  Similarity=-0.132  Sum_probs=25.9

Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+|..+...+...|++++|...|+++.+..|.
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence            46778888999999999999999998887663

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 ....

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.82  E-value=3.1  Score=39.98  Aligned_cols=99  Identities=18%  Similarity=0.140  Sum_probs=48.2

Q ss_pred             hccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhH
Q 011236          218 GARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE  297 (490)
Q Consensus       218 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  297 (490)
                      .+.|+++.|.++..+..       +..-|..|.++....+++..|.+.|.....          |..|+-.+...|+-+.
T Consensus       648 l~lgrl~iA~~la~e~~-------s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d----------~~~LlLl~t~~g~~~~  710 (794)
T KOG0276|consen  648 LKLGRLDIAFDLAVEAN-------SEVKWRQLGDAALSAGELPLASECFLRARD----------LGSLLLLYTSSGNAEG  710 (794)
T ss_pred             hhcCcHHHHHHHHHhhc-------chHHHHHHHHHHhhcccchhHHHHHHhhcc----------hhhhhhhhhhcCChhH
Confidence            34566666666555442       233455666666666666666666655322          3344445555555444


Q ss_pred             HHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          298 MMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEE  339 (490)
Q Consensus       298 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  339 (490)
                      ...+-......+. .+.     ..-+|...|+++++.+++..
T Consensus       711 l~~la~~~~~~g~-~N~-----AF~~~~l~g~~~~C~~lLi~  746 (794)
T KOG0276|consen  711 LAVLASLAKKQGK-NNL-----AFLAYFLSGDYEECLELLIS  746 (794)
T ss_pred             HHHHHHHHHhhcc-cch-----HHHHHHHcCCHHHHHHHHHh
Confidence            3333333333332 222     11223345666666555543

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=89.75  E-value=8  Score=30.05  Aligned_cols=57  Identities=7%  Similarity=-0.149  Sum_probs=38.5

Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCCh
Q 011236           80 RSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVD  137 (490)
Q Consensus        80 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~  137 (490)
                      ....+++++..+++.|.-.. |-.+..-..-...+...|++++|.++|+.+.+..+..
T Consensus        21 L~~~d~~D~e~lLdALrvLr-P~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~~~~   77 (153)
T TIGR02561        21 LRSADPYDAQAMLDALRVLR-PNLKELDMFDGWLLIARGNYDEAARILRELLSSAGAP   77 (153)
T ss_pred             HhcCCHHHHHHHHHHHHHhC-CCccccchhHHHHHHHcCCHHHHHHHHHhhhccCCCc
Confidence            45677888888888777665 2333333444456677888888888888888776543

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=89.71  E-value=0.96  Score=24.58  Aligned_cols=31  Identities=6%  Similarity=-0.199  Sum_probs=24.8

Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      ..+..+...+...|++++|.+.+++..+..|
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p   32 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDP   32 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCc
Confidence            3566778888999999999999999887765

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 ....

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=89.61  E-value=2.7  Score=34.88  Aligned_cols=75  Identities=16%  Similarity=0.188  Sum_probs=55.4

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC----ChhHHHHHHHH
Q 011236           71 ELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK----VDKLYGALLNC  146 (490)
Q Consensus        71 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p----~~~~~~~li~~  146 (490)
                      +.+..++.+.+.+..++++...+.-.+.+ |.+...-..++..+|-.|+++.|..-++......|    -...|..+|.+
T Consensus         3 Tl~~t~seLL~~~sL~dai~~a~~qVkak-Ptda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           3 TLRDTISELLDDNSLQDAIGLARDQVKAK-PTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             chHHHHHHHHHhccHHHHHHHHHHHHhcC-CccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            34556677778888888888888877776 56677777888888889999988887777666554    34556666654

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=89.36  E-value=4.4  Score=28.65  Aligned_cols=46  Identities=9%  Similarity=-0.046  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhh
Q 011236          225 SMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCED  271 (490)
Q Consensus       225 ~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  271 (490)
                      ++.+-++.+- ..++.|++....+.+++|.+.+++.-|.++|+.++.
T Consensus        25 e~rr~mN~l~-~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~   70 (103)
T cd00923          25 ELRRGLNNLF-GYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKD   70 (103)
T ss_pred             HHHHHHHHHh-ccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3444444444 455555555555555555555555555555555543

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.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=89.12  E-value=16  Score=32.69  Aligned_cols=129  Identities=10%  Similarity=0.028  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHh--cC----CHHHHHHHHHHHHhcCC---CCCchhHHHHHHHHHhcCC---
Q 011236          297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVK--IG----ELEEAEKMLEEWELSCY---CYDFRVPNIILLGYSQKGM---  364 (490)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~----~~~~a~~~~~~~~~~~~---~~~~~~~~~l~~~~~~~g~---  364 (490)
                      +...+++.+...+..-+..+|.+..-....  ..    ....+..+++.|++.-+   .++...+..++..  ..++   
T Consensus        80 ~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e~  157 (297)
T PF13170_consen   80 EVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVEE  157 (297)
T ss_pred             HHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHHH
Confidence            445566666666555555555443222222  12    23456667777766421   2223333433332  2222   


Q ss_pred             -HHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHhccCC-HH--HHHHHHHHHHHhhhcCcCCCcchhhHHHHHH
Q 011236          365 -IEKADAVLKEIVKKGKTPTPN-SWSIIAAGYADKNN-ME--KAFECMKEALAVHEENKFWRPKPSLVSSILD  432 (490)
Q Consensus       365 -~~~A~~~~~~m~~~~~~p~~~-~~~~l~~~~~~~~~-~~--~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~  432 (490)
                       .+.+..+|+.+.+.|...+-. -+.+-+-++..... ..  ++.++++.+.+     .|+++....|..+.-
T Consensus       158 l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~-----~~~kik~~~yp~lGl  225 (297)
T PF13170_consen  158 LAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKK-----NGVKIKYMHYPTLGL  225 (297)
T ss_pred             HHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHH-----cCCccccccccHHHH
Confidence             245556666666666654332 22222333333222 22  44555666655     566666655554443

>PRK11619 lytic murein transglycosylase; Provisional

Probab=88.90  E-value=28  Score=35.20  Aligned_cols=317  Identities=8%  Similarity=-0.035  Sum_probs=146.9

Q ss_pred             HHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcc-hHHHHHHHHHhcCCcCc
Q 011236          113 LIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSAL-NYNGIMCLYTNTGQHEK  190 (490)
Q Consensus       113 ~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~-~~~~l~~~~~~~~~~~~  190 (490)
                      -..+.|++..+.++...+..... .-..|..|..... ....++...++++-..   .|-.. .-...+..+.+.+++..
T Consensus        42 ~a~~~g~~~~~~~~~~~l~d~pL~~yl~y~~L~~~l~-~~~~~ev~~Fl~~~~~---~P~~~~Lr~~~l~~La~~~~w~~  117 (644)
T PRK11619         42 QAWDNRQMDVVEQLMPTLKDYPLYPYLEYRQLTQDLM-NQPAVQVTNFIRANPT---LPPARSLQSRFVNELARREDWRG  117 (644)
T ss_pred             HHHHCCCHHHHHHHHHhccCCCcHhHHHHHHHHhccc-cCCHHHHHHHHHHCCC---CchHHHHHHHHHHHHHHccCHHH
Confidence            34466778887777776643211 1122333222111 2234444433332211   11111 11223334445556655


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Q 011236          191 IPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCE  270 (490)
Q Consensus       191 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  270 (490)
                      ..+.+    .. .+.+...-.....+....|+.++|......+= ..|- .....++.++..+.+.|...... +..+|.
T Consensus       118 ~~~~~----~~-~p~~~~~~c~~~~A~~~~G~~~~A~~~a~~lW-~~g~-~~p~~cd~l~~~~~~~g~lt~~d-~w~R~~  189 (644)
T PRK11619        118 LLAFS----PE-KPKPVEARCNYYYAKWATGQQQEAWQGAKELW-LTGK-SLPNACDKLFSVWQQSGKQDPLA-YLERIR  189 (644)
T ss_pred             HHHhc----CC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHh-ccCC-CCChHHHHHHHHHHHcCCCCHHH-HHHHHH
Confidence            55422    11 23344444556667777788777776666665 3333 34556677777777777654432 333333


Q ss_pred             hhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHh---------cCCCChhhHHHHHHHHHh--cCCHHHHHHHHHH
Q 011236          271 DIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIK---------CKKQLNRDYITMLGSLVK--IGELEEAEKMLEE  339 (490)
Q Consensus       271 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~  339 (490)
                      ..... .+...-..+...+ . .+.....+.+..+...         ...++...-..++.++.+  ..+.+.|...+..
T Consensus       190 ~al~~-~~~~lA~~l~~~l-~-~~~~~~a~a~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~l~Rlar~d~~~A~~~~~~  266 (644)
T PRK11619        190 LAMKA-GNTGLVTYLAKQL-P-ADYQTIASALIKLQNDPNTVETFARTTGPTDFTRQMAAVAFASVARQDAENARLMIPS  266 (644)
T ss_pred             HHHHC-CCHHHHHHHHHhc-C-hhHHHHHHHHHHHHHCHHHHHHHhhccCCChhhHHHHHHHHHHHHHhCHHHHHHHHHH
Confidence            22222 3333333333322 1 1111111111111110         001122111222222222  3456777777776


Q ss_pred             HHhcC-CCCCc--hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhc
Q 011236          340 WELSC-YCYDF--RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEE  416 (490)
Q Consensus       340 ~~~~~-~~~~~--~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  416 (490)
                      ..... ..+..  .++..+.......+..++|...++......  .|......-+..-...++++.+...+..|-.    
T Consensus       267 ~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~~~--~~~~~~e~r~r~Al~~~dw~~~~~~i~~L~~----  340 (644)
T PRK11619        267 LVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVIMRS--QSTSLLERRVRMALGTGDRRGLNTWLARLPM----  340 (644)
T ss_pred             HHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhccccc--CCcHHHHHHHHHHHHccCHHHHHHHHHhcCH----
Confidence            64432 22211  123333333333322455656555544322  2344445555555577888877777777644    


Q ss_pred             CcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          417 NKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       417 ~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                        ...-...-..-+.+++...|+.++|..+|+.+..
T Consensus       341 --~~~~~~rw~YW~aRa~~~~g~~~~A~~~~~~~a~  374 (644)
T PRK11619        341 --EAKEKDEWRYWQADLLLEQGRKAEAEEILRQLMQ  374 (644)
T ss_pred             --hhccCHhhHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence              2222334455666776677888888888888743

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.84  E-value=28  Score=35.06  Aligned_cols=152  Identities=18%  Similarity=0.212  Sum_probs=90.4

Q ss_pred             HHHHHhhcCHHHHHHHHHHccccCC---ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCC
Q 011236          111 LDLIGKVRGLESAETYFNSLNDEDK---VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQ  187 (490)
Q Consensus       111 ~~~~~~~~~~~~A~~~~~~~~~~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  187 (490)
                      ++.+.+.+.+++|+...+......|   ...++...|..+...|++++|-...-.|...    +..-|...+..+...++
T Consensus       363 i~Wll~~k~yeeAl~~~k~~~~~~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn----~~~eWe~~V~~f~e~~~  438 (846)
T KOG2066|consen  363 IDWLLEKKKYEEALDAAKASIGNEERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGN----NAAEWELWVFKFAELDQ  438 (846)
T ss_pred             HHHHHHhhHHHHHHHHHHhccCCccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcc----hHHHHHHHHHHhccccc
Confidence            6677788888888888887766544   3556888888888889999988888888765    66667766666666665


Q ss_pred             cCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHH--------------HHHHHHh--CCCCCCCHHHHHHHHH
Q 011236          188 HEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMEN--------------VLQEMES--QSHISMDWGTYSTVAN  251 (490)
Q Consensus       188 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~--------------~~~~~~~--~~~~~~~~~~~~~li~  251 (490)
                      ......++   .......+...|..++..+.. .+...-.+              +.+....  +.+- .+...-..|+.
T Consensus       439 l~~Ia~~l---Pt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q~S-e~~~L~e~La~  513 (846)
T KOG2066|consen  439 LTDIAPYL---PTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTIISATEPQIKQNS-ESTALLEVLAH  513 (846)
T ss_pred             cchhhccC---CCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHHhhcchHHHhhc-cchhHHHHHHH
Confidence            54433221   111111233445555554443 22111111              1111110  0011 12223334888


Q ss_pred             HHHHcCCHHHHHHHHHHHhh
Q 011236          252 YYIIAGLKEKAIIYLKKCED  271 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~  271 (490)
                      .|...++++.|..++-..++
T Consensus       514 LYl~d~~Y~~Al~~ylklk~  533 (846)
T KOG2066|consen  514 LYLYDNKYEKALPIYLKLQD  533 (846)
T ss_pred             HHHHccChHHHHHHHHhccC
Confidence            88899999999988877544

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=88.51  E-value=1.2  Score=25.65  Aligned_cols=30  Identities=27%  Similarity=0.475  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhh
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  414 (490)
                      .+++.|...|...|++++|..++++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~   32 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALEIR   32 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHHHH
Confidence            466777777777777777777777776633

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=88.27  E-value=14  Score=30.86  Aligned_cols=186  Identities=15%  Similarity=-0.021  Sum_probs=108.6

Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHH
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELE  331 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  331 (490)
                      .|-..|-++-|.-=|.+.....+  .-+..||-+.-.+...|+++.|.+.|+...+-++ ....+...-.-++--.|++.
T Consensus        74 lYDSlGL~~LAR~DftQaLai~P--~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp-~y~Ya~lNRgi~~YY~gR~~  150 (297)
T COG4785          74 LYDSLGLRALARNDFSQALAIRP--DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP-TYNYAHLNRGIALYYGGRYK  150 (297)
T ss_pred             hhhhhhHHHHHhhhhhhhhhcCC--CcHHHHHHHHHHHHhcccchHHHHHhhhHhccCC-cchHHHhccceeeeecCchH
Confidence            46667777777777777766554  4567788888888889999999999987776655 22233222222334468888


Q ss_pred             HHHHHHHHHHhcCCCCCchhHHHHHHHHHh--cCCHHHHHHHH-HHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHH
Q 011236          332 EAEKMLEEWELSCYCYDFRVPNIILLGYSQ--KGMIEKADAVL-KEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMK  408 (490)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~g~~~~A~~~~-~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~  408 (490)
                      -|.+-+...-+... .|+  |.+ +..|..  .-++.+|..-+ ++....    |..-|...|..|.-..-.  ...+++
T Consensus       151 LAq~d~~~fYQ~D~-~DP--fR~-LWLYl~E~k~dP~~A~tnL~qR~~~~----d~e~WG~~iV~~yLgkiS--~e~l~~  220 (297)
T COG4785         151 LAQDDLLAFYQDDP-NDP--FRS-LWLYLNEQKLDPKQAKTNLKQRAEKS----DKEQWGWNIVEFYLGKIS--EETLME  220 (297)
T ss_pred             hhHHHHHHHHhcCC-CCh--HHH-HHHHHHHhhCCHHHHHHHHHHHHHhc----cHhhhhHHHHHHHHhhcc--HHHHHH
Confidence            88777666655421 122  222 222322  23455665433 333332    445555544443322211  233444


Q ss_pred             HHHHhhhcCcCCCcc-------hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          409 EALAVHEENKFWRPK-------PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       409 ~~~~~~~~~~~~~p~-------~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+..      +-.-+       ..||--+..-+...|+.++|..+|+-......-
T Consensus       221 ~~~a------~a~~n~~~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLaiannVy  269 (297)
T COG4785         221 RLKA------DATDNTSLAEHLTETYFYLGKYYLSLGDLDEATALFKLAVANNVY  269 (297)
T ss_pred             HHHh------hccchHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhHH
Confidence            4444      21211       246667777888899999999999987776544

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=88.16  E-value=56  Score=37.74  Aligned_cols=146  Identities=12%  Similarity=-0.007  Sum_probs=94.1

Q ss_pred             HHHhcCChhHHHHHHHHH----HhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCCh
Q 011236           78 QLRSRKRFKHALQVSEWM----SGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLV  153 (490)
Q Consensus        78 ~~~~~~~~~~a~~~~~~~----~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~  153 (490)
                      +--+.+.+..|+..++.-    .+..  .....+..+...|+..+++|....+...-. ..|+  .+. -|-.....|++
T Consensus      1392 aSfrc~~y~RalmylEs~~~~ek~~~--~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~-a~~s--l~~-qil~~e~~g~~ 1465 (2382)
T KOG0890|consen 1392 ASFRCKAYARALMYLESHRSTEKEKE--TEEALYFLLQNLYGSIHDPDGVEGVSARRF-ADPS--LYQ-QILEHEASGNW 1465 (2382)
T ss_pred             HHHhhHHHHHHHHHHHHhccccchhH--HHHHHHHHHHHHHHhcCCcchhhhHHHHhh-cCcc--HHH-HHHHHHhhccH
Confidence            444567788898888883    2222  233444455559999999998888776411 1133  233 34455678999


Q ss_pred             hHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHH-HHHHHhccCChHHHHHHHH
Q 011236          154 DESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRI-CINSYGARSELSSMENVLQ  231 (490)
Q Consensus       154 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~-li~~~~~~g~~~~a~~~~~  231 (490)
                      ..|...|+.+.+.+.. ...+++-++......|.++.+.-..+-.... ..+....++. -+.+--+.++++.......
T Consensus      1466 ~da~~Cye~~~q~~p~-~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~-~se~~~~~~s~~~eaaW~l~qwD~~e~~l~ 1542 (2382)
T KOG0890|consen 1466 ADAAACYERLIQKDPD-KEKHHSGVLKSMLAIQHLSTEILHLDGLIIN-RSEEVDELNSLGVEAAWRLSQWDLLESYLS 1542 (2382)
T ss_pred             HHHHHHHHHhhcCCCc-cccchhhHHHhhhcccchhHHHhhhcchhhc-cCHHHHHHHHHHHHHHhhhcchhhhhhhhh
Confidence            9999999999988543 5777887777777778877777655544433 2233333333 3445567778887766654

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=88.03  E-value=22  Score=32.82  Aligned_cols=66  Identities=14%  Similarity=-0.037  Sum_probs=39.8

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC--CChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS--KDALGYNHLISHYASLGNKDEMMKFWGLQKI  307 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  307 (490)
                      ...++..++..+.+.|.++.|...+..+.......  ..+.....-....-..|+..+|+..++....
T Consensus       145 ~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  145 LAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34556667777777777777777777766543210  1233344445555566777777777766655

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=87.97  E-value=32  Score=34.73  Aligned_cols=408  Identities=11%  Similarity=0.059  Sum_probs=202.3

Q ss_pred             HHHHHHHHHH-hcCChhHHHHHHHHHHhCCCCCChh-----hHHHHHHHHHhhcCHHHHHHHHHHccccC---C-Ch--h
Q 011236           71 ELQRVIRQLR-SRKRFKHALQVSEWMSGQGLAFSVH-----DHAVQLDLIGKVRGLESAETYFNSLNDED---K-VD--K  138 (490)
Q Consensus        71 ~~~~ll~~~~-~~~~~~~a~~~~~~~~~~~~~~~~~-----~~~~l~~~~~~~~~~~~A~~~~~~~~~~~---p-~~--~  138 (490)
                      ++-.+...+. ...+++.|...+++.......++-.     ....++..+.+.+... |...+++..+.-   + +.  .
T Consensus        61 ~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d~k~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~~~~w~~  139 (608)
T PF10345_consen   61 VRLRLASILLEETENLDLAETYLEKAILLCERHRLTDLKFRCQFLLARIYFKTNPKA-ALKNLDKAIEDSETYGHSAWYY  139 (608)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccCchhHHH
Confidence            3445555554 6688999999999875544322222     2234556666666555 888888765532   1 12  2


Q ss_pred             HHHHH-HHHHHhcCChhHHHHHHHHHHhcC---CCCCcchHHHHHHHHH--hcCCcCcHHHHHHHHHHCC--C-------
Q 011236          139 LYGAL-LNCYVREGLVDESLSLMQKMKEMG---SFGSALNYNGIMCLYT--NTGQHEKIPDVLLDMKENG--V-------  203 (490)
Q Consensus       139 ~~~~l-i~~~~~~g~~~~a~~~~~~m~~~~---~~p~~~~~~~l~~~~~--~~~~~~~a~~~~~~m~~~~--~-------  203 (490)
                      .+.-+ +..+...+++..|.+.++.+...-   ..|-..++-.++.+..  ..+..+.+.+.++.+....  +       
T Consensus       140 ~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~~~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~  219 (608)
T PF10345_consen  140 AFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPAVFVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVH  219 (608)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCC
Confidence            22333 333333479999999999886542   3334445555555544  4456777888777774321  1       


Q ss_pred             CCCHHHHHHHHHHHh--ccCChHHHHHHHHHHHh------CCC----------CC-------------CCH---------
Q 011236          204 PPDNFSYRICINSYG--ARSELSSMENVLQEMES------QSH----------IS-------------MDW---------  243 (490)
Q Consensus       204 ~p~~~~~~~li~~~~--~~g~~~~a~~~~~~~~~------~~~----------~~-------------~~~---------  243 (490)
                      .|-..+|..+++.++  ..|+++.+...++++..      +..          ++             +..         
T Consensus       220 ~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq~~~~~~~~~~~w~~~~~d~~i~l~~~~~~~~~~~~~~~f~wl~~~~l  299 (608)
T PF10345_consen  220 IPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQQFLDEIKKSPSWPSWDEDGSIPLNIGEGSSNSGGTPLVFSWLPKEEL  299 (608)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCccCCCcCCCeeEEeecccccccCCCceeEEeecCHHHH
Confidence            345566777776554  56776666665554431      111          00             000         


Q ss_pred             HHHHHHHH--HHHHcCCHHHHHHHHHHHhhh----h---ccCCC--------hhhHHHHHHH---------HHhcCChhH
Q 011236          244 GTYSTVAN--YYIIAGLKEKAIIYLKKCEDI----V---SKSKD--------ALGYNHLISH---------YASLGNKDE  297 (490)
Q Consensus       244 ~~~~~li~--~~~~~~~~~~a~~~~~~~~~~----~---~~~~~--------~~~~~~l~~~---------~~~~~~~~~  297 (490)
                      .....++.  .++..+..++|.+++++..+.    .   ...+.        ...|...+..         .+-.+++..
T Consensus       300 ~~L~y~lS~l~~~~~~~~~ks~k~~~k~l~~i~~~~~~~~~~~~~sl~~~~~~~~~~~~l~~~~~~y~~~~~~~~~~~~~  379 (608)
T PF10345_consen  300 YALVYFLSGLHNLYKGSMDKSEKFLEKALKQIEKLKIKSPSAPSESLSEASERIQWLRYLQCYLLFYQIWCNFIRGDWSK  379 (608)
T ss_pred             HHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHhhccCCCCCCcCHHHHHHhHHHHHHHHHHHHHHHHHHHHHCcCHHH
Confidence            01111222  223344444555555443221    1   11011        1222222222         235788999


Q ss_pred             HHHHHHHHHHhcC-CCC-------hhhHHHHHHHHHhcCCHHHHHHHHH--------HHHhcCCCCCchhHHH--HHHHH
Q 011236          298 MMKFWGLQKIKCK-KQL-------NRDYITMLGSLVKIGELEEAEKMLE--------EWELSCYCYDFRVPNI--ILLGY  359 (490)
Q Consensus       298 a~~~~~~~~~~~~-~~~-------~~~~~~l~~~~~~~~~~~~a~~~~~--------~~~~~~~~~~~~~~~~--l~~~~  359 (490)
                      |...++.+..... .|+       +..+....-.+-..|+.+.|...|.        .....+...+..++..  ++..+
T Consensus       380 a~~~l~~~~~~~~~~~~~~~~~~~~~~~yL~gl~~q~~g~l~~A~~~y~~~~~~~~~~~~~~~~~~El~ila~LNl~~I~  459 (608)
T PF10345_consen  380 ATQELEFMRQLCQRSPSKLYESLYPLLHYLLGLYYQSTGDLEAALYQYQKPRFLLCEAANRKSKFRELYILAALNLAIIL  459 (608)
T ss_pred             HHHHHHHHHHHHhcCccchhhhhhHHHHHHHHHHHHHcCCHHHHHHHHhhhHHhhhhhhccCCcchHHHHHHHHHHHHHh
Confidence            9999998876543 122       1222222233345799999999998        4444444444444432  11122


Q ss_pred             Hhc--CCHHH--HHHHHHHHHHc-CCCC--CHHHHHHH-HHHHhcc--CCHHHHHHHHHHHHHhhhcCcCCCcch---hh
Q 011236          360 SQK--GMIEK--ADAVLKEIVKK-GKTP--TPNSWSII-AAGYADK--NNMEKAFECMKEALAVHEENKFWRPKP---SL  426 (490)
Q Consensus       360 ~~~--g~~~~--A~~~~~~m~~~-~~~p--~~~~~~~l-~~~~~~~--~~~~~a~~~~~~~~~~~~~~~~~~p~~---~~  426 (490)
                      ...  ...++  +..+++.+... .-.|  +..++..+ +.++...  -...++...+.+.++...  .....+.   .+
T Consensus       460 ~~~~~~~~~~~~~~~l~~~i~p~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ne~k~~l~~~L~~~~--~~~~n~~l~~~~  537 (608)
T PF10345_consen  460 QYESSRDDSESELNELLEQIEPLCSNSPNSYNRTAYCLVLATYNTFEPFSSNEAKRHLQEALKMAN--NKLGNSQLLAIL  537 (608)
T ss_pred             HhhcccchhhhHHHHHHHhcCccccCCccHHHHHHHHHHHHHHhhCCccccHHHHHHHHHHHHHHH--HhhccchHHHHH
Confidence            222  22233  66666665432 1122  33344444 3333322  223466666666555220  0111222   22


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHh---cccc--hhhhH-----HHHHHHHhcC--CcHHHHHHHHH
Q 011236          427 VSSILDWLGDNRDVEEVEAFVSSLKI---KVQK--RNMYH-----ALTEAHIRSG--QEVDGLLESMK  482 (490)
Q Consensus       427 ~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~--~~~~~-----~l~~~~~~~g--~~a~~~~~~m~  482 (490)
                      ++.+...+. .|+..+..+.......   ..++  ...|.     .+.+.+...|  ++|.....+..
T Consensus       538 L~lm~~~lf-~~~~~e~~~~s~~a~~~A~k~~d~~~~LW~~v~~~~l~~~~~~~G~~~ka~~~~~~~~  604 (608)
T PF10345_consen  538 LNLMGHRLF-EGDVGEQAKKSARAFQLAKKSSDYSDQLWHLVASGMLADSYEVQGDRDKAEEARQQLD  604 (608)
T ss_pred             HHHHHHHHH-cCCHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHH
Confidence            333333333 6787776555543221   1222  44553     3444466777  67776665543

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=87.80  E-value=26  Score=33.45  Aligned_cols=179  Identities=13%  Similarity=0.095  Sum_probs=111.7

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011236          136 VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICIN  215 (490)
Q Consensus       136 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~  215 (490)
                      |....-+++..+.....+.-...+..+|...|-  +-..|-.++.+|..+ ..+.-..+++++.+..+. |+..-..|..
T Consensus        65 ~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~e--~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~~ReLa~  140 (711)
T COG1747          65 DDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYGE--SKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVIGRELAD  140 (711)
T ss_pred             cchHHHHHHHHhccchHHHHHHHHHHHHHHhcc--hHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHHHHHHHH
Confidence            555667778888877777788888888887653  666778888888777 556777788877776552 4444444555


Q ss_pred             HHhccCChHHHHHHHHHHHhCCCCCCC------HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHH
Q 011236          216 SYGARSELSSMENVLQEMESQSHISMD------WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHY  289 (490)
Q Consensus       216 ~~~~~g~~~~a~~~~~~~~~~~~~~~~------~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  289 (490)
                      .|-+ ++.+.+..+|.++. ..=+ |.      ...|.-+...  -..+.|....+..++........-.+.+.-+-.-|
T Consensus       141 ~yEk-ik~sk~a~~f~Ka~-yrfI-~~~q~~~i~evWeKL~~~--i~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Y  215 (711)
T COG1747         141 KYEK-IKKSKAAEFFGKAL-YRFI-PRRQNAAIKEVWEKLPEL--IGDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKY  215 (711)
T ss_pred             HHHH-hchhhHHHHHHHHH-HHhc-chhhhhhHHHHHHHHHHh--ccccHHHHHHHHHHHHHhhccchHHHHHHHHHHHh
Confidence            5544 77777777877776 3222 21      1122222211  13456667777666665544324445556666667


Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHH
Q 011236          290 ASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSL  324 (490)
Q Consensus       290 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  324 (490)
                      ....++++|++++....+... .|..+-..++.-+
T Consensus       216 s~~eN~~eai~Ilk~il~~d~-k~~~ar~~~i~~l  249 (711)
T COG1747         216 SENENWTEAIRILKHILEHDE-KDVWARKEIIENL  249 (711)
T ss_pred             ccccCHHHHHHHHHHHhhhcc-hhhhHHHHHHHHH
Confidence            777788888888876666544 5555555555443

>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat

Probab=87.69  E-value=5.4  Score=27.61  Aligned_cols=66  Identities=11%  Similarity=0.078  Sum_probs=46.4

Q ss_pred             HHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHH
Q 011236           88 ALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESL  157 (490)
Q Consensus        88 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~  157 (490)
                      +.++++.+.+.|+ .+......+-..-...|+.+.|.++++.+. ++|+  .|...+.++-+.|.-+-|.
T Consensus        21 ~~~v~d~ll~~~i-lT~~d~e~I~aa~~~~g~~~~ar~LL~~L~-rg~~--aF~~Fl~aLreT~~~~LA~   86 (88)
T cd08819          21 TRDVCDKCLEQGL-LTEEDRNRIEAATENHGNESGARELLKRIV-QKEG--WFSKFLQALRETEHHELAR   86 (88)
T ss_pred             HHHHHHHHHhcCC-CCHHHHHHHHHhccccCcHHHHHHHHHHhc-cCCc--HHHHHHHHHHHcCchhhhh
Confidence            4567777777774 555555555444446688888888888888 6666  4778888888777765554

Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=87.45  E-value=1.2  Score=24.20  Aligned_cols=27  Identities=22%  Similarity=0.379  Sum_probs=18.3

Q ss_pred             HHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          386 SWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       386 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +|..+...|...|++++|...|+++++
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~   29 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            455666666777777777777777666

...

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=87.41  E-value=1.7  Score=38.60  Aligned_cols=93  Identities=16%  Similarity=0.063  Sum_probs=59.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHH
Q 011236          356 LLGYSQKGMIEKADAVLKEIVKKGKTP-TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWL  434 (490)
Q Consensus       356 ~~~~~~~g~~~~A~~~~~~m~~~~~~p-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~  434 (490)
                      ...|.++|.+++|+..|...+.  ..| |++++..-..+|.+...+..|..-...++.+..      .-...|..-+.+-
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia--~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd~------~Y~KAYSRR~~AR  175 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIA--VYPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALDK------LYVKAYSRRMQAR  175 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhc--cCCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhhH------HHHHHHHHHHHHH
Confidence            4457778888888888766543  677 777788888888888888777777777766210      1112333333344


Q ss_pred             HcCCCHHHHHHHHHHHHhcccc
Q 011236          435 GDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       435 ~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ...|..++|.+-++...+..|.
T Consensus       176 ~~Lg~~~EAKkD~E~vL~LEP~  197 (536)
T KOG4648|consen  176 ESLGNNMEAKKDCETVLALEPK  197 (536)
T ss_pred             HHHhhHHHHHHhHHHHHhhCcc
Confidence            4456666666666666666665

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=87.23  E-value=8.9  Score=27.50  Aligned_cols=49  Identities=8%  Similarity=-0.063  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhc
Q 011236          225 SMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVS  274 (490)
Q Consensus       225 ~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~  274 (490)
                      +..+-++.+- ..++.|++....+.+.+|.+.+++.-|.++|+.++....
T Consensus        28 e~rrglN~l~-~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~   76 (108)
T PF02284_consen   28 ELRRGLNNLF-GYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG   76 (108)
T ss_dssp             HHHHHHHHHT-TSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHh-ccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc
Confidence            3444555555 556666666666666666666666666666666665443

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 ....

>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]

Probab=87.02  E-value=5  Score=29.91  Aligned_cols=60  Identities=12%  Similarity=0.153  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHH
Q 011236          403 AFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAH  467 (490)
Q Consensus       403 a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~  467 (490)
                      ..+-++....     ..+.|++.....-+++|.+.+|+..|.++|+-++...+. ..+|-.+++-+
T Consensus        68 vrkglN~l~~-----yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K~g~~k~~Y~y~v~el  128 (149)
T KOG4077|consen   68 VRKGLNNLFD-----YDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDKCGAQKQVYPYYVKEL  128 (149)
T ss_pred             HHHHHHhhhc-----cccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            3444555555     567788888888888888888888888888888777666 44566665543

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=86.54  E-value=17  Score=29.88  Aligned_cols=143  Identities=11%  Similarity=0.148  Sum_probs=86.1

Q ss_pred             HHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHH-----HHHHHHhcCCHHHHHHHH
Q 011236          298 MMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNI-----ILLGYSQKGMIEKADAVL  372 (490)
Q Consensus       298 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-----l~~~~~~~g~~~~A~~~~  372 (490)
                      ..++|..........-...|..++.+.. .+.. +......++....   ...+|..     +...+...|++++|..-+
T Consensus        38 GW~ywq~~q~~q~~~AS~~Y~~~i~~~~-ak~~-~~~~~~ekf~~~n---~~t~Ya~laaL~lAk~~ve~~~~d~A~aqL  112 (207)
T COG2976          38 GWRYWQSHQVEQAQEASAQYQNAIKAVQ-AKKP-KSIAAAEKFVQAN---GKTIYAVLAALELAKAEVEANNLDKAEAQL  112 (207)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCc-hhHHHHHHHHhhc---cccHHHHHHHHHHHHHHHhhccHHHHHHHH
Confidence            4555554333333334456777777654 3333 4455555555541   2333332     334577888999998888


Q ss_pred             HHHHHcCCCCCHHHHH-----HHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHH
Q 011236          373 KEIVKKGKTPTPNSWS-----IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFV  447 (490)
Q Consensus       373 ~~m~~~~~~p~~~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~  447 (490)
                      +.....   |....+.     .|.+.....|.+++|+.+++....     .++  .......-.+.+...|+-++|+.-|
T Consensus       113 ~~~l~~---t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~-----~~w--~~~~~elrGDill~kg~k~~Ar~ay  182 (207)
T COG2976         113 KQALAQ---TKDENLKALAALRLARVQLQQKKADAALKTLDTIKE-----ESW--AAIVAELRGDILLAKGDKQEARAAY  182 (207)
T ss_pred             HHHHcc---chhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcccc-----ccH--HHHHHHHhhhHHHHcCchHHHHHHH
Confidence            877754   2222333     344567778888888888887655     221  2233444556788889999999888


Q ss_pred             HHHHhccc
Q 011236          448 SSLKIKVQ  455 (490)
Q Consensus       448 ~~~~~~~~  455 (490)
                      ++....++
T Consensus       183 ~kAl~~~~  190 (207)
T COG2976         183 EKALESDA  190 (207)
T ss_pred             HHHHHccC
Confidence            88877753

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=86.36  E-value=21  Score=30.88  Aligned_cols=209  Identities=10%  Similarity=0.013  Sum_probs=135.8

Q ss_pred             cCCCCCcchHHHHHHHH-HhcCCcCcHHHHHHHHHHCCCCCCH---HHHHHHHHHHhccCChHHHHHHHHHHHh--CC--
Q 011236          166 MGSFGSALNYNGIMCLY-TNTGQHEKIPDVLLDMKENGVPPDN---FSYRICINSYGARSELSSMENVLQEMES--QS--  237 (490)
Q Consensus       166 ~~~~p~~~~~~~l~~~~-~~~~~~~~a~~~~~~m~~~~~~p~~---~~~~~li~~~~~~g~~~~a~~~~~~~~~--~~--  237 (490)
                      .+-.||+..-|.--..- .+...+++|+.-|++..+.......   .....++....+.|++++....|.++..  +.  
T Consensus        20 s~sEpdVDlENQYYnsK~l~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQmiKI~f~l~~~~eMm~~Y~qlLTYIkSAV   99 (440)
T KOG1464|consen   20 SNSEPDVDLENQYYNSKGLKEDEPKEALSSFQKVLELEGEKGEWGFKALKQMIKINFRLGNYKEMMERYKQLLTYIKSAV   99 (440)
T ss_pred             cCCCCCcchHhhhhccccccccCHHHHHHHHHHHHhcccccchhHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Confidence            34567777655433221 2345788999999999874322222   2445678899999999999999998861  11  


Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChh----hHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC
Q 011236          238 HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDAL----GYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL  313 (490)
Q Consensus       238 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  313 (490)
                      .-..+....|++++.-..+.+.+--..+|+.-.+......|..    |-+-|...|...+++.....+++++...+...+
T Consensus       100 TrNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~ed  179 (440)
T KOG1464|consen  100 TRNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTED  179 (440)
T ss_pred             hccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhcccc
Confidence            1123456677888888888888887777776544322213433    335678888889999999999998887765222


Q ss_pred             h-----------hhHHHHHHHHHhcCCHHHHHHHHHHHHhcC-CCCCchhHHHHHHH-----HHhcCCHHHHHHHHHHH
Q 011236          314 N-----------RDYITMLGSLVKIGELEEAEKMLEEWELSC-YCYDFRVPNIILLG-----YSQKGMIEKADAVLKEI  375 (490)
Q Consensus       314 ~-----------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~-----~~~~g~~~~A~~~~~~m  375 (490)
                      .           ..|..=|..|....+-.....++++..... --|.+.... +|+-     ..+.|++++|..-|-+.
T Consensus       180 GedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlImG-vIRECGGKMHlreg~fe~AhTDFFEA  257 (440)
T KOG1464|consen  180 GEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLIMG-VIRECGGKMHLREGEFEKAHTDFFEA  257 (440)
T ss_pred             CchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHHHh-HHHHcCCccccccchHHHHHhHHHHH
Confidence            2           346777888888888888888888765432 223433333 3333     35678888886544333

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=86.15  E-value=38  Score=33.68  Aligned_cols=273  Identities=15%  Similarity=0.045  Sum_probs=156.9

Q ss_pred             HHHHHHHHHHccccCCC-hhHHHHHH--HH-HHhcCChhHHHHHHHHHHh-------cCCCCCcchHHHHHHHHHhcC--
Q 011236          120 LESAETYFNSLNDEDKV-DKLYGALL--NC-YVREGLVDESLSLMQKMKE-------MGSFGSALNYNGIMCLYTNTG--  186 (490)
Q Consensus       120 ~~~A~~~~~~~~~~~p~-~~~~~~li--~~-~~~~g~~~~a~~~~~~m~~-------~~~~p~~~~~~~l~~~~~~~~--  186 (490)
                      ...|..+++.....+-. ......++  .+ +....+.+.|+..|+.+.+       .|   +....+-+..+|.+..  
T Consensus       228 ~~~a~~~~~~~a~~g~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g~~~  304 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLGHSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQGLGV  304 (552)
T ss_pred             hhHHHHHHHHHHhhcchHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcCCCC
Confidence            45788888888776632 22222222  22 4467789999999999877       55   4556777888887765  


Q ss_pred             ---CcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhc-cCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH----HcCC
Q 011236          187 ---QHEKIPDVLLDMKENGVPPDNFSYRICINSYGA-RSELSSMENVLQEMESQSHISMDWGTYSTVANYYI----IAGL  258 (490)
Q Consensus       187 ---~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~-~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~----~~~~  258 (490)
                         +.+.|..++...-+.|. |+...+-..+..... ..+...|.++|.... +.|. +...-+  +..+|.    -..+
T Consensus       305 ~~~d~~~A~~~~~~aA~~g~-~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa-~~G~-~~A~~~--la~~y~~G~gv~r~  379 (552)
T KOG1550|consen  305 EKIDYEKALKLYTKAAELGN-PDAQYLLGVLYETGTKERDYRRAFEYYSLAA-KAGH-ILAIYR--LALCYELGLGVERN  379 (552)
T ss_pred             ccccHHHHHHHHHHHHhcCC-chHHHHHHHHHHcCCccccHHHHHHHHHHHH-HcCC-hHHHHH--HHHHHHhCCCcCCC
Confidence               44558999999888876 565554444443333 356789999999998 6665 333332  333332    2347


Q ss_pred             HHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHH-H---Hh----cCCH
Q 011236          259 KEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGS-L---VK----IGEL  330 (490)
Q Consensus       259 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~---~~----~~~~  330 (490)
                      .+.|..++.+.-+.+.  +...--...+..+.. ++++.+...+..+...+. ....+-...+.. .   ..    ..+.
T Consensus       380 ~~~A~~~~k~aA~~g~--~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~g~-~~~q~~a~~l~~~~~~~~~~~~~~~~~  455 (552)
T KOG1550|consen  380 LELAFAYYKKAAEKGN--PSAAYLLGAFYEYGV-GRYDTALALYLYLAELGY-EVAQSNAAYLLDQSEEDLFSRGVISTL  455 (552)
T ss_pred             HHHHHHHHHHHHHccC--hhhHHHHHHHHHHcc-ccccHHHHHHHHHHHhhh-hHHhhHHHHHHHhccccccccccccch
Confidence            8889999999887774  333223333444444 777777777775655544 222222211111 1   11    1244


Q ss_pred             HHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc----CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHh----ccCCHHH
Q 011236          331 EEAEKMLEEWELSCYCYDFRVPNIILLGYSQK----GMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA----DKNNMEK  402 (490)
Q Consensus       331 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~----~~~~~~~  402 (490)
                      ..+...+......|   +......+-+.|...    .+++.|...+......+    ....-.+...+-    -.. +..
T Consensus       456 ~~~~~~~~~a~~~g---~~~a~~~lgd~y~~g~g~~~d~~~a~~~y~~a~~~~----~~~~~nlg~~~e~g~g~~~-~~~  527 (552)
T KOG1550|consen  456 ERAFSLYSRAAAQG---NADAILKLGDYYYYGLGTGRDPEKAAAQYARASEQG----AQALFNLGYMHEHGEGIKV-LHL  527 (552)
T ss_pred             hHHHHHHHHHHhcc---CHHHHhhhcceeeecCCCCCChHHHHHHHHHHHHhh----hHHHhhhhhHHhcCcCcch-hHH
Confidence            55555565555443   333334444444332    34777777777776654    222222222221    223 677


Q ss_pred             HHHHHHHHHH
Q 011236          403 AFECMKEALA  412 (490)
Q Consensus       403 a~~~~~~~~~  412 (490)
                      |.++++.+.+
T Consensus       528 a~~~~~~~~~  537 (552)
T KOG1550|consen  528 AKRYYDQASE  537 (552)
T ss_pred             HHHHHHHHHh
Confidence            7788877766

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=86.01  E-value=1.2  Score=23.91  Aligned_cols=26  Identities=12%  Similarity=0.085  Sum_probs=14.0

Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      +..++.+.|++++|.+.|+++.+..|
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~~P   31 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKRYP   31 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHCc
Confidence            34444555556666665555555444

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=85.62  E-value=15  Score=31.06  Aligned_cols=142  Identities=13%  Similarity=0.104  Sum_probs=89.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      ..--+..|.+.-++.-|.....++.+    | ..+ .+-+--|.+..+..--.++.+-....++.-+......++  +..
T Consensus       133 lRRtMEiyS~ttRFalaCN~s~KIiE----P-IQS-RCAiLRysklsd~qiL~Rl~~v~k~Ekv~yt~dgLeaii--fta  204 (333)
T KOG0991|consen  133 LRRTMEIYSNTTRFALACNQSEKIIE----P-IQS-RCAILRYSKLSDQQILKRLLEVAKAEKVNYTDDGLEAII--FTA  204 (333)
T ss_pred             HHHHHHHHcccchhhhhhcchhhhhh----h-HHh-hhHhhhhcccCHHHHHHHHHHHHHHhCCCCCcchHHHhh--hhc
Confidence            34445556666666655555555543    1 111 122233444444444444444444455555555555554  567


Q ss_pred             cCCHHHHHHHHHHHHHhhhcCcCC-----------CcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHH
Q 011236          397 KNNMEKAFECMKEALAVHEENKFW-----------RPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALT  464 (490)
Q Consensus       397 ~~~~~~a~~~~~~~~~~~~~~~~~-----------~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~  464 (490)
                      .|+...|+..++.-...    .|.           .|.+.....++..|.+ +++++|.+++.++.+.|.. .+..+++.
T Consensus       205 ~GDMRQalNnLQst~~g----~g~Vn~enVfKv~d~PhP~~v~~ml~~~~~-~~~~~A~~il~~lw~lgysp~Dii~~~F  279 (333)
T KOG0991|consen  205 QGDMRQALNNLQSTVNG----FGLVNQENVFKVCDEPHPLLVKKMLQACLK-RNIDEALKILAELWKLGYSPEDIITTLF  279 (333)
T ss_pred             cchHHHHHHHHHHHhcc----ccccchhhhhhccCCCChHHHHHHHHHHHh-ccHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            89999999988887761    221           4677777788877765 6899999999999999888 88888888


Q ss_pred             HHHHhcC
Q 011236          465 EAHIRSG  471 (490)
Q Consensus       465 ~~~~~~g  471 (490)
                      +.+....
T Consensus       280 Rv~K~~~  286 (333)
T KOG0991|consen  280 RVVKNMD  286 (333)
T ss_pred             HHHHhcc
Confidence            8877666

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=85.42  E-value=2.4  Score=24.29  Aligned_cols=28  Identities=29%  Similarity=0.458  Sum_probs=18.2

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHh
Q 011236          138 KLYGALLNCYVREGLVDESLSLMQKMKE  165 (490)
Q Consensus       138 ~~~~~li~~~~~~g~~~~a~~~~~~m~~  165 (490)
                      .+++.|...|...|++++|..++++...
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            3566677777777777777777776544

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=85.07  E-value=13  Score=32.42  Aligned_cols=87  Identities=11%  Similarity=0.015  Sum_probs=43.1

Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh----
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ----  361 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----  361 (490)
                      |++++..++|.+++...-+.-....+........-|-.|.+.++...+.++-.......-.-+..-|..++..|..    
T Consensus        90 IQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~VLl  169 (309)
T PF07163_consen   90 IQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHVLL  169 (309)
T ss_pred             HHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHHHh
Confidence            4555566666665554333333222333444444455556666666666655555543222223335555544433    


Q ss_pred             -cCCHHHHHHHH
Q 011236          362 -KGMIEKADAVL  372 (490)
Q Consensus       362 -~g~~~~A~~~~  372 (490)
                       .|.+++|+++.
T Consensus       170 PLG~~~eAeelv  181 (309)
T PF07163_consen  170 PLGHFSEAEELV  181 (309)
T ss_pred             ccccHHHHHHHH
Confidence             46666665554

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=84.87  E-value=47  Score=33.59  Aligned_cols=373  Identities=15%  Similarity=0.075  Sum_probs=179.8

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCC----CChhhHHHH-HHHHHhhcCHHHHHHHHHHccccC-----CChhHHHHH
Q 011236           74 RVIRQLRSRKRFKHALQVSEWMSGQGLA----FSVHDHAVQ-LDLIGKVRGLESAETYFNSLNDED-----KVDKLYGAL  143 (490)
Q Consensus        74 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~l-~~~~~~~~~~~~A~~~~~~~~~~~-----p~~~~~~~l  143 (490)
                      .++..+.+.+. ..|...+++.++.--.    +-...+..+ +..+...++...|.+.++.+....     |...++-.+
T Consensus       105 ll~~i~~~~~~-~~a~~~l~~~I~~~~~~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~~~v~~~l  183 (608)
T PF10345_consen  105 LLARIYFKTNP-KAALKNLDKAIEDSETYGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPAVFVLASL  183 (608)
T ss_pred             HHHHHHHhcCH-HHHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHHHHHHHHH
Confidence            34455555554 4488888887664322    222223333 223333479999999988765532     334455555


Q ss_pred             HHHHH--hcCChhHHHHHHHHHHhcCC---------CCCcchHHHHHHHHH--hcCCcCcHHHHHHHHHH-------CC-
Q 011236          144 LNCYV--REGLVDESLSLMQKMKEMGS---------FGSALNYNGIMCLYT--NTGQHEKIPDVLLDMKE-------NG-  202 (490)
Q Consensus       144 i~~~~--~~g~~~~a~~~~~~m~~~~~---------~p~~~~~~~l~~~~~--~~~~~~~a~~~~~~m~~-------~~-  202 (490)
                      +.+..  +.+..+++.+.++++.....         .|-..+|..+++.++  ..|+++.+...++++.+       .. 
T Consensus       184 ~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq~~~~~~~~~~~  263 (608)
T PF10345_consen  184 SEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQQFLDEIKKSPS  263 (608)
T ss_pred             HHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCcc
Confidence            55544  45667778888877743321         234556666766554  56666676665554432       11 


Q ss_pred             C---C-------------------CCHHHH---------HHHHH--HHhccCChHHHHHHHHHHHh---C-----C-CCC
Q 011236          203 V---P-------------------PDNFSY---------RICIN--SYGARSELSSMENVLQEMES---Q-----S-HIS  240 (490)
Q Consensus       203 ~---~-------------------p~~~~~---------~~li~--~~~~~g~~~~a~~~~~~~~~---~-----~-~~~  240 (490)
                      .   .                   |....|         .-++.  ..+..+..+.|.+++++...   +     . ...
T Consensus       264 w~~~~~d~~i~l~~~~~~~~~~~~~~~f~wl~~~~l~~L~y~lS~l~~~~~~~~~ks~k~~~k~l~~i~~~~~~~~~~~~  343 (608)
T PF10345_consen  264 WPSWDEDGSIPLNIGEGSSNSGGTPLVFSWLPKEELYALVYFLSGLHNLYKGSMDKSEKFLEKALKQIEKLKIKSPSAPS  343 (608)
T ss_pred             CCCcCCCeeEEeecccccccCCCceeEEeecCHHHHHHHHHHHHHHHHhhccCchHHHHHHHHHHHHHHHhhccCCCCCC
Confidence            0   0                   111111         11111  22334444455555554331   0     1 111


Q ss_pred             CCH------HHHHH---------HHHHHHHcCCHHHHHHHHHHHhhhhccCCC-------hhhHHHHHHHHHhcCChhHH
Q 011236          241 MDW------GTYST---------VANYYIIAGLKEKAIIYLKKCEDIVSKSKD-------ALGYNHLISHYASLGNKDEM  298 (490)
Q Consensus       241 ~~~------~~~~~---------li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~~l~~~~~~~~~~~~a  298 (490)
                      .+.      ..+..         .+-..+-.+++..|...++.+.......|+       ...+....-.+...|+.+.|
T Consensus       344 ~sl~~~~~~~~~~~~l~~~~~~y~~~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~~yL~gl~~q~~g~l~~A  423 (608)
T PF10345_consen  344 ESLSEASERIQWLRYLQCYLLFYQIWCNFIRGDWSKATQELEFMRQLCQRSPSKLYESLYPLLHYLLGLYYQSTGDLEAA  423 (608)
T ss_pred             cCHHHHHHhHHHHHHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcCccchhhhhhHHHHHHHHHHHHHcCCHHHH
Confidence            111      11111         122334578999999999998865432122       22222233334457999999


Q ss_pred             HHHHH--------HHHHhcCCCChhhHHHH--HHHHHhc--CCHHH--HHHHHHHHHhc-CCCC--CchhHHH-HHHHHH
Q 011236          299 MKFWG--------LQKIKCKKQLNRDYITM--LGSLVKI--GELEE--AEKMLEEWELS-CYCY--DFRVPNI-ILLGYS  360 (490)
Q Consensus       299 ~~~~~--------~~~~~~~~~~~~~~~~l--~~~~~~~--~~~~~--a~~~~~~~~~~-~~~~--~~~~~~~-l~~~~~  360 (490)
                      ...|.        .....+...+...+..+  +-.+...  ....+  +.++++.+... .-.|  +..++.. ++.++.
T Consensus       424 ~~~y~~~~~~~~~~~~~~~~~~El~ila~LNl~~I~~~~~~~~~~~~~~~~l~~~i~p~~~~~~~~~~~~a~~~~~~~~~  503 (608)
T PF10345_consen  424 LYQYQKPRFLLCEAANRKSKFRELYILAALNLAIILQYESSRDDSESELNELLEQIEPLCSNSPNSYNRTAYCLVLATYN  503 (608)
T ss_pred             HHHHhhhHHhhhhhhccCCcchHHHHHHHHHHHHHhHhhcccchhhhHHHHHHHhcCccccCCccHHHHHHHHHHHHHHh
Confidence            99997        33333333333333321  1112222  22223  66777766542 1122  2223333 333333


Q ss_pred             hcCC--HHHHHHHHHHHHH-----cCCC-CCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc--hhhHH--
Q 011236          361 QKGM--IEKADAVLKEIVK-----KGKT-PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK--PSLVS--  428 (490)
Q Consensus       361 ~~g~--~~~A~~~~~~m~~-----~~~~-p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~--~~~~~--  428 (490)
                      ....  ..++...+.+..+     .+.. --..+++.+..-+. .|+..+.............    -.||  ...|.  
T Consensus       504 ~~~~~~~ne~k~~l~~~L~~~~~~~~n~~l~~~~L~lm~~~lf-~~~~~e~~~~s~~a~~~A~----k~~d~~~~LW~~v  578 (608)
T PF10345_consen  504 TFEPFSSNEAKRHLQEALKMANNKLGNSQLLAILLNLMGHRLF-EGDVGEQAKKSARAFQLAK----KSSDYSDQLWHLV  578 (608)
T ss_pred             hCCccccHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHHHHH----hhhhhhhHHHHHH
Confidence            2221  2244443332222     1111 11123343333444 6777776666555444221    1122  24453  


Q ss_pred             ---HHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          429 ---SILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       429 ---~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                         .+...+...|+.++|.....+...
T Consensus       579 ~~~~l~~~~~~~G~~~ka~~~~~~~~~  605 (608)
T PF10345_consen  579 ASGMLADSYEVQGDRDKAEEARQQLDR  605 (608)
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHH
Confidence               333457778999999988877653

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=84.48  E-value=53  Score=33.85  Aligned_cols=226  Identities=12%  Similarity=0.046  Sum_probs=114.1

Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCcc-------hHHHHHH-HHHhcCCcCcHHHHHHHHHHC----CCCCCHHHHHHHHH
Q 011236          148 VREGLVDESLSLMQKMKEMGSFGSAL-------NYNGIMC-LYTNTGQHEKIPDVLLDMKEN----GVPPDNFSYRICIN  215 (490)
Q Consensus       148 ~~~g~~~~a~~~~~~m~~~~~~p~~~-------~~~~l~~-~~~~~~~~~~a~~~~~~m~~~----~~~p~~~~~~~li~  215 (490)
                      ....++++|..++.+....-..|+..       .|+.|-. .....|+++++.++.+.....    -..+....+..+..
T Consensus       426 ~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~~~  505 (894)
T COG2909         426 ASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLGE  505 (894)
T ss_pred             HHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhhhH
Confidence            45788899998888876653333332       2333322 223567888888887776553    12345556667777


Q ss_pred             HHhccCChHHHHHHHHHHHhCCCCCCCHHHHH---HH--HHHHHHcCC--HHHHHHHHHHHhhhhccCC-----ChhhHH
Q 011236          216 SYGARSELSSMENVLQEMESQSHISMDWGTYS---TV--ANYYIIAGL--KEKAIIYLKKCEDIVSKSK-----DALGYN  283 (490)
Q Consensus       216 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~---~l--i~~~~~~~~--~~~a~~~~~~~~~~~~~~~-----~~~~~~  283 (490)
                      +..-.|++++|..+..+.. +..-..+...+.   .+  ...+...|+  +.+.+..|...........     -..++.
T Consensus       506 a~~~~G~~~~Al~~~~~a~-~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r~  584 (894)
T COG2909         506 AAHIRGELTQALALMQQAE-QMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIRA  584 (894)
T ss_pred             HHHHhchHHHHHHHHHHHH-HHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHH
Confidence            7778899999888776665 322122323332   22  223455563  3333344444332211101     123344


Q ss_pred             HHHHHHHh-cCChhHHHHHHHHHHHhcCCCChhh--HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCch----hHHHHH
Q 011236          284 HLISHYAS-LGNKDEMMKFWGLQKIKCKKQLNRD--YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFR----VPNIIL  356 (490)
Q Consensus       284 ~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~----~~~~l~  356 (490)
                      .+..++.+ .+...++..-++......+.|-...  +..|+......|+.++|...++++......+...    .-...+
T Consensus       585 ~ll~~~~r~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a~~~~v  664 (894)
T COG2909         585 QLLRAWLRLDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLAAAYKV  664 (894)
T ss_pred             HHHHHHHHHhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHHHHHHh
Confidence            44444443 1111222222221111111122222  2366777778899999998888877654333211    111122


Q ss_pred             HH--HHhcCCHHHHHHHHHH
Q 011236          357 LG--YSQKGMIEKADAVLKE  374 (490)
Q Consensus       357 ~~--~~~~g~~~~A~~~~~~  374 (490)
                      ..  ....|+.+.+.....+
T Consensus       665 ~~~lwl~qg~~~~a~~~l~~  684 (894)
T COG2909         665 KLILWLAQGDKELAAEWLLK  684 (894)
T ss_pred             hHHHhcccCCHHHHHHHHHh
Confidence            22  3446777766665544

>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=84.47  E-value=13  Score=30.79  Aligned_cols=72  Identities=15%  Similarity=0.148  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHccccC--CChhHHHHHHHHHHhcCChhHHHHHHHHHHhc---CCCCCcchHHHHHHHHHhcCCcCcHH
Q 011236          120 LESAETYFNSLNDED--KVDKLYGALLNCYVREGLVDESLSLMQKMKEM---GSFGSALNYNGIMCLYTNTGQHEKIP  192 (490)
Q Consensus       120 ~~~A~~~~~~~~~~~--p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~---~~~p~~~~~~~l~~~~~~~~~~~~a~  192 (490)
                      -+.|++.|-.+...+  -++.....|...|. ..+.++++.++.+..+.   +-.+|+..+.+|+..+.+.|+++.|.
T Consensus       122 d~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  122 DQEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            456777777776665  25555566665555 67788888888887664   33668888899999999988888774

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=84.46  E-value=7.6  Score=34.68  Aligned_cols=54  Identities=15%  Similarity=0.048  Sum_probs=37.3

Q ss_pred             HHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          288 HYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       288 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      -|.+.|.+++|++.|...+...+ -+..++..-..+|.+...+..|+.-......
T Consensus       106 ~yFKQgKy~EAIDCYs~~ia~~P-~NpV~~~NRA~AYlk~K~FA~AE~DC~~Aia  159 (536)
T KOG4648|consen  106 TYFKQGKYEEAIDCYSTAIAVYP-HNPVYHINRALAYLKQKSFAQAEEDCEAAIA  159 (536)
T ss_pred             hhhhccchhHHHHHhhhhhccCC-CCccchhhHHHHHHHHHHHHHHHHhHHHHHH
Confidence            47777888888888776665543 4667777777777777777777666555544

>KOG0403 consensus Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms]

Probab=84.35  E-value=36  Score=31.88  Aligned_cols=24  Identities=21%  Similarity=0.236  Sum_probs=14.2

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHH
Q 011236          141 GALLNCYVREGLVDESLSLMQKMK  164 (490)
Q Consensus       141 ~~li~~~~~~g~~~~a~~~~~~m~  164 (490)
                      |-.+.-|...|+..+|.+..+++.
T Consensus       218 n~~l~eyv~~getrea~rciR~L~  241 (645)
T KOG0403|consen  218 NGNLIEYVEIGETREACRCIRELG  241 (645)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHhC
Confidence            344555666666666666665553

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=84.31  E-value=1.3  Score=23.74  Aligned_cols=16  Identities=31%  Similarity=0.482  Sum_probs=6.3

Q ss_pred             hhcCHHHHHHHHHHcc
Q 011236          116 KVRGLESAETYFNSLN  131 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~  131 (490)
                      +.|++++|.+.|+.+.
T Consensus        12 ~~g~~~~A~~~~~~~~   27 (33)
T PF13174_consen   12 KLGDYDEAIEYFQRLI   27 (33)
T ss_dssp             HHCHHHHHHHHHHHHH
T ss_pred             HccCHHHHHHHHHHHH
Confidence            3334444444443333

>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane

Probab=84.07  E-value=3.8  Score=27.71  Aligned_cols=48  Identities=17%  Similarity=0.165  Sum_probs=34.0

Q ss_pred             ccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHH
Q 011236          396 DKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFV  447 (490)
Q Consensus       396 ~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~  447 (490)
                      ...+.++|+..|+.+++..    .-.|+. .++..++.+++..|++++++++-
T Consensus        18 ~~~~~~~Al~~W~~aL~k~----~~~~~rf~~lG~l~qA~~e~Gkyr~~L~fA   66 (80)
T PF10579_consen   18 HQNETQQALQKWRKALEKI----TDREDRFRVLGYLIQAHMEWGKYREMLAFA   66 (80)
T ss_pred             ccchHHHHHHHHHHHHhhc----CChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6777888888888888722    112222 57778888888888888877654

Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane

>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=84.03  E-value=14  Score=26.82  Aligned_cols=82  Identities=13%  Similarity=0.160  Sum_probs=49.5

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHH
Q 011236           81 SRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLM  160 (490)
Q Consensus        81 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  160 (490)
                      .....++|..+.+++...+. ....+...-+..+.+.|++++|  +..-.....||...|-+|..  .+.|--+++...+
T Consensus        18 G~HcH~EA~tIa~wL~~~~~-~~E~v~lIr~~sLmNrG~Yq~A--Ll~~~~~~~pdL~p~~AL~a--~klGL~~~~e~~l   92 (116)
T PF09477_consen   18 GHHCHQEANTIADWLEQEGE-MEEVVALIRLSSLMNRGDYQEA--LLLPQCHCYPDLEPWAALCA--WKLGLASALESRL   92 (116)
T ss_dssp             TTT-HHHHHHHHHHHHHTTT-THHHHHHHHHHHHHHTT-HHHH--HHHHTTS--GGGHHHHHHHH--HHCT-HHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHhhHHHHHH--HHhcccCCCccHHHHHHHHH--HhhccHHHHHHHH
Confidence            45667888888888888873 2233333345566788888888  33334333477777765543  4777777887777


Q ss_pred             HHHHhcC
Q 011236          161 QKMKEMG  167 (490)
Q Consensus       161 ~~m~~~~  167 (490)
                      .++...|
T Consensus        93 ~rla~~g   99 (116)
T PF09477_consen   93 TRLASSG   99 (116)
T ss_dssp             HHHCT-S
T ss_pred             HHHHhCC
Confidence            7776554

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.

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=83.80  E-value=13  Score=30.00  Aligned_cols=62  Identities=21%  Similarity=0.250  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC-----------CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHH
Q 011236          366 EKADAVLKEIVKKGKTPTPNSWSIIAAGYADKN-----------NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWL  434 (490)
Q Consensus       366 ~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-----------~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~  434 (490)
                      ++|..-|++.+..++. ...++..+..+|...+           .+++|.+.|+++.+       ..|+..+|..-+...
T Consensus        52 edAisK~eeAL~I~P~-~hdAlw~lGnA~ts~A~l~~d~~~A~~~F~kA~~~FqkAv~-------~~P~ne~Y~ksLe~~  123 (186)
T PF06552_consen   52 EDAISKFEEALKINPN-KHDALWCLGNAYTSLAFLTPDTAEAEEYFEKATEYFQKAVD-------EDPNNELYRKSLEMA  123 (186)
T ss_dssp             HHHHHHHHHHHHH-TT--HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH-------H-TT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCc-hHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHh-------cCCCcHHHHHHHHHH
Confidence            4444444555544322 2345666666654432           25566666666665       568888888877766


Q ss_pred             H
Q 011236          435 G  435 (490)
Q Consensus       435 ~  435 (490)
                      .
T Consensus       124 ~  124 (186)
T PF06552_consen  124 A  124 (186)
T ss_dssp             H
T ss_pred             H
Confidence            4

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=83.27  E-value=42  Score=31.79  Aligned_cols=125  Identities=10%  Similarity=0.033  Sum_probs=81.1

Q ss_pred             HhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCH
Q 011236           41 SRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGL  120 (490)
Q Consensus        41 ~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  120 (490)
                      ..-...|+...+-.+++..+++....|+...+.+.|  +...|+++.+.+.+......- .....+...+++...+.|++
T Consensus       297 ~k~~~~gd~~aas~~~~~~lr~~~~~p~~i~l~~~i--~~~lg~ye~~~~~~s~~~~~~-~s~~~~~~~~~r~~~~l~r~  373 (831)
T PRK15180        297 TKQLADGDIIAASQQLFAALRNQQQDPVLIQLRSVI--FSHLGYYEQAYQDISDVEKII-GTTDSTLRCRLRSLHGLARW  373 (831)
T ss_pred             HHHhhccCHHHHHHHHHHHHHhCCCCchhhHHHHHH--HHHhhhHHHHHHHhhchhhhh-cCCchHHHHHHHhhhchhhH
Confidence            333445666666666777666555555554444443  446788888888877655432 34566777788888888899


Q ss_pred             HHHHHHHHHccccC-CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCC
Q 011236          121 ESAETYFNSLNDED-KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGS  168 (490)
Q Consensus       121 ~~A~~~~~~~~~~~-p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~  168 (490)
                      ++|..+-+-|.... .++.+........-..|-++++...|++....+.
T Consensus       374 ~~a~s~a~~~l~~eie~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~~  422 (831)
T PRK15180        374 REALSTAEMMLSNEIEDEEVLTVAAGSADALQLFDKSYHYWKRVLLLNP  422 (831)
T ss_pred             HHHHHHHHHHhccccCChhheeeecccHHHHhHHHHHHHHHHHHhccCC
Confidence            99988888887665 2444444433444456778888888888766543

>PRK09687 putative lyase; Provisional

Probab=82.77  E-value=34  Score=30.41  Aligned_cols=78  Identities=15%  Similarity=0.178  Sum_probs=33.5

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCH----HHHHHHHHHccccCCChhHHHHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGL----ESAETYFNSLNDEDKVDKLYGAL  143 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~A~~~~~~~~~~~p~~~~~~~l  143 (490)
                      |.......+..+...|. +.+...+..+.+.   .++..-...+.+++..|+.    .++...+..+...+++..+-...
T Consensus        36 d~~vR~~A~~aL~~~~~-~~~~~~l~~ll~~---~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~D~d~~VR~~A  111 (280)
T PRK09687         36 NSLKRISSIRVLQLRGG-QDVFRLAIELCSS---KNPIERDIGADILSQLGMAKRCQDNVFNILNNLALEDKSACVRASA  111 (280)
T ss_pred             CHHHHHHHHHHHHhcCc-chHHHHHHHHHhC---CCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhcCCCHHHHHHH
Confidence            44444444555544443 2233333333332   2444444455555555542    33444444443334444444444


Q ss_pred             HHHHHh
Q 011236          144 LNCYVR  149 (490)
Q Consensus       144 i~~~~~  149 (490)
                      +.++..
T Consensus       112 ~~aLG~  117 (280)
T PRK09687        112 INATGH  117 (280)
T ss_pred             HHHHhc
Confidence            444433

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=82.39  E-value=42  Score=31.11  Aligned_cols=95  Identities=12%  Similarity=0.071  Sum_probs=62.0

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHhcC--CCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHC---------CCCCC
Q 011236          138 KLYGALLNCYVREGLVDESLSLMQKMKEMG--SFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKEN---------GVPPD  206 (490)
Q Consensus       138 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~--~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~---------~~~p~  206 (490)
                      ..+.-+.+.|..+|+++.|++.|.+.+..-  .+-.+..|-.+|..-.-.|+|..+.....+..+.         -+++-
T Consensus       151 ra~~Dl~dhy~~cG~l~~Alr~YsR~RdYCTs~khvInm~ln~i~VSI~~~nw~hv~sy~~~A~st~~~~~~~~q~v~~k  230 (466)
T KOG0686|consen  151 RALEDLGDHYLDCGQLDNALRCYSRARDYCTSAKHVINMCLNLILVSIYMGNWGHVLSYISKAESTPDANENLAQEVPAK  230 (466)
T ss_pred             HHHHHHHHHHHHhccHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHhCchhhhhHHHhcCcc
Confidence            456778888999999999999999865431  1113445666777777788988888777776654         13334


Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHH
Q 011236          207 NFSYRICINSYGARSELSSMENVLQEME  234 (490)
Q Consensus       207 ~~~~~~li~~~~~~g~~~~a~~~~~~~~  234 (490)
                      ...+..+.+.+.+  ++..|.+.|-...
T Consensus       231 l~C~agLa~L~lk--kyk~aa~~fL~~~  256 (466)
T KOG0686|consen  231 LKCAAGLANLLLK--KYKSAAKYFLLAE  256 (466)
T ss_pred             hHHHHHHHHHHHH--HHHHHHHHHHhCC
Confidence            4445555544443  6676666655443

>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=82.33  E-value=3.1  Score=22.50  Aligned_cols=31  Identities=10%  Similarity=-0.070  Sum_probs=25.2

Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      .+|..+...+...|++++|...|++..+..|
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~   32 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP   32 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            3567788888999999999999998876544

...

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=81.52  E-value=64  Score=32.64  Aligned_cols=89  Identities=19%  Similarity=0.192  Sum_probs=42.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC-CCChhhHHHHHHHHHh-
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK-KQLNRDYITMLGSLVK-  326 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~-  326 (490)
                      ....+.-.|+++.|++++-...  ... .+.+++...+..|.-.+-.+...   ..+..... .|....+..||..|++ 
T Consensus       264 Yf~~LlLtgqFE~AI~~L~~~~--~~~-~dAVH~AIaL~~~gLL~~~~~~~---~~lls~~~~~~~~ln~arLI~~Y~~~  337 (613)
T PF04097_consen  264 YFQVLLLTGQFEAAIEFLYRNE--FNR-VDAVHFAIALAYYGLLRVSDSSS---APLLSVDPGDPPPLNFARLIGQYTRS  337 (613)
T ss_dssp             HHHHHHHTT-HHHHHHHHHT----T-H-HHHHHHHHHHHHTT---------------------------HHHHHHHHHHT
T ss_pred             HHHHHHHHhhHHHHHHHHHhhc--cCc-ccHHHHHHHHHHcCCCCCCCccc---cceeeecCCCCCCcCHHHHHHHHHHH
Confidence            4456777899999999887711  222 45566655555443322222211   22222211 1223668888888876 


Q ss_pred             --cCCHHHHHHHHHHHHhc
Q 011236          327 --IGELEEAEKMLEEWELS  343 (490)
Q Consensus       327 --~~~~~~a~~~~~~~~~~  343 (490)
                        ..+..+|.+.+-.+...
T Consensus       338 F~~td~~~Al~Y~~li~~~  356 (613)
T PF04097_consen  338 FEITDPREALQYLYLICLF  356 (613)
T ss_dssp             TTTT-HHHHHHHHHGGGGS
T ss_pred             HhccCHHHHHHHHHHHHHc
Confidence              45777888887766553

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.

>PHA02875 ankyrin repeat protein; Provisional

Probab=81.41  E-value=50  Score=31.37  Aligned_cols=15  Identities=13%  Similarity=0.060  Sum_probs=7.4

Q ss_pred             HHhhcCHHHHHHHHH
Q 011236          114 IGKVRGLESAETYFN  128 (490)
Q Consensus       114 ~~~~~~~~~A~~~~~  128 (490)
                      .+..|+.+.+..+++
T Consensus         9 A~~~g~~~iv~~Ll~   23 (413)
T PHA02875          9 AILFGELDIARRLLD   23 (413)
T ss_pred             HHHhCCHHHHHHHHH
Confidence            334455555555444

>PF07575 Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR011502 This is a family of nucleoporins conserved from yeast to human

Probab=81.10  E-value=63  Score=32.33  Aligned_cols=145  Identities=12%  Similarity=0.050  Sum_probs=58.6

Q ss_pred             cCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHH------H----HH-HHHHHhhhhccCCChhhHHHHHHH
Q 011236          220 RSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEK------A----II-YLKKCEDIVSKSKDALGYNHLISH  288 (490)
Q Consensus       220 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~------a----~~-~~~~~~~~~~~~~~~~~~~~l~~~  288 (490)
                      .|++..+++....+-      .+..+-..+.+.+...|-.+.      .    .+ ++-.--..-.  .+...|..-+..
T Consensus       310 ~~d~~~vL~~~~~~~------~~~w~aahladLl~~~g~L~~~~~~~~~~~~lre~~ll~YA~~L~--s~~~lW~vai~y  381 (566)
T PF07575_consen  310 EGDIESVLKEISSLF------DDWWFAAHLADLLEHKGLLEDSEQEDFGGSSLREYLLLEYASSLM--SHHSLWQVAIGY  381 (566)
T ss_dssp             TS--GGGHHHHHHH--------HHHHHHHHHHHHHHTTSS--SS-----TS-HHHHHHHHHHHHHH--T-TTTHHHHHHH
T ss_pred             ccCHHHHHHHHHHHc------cchhHHHHHHHHHHhcCccccccccccccccHHHHHHHHHHHHHh--cCcchHHHHHHH
Confidence            577777777776663      232333345555555555441      0    00 0000000011  233334444444


Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 011236          289 YASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKA  368 (490)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  368 (490)
                      +...++..  ....+..+.+-+..+.....-++..|.+.|-.+.+.++.+.+-..-.  ...-|..-+..+.++|+....
T Consensus       382 L~~c~~~g--~~~i~~lL~~~p~~t~~~~~k~l~iC~~~~L~~~a~~I~~~~~~~~~--~~~~~g~AL~~~~ra~d~~~v  457 (566)
T PF07575_consen  382 LSSCPDEG--RERIEELLPRVPLDTNDDAEKLLEICAELGLEDVAREICKILGQRLL--KEGRYGEALSWFIRAGDYSLV  457 (566)
T ss_dssp             HHS-SSS---HHHHHHHGGG----SHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHH--HHHHHHHHHHHHH--------
T ss_pred             HHHCChhh--HHHHHHHHhhCCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH--HCCCHHHHHHHHHHCCCHHHH
Confidence            44333222  45555555555556666677788888888888888887776654311  122344455556666666555


Q ss_pred             HHHHHHHH
Q 011236          369 DAVLKEIV  376 (490)
Q Consensus       369 ~~~~~~m~  376 (490)
                      ..+...+.
T Consensus       458 ~~i~~~ll  465 (566)
T PF07575_consen  458 TRIADRLL  465 (566)
T ss_dssp             --------
T ss_pred             HHHHHHHH
Confidence            55544444

Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [, , ]. ; PDB: 3F3F_D 3F3P_G 3F3G_G 3EWE_B.

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=80.90  E-value=38  Score=29.68  Aligned_cols=19  Identities=11%  Similarity=0.165  Sum_probs=9.6

Q ss_pred             HHHHHHHcCCCHHHHHHHH
Q 011236          429 SILDWLGDNRDVEEVEAFV  447 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~~~  447 (490)
                      -++..+.+.|.+.+|..+.
T Consensus       130 Kli~l~y~~~~YsdalalI  148 (421)
T COG5159         130 KLIYLLYKTGKYSDALALI  148 (421)
T ss_pred             HHHHHHHhcccHHHHHHHH
Confidence            3444455555555555443

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=80.72  E-value=74  Score=32.88  Aligned_cols=223  Identities=13%  Similarity=0.052  Sum_probs=123.2

Q ss_pred             HhcCCcCcHHHHHHHHHHCCCCCCH----H---HHHHHHH-HHhccCChHHHHHHHHHHHh---CCCCCCCHHHHHHHHH
Q 011236          183 TNTGQHEKIPDVLLDMKENGVPPDN----F---SYRICIN-SYGARSELSSMENVLQEMES---QSHISMDWGTYSTVAN  251 (490)
Q Consensus       183 ~~~~~~~~a~~~~~~m~~~~~~p~~----~---~~~~li~-~~~~~g~~~~a~~~~~~~~~---~~~~~~~~~~~~~li~  251 (490)
                      ....++.+|..+..+....-..|+.    .   .++.+-. .....|+++.|.++.+....   .....+....+..+..
T Consensus       426 ~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~~~  505 (894)
T COG2909         426 ASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLGE  505 (894)
T ss_pred             HHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhhhH
Confidence            3567889999998887654222222    1   2333322 22346888998888776652   2223355677777888


Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccCCChhhH---HHHHH--HHHhcCChh--HHHHHHHHHHHhcC------CCChhhHH
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKSKDALGY---NHLIS--HYASLGNKD--EMMKFWGLQKIKCK------KQLNRDYI  318 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~---~~l~~--~~~~~~~~~--~a~~~~~~~~~~~~------~~~~~~~~  318 (490)
                      +..-.|++++|..+..+..+.... -+...+   ..+..  .+...|+..  +....+........      .+-..++.
T Consensus       506 a~~~~G~~~~Al~~~~~a~~~a~~-~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r~  584 (894)
T COG2909         506 AAHIRGELTQALALMQQAEQMARQ-HDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIRA  584 (894)
T ss_pred             HHHHhchHHHHHHHHHHHHHHHHH-cccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHH
Confidence            888999999999998887765443 444433   33322  234456322  23333332222211      12223455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcC--CCCCc--hh--HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC----CHHHHH
Q 011236          319 TMLGSLVKIGELEEAEKMLEEWELSC--YCYDF--RV--PNIILLGYSQKGMIEKADAVLKEIVKKGKTP----TPNSWS  388 (490)
Q Consensus       319 ~l~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~--~~--~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p----~~~~~~  388 (490)
                      .+..++.+   .+.+..-.....+.|  ..|..  ..  +..|+..+...|+.++|...++++......+    +..+-.
T Consensus       585 ~ll~~~~r---~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a~~  661 (894)
T COG2909         585 QLLRAWLR---LDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLAAA  661 (894)
T ss_pred             HHHHHHHH---HhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHHHH
Confidence            55555555   333332222222221  12221  12  2357777888999999999999887653333    322222


Q ss_pred             HHHH--HHhccCCHHHHHHHHHH
Q 011236          389 IIAA--GYADKNNMEKAFECMKE  409 (490)
Q Consensus       389 ~l~~--~~~~~~~~~~a~~~~~~  409 (490)
                      ..+.  .....|+...+.....+
T Consensus       662 ~~v~~~lwl~qg~~~~a~~~l~~  684 (894)
T COG2909         662 YKVKLILWLAQGDKELAAEWLLK  684 (894)
T ss_pred             HHhhHHHhcccCCHHHHHHHHHh
Confidence            2222  33467888888777766

>PF07163 Pex26: Pex26 protein; InterPro: IPR010797 This family consists of Pex26 and related mammalian proteins

Probab=80.10  E-value=24  Score=30.77  Aligned_cols=87  Identities=15%  Similarity=0.097  Sum_probs=43.9

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccC--CChhHHHHHHHHHH---
Q 011236           74 RVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDED--KVDKLYGALLNCYV---  148 (490)
Q Consensus        74 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~li~~~~---  148 (490)
                      .=|.+++..++|.+++...-+.-+..-+..+.+...-|-.|.+.+.+..+.++-..-.+..  .+..-|.+++..|.   
T Consensus        88 vGIQALAEmnrWreVLsWvlqyYq~pEklPpkIleLCILLysKv~Ep~amlev~~~WL~~p~Nq~lp~y~~vaELyLl~V  167 (309)
T PF07163_consen   88 VGIQALAEMNRWREVLSWVLQYYQVPEKLPPKILELCILLYSKVQEPAAMLEVASAWLQDPSNQSLPEYGTVAELYLLHV  167 (309)
T ss_pred             hhHHHHHHHhhHHHHHHHHHHHhcCcccCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhCcccCCchhhHHHHHHHHHHH
Confidence            3355666666666655544333333224455555555666666666666655554433321  12222544444333   


Q ss_pred             --hcCChhHHHHHH
Q 011236          149 --REGLVDESLSLM  160 (490)
Q Consensus       149 --~~g~~~~a~~~~  160 (490)
                        =.|.+++|+++.
T Consensus       168 LlPLG~~~eAeelv  181 (309)
T PF07163_consen  168 LLPLGHFSEAEELV  181 (309)
T ss_pred             HhccccHHHHHHHH
Confidence              356666666555

Pex26 is a type II peroxisomal membrane protein that recruits Pex6-Pex1 complexes to peroxisomes []. Mutations in Pex26 can lead to human disorders [].; GO: 0032403 protein complex binding, 0045046 protein import into peroxisome membrane, 0005779 integral to peroxisomal membrane

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	490
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	5e-12
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	4e-07
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	3e-06
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	1e-05
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	1e-04
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	4e-04

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 67.5 bits (163), Expect = 5e-12
 Identities = 36/250 (14%), Positives = 80/250 (32%), Gaps = 16/250 (6%)

Query: 140 YGALLNCYVREGLVDESLSLMQKMKEMGSFGSALN---YNGIMCLYTNTGQHEKIPDVLL 196
             A   C +    +  +  L+            L    YN +M  +   G  +++  VL 
Sbjct: 130 LLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLF 189

Query: 197 DMKENGVPPDNFSYRICINSYGARSELS-SMENVLQEMESQSHISMDWGTYSTVANYYII 255
            +K+ G+ PD  SY   +   G + + + ++E  L++M  +        T   ++     
Sbjct: 190 MVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDR- 248

Query: 256 AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQK---IKCKKQ 312
                KA+  +K    +  +    +  + L+    +   +    K     K      +KQ
Sbjct: 249 -ATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQ 307

Query: 313 LNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVL 372
           L+ +       L     +   EK     +   +              +    + +    L
Sbjct: 308 LHME-------LASRVCVVSVEKPTLPSKEVKHARKTLKTLRDQWEKALCRALRETKNRL 360

Query: 373 KEIVKKGKTP 382
           +  V +G+  
Sbjct: 361 EREVYEGRFS 370

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 51.7 bits (122), Expect = 4e-07
 Identities = 28/212 (13%), Positives = 65/212 (30%), Gaps = 7/212 (3%)

Query: 49  PDVSLTPVLDQWVLE-GQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDH 107
               +   L+    +  +   E +L R++++   +         S   S   L+      
Sbjct: 71  LSKQMAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRL 130

Query: 108 AVQLDLIGKVRGLESAETYFNSLNDEDKVDK-----LYGALLNCYVREGLVDESLSLMQK 162
                       L  A       + + +  K     +Y A++  + R+G   E + ++  
Sbjct: 131 LAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFM 190

Query: 163 MKEMGSFGSALNYNGIMCLYTNTGQHEK-IPDVLLDMKENGVPPDNFSYRICINSYGARS 221
           +K+ G     L+Y   +       Q    I   L  M + G+        + ++     +
Sbjct: 191 VKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRAT 250

Query: 222 ELSSMENVLQEMESQSHISMDWGTYSTVANYY 253
            L ++  V         +     T   + + Y
Sbjct: 251 VLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVY 282

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 46.3 bits (108), Expect = 2e-05
 Identities = 20/146 (13%), Positives = 43/146 (29%), Gaps = 3/146 (2%)

Query: 265 YLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSL 324
            L+ C     +S        L+       + D      G           +  +      
Sbjct: 78  CLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCC 137

Query: 325 VKIGELEEAEKMLEEWELSC---YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT 381
           +   +L  A  +L                + N ++LG++++G  ++   VL  +   G T
Sbjct: 138 LLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLT 197

Query: 382 PTPNSWSIIAAGYADKNNMEKAFECM 407
           P   S++        ++      E  
Sbjct: 198 PDLLSYAAALQCMGRQDQDAGTIERC 223

>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 = 63.7 bits (154), Expect = 8e-11
 Identities = 58/422 (13%), Positives = 132/422 (31%), Gaps = 126/422 (29%)

Query: 37  NNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSE--W 94
             L  +I P      + T   D       K+    +Q  +R+L   K +++ L V     
Sbjct: 203 QKLLYQIDP------NWTSRSDH--SSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254

Query: 95  MSGQGLAFSVH--------DHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNC 146
            +    AF++            V   L        S + +  +L   D+V  L    L+C
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT-PDEVKSLLLKYLDC 313

Query: 147 YVREGLVDESLS---LMQKMKEMGSFGSAL--------NYNGIMCLYTNTGQHEKIPDVL 195
             ++ L  E L+       +        ++        N+      + N  +   I +  
Sbjct: 314 RPQD-LPREVLTTNPRRLSI-----IAESIRDGLATWDNW-----KHVNCDKLTTIIESS 362

Query: 196 L------DMKEN----GVPPDNF---SYRICINSYGARSELSSMENVLQEMESQSHISMD 242
           L      + ++      V P +    +  + +         S +  V+ ++   S +   
Sbjct: 363 LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL--IWFDVIKSDVMVVVNKLHKYSLVEKQ 420

Query: 243 WGTYSTVANYYI----------IAGLKE--KAII--Y-LKKC---EDIVSKSKDALGYNH 284
               +      I          +       ++I+  Y + K    +D++    D   Y+H
Sbjct: 421 PKEST----ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476

Query: 285 LISHYASLGNKDEMMKF--------WGLQKIK--------CKKQLN--------RDYIT- 319
           +  H  ++ + + M  F        +  QKI+            LN        + YI  
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICD 536

Query: 320 -------MLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVL 372
                  ++ ++            L + E +  C  +   +++     +  ++ + +A+ 
Sbjct: 537 NDPKYERLVNAI---------LDFLPKIEENLICSKYT--DLL-----RIALMAEDEAIF 580

Query: 373 KE 374
           +E
Sbjct: 581 EE 582

>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 = 51.0 bits (121), Expect = 7e-07
 Identities = 66/516 (12%), Positives = 145/516 (28%), Gaps = 153/516 (29%)

Query: 28  YRAVKPVARNNLYSRISPLGDPDV--SLTPVLDQWVLE---GQKISELELQRVIRQLRSR 82
           Y+ +  V  +     +      DV      +L +  ++     K +     R+   L S+
Sbjct: 18  YKDILSVFEDAF---VDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK 74

Query: 83  -----KRF-KHALQVS-EWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSL-NDED 134
                ++F +  L+++ +++             ++ +               + L ND  
Sbjct: 75  QEEMVQKFVEEVLRINYKFLM----------SPIKTEQRQPSMMTRMYIEQRDRLYNDNQ 124

Query: 135 KVDKLYGALLNCYV-REGLVDESLSLMQKMKE--------MGSFG------SALNYNGIM 179
              K         V R     +    + +++         +   G             + 
Sbjct: 125 VFAKYN-------VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQ 177

Query: 180 CL------YTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEM 233
           C       + N       P+ +L+M +         Y+I  N     S      N+   +
Sbjct: 178 CKMDFKIFWLNLKN-CNSPETVLEMLQK------LLYQIDPNW---TSRSDHSSNIKLRI 227

Query: 234 ESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG 293
            S                      ++ +    LK         ++ L    L+     L 
Sbjct: 228 HS----------------------IQAELRRLLKS-----KPYENCL----LV-----LL 251

Query: 294 N---KDEMMKFWGLQKIKCK-------KQLNRDYITMLGSLVKIGEL------EEAEKML 337
           N         F     + CK       KQ+         + + +         +E + +L
Sbjct: 252 NVQNAKAWNAF----NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307

Query: 338 EEWELSCYCYDFRV------PNII-LLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSII 390
            ++ L C   D         P  + ++  S +  +   D        K  T       II
Sbjct: 308 LKY-LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT-------II 359

Query: 391 AAGYA--DKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLG-DNRDVEEV--EA 445
            +     +     K F+     L+V   +      P+++ S++ W      DV  V  + 
Sbjct: 360 ESSLNVLEPAEYRKMFD----RLSVFPPSA---HIPTILLSLI-WFDVIKSDVMVVVNKL 411

Query: 446 FVSSLKIKVQKRNMY--HALTEAHIRSGQEVDGLLE 479
              SL  K  K +     ++   ++    +++    
Sbjct: 412 HKYSLVEKQPKESTISIPSI---YLELKVKLENEYA 444

>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 = 50.6 bits (120), Expect = 1e-06
 Identities = 54/463 (11%), Positives = 124/463 (26%), Gaps = 134/463 (28%)

Query: 4   KLFSTIFNNKRN----FTKTNLE-----IFTR-AYRAVKPVARNNLY-SRISPL-GDPDV 51
           +LF T+ + +      F +  L      + +       +P     +Y  +   L  D   
Sbjct: 66  RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ- 124

Query: 52  SLTPVLDQWVLEGQKISELELQRVIRQLRSRKR-FKHALQVSEWMSGQG---LAFSV-HD 106
                    V   Q    L+L++ + +LR  K            + G G   +A  V   
Sbjct: 125 ---VFAKYNVSRLQPY--LKLRQALLELRPAKNVLIDG------VLGSGKTWVALDVCLS 173

Query: 107 HAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEM 166
           + VQ  +  K+        ++ +L + +  + +   L     +         +       
Sbjct: 174 YKVQCKMDFKI--------FWLNLKNCNSPETVLEMLQKLLYQ---------IDPNWTSR 216

Query: 167 GSFGSA--LNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSEL- 223
               S   L  + I        + +   + LL +        N       N++    ++ 
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL-------LNVQNAKAWNAFNLSCKIL 269

Query: 224 -----SSMENVLQEMESQSHISMD---WG-----TYSTVANYY----------------- 253
                  + + L    + +HIS+D            S +  Y                  
Sbjct: 270 LTTRFKQVTDFLSA-ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328

Query: 254 ----IIAGLKEKAIIY-------LKKCEDIVSKSKDALGYNHLISHYASLG--NKDE--- 297
               I   +++    +         K   I+  S + L        +  L          
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIP 388

Query: 298 ---MMKFWG----------LQKIKCKKQLNRD------YITMLGSLVKIGELEEAE---K 335
              +   W           + K+     + +        I  +   +K+    E      
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRS 448

Query: 336 MLEEWEL-SCYCYDFRVPNII------LLGY--SQKGMIEKAD 369
           +++ + +   +  D  +P  +       +G+        E+  
Sbjct: 449 IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMT 491

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 45.6 bits (107), Expect = 4e-05
 Identities = 54/347 (15%), Positives = 103/347 (29%), Gaps = 103/347 (29%)

Query: 183 TNTGQHE-KIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSME--NVLQEMESQSHI 239
             TG+H+ +  D+L   ++  V  DNF  +   +    +S LS  E  +++   ++ S  
Sbjct: 9   FETGEHQYQYKDILSVFEDAFV--DNFDCKDVQDM--PKSILSKEEIDHIIMSKDAVSGT 64

Query: 240 SMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK---SKDALGYNHLISHYASLGNKD 296
                         +           L K E++V K       + Y  L+S   +   + 
Sbjct: 65  ------------LRLF-------WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQP 105

Query: 297 EMM---------KFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY 347
            MM         + +   ++  K  ++R        L    +L +A   L          
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKYNVSR--------LQPYLKLRQALLELR--------- 148

Query: 348 DFRVPNIILLGYSQKGM--IEK---ADAVLKEIVKKGKTPTPNSWSIIAAGYADK----- 397
                N+++      G+    K   A  V      + K      W  +     +      
Sbjct: 149 --PAKNVLI-----DGVLGSGKTWVALDVCLSYKVQCKMDFKIFW--LNLKNCNSPETVL 199

Query: 398 ---NNMEKAFECMKEALAVHEEN-------------KFWRPKP---SLVSSILDWLGDNR 438
                +    +    + + H  N             +  + KP    L+  +L    + +
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL--VLL---NVQ 254

Query: 439 DVEEVEAFVSSLKIKVQKRN-----MYHALTEAHIRSGQEVDGLLES 480
           + +   AF  S KI +  R         A T  HI        L   
Sbjct: 255 NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis} Length = 378

 Score = 48.3 bits (115), Expect = 3e-06
 Identities = 46/338 (13%), Positives = 109/338 (32%), Gaps = 40/338 (11%)

Query: 111 LDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKM-KEMGSF 169
              I ++   +    Y++ +    ++   Y      Y     V E L  ++   K++   
Sbjct: 39  EQDIQQMEEDQDLLIYYSLMCFRHQLMLDYLEPGKTYGNRPTVTELLETIETPQKKLTGL 98

Query: 170 GSALNYNGIMCLYTNTGQH----------EKIPDVLLDMKENGVPPDNFSYRICINSYGA 219
               +         +  ++          EK    + D  E       F +++    Y  
Sbjct: 99  LKYYSLFFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKA----EFHFKVAEAYYHM 154

Query: 220 RSELSSMENVLQEMESQSHISMD----WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSK 275
           +    SM ++LQ ++   +  +       +   +A  Y      +KA+ +L+   ++   
Sbjct: 155 KQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMD 214

Query: 276 SKD----ALGYNHLISHYASLGNKDEMMKFWGLQK-IKCKKQLNRDYIT----MLGS-LV 325
            ++    A+   ++ + Y   G+    ++    QK  K  ++   D +      L   L 
Sbjct: 215 IQNDRFIAISLLNIANSYDRSGDDQMAVEH--FQKAAKVSREKVPDLLPKVLFGLSWTLC 272

Query: 326 KIGELEEAEKMLE-------EWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK 378
           K G+ ++A + +E             Y   F     +      +  I    +  ++  K 
Sbjct: 273 KAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEK--KN 330

Query: 379 GKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEE 416
                       AA +    + E+A    ++ L   E+
Sbjct: 331 LHAYIEACARSAAAVFESSCHFEQAAAFYRKVLKAQED 368

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis} Length = 378

 Score = 46.7 bits (111), Expect = 1e-05
 Identities = 33/237 (13%), Positives = 67/237 (28%), Gaps = 25/237 (10%)

Query: 207 NFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGT------YSTVANYYIIAGLKE 260
            F +++ ++         +   V + +E+                      Y        
Sbjct: 59  CFRHQLMLDYLEPGKTYGNRPTVTELLETIETPQKKLTGLLKYYSLFFRGMYEFDQKEYV 118

Query: 261 KAIIYLKKCEDIVSKSKDALG----YNHLISHYASLGNKDEMMKFW--GLQKIKCKKQLN 314
           +AI Y ++ E  +    D +     +  +   Y  +      M      L   +     +
Sbjct: 119 EAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYS 178

Query: 315 RDYITMLGSL----VKIGELEEAEKMLEEW-ELSCYCYDFRVPNIIL--LG--YSQKGMI 365
              I  L  +          ++A   LE   EL+    + R   I L  +   Y + G  
Sbjct: 179 IRTIQSLFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDD 238

Query: 366 EKA----DAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENK 418
           + A        K   +K     P     ++         +KAF+ ++E L       
Sbjct: 239 QMAVEHFQKAAKVSREKVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARS 295

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} Length = 383

 Score = 43.3 bits (102), Expect = 1e-04
 Identities = 22/191 (11%), Positives = 57/191 (29%), Gaps = 24/191 (12%)

Query: 245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD----ALGYNHLISHYASLGNKDEMMK 300
            +S  A  ++     E AI + +K   +    K          ++     S    ++ + 
Sbjct: 186 CHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIP 245

Query: 301 FWGLQK---IKCKKQLNRDYITMLGSL----VKIGELEEAEKMLE-------EWELSCYC 346
           +   ++   +  +  +          +     K+G++++A +          +     Y 
Sbjct: 246 Y--FKRAIAVFEESNILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYL 303

Query: 347 YDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTP-TPNSWSIIAAGYADKNNMEKAFE 405
            +F     +   Y      E        +  K       +    +A  Y ++ N +KA  
Sbjct: 304 SEF---EFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASA 360

Query: 406 CMKEALAVHEE 416
              +   V + 
Sbjct: 361 YFLKVEQVRQL 371

>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} Length = 307

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 28/233 (12%), Positives = 77/233 (33%), Gaps = 35/233 (15%)

Query: 246 YSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD----ALGYNHLISHYASLGNKDEMMKF 301
           Y+  A  +  A   E+A     +  +  + ++     A  +         L    E +++
Sbjct: 39  YAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQY 98

Query: 302 WGLQKIKCKKQLNR-----DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNI-- 354
              +      +          +   G L++  +L +A  + ++   + +  + R+     
Sbjct: 99  I-EKASVMYVENGTPDTAAMALDRAGKLMEPLDLSKAVHLYQQ-AAAVFENEERLRQAAE 156

Query: 355 ----ILLGYSQKGMIEKADAVLK---EIVKKGKTPTPNSWSIIAAG--YADKNNMEKAFE 405
                     ++   ++A A L+    + K+ +         IA       + +   A +
Sbjct: 157 LIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQK 216

Query: 406 CMKEALAVH-----EENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK 453
           C++E+ ++      E+         L+ +      D +D E++     S  + 
Sbjct: 217 CVRESYSIPGFSGSEDCAALE---DLLQAY-----DEQDEEQLLRVCRSPLVT 261

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	490
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.96
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.95
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.93
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.89
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.89
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.88
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.88
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.87
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.87
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.85
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.84
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.84
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.83
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.83
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.83
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.82
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.82
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.81
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.8
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.8
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.8
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.78
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.78
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.77
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.76
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.75
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.73
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.73
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.72
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.71
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.7
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.7
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.69
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.69
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.68
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.68
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.67
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.67
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.67
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.66
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.66
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.66
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.66
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.65
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.65
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.64
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.63
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.63
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.63
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.63
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.63
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.61
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.6
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.57
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.56
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.55
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.55
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.54
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.53
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.52
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.51
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.51
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.5
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.49
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.48
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.46
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.44
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.42
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.4
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.4
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.38
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.37
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.34
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.33
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.33
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.3
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.28
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.23
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.21
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.18
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.18
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.18
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.17
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.17
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.15
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	99.14
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.13
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.13
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.11
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.1
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.1
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.1
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.08
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.07
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.04
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.04
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.03
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.02
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.02
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.01
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.01
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.0
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.0
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.99
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.92
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.89
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.89
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.89
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.88
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.87
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.87
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.87
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.85
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.82
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.81
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.8
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.79
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.79
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.79
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.78
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.77
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.77
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.76
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.76
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.75
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.75
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.74
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.74
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.72
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.72
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.71
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.69
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.69
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.68
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.68
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.67
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.66
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.66
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.65
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.62
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.62
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.61
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.6
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.6
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.59
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.58
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.57
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.57
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.56
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.55
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.54
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.54
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.52
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.51
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.49
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.48
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.47
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.47
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.44
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.43
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.43
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.39
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.38
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.38
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.37
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.36
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.36
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.34
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.33
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.32
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.29
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.28
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.25
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.21
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.17
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.17
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.15
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.1
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.09
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.09
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.08
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.08
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.08
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.03
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.97
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.89
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.89
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.87
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.84
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.82
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.82
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.8
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.75
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.7
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.68
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.68
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.62
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.55
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.38
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.27
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.26
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.26
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.14
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	97.13
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.09
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.05
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.95
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.86
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.7
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	96.65
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.62
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.58
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.45
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	96.04
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.02
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.0
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.95
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.83
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.82
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.75
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.7
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.66
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	95.59
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.39
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	95.15
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.87
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.85
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	94.8
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	94.76
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	94.56
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	94.07
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	94.02
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	93.79
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.75
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	92.66
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	91.95
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	91.23
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	91.23
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	90.67
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	90.64
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	90.55
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	89.6
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	89.57
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	89.44
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	89.43
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	88.85
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	88.47
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	86.66
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	86.47
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	86.45
2p58_C	116	Putative type III secretion protein YSCG; type III	86.27
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	86.26
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	86.19
4g8k_A	337	2-5A-dependent ribonuclease; ankyrin-repeat domain	86.12
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	84.32
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	82.8
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	82.76
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	80.4

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=8.1e-41  Score=332.07  Aligned_cols=436  Identities=10%  Similarity=-0.031  Sum_probs=378.6

Q ss_pred             CCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011236           34 VARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDL  113 (490)
Q Consensus        34 ~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  113 (490)
                      ..|+.++..+.+.|++++++. +++++..  ..|+..++..++..|.+.|++++|..+|+.+...  ++++.++..++.+
T Consensus        85 ~~~~~~~~~~~~~g~~~~A~~-~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~  159 (597)
T 2xpi_A           85 DYLRLWRHDALMQQQYKCAAF-VGEKVLD--ITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYLAAFC  159 (597)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHH-HHHHHHH--HHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCchHHHH-HHHHHHh--hCCCchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHHHHHH
Confidence            447888899999999888887 7787773  4568889999999999999999999999988654  5688899999999


Q ss_pred             HHhhcCHHHHHHHHHHccccC-----------------CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHH
Q 011236          114 IGKVRGLESAETYFNSLNDED-----------------KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYN  176 (490)
Q Consensus       114 ~~~~~~~~~A~~~~~~~~~~~-----------------p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~  176 (490)
                      |.+.|++++|.++|+++....                 ++..+|+.++.+|.+.|++++|+++|++|.+.++. +...+.
T Consensus       160 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~-~~~~~~  238 (597)
T 2xpi_A          160 LVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAK-CYEAFD  238 (597)
T ss_dssp             HHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHH
T ss_pred             HHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCch-hhHHHH
Confidence            999999999999999543322                 24788999999999999999999999999887533 333333


Q ss_pred             HH--------------------------------------HHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHh
Q 011236          177 GI--------------------------------------MCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYG  218 (490)
Q Consensus       177 ~l--------------------------------------~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  218 (490)
                      .+                                      +..|.+.|++++|.++|+++.+.  +++..++..++.+|.
T Consensus       239 ~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~  316 (597)
T 2xpi_A          239 QLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL--EKSSDLLLCKADTLF  316 (597)
T ss_dssp             HHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG--GGCHHHHHHHHHHHH
T ss_pred             HHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC--CchHHHHHHHHHHHH
Confidence            22                                      44556778889999999998765  588999999999999


Q ss_pred             ccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHH
Q 011236          219 ARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEM  298 (490)
Q Consensus       219 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  298 (490)
                      +.|++++|.++|+++. +.+. .+..+++.++.+|.+.|++++|..+++++....+  .+..+|+.++.+|.+.|++++|
T Consensus       317 ~~g~~~~A~~~~~~~~-~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A  392 (597)
T 2xpi_A          317 VRSRFIDVLAITTKIL-EIDP-YNLDVYPLHLASLHESGEKNKLYLISNDLVDRHP--EKAVTWLAVGIYYLCVNKISEA  392 (597)
T ss_dssp             HTTCHHHHHHHHHHHH-HHCT-TCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCT--TSHHHHHHHHHHHHHTTCHHHH
T ss_pred             HhcCHHHHHHHHHHHH-HcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCc--ccHHHHHHHHHHHHHhccHHHH
Confidence            9999999999999998 5454 4778899999999999999999999999986554  6889999999999999999999


Q ss_pred             HHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011236          299 MKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      .++|+++....+ .+..+|..++.+|.+.|++++|.++|+++.+. .+.+..+|+.++.+|.+.|++++|.++|+++.+.
T Consensus       393 ~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  470 (597)
T 2xpi_A          393 RRYFSKSSTMDP-QFGPAWIGFAHSFAIEGEHDQAISAYTTAARL-FQGTHLPYLFLGMQHMQLGNILLANEYLQSSYAL  470 (597)
T ss_dssp             HHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT-TTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            999999988765 67889999999999999999999999999986 3457889999999999999999999999999987


Q ss_pred             CCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc--hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          379 GKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK--PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       379 ~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+. +..+|+.++..|.+.|++++|.++|+++.+..++ .+..|+  ..+|..++.+|.+.|++++|.++++++.+.+|.
T Consensus       471 ~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~  548 (597)
T 2xpi_A          471 FQY-DPLLLNELGVVAFNKSDMQTAINHFQNALLLVKK-TQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTN  548 (597)
T ss_dssp             CCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-SCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSC
T ss_pred             CCC-ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhc-cccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC
Confidence            655 8899999999999999999999999999984431 155787  689999999999999999999999999999998


Q ss_pred             -hhhhHHHHHHHHhcC--CcHHHHHHHHHhCC
Q 011236          457 -RNMYHALTEAHIRSG--QEVDGLLESMKADD  485 (490)
Q Consensus       457 -~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~  485 (490)
                       ..+|..++.+|.+.|  ++|.++++++.+..
T Consensus       549 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~  580 (597)
T 2xpi_A          549 DANVHTAIALVYLHKKIPGLAITHLHESLAIS  580 (597)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             ChHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC
Confidence             999999999999999  99999999998743

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.4e-37  Score=308.81  Aligned_cols=403  Identities=11%  Similarity=-0.001  Sum_probs=354.1

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHH
Q 011236           66 KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLN  145 (490)
Q Consensus        66 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~  145 (490)
                      .++...|+.++..+.+.|++++|+.+|+++....  |+..++..++.+|.+.|++++|..+|+.+....++..+++.++.
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~--p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~  158 (597)
T 2xpi_A           81 LSREDYLRLWRHDALMQQQYKCAAFVGEKVLDIT--GNPNDAFWLAQVYCCTGDYARAKCLLTKEDLYNRSSACRYLAAF  158 (597)
T ss_dssp             -CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGGGTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHccCchHHHHHHHHHHhhC--CCchHHHHHHHHHHHcCcHHHHHHHHHHHhccccchhHHHHHHH
Confidence            3678899999999999999999999999999654  57788899999999999999999999999776678999999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhc---------------CCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHH
Q 011236          146 CYVREGLVDESLSLMQKMKEM---------------GSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSY  210 (490)
Q Consensus       146 ~~~~~g~~~~a~~~~~~m~~~---------------~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~  210 (490)
                      +|.+.|++++|.++|+++...               +.+++..+|+.++.+|.+.|++++|.++|++|.+.+.. +...+
T Consensus       159 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~-~~~~~  237 (597)
T 2xpi_A          159 CLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAK-CYEAF  237 (597)
T ss_dssp             HHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHH
T ss_pred             HHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCch-hhHHH
Confidence            999999999999999953221               22345789999999999999999999999999885422 23333


Q ss_pred             H--------------------------------------HHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHH
Q 011236          211 R--------------------------------------ICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANY  252 (490)
Q Consensus       211 ~--------------------------------------~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  252 (490)
                      .                                      .++..|.+.|++++|.++|+++. +.  +++..+++.++.+
T Consensus       238 ~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~-~~--~~~~~~~~~l~~~  314 (597)
T 2xpi_A          238 DQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSIN-GL--EKSSDLLLCKADT  314 (597)
T ss_dssp             HHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTST-TG--GGCHHHHHHHHHH
T ss_pred             HHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhh-cC--CchHHHHHHHHHH
Confidence            2                                      23556778899999999999997 44  4889999999999


Q ss_pred             HHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHH
Q 011236          253 YIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEE  332 (490)
Q Consensus       253 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  332 (490)
                      |.+.|++++|..+|+++....+  .+..+++.++.++.+.|++++|..+++.+....+ .+..++..++..|.+.|++++
T Consensus       315 ~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~  391 (597)
T 2xpi_A          315 LFVRSRFIDVLAITTKILEIDP--YNLDVYPLHLASLHESGEKNKLYLISNDLVDRHP-EKAVTWLAVGIYYLCVNKISE  391 (597)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCT--TCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TSHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHhcCHHHHHHHHHHHHHcCc--ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCc-ccHHHHHHHHHHHHHhccHHH
Confidence            9999999999999999998765  6888999999999999999999999999986654 778899999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          333 AEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       333 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      |.++|+++.+. .+.+..+|+.++.+|.+.|++++|.++|+++.+.++. +..+|..++.+|.+.|++++|.++|+++.+
T Consensus       392 A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  469 (597)
T 2xpi_A          392 ARRYFSKSSTM-DPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQG-THLPYLFLGMQHMQLGNILLANEYLQSSYA  469 (597)
T ss_dssp             HHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTT-CSHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999886 2346779999999999999999999999999987654 889999999999999999999999999998


Q ss_pred             hhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhc------ccc--hhhhHHHHHHHHhcC--CcHHHHHHHHH
Q 011236          413 VHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK------VQK--RNMYHALTEAHIRSG--QEVDGLLESMK  482 (490)
Q Consensus       413 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~------~~~--~~~~~~l~~~~~~~g--~~a~~~~~~m~  482 (490)
                      ..      ..+..+|..++..|.+.|++++|.++|+++.+.      .|.  ..+|..++.+|.+.|  ++|.++++++.
T Consensus       470 ~~------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  543 (597)
T 2xpi_A          470 LF------QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGL  543 (597)
T ss_dssp             HC------CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             hC------CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            32      245789999999999999999999999999887      444  578999999999999  99999999998


Q ss_pred             hCC
Q 011236          483 ADD  485 (490)
Q Consensus       483 ~~~  485 (490)
                      +.+
T Consensus       544 ~~~  546 (597)
T 2xpi_A          544 LLS  546 (597)
T ss_dssp             HHS
T ss_pred             HhC
Confidence            765

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=100.00  E-value=8.4e-31  Score=245.55  Aligned_cols=380  Identities=11%  Similarity=0.003  Sum_probs=334.7

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCCh
Q 011236           75 VIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLV  153 (490)
Q Consensus        75 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~  153 (490)
                      +...+.+.|++++|.+.++.+.+.. |.+...+..+...+...|++++|...++......| +..+|..+...+.+.|++
T Consensus         5 ~a~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~~g~~   83 (388)
T 1w3b_A            5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQL   83 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCH
Confidence            3456678999999999999998876 45667777888889999999999999999988877 688999999999999999


Q ss_pred             hHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          154 DESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       154 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      ++|+..|+++.+..+. +..+|..+..++...|++++|.+.|+++.+.+. .+...+..+...+...|++++|.+.|+++
T Consensus        84 ~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  161 (388)
T 1w3b_A           84 QEAIEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNP-DLYCVRSDLGNLLKALGRLEEAKACYLKA  161 (388)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCcc-hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            9999999999987533 566799999999999999999999999988532 24456777888999999999999999999


Q ss_pred             HhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC
Q 011236          234 ESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL  313 (490)
Q Consensus       234 ~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  313 (490)
                      . ...+ .+..+|..+..++...|++++|+..|+++....+  .+...|..+...+...|++++|...+++.....+ .+
T Consensus       162 l-~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p--~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~  236 (388)
T 1w3b_A          162 I-ETQP-NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP--NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-NH  236 (388)
T ss_dssp             H-HHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TC
T ss_pred             H-HhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC--CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc-CC
Confidence            8 4443 5678899999999999999999999999998765  5788899999999999999999999998888765 56


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011236          314 NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG  393 (490)
Q Consensus       314 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~  393 (490)
                      ..++..+..++.+.|++++|...++++.+.. +.+..++..+...|.+.|++++|...|+++.+..+. +..+|..+...
T Consensus       237 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~  314 (388)
T 1w3b_A          237 AVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPT-HADSLNNLANI  314 (388)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcc-cHHHHHHHHHH
Confidence            7889999999999999999999999999863 335678999999999999999999999999988643 88899999999


Q ss_pred             HhccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC
Q 011236          394 YADKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG  471 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g  471 (490)
                      +.+.|++++|...++++++       ..| +..++..+...+.+.|++++|...++++.+..|. ...|..+...+...|
T Consensus       315 ~~~~g~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~a~~~lg~~~~~~~  387 (388)
T 1w3b_A          315 KREQGNIEEAVRLYRKALE-------VFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQ  387 (388)
T ss_dssp             HHTTTCHHHHHHHHHHHTT-------SCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTC
T ss_pred             HHHcCCHHHHHHHHHHHHh-------cCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHhHHHHHHHcc
Confidence            9999999999999999987       334 4578999999999999999999999999999998 999999998887654

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=100.00  E-value=3.2e-29  Score=234.76  Aligned_cols=360  Identities=13%  Similarity=0.060  Sum_probs=319.3

Q ss_pred             HHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCc
Q 011236          110 QLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQH  188 (490)
Q Consensus       110 l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  188 (490)
                      +...+.+.|++++|.+.++.+....| +...+..+...+.+.|++++|...++......+ .+..+|..+...+.+.|++
T Consensus         5 ~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~p-~~~~~~~~lg~~~~~~g~~   83 (388)
T 1w3b_A            5 LAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNP-LLAEAYSNLGNVYKERGQL   83 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CchHHHHHHHHHHHHCCCH
Confidence            34567789999999999999988888 467788888899999999999999999888753 4788999999999999999


Q ss_pred             CcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011236          189 EKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK  268 (490)
Q Consensus       189 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  268 (490)
                      ++|.+.|+++.+.. +.+..+|..+..++.+.|++++|.+.|+++. +.++ .+...+..+...+...|++++|.+.|++
T Consensus        84 ~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al-~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~  160 (388)
T 1w3b_A           84 QEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSAL-QYNP-DLYCVRSDLGNLLKALGRLEEAKACYLK  160 (388)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHH-HHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-CcHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            99999999998853 2345679999999999999999999999998 5443 4466777889999999999999999999


Q ss_pred             HhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC
Q 011236          269 CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD  348 (490)
Q Consensus       269 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  348 (490)
                      +....+  .+..+|..+...+...|++++|...|+++....+ .+...+..+...+...|++++|...+++..+.. +.+
T Consensus       161 al~~~p--~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~  236 (388)
T 1w3b_A          161 AIETQP--NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP-NFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNH  236 (388)
T ss_dssp             HHHHCT--TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTC
T ss_pred             HHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCC
Confidence            988665  5788999999999999999999999999988776 667889999999999999999999999998863 335


Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHH
Q 011236          349 FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVS  428 (490)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~  428 (490)
                      ..++..+...|.+.|++++|...|+++.+.++. +..+|..+...+.+.|++++|.+.|+++++..      +.+..++.
T Consensus       237 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~------p~~~~~~~  309 (388)
T 1w3b_A          237 AVVHGNLACVYYEQGLIDLAIDTYRRAIELQPH-FPDAYCNLANALKEKGSVAEAEDCYNTALRLC------PTHADSLN  309 (388)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHC------TTCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC------cccHHHHH
Confidence            678899999999999999999999999998654 67889999999999999999999999999832      34568899


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          429 SILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      .+...+...|++++|...++++.+..|. ...+..++..|.+.|  ++|...++++.+.
T Consensus       310 ~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  368 (388)
T 1w3b_A          310 NLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            9999999999999999999999999998 999999999999999  9999999999874

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.98  E-value=4.6e-31  Score=251.23  Aligned_cols=212  Identities=11%  Similarity=0.120  Sum_probs=104.5

Q ss_pred             HHHHHHHHHHCCCCCCH-HHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011236          191 IPDVLLDMKENGVPPDN-FSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKC  269 (490)
Q Consensus       191 a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  269 (490)
                      +..+.+++.+.+..+.+ ..++.+|++|++.|++++|.++|++|. +.|+.||..+||+||.+|++.+..+++       
T Consensus         9 ~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~-~~Gv~pd~~tyn~Li~~c~~~~~~~~~-------   80 (501)
T 4g26_A            9 SENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEAR-RNGVQLSQYHYNVLLYVCSLAEAATES-------   80 (501)
T ss_dssp             ---------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHH-HHTCCCCHHHHHHHHHHHTTCCCCSSS-------
T ss_pred             HHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHH-HcCCCCCHhHHHHHHHHHHhCCchhhh-------
Confidence            34444555555444332 235555666666666666666666666 556666666666666666554431000       


Q ss_pred             hhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc
Q 011236          270 EDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDF  349 (490)
Q Consensus       270 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  349 (490)
                                          ...+.+++|.++|++|...+..||..||+++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus        81 --------------------~~~~~l~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~  140 (501)
T 4g26_A           81 --------------------SPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRL  140 (501)
T ss_dssp             --------------------SCCHHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCH
T ss_pred             --------------------hhcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCcc
Confidence                                001113445555555555555555555555555555555555555555555555555555


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                      .+|+++|.+|++.|++++|.++|++|.+.|+.||..||++||.+|++.|+.++|.++|++|.+     .|..|+..||+.
T Consensus       141 ~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~-----~g~~ps~~T~~~  215 (501)
T 4g26_A          141 RSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRD-----LVRQVSKSTFDM  215 (501)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-----HTSSBCHHHHHH
T ss_pred             ceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHH-----hCCCcCHHHHHH
Confidence            555555555555555555555555555555555555555555555555555555555555555     455555555555


Q ss_pred             HHHHHH
Q 011236          430 ILDWLG  435 (490)
Q Consensus       430 l~~~~~  435 (490)
                      ++..|.
T Consensus       216 l~~~F~  221 (501)
T 4g26_A          216 IEEWFK  221 (501)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            555444

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.98  E-value=3.6e-31  Score=251.95  Aligned_cols=206  Identities=12%  Similarity=0.082  Sum_probs=134.6

Q ss_pred             hHHHHHHHHHHhcCCCCCcc-hHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC---------h
Q 011236          154 DESLSLMQKMKEMGSFGSAL-NYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSE---------L  223 (490)
Q Consensus       154 ~~a~~~~~~m~~~~~~p~~~-~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~---------~  223 (490)
                      ..+..+.+++.+.+..+.+. .++.+|++|++.|++++|+++|++|.+.|++||..||++||.+|++.+.         +
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l   86 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGL   86 (501)
T ss_dssp             -----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHH
T ss_pred             chHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchH
Confidence            44566777888887765543 5889999999999999999999999999999999999999999998765         4


Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHH
Q 011236          224 SSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWG  303 (490)
Q Consensus       224 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  303 (490)
                      +.|.++|++|. ..|+.||..||+++|.+|++.|++++|.++|++|...+.. ||..+|+.+|.+|++.|++++|.++|+
T Consensus        87 ~~A~~lf~~M~-~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~-Pd~~tyn~lI~~~~~~g~~~~A~~l~~  164 (501)
T 4g26_A           87 SRGFDIFKQMI-VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQ-PRLRSYGPALFGFCRKGDADKAYEVDA  164 (501)
T ss_dssp             HHHHHHHHHHH-HTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCC-CCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CccceehHHHHHHHHCCCHHHHHHHHH
Confidence            55666666666 5666666666666666666666666666666666666655 666666666666666666666666666


Q ss_pred             HHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Q 011236          304 LQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ  361 (490)
Q Consensus       304 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (490)
                      +|...+..||..||++||.+|++.|++++|.+++++|.+.|..|+..||+.++..|+.
T Consensus       165 ~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          165 HMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHS
T ss_pred             HHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhc
Confidence            6666666666666666666666666666666666666666666666666666655554

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.96  E-value=1.7e-25  Score=217.54  Aligned_cols=405  Identities=10%  Similarity=0.000  Sum_probs=235.0

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHH
Q 011236           69 ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCY  147 (490)
Q Consensus        69 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~  147 (490)
                      ...+......+.+.|++++|+..|+++.+..  |++..+..+..++...|++++|...|+.+...+| +..+|..+..++
T Consensus         6 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~   83 (514)
T 2gw1_A            6 ALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASAN   83 (514)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHH
Confidence            4556777788889999999999999999886  5788888899999999999999999999988887 577899999999


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcC-----------------------------------cHH
Q 011236          148 VREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHE-----------------------------------KIP  192 (490)
Q Consensus       148 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~-----------------------------------~a~  192 (490)
                      .+.|++++|...|+++...+.. +......++..+.......                                   ...
T Consensus        84 ~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (514)
T 2gw1_A           84 EGLGKFADAMFDLSVLSLNGDF-NDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVT  162 (514)
T ss_dssp             HHTTCHHHHHHHHHHHHHSSSC-CGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHH
T ss_pred             HHHhhHHHHHHHHHHHHhcCCC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhH
Confidence            9999999999999999887542 3333322222222111100                                   000


Q ss_pred             HHHHHHHHCCCC--------C-CHHHHHHHHHHHh---ccCChHHHHHHHHHHHhC-----C--CC------CCCHHHHH
Q 011236          193 DVLLDMKENGVP--------P-DNFSYRICINSYG---ARSELSSMENVLQEMESQ-----S--HI------SMDWGTYS  247 (490)
Q Consensus       193 ~~~~~m~~~~~~--------p-~~~~~~~li~~~~---~~g~~~~a~~~~~~~~~~-----~--~~------~~~~~~~~  247 (490)
                      .+...+......        | +...+......+.   +.|++++|..+|+++. .     .  ..      +.+..++.
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  241 (514)
T 2gw1_A          163 SMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAA-RLFEEQLDKNNEDEKLKEKLAISLE  241 (514)
T ss_dssp             HHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHH-HHHHHHTTTSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHH-HHhhhhhccCccccccChHHHHHHH
Confidence            110000000000        0 1222222222222   2556666666666555 2     1  10      11234445


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  327 (490)
                      .+...+...|++++|...|+++....+  . ..++..+..++...|++++|...++......+ .+...+..+...+...
T Consensus       242 ~~~~~~~~~~~~~~A~~~~~~~l~~~~--~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~  317 (514)
T 2gw1_A          242 HTGIFKFLKNDPLGAHEDIKKAIELFP--R-VNSYIYMALIMADRNDSTEYYNYFDKALKLDS-NNSSVYYHRGQMNFIL  317 (514)
T ss_dssp             HHHHHHHHSSCHHHHHHHHHHHHHHCC--C-HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCT-TCTHHHHHHHHHHHHT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhCc--c-HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCc-CCHHHHHHHHHHHHHh
Confidence            555556666666666666666555432  2 55555556666666666666666665554433 3445555566666666


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHH
Q 011236          328 GELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECM  407 (490)
Q Consensus       328 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~  407 (490)
                      |++++|...++++.+.. +.+...+..+...|...|++++|...++++.+..+. +..+|..+...+...|++++|...+
T Consensus       318 ~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~  395 (514)
T 2gw1_A          318 QNYDQAGKDFDKAKELD-PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPE-APEVPNFFAEILTDKNDFDKALKQY  395 (514)
T ss_dssp             TCTTHHHHHHHHHHHTC-SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHccc-CHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            66666666666655542 224445555555666666666666666666554332 4455555666666666666666666


Q ss_pred             HHHHHhhhcCcCCCcchhhHHHHHHHHHc---CCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHH
Q 011236          408 KEALAVHEENKFWRPKPSLVSSILDWLGD---NRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESM  481 (490)
Q Consensus       408 ~~~~~~~~~~~~~~p~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m  481 (490)
                      +++....+......-....+..+...+..   .|++++|...++++.+..|. ...+..++..|.+.|  ++|...+++.
T Consensus       396 ~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  475 (514)
T 2gw1_A          396 DLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITLFEES  475 (514)
T ss_dssp             HHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            66655332111111112255555555555   56666666666666655555 555666666666666  5566666555


Q ss_pred             Hh
Q 011236          482 KA  483 (490)
Q Consensus       482 ~~  483 (490)
                      .+
T Consensus       476 ~~  477 (514)
T 2gw1_A          476 AD  477 (514)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.95  E-value=5.3e-25  Score=210.40  Aligned_cols=366  Identities=11%  Similarity=0.019  Sum_probs=241.9

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHH
Q 011236           66 KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALL  144 (490)
Q Consensus        66 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li  144 (490)
                      +.+...+..+...+.+.|++++|+++|+.+.+.. +.++..+..+..++...|++++|...|+.+...+| +..+|..+.
T Consensus        23 p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~  101 (450)
T 2y4t_A           23 MADVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRG  101 (450)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHH
Confidence            3455566666666666666666666666666554 34555666666666666666666666666666555 355666666


Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCc---chHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccC
Q 011236          145 NCYVREGLVDESLSLMQKMKEMGSFGSA---LNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARS  221 (490)
Q Consensus       145 ~~~~~~g~~~~a~~~~~~m~~~~~~p~~---~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g  221 (490)
                      ..|.+.|++++|...|+++.+.+.. +.   ..+..+...+..                       ..+..+...+...|
T Consensus       102 ~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~-----------------------~~~~~~a~~~~~~~  157 (450)
T 2y4t_A          102 HLLLKQGKLDEAEDDFKKVLKSNPS-ENEEKEAQSQLIKSDEM-----------------------QRLRSQALNAFGSG  157 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHH-----------------------HHHHHHHHHHHHHT
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHHHHH-----------------------HHHHHHHHHHHHcC
Confidence            6666666666666666666654321 22   344444333110                       11222344566777


Q ss_pred             ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHH
Q 011236          222 ELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKF  301 (490)
Q Consensus       222 ~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  301 (490)
                      ++++|...|+++. .... .+..++..++.+|...|++++|+..|+++....+  .+..++..+..+|...|++++|...
T Consensus       158 ~~~~A~~~~~~~~-~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~  233 (450)
T 2y4t_A          158 DYTAAIAFLDKIL-EVCV-WDAELRELRAECFIKEGEPRKAISDLKAASKLKN--DNTEAFYKISTLYYQLGDHELSLSE  233 (450)
T ss_dssp             CHHHHHHHHHHHH-HHCT-TCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHC--SCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CHHHHHHHHHHHH-HhCC-CChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            8888888887776 4333 4667777777888888888888888887777655  5677777888888888888888888


Q ss_pred             HHHHHHhcCCCChhhHHHH------------HHHHHhcCCHHHHHHHHHHHHhcCCCCC-----chhHHHHHHHHHhcCC
Q 011236          302 WGLQKIKCKKQLNRDYITM------------LGSLVKIGELEEAEKMLEEWELSCYCYD-----FRVPNIILLGYSQKGM  364 (490)
Q Consensus       302 ~~~~~~~~~~~~~~~~~~l------------~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~  364 (490)
                      |+.+....+ .+...+..+            ...+.+.|++++|...++++.+.  .|+     ...+..+...+.+.|+
T Consensus       234 ~~~~~~~~p-~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~  310 (450)
T 2y4t_A          234 VRECLKLDQ-DHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEK  310 (450)
T ss_dssp             HHHHHHHCT-TCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHhCC-ChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCC
Confidence            887776544 333444333            77888888888888888888875  333     3367778888888888


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHH-----------
Q 011236          365 IEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILD-----------  432 (490)
Q Consensus       365 ~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~-----------  432 (490)
                      +++|...++++.+..+. +..+|..+..+|...|++++|...++++++       +.|+. ..+..+..           
T Consensus       311 ~~~A~~~~~~a~~~~p~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~~~~~~~~~~  382 (450)
T 2y4t_A          311 PVEAIRVCSEVLQMEPD-NVNALKDRAEAYLIEEMYDEAIQDYETAQE-------HNENDQQIREGLEKAQRLLKQSQKR  382 (450)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT-------TSSSCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHhCcc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-------hCcchHHHHHHHHHHHHHhhcccch
Confidence            99998888888876533 678888888888888899999988888887       34544 44444442           


Q ss_pred             -HHHcCC-----CHHHHHHHHHH-HHhcccc-----------hhhhHHHHHHHHhcC
Q 011236          433 -WLGDNR-----DVEEVEAFVSS-LKIKVQK-----------RNMYHALTEAHIRSG  471 (490)
Q Consensus       433 -~~~~~g-----~~~~a~~~~~~-~~~~~~~-----------~~~~~~l~~~~~~~g  471 (490)
                       .|...|     +.+++.+.+++ ..+..|+           ...|..+..+|...|
T Consensus       383 ~~y~~lg~~~~~~~~~~~~~y~~~~l~~~pd~~~~~~~~~~a~~~~~~i~~ay~~L~  439 (450)
T 2y4t_A          383 DYYKILGVKRNAKKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKFIDIAAAKEVLS  439 (450)
T ss_dssp             CSGGGSCSSTTCCTTHHHHHHHHHHHHSCGGGCCSHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             hHHHHhCCCccCCHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHHHHHhC
Confidence             233333     55677777775 4444443           226777777777777

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.95  E-value=4.4e-25  Score=211.00  Aligned_cols=377  Identities=11%  Similarity=-0.016  Sum_probs=225.6

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQL  111 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  111 (490)
                      ++..+..+...+.+.|+.++++. +++++... .+.+...+..+...+...|++++|+..|+.+.+.+ +.+...+..+.
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~-~~~~~l~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~  101 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALS-QFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRG  101 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHH-HHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHH-HHHHHHHh-CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHH
Confidence            45667788888999999998888 77777765 45578999999999999999999999999999987 46788899999


Q ss_pred             HHHHhhcCHHHHHHHHHHccccCCC-h---hHHHHHHHH------------HHhcCChhHHHHHHHHHHhcCCCCCcchH
Q 011236          112 DLIGKVRGLESAETYFNSLNDEDKV-D---KLYGALLNC------------YVREGLVDESLSLMQKMKEMGSFGSALNY  175 (490)
Q Consensus       112 ~~~~~~~~~~~A~~~~~~~~~~~p~-~---~~~~~li~~------------~~~~g~~~~a~~~~~~m~~~~~~p~~~~~  175 (490)
                      .++...|++++|...|+.+....|+ .   .++..++..            +.+.|++++|+..|+++.+.... +..++
T Consensus       102 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~  180 (450)
T 2y4t_A          102 HLLLKQGKLDEAEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVW-DAELR  180 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHH
Confidence            9999999999999999999998875 4   677777554            66667777777777766665332 55566


Q ss_pred             HHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH
Q 011236          176 NGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII  255 (490)
Q Consensus       176 ~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~  255 (490)
                      ..+..++...|++++|.++|+++.+.. +.+..++..+..++...|++++|...|+++. .... .+...+..+...   
T Consensus       181 ~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~p-~~~~~~~~~~~~---  254 (450)
T 2y4t_A          181 ELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECL-KLDQ-DHKRCFAHYKQV---  254 (450)
T ss_dssp             HHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCT-TCHHHHHHHHHH---
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-ChHHHHHHHHHH---
Confidence            666666666666666666666665532 2345566666666666666666666666665 2222 223333222000   


Q ss_pred             cCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC----hhhHHHHHHHHHhcCCHH
Q 011236          256 AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL----NRDYITMLGSLVKIGELE  331 (490)
Q Consensus       256 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~  331 (490)
                                           .....+..+...+...|++++|...|+.+....+. +    ...+..+..++.+.|+++
T Consensus       255 ---------------------~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~l~~~~~~~g~~~  312 (450)
T 2y4t_A          255 ---------------------KKLNKLIESAEELIRDGRYTDATSKYESVMKTEPS-IAEYTVRSKERICHCFSKDEKPV  312 (450)
T ss_dssp             ---------------------HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHTTTCHH
T ss_pred             ---------------------HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHHHHHCCCHH
Confidence                                 00000111144444455555555555544443321 1    123444455555555555


Q ss_pred             HHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH------------HHhccC-
Q 011236          332 EAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAA------------GYADKN-  398 (490)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~------------~~~~~~-  398 (490)
                      +|...++++.+. .+.+...|..+..+|...|++++|...++++.+..+. +...+..+..            .|...| 
T Consensus       313 ~A~~~~~~a~~~-~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~~~~~~y~~lg~  390 (450)
T 2y4t_A          313 EAIRVCSEVLQM-EPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNEN-DQQIREGLEKAQRLLKQSQKRDYYKILGV  390 (450)
T ss_dssp             HHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSS-CHHHHHHHHHHHHHHHHHHSCCSGGGSCS
T ss_pred             HHHHHHHHHHHh-CcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcc-hHHHHHHHHHHHHHhhcccchhHHHHhCC
Confidence            555555555443 1223444555555555555555555555555544322 3333433331            233333 


Q ss_pred             ----CHHHHHHHHHH-HHHhhhcCcCCCc----chhhHHHHHHHHHcCCCHHH
Q 011236          399 ----NMEKAFECMKE-ALAVHEENKFWRP----KPSLVSSILDWLGDNRDVEE  442 (490)
Q Consensus       399 ----~~~~a~~~~~~-~~~~~~~~~~~~p----~~~~~~~l~~~~~~~g~~~~  442 (490)
                          +.+++.+.+++ ++..+|++..-.+    ....+..+..+|...+|.+.
T Consensus       391 ~~~~~~~~~~~~y~~~~l~~~pd~~~~~~~~~~a~~~~~~i~~ay~~L~d~~~  443 (450)
T 2y4t_A          391 KRNAKKQEIIKAYRKLALQWHPDNFQNEEEKKKAEKKFIDIAAAKEVLSDPEM  443 (450)
T ss_dssp             STTCCTTHHHHHHHHHHHHSCGGGCCSHHHHHHHHHHHHHHHHHHHHSSGGGG
T ss_pred             CccCCHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHHHHHHHHHhCCHHH
Confidence                56677878876 5553332211100    11355566666666655443

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.95  E-value=1.7e-24  Score=211.80  Aligned_cols=403  Identities=11%  Similarity=0.042  Sum_probs=275.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHH
Q 011236           69 ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCY  147 (490)
Q Consensus        69 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~  147 (490)
                      ...+..+...+.+.|++++|++.|+++.+.. +.++..+..+..++...|++++|.+.|+.+...+| +..+|..+..++
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~  103 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRASAN  103 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHH
Confidence            3455666666677777777777777776665 45566666677777777777777777777766665 466666677777


Q ss_pred             HhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHC------CCCCCHH-------------
Q 011236          148 VREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKEN------GVPPDNF-------------  208 (490)
Q Consensus       148 ~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~------~~~p~~~-------------  208 (490)
                      ...|++++|+..|+ .....  |+.  .+..+..+...+....+...++++...      ...|+..             
T Consensus       104 ~~~g~~~~A~~~~~-~~~~~--~~~--~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (537)
T 3fp2_A          104 ESLGNFTDAMFDLS-VLSLN--GDF--DGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHL  178 (537)
T ss_dssp             HHHTCHHHHHHHHH-HHC---------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHH
T ss_pred             HHcCCHHHHHHHHH-HHhcC--CCC--ChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHH
Confidence            77777777777775 22221  111  111122223333334455555555332      0111111             


Q ss_pred             -----------------HHHHHHHHHhc--------cCChHHHHHHHHHHHhCCCCCCC-------HHHHHHHHHHHHHc
Q 011236          209 -----------------SYRICINSYGA--------RSELSSMENVLQEMESQSHISMD-------WGTYSTVANYYIIA  256 (490)
Q Consensus       209 -----------------~~~~li~~~~~--------~g~~~~a~~~~~~~~~~~~~~~~-------~~~~~~li~~~~~~  256 (490)
                                       ....+...+..        .|++++|..+|+++. +... .+       ..++..+...+...
T Consensus       179 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l-~~~p-~~~~~~~~~~~~~~~~g~~~~~~  256 (537)
T 3fp2_A          179 EVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLL-SANT-VDDPLRENAALALCYTGIFHFLK  256 (537)
T ss_dssp             HHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHH-C--C-CCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHH-HHCC-CcchhhHHHHHHHHHHHHHHHhc
Confidence                             12222222222        247888888888887 5443 22       23466667788888


Q ss_pred             CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011236          257 GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM  336 (490)
Q Consensus       257 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  336 (490)
                      |++++|...|+++....   |+..++..+...+...|++++|...+++.....+ .+..++..+...+...|++++|...
T Consensus       257 ~~~~~A~~~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~  332 (537)
T 3fp2_A          257 NNLLDAQVLLQESINLH---PTPNSYIFLALTLADKENSQEFFKFFQKAVDLNP-EYPPTYYHRGQMYFILQDYKNAKED  332 (537)
T ss_dssp             TCHHHHHHHHHHHHHHC---CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             ccHHHHHHHHHHHHhcC---CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCC-CCHHHHHHHHHHHHhcCCHHHHHHH
Confidence            89999999998887754   4477788888888889999999999988877765 5677888888888889999999999


Q ss_pred             HHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhc
Q 011236          337 LEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEE  416 (490)
Q Consensus       337 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  416 (490)
                      ++++.+.. +.+...+..+...|...|++++|...++++.+..+. +...+..+...+...|++++|...++++++..+.
T Consensus       333 ~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~  410 (537)
T 3fp2_A          333 FQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPT-LPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEV  410 (537)
T ss_dssp             HHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCc
Confidence            98888763 335677888888888999999999999888887544 6678888888888999999999999988886654


Q ss_pred             CcCCCcchhhHHHHHHHHHcC----------CCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHh
Q 011236          417 NKFWRPKPSLVSSILDWLGDN----------RDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       417 ~~~~~p~~~~~~~l~~~~~~~----------g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~  483 (490)
                      ..........+......+...          |++++|...++++.+..|. ...+..++..|.+.|  ++|.+.+++..+
T Consensus       411 ~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  490 (537)
T 3fp2_A          411 QEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAI  490 (537)
T ss_dssp             CSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            433333334455555667777          8899999999998888888 888888999999888  888888888776


Q ss_pred             CC
Q 011236          484 DD  485 (490)
Q Consensus       484 ~~  485 (490)
                      ..
T Consensus       491 ~~  492 (537)
T 3fp2_A          491 LA  492 (537)
T ss_dssp             HC
T ss_pred             hC
Confidence            43

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.95  E-value=3.3e-25  Score=215.63  Aligned_cols=411  Identities=10%  Similarity=-0.046  Sum_probs=326.4

Q ss_pred             cccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011236           36 RNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIG  115 (490)
Q Consensus        36 ~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  115 (490)
                      +......+.+.|++++++. .+++.....  |+...+..+...+...|++++|++.++.+.+.+ +.+...+..+..++.
T Consensus         9 ~~~~g~~~~~~g~~~~A~~-~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~   84 (514)
T 2gw1_A            9 LKDKGNQFFRNKKYDDAIK-YYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANE   84 (514)
T ss_dssp             HHHHHHHHHHTSCHHHHHH-HHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHH-HHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHH
Confidence            3344566777889888888 777777665  689999999999999999999999999999887 567788999999999


Q ss_pred             hhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhc----------------------------
Q 011236          116 KVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEM----------------------------  166 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----------------------------  166 (490)
                      ..|++++|...|+.+...+| +......++..+........+.+.+..+...                            
T Consensus        85 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (514)
T 2gw1_A           85 GLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSM  164 (514)
T ss_dssp             HTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHH
T ss_pred             HHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHH
Confidence            99999999999999988775 4444445554444433333333222111110                            


Q ss_pred             -------CCC---------CCcchHHHHHHHHHh---cCCcCcHHHHHHHHHH-----CCCC--------CCHHHHHHHH
Q 011236          167 -------GSF---------GSALNYNGIMCLYTN---TGQHEKIPDVLLDMKE-----NGVP--------PDNFSYRICI  214 (490)
Q Consensus       167 -------~~~---------p~~~~~~~l~~~~~~---~~~~~~a~~~~~~m~~-----~~~~--------p~~~~~~~li  214 (490)
                             ...         .+...+..+...+..   .|++++|..+|+++.+     ..-.        .+..++..+.
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (514)
T 2gw1_A          165 ASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTG  244 (514)
T ss_dssp             HHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHH
Confidence                   000         113334444444444   8999999999999987     3111        2345778888


Q ss_pred             HHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCC
Q 011236          215 NSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGN  294 (490)
Q Consensus       215 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  294 (490)
                      ..+...|++++|...|+++. +.+.  +..++..+..+|...|++++|...++++....+  .+..++..+...+...|+
T Consensus       245 ~~~~~~~~~~~A~~~~~~~l-~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~  319 (514)
T 2gw1_A          245 IFKFLKNDPLGAHEDIKKAI-ELFP--RVNSYIYMALIMADRNDSTEYYNYFDKALKLDS--NNSSVYYHRGQMNFILQN  319 (514)
T ss_dssp             HHHHHSSCHHHHHHHHHHHH-HHCC--CHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCT--TCTHHHHHHHHHHHHTTC
T ss_pred             HHHHHCCCHHHHHHHHHHHH-hhCc--cHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCc--CCHHHHHHHHHHHHHhCC
Confidence            99999999999999999998 5444  388889999999999999999999999988665  577889999999999999


Q ss_pred             hhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          295 KDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKE  374 (490)
Q Consensus       295 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  374 (490)
                      +++|...+++.....+ .+...+..+...+...|++++|...++++.+. .+.+...+..+...|.+.|++++|...+++
T Consensus       320 ~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  397 (514)
T 2gw1_A          320 YDQAGKDFDKAKELDP-ENIFPYIQLACLAYRENKFDDCETLFSEAKRK-FPEAPEVPNFFAEILTDKNDFDKALKQYDL  397 (514)
T ss_dssp             TTHHHHHHHHHHHTCS-SCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHH-STTCSHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCh-hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-cccCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            9999999998888765 56778999999999999999999999999886 344677889999999999999999999999


Q ss_pred             HHHcCCC-CC----HHHHHHHHHHHhc---cCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHH
Q 011236          375 IVKKGKT-PT----PNSWSIIAAGYAD---KNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAF  446 (490)
Q Consensus       375 m~~~~~~-p~----~~~~~~l~~~~~~---~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  446 (490)
                      +.+..+. ++    ..+|..+...+..   .|++++|...+++++...      +.+..++..+...+.+.|++++|...
T Consensus       398 a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~------~~~~~~~~~la~~~~~~g~~~~A~~~  471 (514)
T 2gw1_A          398 AIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLD------PRSEQAKIGLAQMKLQQEDIDEAITL  471 (514)
T ss_dssp             HHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHC------TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhC------cccHHHHHHHHHHHHHhcCHHHHHHH
Confidence            9875433 11    3489999999999   999999999999999832      23457888999999999999999999


Q ss_pred             HHHHHhcccc-hhhhHHH
Q 011236          447 VSSLKIKVQK-RNMYHAL  463 (490)
Q Consensus       447 ~~~~~~~~~~-~~~~~~l  463 (490)
                      ++++.+..|. ...+..+
T Consensus       472 ~~~a~~~~~~~~~~~~~~  489 (514)
T 2gw1_A          472 FEESADLARTMEEKLQAI  489 (514)
T ss_dssp             HHHHHHHCSSHHHHHHHH
T ss_pred             HHHHHHhccccHHHHHHH
Confidence            9999999998 6665554

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.93  E-value=1.2e-21  Score=191.48  Aligned_cols=403  Identities=11%  Similarity=0.036  Sum_probs=300.9

Q ss_pred             CCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHH
Q 011236           34 VARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDL  113 (490)
Q Consensus        34 ~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  113 (490)
                      ..+..+...+.+.|+.++|+. .+++..... +.+...+..+...+...|++++|++.++++.+.+ +.++..+..+..+
T Consensus        26 ~~~~~~g~~~~~~g~~~~A~~-~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~  102 (537)
T 3fp2_A           26 VQLKNRGNHFFTAKNFNEAIK-YYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASA  102 (537)
T ss_dssp             HHHHHHHHHHHHTTCCC-CHH-HHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHH-HHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHH
Confidence            346667778888999999998 777777653 4588999999999999999999999999999987 5678889999999


Q ss_pred             HHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcC------CCCC----------------
Q 011236          114 IGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMG------SFGS----------------  171 (490)
Q Consensus       114 ~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~------~~p~----------------  171 (490)
                      +...|++++|...|+.+ ...|+.  .+..+..+...+....|...++++....      ..|+                
T Consensus       103 ~~~~g~~~~A~~~~~~~-~~~~~~--~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  179 (537)
T 3fp2_A          103 NESLGNFTDAMFDLSVL-SLNGDF--DGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLE  179 (537)
T ss_dssp             HHHHTCHHHHHHHHHHH-C-------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHH
T ss_pred             HHHcCCHHHHHHHHHHH-hcCCCC--ChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHH
Confidence            99999999999999744 333332  2223444555555677777777774431      0111                


Q ss_pred             ----------cc----hHHHHHHHHHh--------cCCcCcHHHHHHHHHHCCCCCC-------HHHHHHHHHHHhccCC
Q 011236          172 ----------AL----NYNGIMCLYTN--------TGQHEKIPDVLLDMKENGVPPD-------NFSYRICINSYGARSE  222 (490)
Q Consensus       172 ----------~~----~~~~l~~~~~~--------~~~~~~a~~~~~~m~~~~~~p~-------~~~~~~li~~~~~~g~  222 (490)
                                ..    ....+...+..        .|++++|..+|+++.+.... +       ..++..+...+...|+
T Consensus       180 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~g~~~~~~~~  258 (537)
T 3fp2_A          180 VSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTV-DDPLRENAALALCYTGIFHFLKNN  258 (537)
T ss_dssp             HHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CC-CHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCC-cchhhHHHHHHHHHHHHHHHhccc
Confidence                      01    12222222222        24788999999998875322 2       2346677778888999


Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHH
Q 011236          223 LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFW  302 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  302 (490)
                      +++|...|+++. ...  |+..++..+...+...|++++|...|+++....+  .+..++..+...+...|++++|...+
T Consensus       259 ~~~A~~~~~~~~-~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~  333 (537)
T 3fp2_A          259 LLDAQVLLQESI-NLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLNP--EYPPTYYHRGQMYFILQDYKNAKEDF  333 (537)
T ss_dssp             HHHHHHHHHHHH-HHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHH-hcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCC--CCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence            999999999988 433  4578888888999999999999999999887665  57788999999999999999999999


Q ss_pred             HHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-
Q 011236          303 GLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-  381 (490)
Q Consensus       303 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-  381 (490)
                      ++.....+ .+...+..+...+...|++++|...++++.+. .+.+...+..+...|...|++++|...|+++.+..+. 
T Consensus       334 ~~a~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~  411 (537)
T 3fp2_A          334 QKAQSLNP-ENVYPYIQLACLLYKQGKFTESEAFFNETKLK-FPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQ  411 (537)
T ss_dssp             HHHHHHCT-TCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcc
Confidence            98888765 55678888999999999999999999998886 3445678888899999999999999999988764321 


Q ss_pred             ----CCHHHHHHHHHHHhcc----------CCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHH
Q 011236          382 ----PTPNSWSIIAAGYADK----------NNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFV  447 (490)
Q Consensus       382 ----p~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~  447 (490)
                          .....+......+...          |++++|...|+++++..      +.+...+..+...+.+.|++++|...|
T Consensus       412 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~------p~~~~~~~~l~~~~~~~g~~~~A~~~~  485 (537)
T 3fp2_A          412 EKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELD------PRSEQAKIGLAQLKLQMEKIDEAIELF  485 (537)
T ss_dssp             SSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHC------TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhC------CCCHHHHHHHHHHHHHhccHHHHHHHH
Confidence                1223355566677777          99999999999998832      133477888889999999999999999


Q ss_pred             HHHHhcccc
Q 011236          448 SSLKIKVQK  456 (490)
Q Consensus       448 ~~~~~~~~~  456 (490)
                      +++.+..|.
T Consensus       486 ~~al~~~~~  494 (537)
T 3fp2_A          486 EDSAILART  494 (537)
T ss_dssp             HHHHHHC--
T ss_pred             HHHHHhCCC
Confidence            999888776

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=5.5e-21  Score=176.54  Aligned_cols=303  Identities=9%  Similarity=-0.034  Sum_probs=189.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNC  146 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~  146 (490)
                      ++..+..+...+...|++++|++.|+.+.+.. +.++..+..+..++...|++++|...|+.+....| +..+|..+...
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~   80 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHH
Confidence            45667778888888999999999999988876 45677888888888899999999999998888777 57788888888


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCC--CCcchHHHH------------HHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHH
Q 011236          147 YVREGLVDESLSLMQKMKEMGSF--GSALNYNGI------------MCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRI  212 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~--p~~~~~~~l------------~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  212 (490)
                      +...|++++|...|+++.+....  .+...+..+            ...+...|++++|.++++++.+.. +.+...+..
T Consensus        81 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~  159 (359)
T 3ieg_A           81 LLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELREL  159 (359)
T ss_dssp             HHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHHH
Confidence            89999999999999988876430  134444444            355566666666666666665542 234555666


Q ss_pred             HHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHH--------
Q 011236          213 CINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNH--------  284 (490)
Q Consensus       213 li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~--------  284 (490)
                      +..++...|++++|...++++. .... .+..++..+...+...|++++|...|++.....+  .+...+..        
T Consensus       160 ~~~~~~~~~~~~~A~~~~~~~~-~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~--~~~~~~~~~~~~~~~~  235 (359)
T 3ieg_A          160 RAECFIKEGEPRKAISDLKAAS-KLKS-DNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQ--DHKRCFAHYKQVKKLN  235 (359)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHH-TTCS-CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc--cchHHHHHHHHHHHHH
Confidence            6666666666666666666665 4333 4555666666666666666666666666655443  23332221        


Q ss_pred             ----HHHHHHhcCChhHHHHHHHHHHHhcCCCCh----hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHH
Q 011236          285 ----LISHYASLGNKDEMMKFWGLQKIKCKKQLN----RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIIL  356 (490)
Q Consensus       285 ----l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  356 (490)
                          +...+...|++++|...++......+. +.    ..+..+..++...|++++|...+++..+. .+.+..++..+.
T Consensus       236 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~  313 (359)
T 3ieg_A          236 KLIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQM-EPDNVNALKDRA  313 (359)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-CcccHHHHHHHH
Confidence                133455555555555555555544331 11    11333444555555555555555555543 122344455555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHc
Q 011236          357 LGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      ..|...|++++|...|+++.+.
T Consensus       314 ~~~~~~g~~~~A~~~~~~a~~~  335 (359)
T 3ieg_A          314 EAYLIEEMYDEAIQDYEAAQEH  335 (359)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHcCCHHHHHHHHHHHHhc
Confidence            5555555555555555555554

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=1e-20  Score=174.80  Aligned_cols=327  Identities=12%  Similarity=0.028  Sum_probs=194.6

Q ss_pred             hhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHH
Q 011236          104 VHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLY  182 (490)
Q Consensus       104 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~  182 (490)
                      +..+..+...+...|++++|...|+.+....| +..+|..+...+...|++++|...++++.+.... +...|..+...+
T Consensus         3 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~   81 (359)
T 3ieg_A            3 VEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMD-FTAARLQRGHLL   81 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-cchHHHHHHHHH
Confidence            34455556666667777777777776666655 4566666666777777777777777766665332 445666666666


Q ss_pred             HhcCCcCcHHHHHHHHHHCCCCC----CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCC
Q 011236          183 TNTGQHEKIPDVLLDMKENGVPP----DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGL  258 (490)
Q Consensus       183 ~~~~~~~~a~~~~~~m~~~~~~p----~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~  258 (490)
                      ...|++++|...|+++.+.  .|    +...+..+.....                        ...+..+...+...|+
T Consensus        82 ~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~------------------------~~~~~~~a~~~~~~~~  135 (359)
T 3ieg_A           82 LKQGKLDEAEDDFKKVLKS--NPSEQEEKEAESQLVKADE------------------------MQRLRSQALDAFDGAD  135 (359)
T ss_dssp             HHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHH------------------------HHHHHHHHHHHHHTTC
T ss_pred             HHcCChHHHHHHHHHHHhc--CCcccChHHHHHHHHHHHH------------------------HHHHHHHHHHHHHccC
Confidence            6666666666666666653  23    2222222210000                        0001112445555666


Q ss_pred             HHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHH
Q 011236          259 KEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLE  338 (490)
Q Consensus       259 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  338 (490)
                      +++|...++++....+  .+...+..+...+...|++++|...++......+ .+...+..+...+...|++++|...++
T Consensus       136 ~~~A~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~  212 (359)
T 3ieg_A          136 YTAAITFLDKILEVCV--WDAELRELRAECFIKEGEPRKAISDLKAASKLKS-DNTEAFYKISTLYYQLGDHELSLSEVR  212 (359)
T ss_dssp             HHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCS-CCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            6666666666555443  3455555556666666666666666665554433 444555556666666666666666666


Q ss_pred             HHHhcCCCCCchhHH------------HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH----HHHHHHHHHHhccCCHHH
Q 011236          339 EWELSCYCYDFRVPN------------IILLGYSQKGMIEKADAVLKEIVKKGKTPTP----NSWSIIAAGYADKNNMEK  402 (490)
Q Consensus       339 ~~~~~~~~~~~~~~~------------~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~----~~~~~l~~~~~~~~~~~~  402 (490)
                      +..+... .+...+.            .+...+.+.|++++|...++++.+..+. +.    ..+..+...+...|++++
T Consensus       213 ~a~~~~~-~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~~~~~~  290 (359)
T 3ieg_A          213 ECLKLDQ-DHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPS-VAEYTVRSKERICHCFSKDEKPVE  290 (359)
T ss_dssp             HHHHHCT-TCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-SHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHhhCc-cchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHHHHHccCHHH
Confidence            6555311 1222221            2255577778888888888877776433 23    224456677777888888


Q ss_pred             HHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHh
Q 011236          403 AFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIR  469 (490)
Q Consensus       403 a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~  469 (490)
                      |...++++++.       .| +..++..+...+...|++++|...++++.+..|. ...+..+..+...
T Consensus       291 A~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~  352 (359)
T 3ieg_A          291 AIRICSEVLQM-------EPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEHNENDQQIREGLEKAQRL  352 (359)
T ss_dssp             HHHHHHHHHHH-------CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh-------CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Confidence            88888887772       24 4567777777778888888888888888877777 6666666655543

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.89  E-value=3e-20  Score=169.50  Aligned_cols=289  Identities=11%  Similarity=-0.010  Sum_probs=149.1

Q ss_pred             ChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHH
Q 011236          103 SVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCL  181 (490)
Q Consensus       103 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~  181 (490)
                      ++..+......+...|++++|..+|+.+....| +..++..++..+...|++++|..+++++.+.... +...|..+...
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~   99 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLYPS-NPVSWFAVGCY   99 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-STHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHHHHHH
Confidence            333444444444444444444444444444443 2333444444444455555555555554444222 34444444444


Q ss_pred             HHhcC-CcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHH
Q 011236          182 YTNTG-QHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKE  260 (490)
Q Consensus       182 ~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~  260 (490)
                      +...| ++++|.+.|++..+... .+...+..+...+...|++++|...|+++. +... .+...+..+...|...|+++
T Consensus       100 ~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~-~~~~-~~~~~~~~l~~~~~~~~~~~  176 (330)
T 3hym_B          100 YLMVGHKNEHARRYLSKATTLEK-TYGPAWIAYGHSFAVESEHDQAMAAYFTAA-QLMK-GCHLPMLYIGLEYGLTNNSK  176 (330)
T ss_dssp             HHHSCSCHHHHHHHHHHHHTTCT-TCTHHHHHHHHHHHHHTCHHHHHHHHHHHH-HHTT-TCSHHHHHHHHHHHHTTCHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHhCC-ccHHHHHHHHHHHHHccCHHHHHHHHHHHH-Hhcc-ccHHHHHHHHHHHHHHhhHH
Confidence            44444 45555555555444321 133444555555555555555555555554 2222 22334444555555555555


Q ss_pred             HHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC--------CCChhhHHHHHHHHHhcCCHHH
Q 011236          261 KAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCK--------KQLNRDYITMLGSLVKIGELEE  332 (490)
Q Consensus       261 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~~~~l~~~~~~~~~~~~  332 (490)
                      +|...++++....+  .+..++..+...+...|++++|...+++......        .....++..+...+...|++++
T Consensus       177 ~A~~~~~~al~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  254 (330)
T 3hym_B          177 LAERFFSQALSIAP--EDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAE  254 (330)
T ss_dssp             HHHHHHHHHHTTCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHhCC--CChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHH
Confidence            55555555555443  3445555555555566666666666555554331        1223456666666666666666


Q ss_pred             HHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-hccCC
Q 011236          333 AEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY-ADKNN  399 (490)
Q Consensus       333 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~-~~~~~  399 (490)
                      |...+++..+.. +.+...+..+...|.+.|++++|...|++..+..+. +...+..+..++ ...|+
T Consensus       255 A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~g~  320 (330)
T 3hym_B          255 ALDYHRQALVLI-PQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRRD-DTFSVTMLGHCIEMYIGD  320 (330)
T ss_dssp             HHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCSC-CHHHHHHHHHHHHTTTTC
T ss_pred             HHHHHHHHHhhC-ccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCCC-chHHHHHHHHHHHHHhCc
Confidence            666666666542 224556666666666777777777777666665433 555666666655 33444

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.89  E-value=1.8e-18  Score=168.40  Aligned_cols=404  Identities=10%  Similarity=0.017  Sum_probs=299.7

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHH
Q 011236           66 KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLN  145 (490)
Q Consensus        66 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~  145 (490)
                      +-+...|..++. +.+.|+++.|..+|+.+.+.. |.+...+...+..+.+.|+++.|..+|++.....|+...|..++.
T Consensus        10 P~~~~~w~~l~~-~~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~~~~   87 (530)
T 2ooe_A           10 PYDLDAWSILIR-EAQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLS   87 (530)
T ss_dssp             TTCHHHHHHHHH-HHHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHH-HHHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHHHHH
Confidence            457889999998 478899999999999999886 577888999999999999999999999999998898888888775


Q ss_pred             HH-HhcCChhHHHH----HHHHHHhc-CCCC-CcchHHHHHHHHHh---------cCCcCcHHHHHHHHHHCCCCCCHHH
Q 011236          146 CY-VREGLVDESLS----LMQKMKEM-GSFG-SALNYNGIMCLYTN---------TGQHEKIPDVLLDMKENGVPPDNFS  209 (490)
Q Consensus       146 ~~-~~~g~~~~a~~----~~~~m~~~-~~~p-~~~~~~~l~~~~~~---------~~~~~~a~~~~~~m~~~~~~p~~~~  209 (490)
                      .. ...|+.+.|.+    +|+..... |..| +...|...+.....         .|+++.|..+|++.++....+....
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            33 45678877765    77766543 5444 44567777766554         6889999999999988321111233


Q ss_pred             HHHHHHHH-------------hccCChHHHHHHHHHHHh-----CCC---CCCC--------HHHHHHHHHHHHHc----
Q 011236          210 YRICINSY-------------GARSELSSMENVLQEMES-----QSH---ISMD--------WGTYSTVANYYIIA----  256 (490)
Q Consensus       210 ~~~li~~~-------------~~~g~~~~a~~~~~~~~~-----~~~---~~~~--------~~~~~~li~~~~~~----  256 (490)
                      |.......             .+.+++..|..++.+...     +..   ++|+        ...|...+......    
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            43322211             134567778777765210     221   3343        23444444332222    


Q ss_pred             CCH----HHHHHHHHHHhhhhccCCChhhHHHHHHHHHh-------cCChh-------HHHHHHHHHHHhcCCCChhhHH
Q 011236          257 GLK----EKAIIYLKKCEDIVSKSKDALGYNHLISHYAS-------LGNKD-------EMMKFWGLQKIKCKKQLNRDYI  318 (490)
Q Consensus       257 ~~~----~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~-------~a~~~~~~~~~~~~~~~~~~~~  318 (490)
                      ++.    +++..+|++.....+  .+...|...+..+..       .|+++       +|..+|++......+.+...|.
T Consensus       248 ~~~~~~~~~a~~~y~~al~~~p--~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~  325 (530)
T 2ooe_A          248 EDQTLITKRVMFAYEQCLLVLG--HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYF  325 (530)
T ss_dssp             SCSHHHHHHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHH
T ss_pred             CcchhHHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHH
Confidence            222    477889999988765  578889888888875       79987       8999999887633324677889


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc--hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-Hh
Q 011236          319 TMLGSLVKIGELEEAEKMLEEWELSCYCYDF--RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG-YA  395 (490)
Q Consensus       319 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~-~~  395 (490)
                      .++..+.+.|++++|..+|+++.+.  .|+.  ..|..++..+.+.|++++|..+|++..+.... +...|...+.. +.
T Consensus       326 ~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~-~~~~~~~~a~~~~~  402 (530)
T 2ooe_A          326 AYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART-RHHVYVTAALMEYY  402 (530)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTC-CTHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCC-chHHHHHHHHHHHH
Confidence            9999999999999999999999985  4543  47888888899999999999999999886432 33344333322 34


Q ss_pred             ccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-----hhhhHHHHHHHHh
Q 011236          396 DKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-----RNMYHALTEAHIR  469 (490)
Q Consensus       396 ~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-----~~~~~~l~~~~~~  469 (490)
                      ..|+.++|..+|+++++..       | +...|..++..+.+.|+.++|..+|++.....+.     ...|...+.....
T Consensus       403 ~~~~~~~A~~~~e~al~~~-------p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~lw~~~~~~e~~  475 (530)
T 2ooe_A          403 CSKDKSVAFKIFELGLKKY-------GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESN  475 (530)
T ss_dssp             HTCCHHHHHHHHHHHHHHH-------TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHHHHHHHHHHHH
T ss_pred             HcCChhHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHH
Confidence            6899999999999999833       4 4578899999999999999999999999987653     4488888998888


Q ss_pred             cC--CcHHHHHHHHHh
Q 011236          470 SG--QEVDGLLESMKA  483 (490)
Q Consensus       470 ~g--~~a~~~~~~m~~  483 (490)
                      .|  +.+..+.+++.+
T Consensus       476 ~G~~~~~~~~~~r~~~  491 (530)
T 2ooe_A          476 IGDLASILKVEKRRFT  491 (530)
T ss_dssp             SSCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            89  778888877764

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.88  E-value=7e-20  Score=167.10  Aligned_cols=290  Identities=10%  Similarity=-0.048  Sum_probs=194.2

Q ss_pred             CChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHH
Q 011236          135 KVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICI  214 (490)
Q Consensus       135 p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li  214 (490)
                      .+...+..+...+...|++++|+++|+++....+. +...+..++..+...|++++|..+++++.+... .+...+..+.
T Consensus        20 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~   97 (330)
T 3hym_B           20 ENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPF-HASCLPVHIGTLVELNKANELFYLSHKLVDLYP-SNPVSWFAVG   97 (330)
T ss_dssp             CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TSTHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-ChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhCc-CCHHHHHHHH
Confidence            35556777777788888888888888888776543 566666777777788888888888888776432 3556677777


Q ss_pred             HHHhccC-ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcC
Q 011236          215 NSYGARS-ELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG  293 (490)
Q Consensus       215 ~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  293 (490)
                      ..+...| ++++|...|+++. +... .+...+..+..++...|++++|+..|+++....+  .+...+..+...+...|
T Consensus        98 ~~~~~~~~~~~~A~~~~~~a~-~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~--~~~~~~~~l~~~~~~~~  173 (330)
T 3hym_B           98 CYYLMVGHKNEHARRYLSKAT-TLEK-TYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMK--GCHLPMLYIGLEYGLTN  173 (330)
T ss_dssp             HHHHHSCSCHHHHHHHHHHHH-TTCT-TCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTT--TCSHHHHHHHHHHHHTT
T ss_pred             HHHHHhhhhHHHHHHHHHHHH-HhCC-ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhcc--ccHHHHHHHHHHHHHHh
Confidence            7777777 7888888888777 5443 4456677777777778888888888777776554  34556666777777777


Q ss_pred             ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC--------CCCchhHHHHHHHHHhcCCH
Q 011236          294 NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY--------CYDFRVPNIILLGYSQKGMI  365 (490)
Q Consensus       294 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--------~~~~~~~~~l~~~~~~~g~~  365 (490)
                      ++++|...+++.....+ .+...+..+...+...|++++|...++++.+...        +.+..++..+...|...|++
T Consensus       174 ~~~~A~~~~~~al~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~  252 (330)
T 3hym_B          174 NSKLAERFFSQALSIAP-EDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKY  252 (330)
T ss_dssp             CHHHHHHHHHHHHTTCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCH
T ss_pred             hHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCH
Confidence            77777777776666554 4556667777777777777777777776665311        22345566666666666666


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHH-HcCCC
Q 011236          366 EKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWL-GDNRD  439 (490)
Q Consensus       366 ~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~-~~~g~  439 (490)
                      ++|...+++..+..+. +...|..+...+...|++++|...++++++       +.|+ ...+..+..++ ...|+
T Consensus       253 ~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~-------~~p~~~~~~~~l~~~~~~~~g~  320 (330)
T 3hym_B          253 AEALDYHRQALVLIPQ-NASTYSAIGYIHSLMGNFENAVDYFHTALG-------LRRDDTFSVTMLGHCIEMYIGD  320 (330)
T ss_dssp             HHHHHHHHHHHHHSTT-CSHHHHHHHHHHHHHTCHHHHHHHHHTTTT-------TCSCCHHHHHHHHHHHHTTTTC
T ss_pred             HHHHHHHHHHHhhCcc-chHHHHHHHHHHHHhccHHHHHHHHHHHHc-------cCCCchHHHHHHHHHHHHHhCc
Confidence            6666666666665433 555666666666666666666666666655       3343 34555555555 33444

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.88  E-value=5.8e-18  Score=163.12  Aligned_cols=368  Identities=11%  Similarity=-0.004  Sum_probs=305.7

Q ss_pred             CCHHHHHHHHHHHHh----cCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHh----hcCHHHHHHHHHHccccCCChh
Q 011236           67 ISELELQRVIRQLRS----RKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGK----VRGLESAETYFNSLNDEDKVDK  138 (490)
Q Consensus        67 ~~~~~~~~ll~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~~~p~~~  138 (490)
                      -+...+..+...+..    .+++++|+..|++..+.|   ++..+..+...|..    .+++++|...|++....+ +..
T Consensus        37 g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~-~~~  112 (490)
T 2xm6_A           37 GEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG-LPQ  112 (490)
T ss_dssp             TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT-CHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-CHH
Confidence            367888888888887    899999999999999886   57788888888888    899999999999988765 566


Q ss_pred             HHHHHHHHHHh----cCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHh----cCCcCcHHHHHHHHHHCCCCCCHHHH
Q 011236          139 LYGALLNCYVR----EGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTN----TGQHEKIPDVLLDMKENGVPPDNFSY  210 (490)
Q Consensus       139 ~~~~li~~~~~----~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~  210 (490)
                      .+..|...|..    .+++++|+..|++..+.|   +...+..|...|..    .+++++|.+.|++..+.|   +...+
T Consensus       113 a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~  186 (490)
T 2xm6_A          113 AQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSC  186 (490)
T ss_dssp             HHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            78888888888    889999999999998875   66788888888887    789999999999998864   67788


Q ss_pred             HHHHHHHhc----cCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHhhhhccCCChhhH
Q 011236          211 RICINSYGA----RSELSSMENVLQEMESQSHISMDWGTYSTVANYYII----AGLKEKAIIYLKKCEDIVSKSKDALGY  282 (490)
Q Consensus       211 ~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  282 (490)
                      ..+...|..    .++.++|.+.|++.. +.+   +...+..+...|..    .+++++|..+|++..+.+    +...+
T Consensus       187 ~~Lg~~y~~g~g~~~~~~~A~~~~~~a~-~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~----~~~a~  258 (490)
T 2xm6_A          187 NQLGYMYSRGLGVERNDAISAQWYRKSA-TSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG----NSIAQ  258 (490)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHH-HTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT----CHHHH
T ss_pred             HHHHHHHhcCCCCCcCHHHHHHHHHHHH-HCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC----CHHHH
Confidence            888888887    899999999999988 443   45677778888887    889999999999987643    45567


Q ss_pred             HHHHHHHHh----cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc-----CCHHHHHHHHHHHHhcCCCCCchhHH
Q 011236          283 NHLISHYAS----LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI-----GELEEAEKMLEEWELSCYCYDFRVPN  353 (490)
Q Consensus       283 ~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~~~~~~~~  353 (490)
                      ..+...|..    .++.++|...|++....   .+...+..+...|...     +++++|...+++..+.|   +...+.
T Consensus       259 ~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~---~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~  332 (490)
T 2xm6_A          259 FRLGYILEQGLAGAKEPLKALEWYRKSAEQ---GNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG---DATAQA  332 (490)
T ss_dssp             HHHHHHHHHTTTSSCCHHHHHHHHHHHHTT---TCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHHHHc---CCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC---CHHHHH
Confidence            778888877    89999999999987655   3456777788888877     89999999999998874   345677


Q ss_pred             HHHHHHHhcC---CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHHHHHHHHHHhhhcCcCCCcchhh
Q 011236          354 IILLGYSQKG---MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAFECMKEALAVHEENKFWRPKPSL  426 (490)
Q Consensus       354 ~l~~~~~~~g---~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~  426 (490)
                      .+...|...|   ++++|...|++..+.|   +...+..+...|..    .+++++|..+|+++.+     .+   +...
T Consensus       333 ~lg~~y~~~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~-----~~---~~~a  401 (490)
T 2xm6_A          333 NLGAIYFRLGSEEEHKKAVEWFRKAAAKG---EKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAE-----QG---LSAA  401 (490)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH-----TT---CHHH
T ss_pred             HHHHHHHhCCCcccHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHh-----CC---CHHH
Confidence            7888888766   7899999999999874   78889999999988    8999999999999988     33   4667


Q ss_pred             HHHHHHHHHc----CCCHHHHHHHHHHHHhccc---c-hhhhHHHHHHHHh
Q 011236          427 VSSILDWLGD----NRDVEEVEAFVSSLKIKVQ---K-RNMYHALTEAHIR  469 (490)
Q Consensus       427 ~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~---~-~~~~~~l~~~~~~  469 (490)
                      +..+...|..    .++.++|...|++..+.++   . +.....+...+..
T Consensus       402 ~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~~a~~~l~~~~~~  452 (490)
T 2xm6_A          402 QVQLGEIYYYGLGVERDYVQAWAWFDTASTNDMNLFGTENRNITEKKLTAK  452 (490)
T ss_dssp             HHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCCCcCCHHHHHHHHhcCHh
Confidence            8888888887    8999999999999999883   3 5555555444443

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.87  E-value=2.2e-20  Score=173.31  Aligned_cols=271  Identities=10%  Similarity=-0.070  Sum_probs=179.0

Q ss_pred             chHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHH
Q 011236          173 LNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANY  252 (490)
Q Consensus       173 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~  252 (490)
                      ..+..+...+...|++++|...|+++.+.. +.+..++..+..++...|++++|...|+++. +.+. .+..++..+..+
T Consensus        65 ~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al-~~~~-~~~~~~~~l~~~  141 (368)
T 1fch_A           65 PQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCL-ELKP-DNQTALMALAVS  141 (368)
T ss_dssp             SSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHH-hcCC-CCHHHHHHHHHH
Confidence            344455555555555555555555555432 1244455555555555555555555555554 3222 345555555555


Q ss_pred             HHHcCCHHHHHHHHHHHhhhhccCCChhhHHH---------------HHHHHHhcCChhHHHHHHHHHHHhcCCC-Chhh
Q 011236          253 YIIAGLKEKAIIYLKKCEDIVSKSKDALGYNH---------------LISHYASLGNKDEMMKFWGLQKIKCKKQ-LNRD  316 (490)
Q Consensus       253 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~---------------l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~  316 (490)
                      |...|++++|...|+++....+.  +...+..               .+..+...|++++|...++++....+.. +..+
T Consensus       142 ~~~~g~~~~A~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~  219 (368)
T 1fch_A          142 FTNESLQRQACEILRDWLRYTPA--YAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDV  219 (368)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTSTT--TGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCcC--cHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHH
Confidence            66666666666666655544332  2222111               1223337888888888888887776522 5778


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      +..+...+...|++++|...++++.+. .+.+..++..+...|...|++++|...|+++.+..+. +..++..+...|.+
T Consensus       220 ~~~l~~~~~~~g~~~~A~~~~~~al~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~l~~~~~~  297 (368)
T 1fch_A          220 QCGLGVLFNLSGEYDKAVDCFTAALSV-RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPG-YIRSRYNLGISCIN  297 (368)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh-CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHH
Confidence            888888888889999999998888876 2335667888888899999999999999998887543 67788889999999


Q ss_pred             cCCHHHHHHHHHHHHHhhhcCcCCC-----cchhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 011236          397 KNNMEKAFECMKEALAVHEENKFWR-----PKPSLVSSILDWLGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       397 ~~~~~~a~~~~~~~~~~~~~~~~~~-----p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  450 (490)
                      .|++++|...|+++++..|+..+..     ....+|..+..++...|++++|..++++.
T Consensus       298 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  356 (368)
T 1fch_A          298 LGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARD  356 (368)
T ss_dssp             HTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTC
T ss_pred             CCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHHH
Confidence            9999999999999988654332211     11577888888899999999888887643

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.87  E-value=3.2e-20  Score=172.20  Aligned_cols=290  Identities=10%  Similarity=-0.041  Sum_probs=208.9

Q ss_pred             hcCHHHHHH-HHHHccccCC-----ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCc
Q 011236          117 VRGLESAET-YFNSLNDEDK-----VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEK  190 (490)
Q Consensus       117 ~~~~~~A~~-~~~~~~~~~p-----~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  190 (490)
                      .|+++.|.. .|++.....|     +...+..+...+.+.|++++|+..|+++.+..+. +..+|..+..++...|++++
T Consensus        38 ~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~~~~  116 (368)
T 1fch_A           38 LSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPK-HMEAWQYLGTTQAENEQELL  116 (368)
T ss_dssp             --------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHCcCHHH
Confidence            466677776 6665544432     2345666677777777777777777777766433 55667777777777777777


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHH---------------HHHHHHH
Q 011236          191 IPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYST---------------VANYYII  255 (490)
Q Consensus       191 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~---------------li~~~~~  255 (490)
                      |...|+++.+.+ +.+..++..+..++...|++++|...|+++. .... .+...+..               .+..+..
T Consensus       117 A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  193 (368)
T 1fch_A          117 AISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWL-RYTP-AYAHLVTPAEEGAGGAGLGPSKRILGSLLS  193 (368)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HTST-TTGGGCC---------------CTTHHHHH
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCc-CcHHHHHHHHHHhhhhcccHHHHHHHHHhh
Confidence            777777776643 2356667777777777777777777777776 3332 11222211               2333348


Q ss_pred             cCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011236          256 AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEK  335 (490)
Q Consensus       256 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  335 (490)
                      .|++++|...|+++....+..++..++..+...+...|++++|...+++.....+ .+...+..+...+...|++++|..
T Consensus       194 ~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~l~~~~~~~g~~~~A~~  272 (368)
T 1fch_A          194 DSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRP-NDYLLWNKLGATLANGNQSEEAVA  272 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHcCCHHHHHH
Confidence            8999999999999988665312678899999999999999999999998888765 567889999999999999999999


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC----------CHHHHHHHHHHHhccCCHHHHHH
Q 011236          336 MLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTP----------TPNSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p----------~~~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      .++++.+.. +.+...+..+...|.+.|++++|...|+++.+..+..          ...+|..+..+|...|++++|..
T Consensus       273 ~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  351 (368)
T 1fch_A          273 AYRRALELQ-PGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGA  351 (368)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHH
T ss_pred             HHHHHHHhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHH
Confidence            999998863 3456788889999999999999999999988754331          16789999999999999999999


Q ss_pred             HHHHHHH
Q 011236          406 CMKEALA  412 (490)
Q Consensus       406 ~~~~~~~  412 (490)
                      ++++.++
T Consensus       352 ~~~~~l~  358 (368)
T 1fch_A          352 ADARDLS  358 (368)
T ss_dssp             HHTTCHH
T ss_pred             hHHHHHH
Confidence            8887665

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.85  E-value=3.5e-19  Score=165.03  Aligned_cols=272  Identities=9%  Similarity=-0.083  Sum_probs=200.8

Q ss_pred             CcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHH
Q 011236          171 SALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVA  250 (490)
Q Consensus       171 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li  250 (490)
                      +...|..+...+.+.|++++|..+|+++.+.. +.+..++..+..++...|++++|...|+++. +.+. .+..++..+.
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~~~p-~~~~~~~~l~  140 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCL-ELQP-NNLKALMALA  140 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCT-TCHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-hcCC-CCHHHHHHHH
Confidence            34446666666666666666666666666543 2355667777777777777777777777776 4333 4567777777


Q ss_pred             HHHHHcCCHHHHHHHHHHHhhhhccCCChhh----------HHHHHHHHHhcCChhHHHHHHHHHHHhcCC-CChhhHHH
Q 011236          251 NYYIIAGLKEKAIIYLKKCEDIVSKSKDALG----------YNHLISHYASLGNKDEMMKFWGLQKIKCKK-QLNRDYIT  319 (490)
Q Consensus       251 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~----------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~  319 (490)
                      .+|...|++++|+..|+++....+.  +...          +..+...+...|++++|...++++....+. ++..++..
T Consensus       141 ~~~~~~g~~~~A~~~~~~al~~~p~--~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~  218 (365)
T 4eqf_A          141 VSYTNTSHQQDACEALKNWIKQNPK--YKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTG  218 (365)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCHH--HHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHH
T ss_pred             HHHHccccHHHHHHHHHHHHHhCcc--chHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHH
Confidence            8888888888888888877665432  2222          334578888999999999999998888662 26788999


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          320 MLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       320 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      +...+...|++++|...++++.+. .+.+..+|..+..+|...|++++|...|+++.+..+. +..+|..+...|...|+
T Consensus       219 l~~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~g~  296 (365)
T 4eqf_A          219 LGVLFHLSGEFNRAIDAFNAALTV-RPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPG-FIRSRYNLGISCINLGA  296 (365)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-chHHHHHHHHHHHHCCC
Confidence            999999999999999999999886 3446778999999999999999999999999987644 68889999999999999


Q ss_pred             HHHHHHHHHHHHHhhhcCcCCC------cchhhHHHHHHHHHcCCCHHHHHHHHHH
Q 011236          400 MEKAFECMKEALAVHEENKFWR------PKPSLVSSILDWLGDNRDVEEVEAFVSS  449 (490)
Q Consensus       400 ~~~a~~~~~~~~~~~~~~~~~~------p~~~~~~~l~~~~~~~g~~~~a~~~~~~  449 (490)
                      +++|...|+++++..|+..+..      .+..+|..+..++...|+.+.+.++.++
T Consensus       297 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          297 YREAVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             CHHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            9999999999999765433311      1357888999999999999988877665

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.84  E-value=5.6e-20  Score=170.39  Aligned_cols=270  Identities=10%  Similarity=-0.067  Sum_probs=163.8

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011236          138 KLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSY  217 (490)
Q Consensus       138 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  217 (490)
                      ..|..+...+.+.|++++|+.+|+++.+..+. +..+|..+...+...|++++|...|+++.+.. +.+..++..+..++
T Consensus        66 ~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~  143 (365)
T 4eqf_A           66 PGAFEEGLKRLKEGDLPVTILFMEAAILQDPG-DAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVSY  143 (365)
T ss_dssp             TTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            33555555555666666666666665555332 45555556666666666666666666655532 12345555666666


Q ss_pred             hccCChHHHHHHHHHHHhCCCCC---------CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHH
Q 011236          218 GARSELSSMENVLQEMESQSHIS---------MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISH  288 (490)
Q Consensus       218 ~~~g~~~~a~~~~~~~~~~~~~~---------~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  288 (490)
                      ...|++++|...|+++. +....         .....+..+...+...|++++|+..|+++....+...+..++..+...
T Consensus       144 ~~~g~~~~A~~~~~~al-~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~~  222 (365)
T 4eqf_A          144 TNTSHQQDACEALKNWI-KQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGVL  222 (365)
T ss_dssp             HHTTCHHHHHHHHHHHH-HHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHHH
T ss_pred             HccccHHHHHHHHHHHH-HhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHHH
Confidence            66666666666666654 21110         011223345667777777777777777777655421256777777777


Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 011236          289 YASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKA  368 (490)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  368 (490)
                      +...|++++|...|++.....+ .+..++..+..+|...|++++|...++++.+.. +.+..++..+...|.+.|++++|
T Consensus       223 ~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A  300 (365)
T 4eqf_A          223 FHLSGEFNRAIDAFNAALTVRP-EDYSLWNRLGATLANGDRSEEAVEAYTRALEIQ-PGFIRSRYNLGISCINLGAYREA  300 (365)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCCHHHH
Confidence            7777777777777777776654 556677777777777777777877777777652 23456677777777788888888


Q ss_pred             HHHHHHHHHcCCC-----------CCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          369 DAVLKEIVKKGKT-----------PTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       369 ~~~~~~m~~~~~~-----------p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...|+++.+..+.           .+...|..+..++...|+.+.+..+.++...
T Consensus       301 ~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~l~  355 (365)
T 4eqf_A          301 VSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLGDLD  355 (365)
T ss_dssp             HHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTTCCG
T ss_pred             HHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHhhHH
Confidence            8888777664321           1246678888888888888877776665433

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.84  E-value=2.3e-16  Score=151.91  Aligned_cols=364  Identities=11%  Similarity=0.040  Sum_probs=302.2

Q ss_pred             HHHHHHHHHHhCCCCCChhhHHHHHHHHHh----hcCHHHHHHHHHHccccCCChhHHHHHHHHHHh----cCChhHHHH
Q 011236           87 HALQVSEWMSGQGLAFSVHDHAVQLDLIGK----VRGLESAETYFNSLNDEDKVDKLYGALLNCYVR----EGLVDESLS  158 (490)
Q Consensus        87 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~  158 (490)
                      .+++.++...+.|   ++.....+...|..    .++++.|...|+...+.+ +..++..|...|..    .++.++|..
T Consensus        25 ~~~~~~~~~a~~g---~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~-~~~a~~~Lg~~y~~g~g~~~~~~~A~~  100 (490)
T 2xm6_A           25 VNLEQLKQKAESG---EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG-YTPAEYVLGLRYMNGEGVPQDYAQAVI  100 (490)
T ss_dssp             CCHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHTSSSCCCHHHHHH
T ss_pred             HHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence            3456666666665   67777888888877    899999999999988764 56788889999998    999999999


Q ss_pred             HHHHHHhcCCCCCcchHHHHHHHHHh----cCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhc----cCChHHHHHHH
Q 011236          159 LMQKMKEMGSFGSALNYNGIMCLYTN----TGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGA----RSELSSMENVL  230 (490)
Q Consensus       159 ~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~  230 (490)
                      .|++..+.|   +...+..|...|..    .+++++|.+.|++..+.|   +...+..+...|..    .+++++|.+.|
T Consensus       101 ~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~  174 (490)
T 2xm6_A          101 WYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRDYVMAREWY  174 (490)
T ss_dssp             HHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            999998875   66788888888888    789999999999998875   56677778888876    78999999999


Q ss_pred             HHHHhCCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHh----cCChhHHHHHH
Q 011236          231 QEMESQSHISMDWGTYSTVANYYII----AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYAS----LGNKDEMMKFW  302 (490)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~  302 (490)
                      ++.. +.+   +...+..+...|..    .+++++|...|++..+.    .+..++..+...|..    .+++++|..+|
T Consensus       175 ~~a~-~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~----~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~  246 (490)
T 2xm6_A          175 SKAA-EQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATS----GDELGQLHLADMYYFGIGVTQDYTQSRVLF  246 (490)
T ss_dssp             HHHH-HTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHH-HCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHC----CCHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            9998 443   57788889999988    89999999999998764    355678888888876    88999999999


Q ss_pred             HHHHHhcCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhc-----CCHHHHHHHHH
Q 011236          303 GLQKIKCKKQLNRDYITMLGSLVK----IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQK-----GMIEKADAVLK  373 (490)
Q Consensus       303 ~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----g~~~~A~~~~~  373 (490)
                      ++....   .+...+..+...|..    .++.++|...|++..+.|   +...+..+...|...     +++++|...|+
T Consensus       247 ~~a~~~---~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~  320 (490)
T 2xm6_A          247 SQSAEQ---GNSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG---NSDGQYYLAHLYDKGAEGVAKNREQAISWYT  320 (490)
T ss_dssp             HHHHTT---TCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHH
T ss_pred             HHHHHC---CCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHH
Confidence            987765   345677777777877    899999999999998764   445677788888887     89999999999


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHhccC---CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc----CCCHHHHHHH
Q 011236          374 EIVKKGKTPTPNSWSIIAAGYADKN---NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD----NRDVEEVEAF  446 (490)
Q Consensus       374 ~m~~~~~~p~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~  446 (490)
                      +..+.|   +...+..+...|...|   +.++|+++|+++.+     .   .+...+..+...|..    .+++++|...
T Consensus       321 ~a~~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~-----~---~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~  389 (490)
T 2xm6_A          321 KSAEQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAA-----K---GEKAAQFNLGNALLQGKGVKKDEQQAAIW  389 (490)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHH-----T---TCHHHHHHHHHHHHHTSSSCCCHHHHHHH
T ss_pred             HHHhcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHH-----C---CCHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence            999875   5677888888888766   78999999999998     3   356778888888888    8999999999


Q ss_pred             HHHHHhcccchhhhHHHHHHHHh----cC--CcHHHHHHHHHhCCC
Q 011236          447 VSSLKIKVQKRNMYHALTEAHIR----SG--QEVDGLLESMKADDI  486 (490)
Q Consensus       447 ~~~~~~~~~~~~~~~~l~~~~~~----~g--~~a~~~~~~m~~~~~  486 (490)
                      |++..+.+. +..+..|...|.+    .+  ++|..+|++..+.+.
T Consensus       390 ~~~A~~~~~-~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~  434 (490)
T 2xm6_A          390 MRKAAEQGL-SAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDM  434 (490)
T ss_dssp             HHHHHHTTC-HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHhCCC-HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC
Confidence            999988654 7778889999987    55  899999999887663

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.83  E-value=1.4e-18  Score=158.15  Aligned_cols=271  Identities=8%  Similarity=-0.139  Sum_probs=171.6

Q ss_pred             HHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Q 011236          175 YNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYI  254 (490)
Q Consensus       175 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~  254 (490)
                      +..+...+...|++++|..+|+++.+... .+...+..+..++...|++++|...++++. +... .+..++..+..+|.
T Consensus        24 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~-~~~~-~~~~~~~~la~~~~  100 (327)
T 3cv0_A           24 PMEEGLSMLKLANLAEAALAFEAVCQAAP-EREEAWRSLGLTQAENEKDGLAIIALNHAR-MLDP-KDIAVHAALAVSHT  100 (327)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-hcCc-CCHHHHHHHHHHHH
Confidence            33344444444444444444444443211 233444444445555555555555555544 2222 33444555555555


Q ss_pred             HcCCHHHHHHHHHHHhhhhccCCChhhHHHH--------------HH-HHHhcCChhHHHHHHHHHHHhcCCCChhhHHH
Q 011236          255 IAGLKEKAIIYLKKCEDIVSKSKDALGYNHL--------------IS-HYASLGNKDEMMKFWGLQKIKCKKQLNRDYIT  319 (490)
Q Consensus       255 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (490)
                      ..|++++|...++++....+  .+...+..+              .. .+...|++++|...+++.....+ .+...+..
T Consensus       101 ~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~  177 (327)
T 3cv0_A          101 NEHNANAALASLRAWLLSQP--QYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNP-NDAQLHAS  177 (327)
T ss_dssp             HTTCHHHHHHHHHHHHHTST--TTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHST-TCHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCC--ccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCC-CCHHHHHH
Confidence            55555555555555544332  222222222              22 36677788888888887777665 56777888


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          320 MLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       320 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      +...+...|++++|...++++.+.. +.+..++..+...|...|++++|...++++.+..+. +..+|..+...|...|+
T Consensus       178 la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~g~  255 (327)
T 3cv0_A          178 LGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDINPG-YVRVMYNMAVSYSNMSQ  255 (327)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhcc
Confidence            8888888888888888888888762 335667888888888999999999999988887544 67788888999999999


Q ss_pred             HHHHHHHHHHHHHhhhcCcCCCc------chhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          400 MEKAFECMKEALAVHEENKFWRP------KPSLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       400 ~~~a~~~~~~~~~~~~~~~~~~p------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      +++|.+.+++++...+...+...      +...+..+..++.+.|++++|..++++..+.
T Consensus       256 ~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  315 (327)
T 3cv0_A          256 YDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEP  315 (327)
T ss_dssp             HHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSHH
T ss_pred             HHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            99999999998885432211111      4578888888999999999998888755443

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.83  E-value=7.1e-19  Score=160.16  Aligned_cols=280  Identities=10%  Similarity=-0.029  Sum_probs=172.9

Q ss_pred             hHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHh
Q 011236          106 DHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTN  184 (490)
Q Consensus       106 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~  184 (490)
                      .+......+...|++++|..+|+.+....| +..+|..+...+...|++++|...++++.+.... +..++..+...+..
T Consensus        23 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~  101 (327)
T 3cv0_A           23 NPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTN  101 (327)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcC-CHHHHHHHHHHHHH
Confidence            344455555566666666666666655554 3555555666666666666666666666555322 44455555555555


Q ss_pred             cCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHH-HH-HHHHcCCHHHH
Q 011236          185 TGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTV-AN-YYIIAGLKEKA  262 (490)
Q Consensus       185 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l-i~-~~~~~~~~~~a  262 (490)
                      .|++++|.+.++++.+.... +...+..+...+                       |+......+ .. .+...|++++|
T Consensus       102 ~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~A  157 (327)
T 3cv0_A          102 EHNANAALASLRAWLLSQPQ-YEQLGSVNLQAD-----------------------VDIDDLNVQSEDFFFAAPNEYREC  157 (327)
T ss_dssp             TTCHHHHHHHHHHHHHTSTT-TTTC-------------------------------------------CCTTSHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHHH-----------------------HHHHHHHHHHHhHHHHHcccHHHH
Confidence            55555555555555543211 111111110000                       000001111 22 25666777778


Q ss_pred             HHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          263 IIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      ...++++....+  .+..++..+...+...|++++|...+++.....+ .+...+..+...+...|++++|...++++.+
T Consensus       158 ~~~~~~~~~~~~--~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~  234 (327)
T 3cv0_A          158 RTLLHAALEMNP--NDAQLHASLGVLYNLSNNYDSAAANLRRAVELRP-DDAQLWNKLGATLANGNRPQEALDAYNRALD  234 (327)
T ss_dssp             HHHHHHHHHHST--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhCC--CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            877777776554  4667777777778888888888888877776654 5566777778888888888888888888777


Q ss_pred             cCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-----------CHHHHHHHHHHHhccCCHHHHHHHHHHHH
Q 011236          343 SCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTP-----------TPNSWSIIAAGYADKNNMEKAFECMKEAL  411 (490)
Q Consensus       343 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p-----------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  411 (490)
                      .. +.+..++..+...|...|++++|...++++.+..+..           +..+|..+..++.+.|++++|..++++++
T Consensus       235 ~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  313 (327)
T 3cv0_A          235 IN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNV  313 (327)
T ss_dssp             HC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCS
T ss_pred             cC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            52 3355677778888888888888888888887754332           36678888888888888888888887766


Q ss_pred             Hhh
Q 011236          412 AVH  414 (490)
Q Consensus       412 ~~~  414 (490)
                      +..
T Consensus       314 ~~~  316 (327)
T 3cv0_A          314 EPF  316 (327)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            533

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.83  E-value=1.5e-16  Score=154.95  Aligned_cols=379  Identities=9%  Similarity=-0.015  Sum_probs=278.1

Q ss_pred             HHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCC
Q 011236           92 SEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFG  170 (490)
Q Consensus        92 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p  170 (490)
                      ++..++.. |.+...+..++.. .+.|+++.|..+|+.+....| +...|..++..+.+.|++++|..+|+++....  |
T Consensus         2 le~al~~~-P~~~~~w~~l~~~-~~~~~~~~a~~~~e~al~~~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--p   77 (530)
T 2ooe_A            2 AEKKLEEN-PYDLDAWSILIRE-AQNQPIDKARKTYERLVAQFPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--L   77 (530)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHH-HHSSCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--C
T ss_pred             hhhHhhhC-CCCHHHHHHHHHH-HHhCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--C
Confidence            44444544 4577788888874 778999999999999999888 67889999999999999999999999998874  5


Q ss_pred             CcchHHHHHHHH-HhcCCcCcHHH----HHHHHHH-CCCCC-CHHHHHHHHHHHhc---------cCChHHHHHHHHHHH
Q 011236          171 SALNYNGIMCLY-TNTGQHEKIPD----VLLDMKE-NGVPP-DNFSYRICINSYGA---------RSELSSMENVLQEME  234 (490)
Q Consensus       171 ~~~~~~~l~~~~-~~~~~~~~a~~----~~~~m~~-~~~~p-~~~~~~~li~~~~~---------~g~~~~a~~~~~~~~  234 (490)
                      ++..|...+... ...|+.+.|.+    +|+.... .|..| +...|...+.....         .|+++.|..+|++..
T Consensus        78 ~~~lw~~~~~~~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al  157 (530)
T 2ooe_A           78 HIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGC  157 (530)
T ss_dssp             CHHHHHHHHHHHHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHH
Confidence            777777777533 45688888776    6776654 35444 45677777766544         688999999999998


Q ss_pred             hCCCCCCCHHHHHHHHHHH-------------HHcCCHHHHHHHHHHHhh------hh---ccCCC--------hhhHHH
Q 011236          235 SQSHISMDWGTYSTVANYY-------------IIAGLKEKAIIYLKKCED------IV---SKSKD--------ALGYNH  284 (490)
Q Consensus       235 ~~~~~~~~~~~~~~li~~~-------------~~~~~~~~a~~~~~~~~~------~~---~~~~~--------~~~~~~  284 (490)
                       +.........|.......             ...++++.|..++..+..      ..   .+ |+        ...|..
T Consensus       158 -~~P~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~-p~~~~~~~~~~~~w~~  235 (530)
T 2ooe_A          158 -VNPMINIEQLWRDYNKYEEGINIHLAKKMIEDRSRDYMNARRVAKEYETVMKGLDRNAPSVP-PQNTPQEAQQVDMWKK  235 (530)
T ss_dssp             -TSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHCCSSSCCCC-CC--CCHHHHHHHHHH
T ss_pred             -hchhhhHHHHHHHHHHHHHhhchhHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCC-CCCChhHHHHHHHHHH
Confidence             521111123333222211             123567777777765321      10   11 22        245555


Q ss_pred             HHHHHHhc----CCh----hHHHHHHHHHHHhcCCCChhhHHHHHHHHHh-------cCCHH-------HHHHHHHHHHh
Q 011236          285 LISHYASL----GNK----DEMMKFWGLQKIKCKKQLNRDYITMLGSLVK-------IGELE-------EAEKMLEEWEL  342 (490)
Q Consensus       285 l~~~~~~~----~~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~~-------~a~~~~~~~~~  342 (490)
                      .+......    ++.    +++..+|++.....+ .+...|..++..+.+       .|+++       +|..++++..+
T Consensus       236 ~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~p-~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~  314 (530)
T 2ooe_A          236 YIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVLG-HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIS  314 (530)
T ss_dssp             HHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHcCCccCCcchhHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHH
Confidence            55443322    232    377889998888766 677888888888775       79987       89999999986


Q ss_pred             cCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCC
Q 011236          343 SCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTP-NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWR  421 (490)
Q Consensus       343 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  421 (490)
                      .-.+.+...|..++..+.+.|++++|..+|+++++..+. +. ..|..++..+.+.|+.++|..+|+++++       ..
T Consensus       315 ~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~-------~~  386 (530)
T 2ooe_A          315 TLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDI-DPTLVYIQYMKFARRAEGIKSGRMIFKKARE-------DA  386 (530)
T ss_dssp             TTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-------CT
T ss_pred             HhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCcccc-CchHHHHHHHHHHHHhcCHHHHHHHHHHHHh-------cc
Confidence            323345778899999999999999999999999996432 33 5899999999999999999999999988       22


Q ss_pred             cc-hhhHHHHHHH-HHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhCC
Q 011236          422 PK-PSLVSSILDW-LGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKADD  485 (490)
Q Consensus       422 p~-~~~~~~l~~~-~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~  485 (490)
                      |+ ...+...... +...|+.++|..+|++..+..|. +..|..++..+.+.|  ++|..+|++....+
T Consensus       387 ~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~  455 (530)
T 2ooe_A          387 RTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  455 (530)
T ss_dssp             TCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSC
T ss_pred             CCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhcc
Confidence            33 2333332222 33689999999999999999998 999999999999999  89999999998764

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.82  E-value=7.4e-17  Score=154.87  Aligned_cols=400  Identities=13%  Similarity=0.007  Sum_probs=253.4

Q ss_pred             CCCCCChHHHHHHHHHc----CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhC-----C---CCCChhhHHHHHHHH
Q 011236           47 GDPDVSLTPVLDQWVLE----GQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQ-----G---LAFSVHDHAVQLDLI  114 (490)
Q Consensus        47 ~~~~~a~~~~~~~~~~~----~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~---~~~~~~~~~~l~~~~  114 (490)
                      ++.+.++..+-+.+...    +.......|+.+...+...|++++|++.|++..+.     +   .+....++..+..+|
T Consensus        25 ~~~~~~l~~~e~~~~~~~~~~~~~~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y  104 (472)
T 4g1t_A           25 MEGENSLDDFEDKVFYRTEFQNREFKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVY  104 (472)
T ss_dssp             TTTCCCHHHHHHHHHHHTTSCC---CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHH
Confidence            34455555444433322    33444667899999999999999999999987652     1   123345677788888


Q ss_pred             HhhcCHHHHHHHHHHcccc--------CC-ChhHHHHHHHHHHhc--CChhHHHHHHHHHHhcCCCCCcchHHHHHHH--
Q 011236          115 GKVRGLESAETYFNSLNDE--------DK-VDKLYGALLNCYVRE--GLVDESLSLMQKMKEMGSFGSALNYNGIMCL--  181 (490)
Q Consensus       115 ~~~~~~~~A~~~~~~~~~~--------~p-~~~~~~~li~~~~~~--g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~--  181 (490)
                      ...|++++|...+++....        .+ ...++..+..++...  +++++|+..|++..+..+. ++..+..+..+  
T Consensus       105 ~~~g~~~~A~~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~-~~~~~~~~~~~~~  183 (472)
T 4g1t_A          105 YHMGRLSDVQIYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPK-NPEFTSGLAIASY  183 (472)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHH
T ss_pred             HHcCChHHHHHHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHH
Confidence            9999999999988876542        12 345666666566554  4688999999998887543 45555555444  


Q ss_pred             -HHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhc----cCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc
Q 011236          182 -YTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGA----RSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIA  256 (490)
Q Consensus       182 -~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~  256 (490)
                       +...++.++|++.+++..+.+. .+..++..+...+..    .|++++|.+++++.. ..+. .+..++..+...|...
T Consensus       184 ~l~~~~~~~~al~~~~~al~l~p-~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al-~~~~-~~~~~~~~lg~~~~~~  260 (472)
T 4g1t_A          184 RLDNWPPSQNAIDPLRQAIRLNP-DNQYLKVLLALKLHKMREEGEEEGEGEKLVEEAL-EKAP-GVTDVLRSAAKFYRRK  260 (472)
T ss_dssp             HHHHSCCCCCTHHHHHHHHHHCS-SCHHHHHHHHHHHHHCC------CHHHHHHHHHH-HHCS-SCHHHHHHHHHHHHHT
T ss_pred             HhcCchHHHHHHHHHHHHhhcCC-cchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH-HhCc-cHHHHHHHHHHHHHHc
Confidence             3456778889999988877532 345555555544443    467788999998887 4444 5677788889999999


Q ss_pred             CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011236          257 GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM  336 (490)
Q Consensus       257 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  336 (490)
                      |++++|+..+++..+..+  .+..++..+..+|...+....+         . .      ...........+..+.|...
T Consensus       261 ~~~~~A~~~~~~al~~~p--~~~~~~~~lg~~y~~~~~~~~~---------~-~------~~~~~~~~~~~~~~~~A~~~  322 (472)
T 4g1t_A          261 DEPDKAIELLKKALEYIP--NNAYLHCQIGCCYRAKVFQVMN---------L-R------ENGMYGKRKLLELIGHAVAH  322 (472)
T ss_dssp             TCHHHHHHHHHHHHHHST--TCHHHHHHHHHHHHHHHHHHHH---------C-------------CHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHhCC--ChHHHHHHHHHHHHHHHHHhhh---------H-H------HHHHHHHHHHHhhHHHHHHH
Confidence            999999999999887665  4667777777666432111000         0 0      00001111122346678888


Q ss_pred             HHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHH--HHHHHHH-HHhccCCHHHHHHHHHHHHHh
Q 011236          337 LEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPN--SWSIIAA-GYADKNNMEKAFECMKEALAV  413 (490)
Q Consensus       337 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~--~~~~l~~-~~~~~~~~~~a~~~~~~~~~~  413 (490)
                      +++..+.. +.+...+..+...|...|++++|...|++..+..+.|...  .+..+.. .+...|+.++|+..|+++++ 
T Consensus       323 ~~~a~~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~-  400 (472)
T 4g1t_A          323 LKKADEAN-DNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK-  400 (472)
T ss_dssp             HHHHHHHC-TTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH-
T ss_pred             HHHHhhcC-CchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-
Confidence            88877763 3456678888899999999999999999988865443221  2333332 24567889999999999988 


Q ss_pred             hhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhCC
Q 011236          414 HEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKADD  485 (490)
Q Consensus       414 ~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~  485 (490)
                            +.|+......         ....+.+++++..+..|. +.+|..++..|...|  ++|++.|++..+.|
T Consensus       401 ------i~~~~~~~~~---------~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~  460 (472)
T 4g1t_A          401 ------INQKSREKEK---------MKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESG  460 (472)
T ss_dssp             ------SCCCCHHHHH---------HHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC-------------
T ss_pred             ------cCcccHHHHH---------HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence                  4465533322         234456677777777888 889999999999998  88999998887654

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.82  E-value=1.8e-16  Score=152.20  Aligned_cols=387  Identities=10%  Similarity=-0.076  Sum_probs=233.1

Q ss_pred             CcccHHHhhccCCCCCCChHHHHHHHHH----c----CCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC------
Q 011236           35 ARNNLYSRISPLGDPDVSLTPVLDQWVL----E----GQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGL------  100 (490)
Q Consensus        35 ~~~~l~~~l~~~~~~~~a~~~~~~~~~~----~----~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~------  100 (490)
                      .++.|-..+...|+.++|+. .+++-.+    .    ..+....+|+.+...+...|++++|...+++..+...      
T Consensus        53 ~yn~Lg~~~~~~G~~~eAl~-~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~~  131 (472)
T 4g1t_A           53 MCNLLAYLKHLKGQNEAALE-CLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSPY  131 (472)
T ss_dssp             HHHHHHHHHHHTTCHHHHHH-HHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCSS
T ss_pred             HHHHHHHHHHHCCCHHHHHH-HHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccccc
Confidence            35666677778899999888 5544332    1    1333567899999999999999999999998765311      


Q ss_pred             -CCChhhHHHHHHHHHhh--cCHHHHHHHHHHccccCC-ChhHHHHHHHH---HHhcCChhHHHHHHHHHHhcCCCCCcc
Q 011236          101 -AFSVHDHAVQLDLIGKV--RGLESAETYFNSLNDEDK-VDKLYGALLNC---YVREGLVDESLSLMQKMKEMGSFGSAL  173 (490)
Q Consensus       101 -~~~~~~~~~l~~~~~~~--~~~~~A~~~~~~~~~~~p-~~~~~~~li~~---~~~~g~~~~a~~~~~~m~~~~~~p~~~  173 (490)
                       ...+.++.....++...  +++++|+..|++....+| ++..+..+..+   +...++.++|++.+++..+..+. +..
T Consensus       132 ~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~-~~~  210 (472)
T 4g1t_A          132 RIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPD-NQY  210 (472)
T ss_dssp             CCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSS-CHH
T ss_pred             chhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCc-chH
Confidence             12344555555455544  468999999999999888 46666665555   34567889999999999887543 556


Q ss_pred             hHHHHHHHHHh----cCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHH
Q 011236          174 NYNGIMCLYTN----TGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTV  249 (490)
Q Consensus       174 ~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  249 (490)
                      ++..+...+..    .+++++|.+++++..... +.+..++..+...+...|++++|...+++.. +..+ -+..++..+
T Consensus       211 ~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al-~~~p-~~~~~~~~l  287 (472)
T 4g1t_A          211 LKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKAL-EYIP-NNAYLHCQI  287 (472)
T ss_dssp             HHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHST-TCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHHH-HhCC-ChHHHHHHH
Confidence            66666655554    467889999999988754 3466788899999999999999999999998 5444 456777777


Q ss_pred             HHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCC
Q 011236          250 ANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGE  329 (490)
Q Consensus       250 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  329 (490)
                      ..+|...+....+.         ..  ..      ........+..+.|...++......+ .+..++..+...+...|+
T Consensus       288 g~~y~~~~~~~~~~---------~~--~~------~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~lg~~~~~~~~  349 (472)
T 4g1t_A          288 GCCYRAKVFQVMNL---------RE--NG------MYGKRKLLELIGHAVAHLKKADEAND-NLFRVCSILASLHALADQ  349 (472)
T ss_dssp             HHHHHHHHHHHHHC-----------------------CHHHHHHHHHHHHHHHHHHHHHCT-TTCCCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhhhH---------HH--HH------HHHHHHHHhhHHHHHHHHHHHhhcCC-chhhhhhhHHHHHHHhcc
Confidence            77665422111100         00  00      00011112234567777776666554 555667777777777788


Q ss_pred             HHHHHHHHHHHHhcCCCCCch--hHHHHHH-HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHH
Q 011236          330 LEEAEKMLEEWELSCYCYDFR--VPNIILL-GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFEC  406 (490)
Q Consensus       330 ~~~a~~~~~~~~~~~~~~~~~--~~~~l~~-~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~  406 (490)
                      +++|...|++..+....+...  .+..+.. .+...|+.++|+..|++.++..  |+......         ....+..+
T Consensus       350 ~~~A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~--~~~~~~~~---------~~~~l~~~  418 (472)
T 4g1t_A          350 YEEAEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKIN--QKSREKEK---------MKDKLQKI  418 (472)
T ss_dssp             HHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSC--CCCHHHHH---------HHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--cccHHHHH---------HHHHHHHH
Confidence            888887777777653322211  1222222 2345677788888887777653  33222211         12334455


Q ss_pred             HHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhH
Q 011236          407 MKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYH  461 (490)
Q Consensus       407 ~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~  461 (490)
                      ++..+...      +.+..+|..+...+...|++++|.+.|++..+.++. +..++
T Consensus       419 ~~~~l~~~------p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~  468 (472)
T 4g1t_A          419 AKMRLSKN------GADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASS  468 (472)
T ss_dssp             HHHHHHHC------C-CTTHHHHHHHHHHHHHHCC---------------------
T ss_pred             HHHHHHhC------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhh
Confidence            55555521      233467777777777788888888888887777666 44443

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.81  E-value=6.1e-19  Score=160.17  Aligned_cols=237  Identities=9%  Similarity=0.005  Sum_probs=55.6

Q ss_pred             CChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHH
Q 011236           83 KRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQK  162 (490)
Q Consensus        83 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  162 (490)
                      |+.++|.++++++      +.+.++..+..++.+.|++++|++.|.+.    +|...|..++..+...|++++|+..++.
T Consensus        17 ~~ld~A~~fae~~------~~~~vWs~La~A~l~~g~~~eAIdsfika----~D~~~y~~V~~~ae~~g~~EeAi~yl~~   86 (449)
T 1b89_A           17 GNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSYIKA----DDPSSYMEVVQAANTSGNWEELVKYLQM   86 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cCHHHHHHHHHhC------CChHHHHHHHHHHHHcCCHHHHHHHHHcC----CCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            4445555555444      12234445555555555555555555332    2333444445555555555555554443


Q ss_pred             HHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC
Q 011236          163 MKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMD  242 (490)
Q Consensus       163 m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~  242 (490)
                      .++.  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|..+...|...|.+++|..+|..+.        
T Consensus        87 ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a~--------  149 (449)
T 1b89_A           87 ARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVS--------  149 (449)
T ss_dssp             ------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHTT--------
T ss_pred             HHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHhh--------
Confidence            3332  2234444445555555555444444442       1344455555555555555555555554441        


Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHH
Q 011236          243 WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLG  322 (490)
Q Consensus       243 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  322 (490)
                        .|..++.++.+.|++++|.+.++++       .++.+|..++.+|+..|+++.|......     ....+.....++.
T Consensus       150 --n~~~LA~~L~~Lg~yq~AVea~~KA-------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~-----L~~~ad~l~~lv~  215 (449)
T 1b89_A          150 --NFGRLASTLVHLGEYQAAVDGARKA-------NSTRTWKEVCFACVDGKEFRLAQMCGLH-----IVVHADELEELIN  215 (449)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHH-------TCHHHHHHHHHHHHHTTCHHHHHHTTTT-----TTTCHHHHHHHHH
T ss_pred             --hHHHHHHHHHHhccHHHHHHHHHHc-------CCchhHHHHHHHHHHcCcHHHHHHHHHH-----HHhCHhhHHHHHH
Confidence              2444555555555555555555443       2334455555555555555555332221     1111122233444


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Q 011236          323 SLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ  361 (490)
Q Consensus       323 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (490)
                      .|.+.|++++|..+++...... +-....|+-|...|++
T Consensus       216 ~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~k  253 (449)
T 1b89_A          216 YYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSK  253 (449)
T ss_dssp             HHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHT
T ss_pred             HHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHh
Confidence            4555555555555555444321 2223344444444443

>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=99.80  E-value=3.1e-18  Score=155.58  Aligned_cols=280  Identities=8%  Similarity=-0.022  Sum_probs=130.3

Q ss_pred             CCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHH
Q 011236           46 LGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAET  125 (490)
Q Consensus        46 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  125 (490)
                      .|+.+++.. +.+++      +++..|..+..++.+.|++++|++.|.+.      +++..+..++..+...|++++|+.
T Consensus        16 ~~~ld~A~~-fae~~------~~~~vWs~La~A~l~~g~~~eAIdsfika------~D~~~y~~V~~~ae~~g~~EeAi~   82 (449)
T 1b89_A           16 IGNLDRAYE-FAERC------NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVK   82 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCHHHHHH-HHHhC------CChHHHHHHHHHHHHcCCHHHHHHHHHcC------CCHHHHHHHHHHHHhCCCHHHHHH
Confidence            344555555 55544      34469999999999999999999999652      467788999999999999999999


Q ss_pred             HHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCC
Q 011236          126 YFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPP  205 (490)
Q Consensus       126 ~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p  205 (490)
                      +++...+..+++.+.+.++.+|.+.|+++++.++++       .|+..+|+.+...|...|.+++|..+|..+       
T Consensus        83 yl~~ark~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a-------  148 (449)
T 1b89_A           83 YLQMARKKARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-------  148 (449)
T ss_dssp             --------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT-------
T ss_pred             HHHHHHHhCccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh-------
Confidence            888777765677889999999999999999988885       367789999999999999999999999876       


Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHH
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHL  285 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  285 (490)
                        ..|..++.++.+.|++++|.+.+.++       .++.+|..++.+|...|+++.|......+.      .++.-...+
T Consensus       149 --~n~~~LA~~L~~Lg~yq~AVea~~KA-------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~------~~ad~l~~l  213 (449)
T 1b89_A          149 --SNFGRLASTLVHLGEYQAAVDGARKA-------NSTRTWKEVCFACVDGKEFRLAQMCGLHIV------VHADELEEL  213 (449)
T ss_dssp             --TCHHHHHHHHHTTTCHHHHHHHHHHH-------TCHHHHHHHHHHHHHTTCHHHHHHTTTTTT------TCHHHHHHH
T ss_pred             --hhHHHHHHHHHHhccHHHHHHHHHHc-------CCchhHHHHHHHHHHcCcHHHHHHHHHHHH------hCHhhHHHH
Confidence              47889999999999999999999988       367889999999999999999966655432      222334468


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc--CCHHHHHHHHHHHHhcCCCC------CchhHHHHHH
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI--GELEEAEKMLEEWELSCYCY------DFRVPNIILL  357 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~a~~~~~~~~~~~~~~------~~~~~~~l~~  357 (490)
                      +..|.+.|++++|..+++..+... +-....|+-+.-+|++-  +++.+..+.|..  +.+++|      +...|.-+..
T Consensus       214 v~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~--~ini~k~~~~~~~~~~w~e~~~  290 (449)
T 1b89_A          214 INYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWS--RVNIPKVLRAAEQAHLWAELVF  290 (449)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHST--TSCHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH--HhcCcHHHHHHHHHHHHHHHHH
Confidence            889999999999999999777554 35566777777777654  344444444432  112233      5678889999


Q ss_pred             HHHhcCCHHHHHH
Q 011236          358 GYSQKGMIEKADA  370 (490)
Q Consensus       358 ~~~~~g~~~~A~~  370 (490)
                      .|...++++.|..
T Consensus       291 ly~~~~e~d~A~~  303 (449)
T 1b89_A          291 LYDKYEEYDNAII  303 (449)
T ss_dssp             HHHHTTCHHHHHH
T ss_pred             HHHhhchHHHHHH
Confidence            9999999998876

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.80  E-value=3.6e-17  Score=145.47  Aligned_cols=251  Identities=11%  Similarity=-0.019  Sum_probs=137.3

Q ss_pred             HHhhcCHHHHHHHHHHccccCCCh--hHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcH
Q 011236          114 IGKVRGLESAETYFNSLNDEDKVD--KLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKI  191 (490)
Q Consensus       114 ~~~~~~~~~A~~~~~~~~~~~p~~--~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  191 (490)
                      ....|++..|+..++......|+.  .....+.++|...|+++.|+..++.    .-+|+..++..+...+...++.++|
T Consensus         9 ~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~~~A   84 (291)
T 3mkr_A            9 AFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRRDAI   84 (291)
T ss_dssp             HHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcHHHH
Confidence            344566666666666555544432  2344455666666666666654433    1234455555566666666666666


Q ss_pred             HHHHHHHHHCCCCC-CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHh
Q 011236          192 PDVLLDMKENGVPP-DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCE  270 (490)
Q Consensus       192 ~~~~~~m~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~  270 (490)
                      .+.++++...+..| +...+..+..++...|++++|++.+++       +.+...+..++..|.+.|++++|.+.|+++.
T Consensus        85 ~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~-------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~  157 (291)
T 3mkr_A           85 VAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ-------GDSLECMAMTVQILLKLDRLDLARKELKKMQ  157 (291)
T ss_dssp             HHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT-------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC-------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            66666665554333 333444445566666666666666643       2455566666666666666666666666665


Q ss_pred             hhhccCCChhh--HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC
Q 011236          271 DIVSKSKDALG--YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD  348 (490)
Q Consensus       271 ~~~~~~~~~~~--~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  348 (490)
                      ...+  .+...  ....+..+...|++++|..+|+++....+ .+...++.+..++.+.|++++|...++++.+.. +-+
T Consensus       158 ~~~p--~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p-~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~-p~~  233 (291)
T 3mkr_A          158 DQDE--DATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCS-PTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD-SGH  233 (291)
T ss_dssp             HHCT--TCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTC
T ss_pred             hhCc--CcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCC
Confidence            5432  11111  01122233334566666666666665544 455556666666666666666666666665542 224


Q ss_pred             chhHHHHHHHHHhcCCHHH-HHHHHHHHHHcC
Q 011236          349 FRVPNIILLGYSQKGMIEK-ADAVLKEIVKKG  379 (490)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~-A~~~~~~m~~~~  379 (490)
                      ..++..++..+...|+.++ +.++++++.+.+
T Consensus       234 ~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~  265 (291)
T 3mkr_A          234 PETLINLVVLSQHLGKPPEVTNRYLSQLKDAH  265 (291)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence            4455556666666666544 445666666554

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.80  E-value=1.8e-17  Score=147.50  Aligned_cols=277  Identities=8%  Similarity=-0.036  Sum_probs=215.2

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhH
Q 011236           76 IRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDE  155 (490)
Q Consensus        76 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~  155 (490)
                      ++.....|+++.|+..++................+.+++...|+++.|+..++..  ..|+..++..+...+...|+.++
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~--~~~~~~a~~~la~~~~~~~~~~~   83 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKPS--SAPELQAVRMFAEYLASHSRRDA   83 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTT--SCHHHHHHHHHHHHHHCSTTHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhccc--CChhHHHHHHHHHHHcCCCcHHH
Confidence            3445578999999999887655432111345566789999999999999877552  23567788889999999999999


Q ss_pred             HHHHHHHHHhcCCCCC-cchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHH
Q 011236          156 SLSLMQKMKEMGSFGS-ALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEME  234 (490)
Q Consensus       156 a~~~~~~m~~~~~~p~-~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  234 (490)
                      |++.++++...+..|+ ...+..+...+...|++++|.+.+++      +.+...+..++..+.+.|++++|.+.|+++.
T Consensus        84 A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~  157 (291)
T 3mkr_A           84 IVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKKMQ  157 (291)
T ss_dssp             HHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            9999999998775554 55567777899999999999999987      4678889999999999999999999999998


Q ss_pred             hCCCCCCCHHHH---HHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC
Q 011236          235 SQSHISMDWGTY---STVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK  311 (490)
Q Consensus       235 ~~~~~~~~~~~~---~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  311 (490)
                       +.+  |+....   ..++..+...|++++|..+|+++....+  .+...++.+..++.+.|++++|...|++.....+ 
T Consensus       158 -~~~--p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p--~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p-  231 (291)
T 3mkr_A          158 -DQD--EDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCS--PTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDS-  231 (291)
T ss_dssp             -HHC--TTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-
T ss_pred             -hhC--cCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCC--CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-
Confidence             443  443211   1233444455899999999999998755  6889999999999999999999999999988876 


Q ss_pred             CChhhHHHHHHHHHhcCCHHH-HHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHH
Q 011236          312 QLNRDYITMLGSLVKIGELEE-AEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAV  371 (490)
Q Consensus       312 ~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  371 (490)
                      .+..++..++..+...|+.++ +.++++++.+.  .|+..   .+.+...+.+.++++..-
T Consensus       232 ~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~--~P~~~---~~~d~~~~~~~fd~~~~~  287 (291)
T 3mkr_A          232 GHPETLINLVVLSQHLGKPPEVTNRYLSQLKDA--HRSHP---FIKEYRAKENDFDRLVLQ  287 (291)
T ss_dssp             TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--CTTCH---HHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh--CCCCh---HHHHHHHHHHHHHHHHHH
Confidence            678889999999999999875 67899998885  44432   233445555555555443

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.78  E-value=2.9e-20  Score=182.04  Aligned_cols=156  Identities=16%  Similarity=0.158  Sum_probs=123.0

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHh---cCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHH
Q 011236          137 DKLYGALLNCYVREGLVDESLSLMQKMKE---MGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRIC  213 (490)
Q Consensus       137 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~---~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l  213 (490)
                      ..+||+||++|++.|++++|.++|++|.+   .|+.||+.|||+||.+|++.|++++|.++|++|.+.|+.||..||+++
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            45799999999999999999999988764   589999999999999999999999999999999999999999999999


Q ss_pred             HHHHhccCCh-HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhc
Q 011236          214 INSYGARSEL-SSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASL  292 (490)
Q Consensus       214 i~~~~~~g~~-~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  292 (490)
                      |.++++.|+. ++|.++|++|. +.|+.||..+|+.++....+.+-++...++...+.......+...+...|.+.|.+.
T Consensus       207 I~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          207 LQCMGRQDQDAGTIERCLEQMS-QEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKD  285 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHH-HHTCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCCCCCCCCCCCCCCCTTTHHHHCCC
T ss_pred             HHHHHhCCCcHHHHHHHHHHHH-HcCCCCChhhcccccChhhHHHHHHHHHHhCcccCCCCCCcccccchHHHHHHHccC
Confidence            9999999985 78899999999 889999999999888766554333333222222111111102245566677777665


Q ss_pred             C
Q 011236          293 G  293 (490)
Q Consensus       293 ~  293 (490)
                      +
T Consensus       286 ~  286 (1134)
T 3spa_A          286 G  286 (1134)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.78  E-value=6.8e-15  Score=149.16  Aligned_cols=355  Identities=11%  Similarity=0.082  Sum_probs=265.6

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCC--CCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHH
Q 011236           66 KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGL--AFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGAL  143 (490)
Q Consensus        66 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~l  143 (490)
                      ..++.-....+++|...|.+.+|+++++++...+.  .-+...-+.++....+. +..+..++.+.+...  +   ...+
T Consensus       982 ~~~PeeVs~~vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~~--d---~~eI 1055 (1630)
T 1xi4_A          982 TQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDNY--D---APDI 1055 (1630)
T ss_pred             ccCHHHhHHHHHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhhc--c---HHHH
Confidence            44666677788888888888888888888885432  12334555566555555 555556655555421  1   3346


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 011236          144 LNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSEL  223 (490)
Q Consensus       144 i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  223 (490)
                      ...+...|.+++|..+|++...     .....+.++.   ..+++++|.++.++.      -+..+|..+..++...|++
T Consensus      1056 A~Iai~lglyEEAf~IYkKa~~-----~~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~~ 1121 (1630)
T 1xi4_A         1056 ANIAISNELFEEAFAIFRKFDV-----NTSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMV 1121 (1630)
T ss_pred             HHHHHhCCCHHHHHHHHHHcCC-----HHHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCCH
Confidence            6778888999999999988521     2222333332   667888888888755      2467888899999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHH
Q 011236          224 SSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWG  303 (490)
Q Consensus       224 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  303 (490)
                      ++|...|.+.       -|...|..++.++.+.|++++|.++|....+...   +....+.++.+|++.+++++...+.+
T Consensus      1122 kEAIdsYiKA-------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~---e~~Idt~LafaYAKl~rleele~fI~ 1191 (1630)
T 1xi4_A         1122 KEAIDSYIKA-------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKAR---ESYVETELIFALAKTNRLAELEEFIN 1191 (1630)
T ss_pred             HHHHHHHHhc-------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcc---cccccHHHHHHHHhhcCHHHHHHHHh
Confidence            9999998654       4566777899999999999999999988776543   33333458888999988886444431


Q ss_pred             HHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC
Q 011236          304 LQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT  383 (490)
Q Consensus       304 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~  383 (490)
                             .++...|..+...|...|++++|..+|...         ..|..+..+|++.|++++|.+.+++.      .+
T Consensus      1192 -------~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n 1249 (1630)
T 1xi4_A         1192 -------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NS 1249 (1630)
T ss_pred             -------CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CC
Confidence                   356677778999999999999999999985         37889999999999999999999876      26


Q ss_pred             HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHH
Q 011236          384 PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHA  462 (490)
Q Consensus       384 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~  462 (490)
                      ..+|..+..+|...|++..|..+... +.         .++..+..++..|.+.|.+++|..+++......+. ...|+-
T Consensus      1250 ~~aWkev~~acve~~Ef~LA~~cgl~-Ii---------v~~deLeeli~yYe~~G~feEAI~LlE~aL~LeraH~gmftE 1319 (1630)
T 1xi4_A         1250 TRTWKEVCFACVDGKEFRLAQMCGLH-IV---------VHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTE 1319 (1630)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHh-hh---------cCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccChhHhHHHHH
Confidence            78899999999999999988876654 22         45667779999999999999999999999888866 889999


Q ss_pred             HHHHHHhcC-CcHHHHHHHHH
Q 011236          463 LTEAHIRSG-QEVDGLLESMK  482 (490)
Q Consensus       463 l~~~~~~~g-~~a~~~~~~m~  482 (490)
                      |...|.+.. ++.++.++--.
T Consensus      1320 LaiLyaKy~peklmEhlk~f~ 1340 (1630)
T 1xi4_A         1320 LAILYSKFKPQKMREHLELFW 1340 (1630)
T ss_pred             HHHHHHhCCHHHHHHHHHHHH
Confidence            999999988 54444444333

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.77  E-value=6.2e-19  Score=172.80  Aligned_cols=113  Identities=9%  Similarity=-0.017  Sum_probs=56.1

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHH---HhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHH
Q 011236          280 LGYNHLISHYASLGNKDEMMKFWGLQK---IKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIIL  356 (490)
Q Consensus       280 ~~~~~l~~~~~~~~~~~~a~~~~~~~~---~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  356 (490)
                      .||+++|.+||+.|++++|.++|++|.   ..+..||..||++||.+||+.|++++|.++|++|.+.|+.||..|||++|
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI  207 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAAL  207 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            345555555555555555555554433   22334555555555555555555555555555555555555555555555


Q ss_pred             HHHHhcCC-HHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011236          357 LGYSQKGM-IEKADAVLKEIVKKGKTPTPNSWSIIAA  392 (490)
Q Consensus       357 ~~~~~~g~-~~~A~~~~~~m~~~~~~p~~~~~~~l~~  392 (490)
                      .++++.|+ .++|.++|++|.+.|+.||..+|+.++.
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~  244 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLS  244 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCC
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccC
Confidence            55555544 2444455555555555555555554443

>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=99.76  E-value=6e-15  Score=149.55  Aligned_cols=379  Identities=10%  Similarity=0.058  Sum_probs=289.0

Q ss_pred             CCCCcccHHHhhccCCCCCCChHHHHHHHHHcCC--CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHH
Q 011236           32 KPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQ--KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAV  109 (490)
Q Consensus        32 ~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  109 (490)
                      +|......++.+...|.+.+++. ++++....+-  .-+....+.++....+. +.....+..+......       ..-
T Consensus       984 ~PeeVs~~vKaf~~aglp~Eaie-LLEKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~~d-------~~e 1054 (1630)
T 1xi4_A          984 DPEEVSVTVKAFMTADLPNELIE-LLEKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDNYD-------APD 1054 (1630)
T ss_pred             CHHHhHHHHHHHHhCCCHHHHHH-HHHHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhhcc-------HHH
Confidence            55667778888889999999888 8888774421  13446666677666666 4566666666554221       233


Q ss_pred             HHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcC
Q 011236          110 QLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHE  189 (490)
Q Consensus       110 l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  189 (490)
                      +...+...|.+++|..+|++...   .....+.++.   ..+++++|.++.++..      +..+|..+..++...|+++
T Consensus      1055 IA~Iai~lglyEEAf~IYkKa~~---~~~A~~VLie---~i~nldrAiE~Aervn------~p~vWsqLAKAql~~G~~k 1122 (1630)
T 1xi4_A         1055 IANIAISNELFEEAFAIFRKFDV---NTSAVQVLIE---HIGNLDRAYEFAERCN------EPAVWSQLAKAQLQKGMVK 1122 (1630)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcCC---HHHHHHHHHH---HHhhHHHHHHHHHhcC------CHHHHHHHHHHHHhCCCHH
Confidence            77788899999999999999742   2333344433   6789999999998652      5789999999999999999


Q ss_pred             cHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011236          190 KIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKC  269 (490)
Q Consensus       190 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  269 (490)
                      +|.+.|.+.      -|...|..++.++.+.|++++|.++|.... +....+...+  .++.+|++.+++++...+..  
T Consensus      1123 EAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mAr-k~~~e~~Idt--~LafaYAKl~rleele~fI~-- 1191 (1630)
T 1xi4_A         1123 EAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMAR-KKARESYVET--ELIFALAKTNRLAELEEFIN-- 1191 (1630)
T ss_pred             HHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHH-hhcccccccH--HHHHHHHhhcCHHHHHHHHh--
Confidence            999999663      477788899999999999999999999877 4442233333  49999999999886544432  


Q ss_pred             hhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc
Q 011236          270 EDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDF  349 (490)
Q Consensus       270 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  349 (490)
                           . ++...|..+...|...|++++|..+|...         ..|..+...+++.|++++|.+.+++.      .+.
T Consensus      1192 -----~-~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEaarKA------~n~ 1250 (1630)
T 1xi4_A         1192 -----G-PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKA------NST 1250 (1630)
T ss_pred             -----C-CCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHHHHHh------CCH
Confidence                 2 66677888999999999999999999963         48999999999999999999999987      356


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHH
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVS  428 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~  428 (490)
                      .+|..+..+|...|++..|......+.     .++..+..++..|.+.|.+++|+.+++..+.       +.|.. ..|+
T Consensus      1251 ~aWkev~~acve~~Ef~LA~~cgl~Ii-----v~~deLeeli~yYe~~G~feEAI~LlE~aL~-------LeraH~gmft 1318 (1630)
T 1xi4_A         1251 RTWKEVCFACVDGKEFRLAQMCGLHIV-----VHADELEELINYYQDRGYFEELITMLEAALG-------LERAHMGMFT 1318 (1630)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHhhh-----cCHHHHHHHHHHHHHcCCHHHHHHHHHHHhc-------cChhHhHHHH
Confidence            889999999999999999988766432     3677788999999999999999999998876       33433 5666


Q ss_pred             HHHHHHHc--CCCHHHHHHHHHHHHhccc-----c-hhhhHHHHHHHHhcC--CcHH
Q 011236          429 SILDWLGD--NRDVEEVEAFVSSLKIKVQ-----K-RNMYHALTEAHIRSG--QEVD  475 (490)
Q Consensus       429 ~l~~~~~~--~g~~~~a~~~~~~~~~~~~-----~-~~~~~~l~~~~~~~g--~~a~  475 (490)
                      .+...+.+  .++..++.+.|..-....+     . ...|.-++..|.+.|  +.|.
T Consensus      1319 ELaiLyaKy~peklmEhlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~ 1375 (1630)
T 1xi4_A         1319 ELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAI 1375 (1630)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhcccHHHHH
Confidence            66666654  4556666666664444333     2 778999999999998  6666

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.75  E-value=6e-16  Score=135.52  Aligned_cols=228  Identities=13%  Similarity=0.044  Sum_probs=172.1

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC-CC----hhh
Q 011236          207 NFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS-KD----ALG  281 (490)
Q Consensus       207 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-~~----~~~  281 (490)
                      ...+..+...+...|++++|..+|+++. +..  .+..++..+..+|...|++++|+..+++.....+.. ++    ..+
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~-~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~   81 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAW-ELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKS   81 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHH-Hhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHH
Confidence            3456677777888888888888888877 444  566777778888888888888888888877655430 11    567


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ  361 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (490)
                      +..+...+...|++++|...|++.....+  +       ...+...|++++|...++.+... .+.+...+..+...+..
T Consensus        82 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~~--~-------~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~  151 (258)
T 3uq3_A           82 FARIGNAYHKLGDLKKTIEYYQKSLTEHR--T-------ADILTKLRNAEKELKKAEAEAYV-NPEKAEEARLEGKEYFT  151 (258)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCC--C-------HHHHHHHHHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHhcCc--h-------hHHHHHHhHHHHHHHHHHHHHHc-CcchHHHHHHHHHHHHH
Confidence            78888888888888888888887777653  2       23455677888888888888775 22345567778888888


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHH
Q 011236          362 KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVE  441 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  441 (490)
                      .|++++|...++++.+..+. +..+|..+...|...|++++|...++++++..      +.+...+..+...+.+.|+++
T Consensus       152 ~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~------~~~~~~~~~l~~~~~~~g~~~  224 (258)
T 3uq3_A          152 KSDWPNAVKAYTEMIKRAPE-DARGYSNRAAALAKLMSFPEAIADCNKAIEKD------PNFVRAYIRKATAQIAVKEYA  224 (258)
T ss_dssp             TTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC------TTCHHHHHHHHHHHHHTTCHH
T ss_pred             hcCHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC------HHHHHHHHHHHHHHHHHhhHH
Confidence            88888888888888887654 67788888888888888888888888888722      123567788888888888888


Q ss_pred             HHHHHHHHHHhcc
Q 011236          442 EVEAFVSSLKIKV  454 (490)
Q Consensus       442 ~a~~~~~~~~~~~  454 (490)
                      +|...++++.+..
T Consensus       225 ~A~~~~~~a~~~~  237 (258)
T 3uq3_A          225 SALETLDAARTKD  237 (258)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC
Confidence            8888888888777

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.73  E-value=1.8e-15  Score=143.57  Aligned_cols=369  Identities=13%  Similarity=0.075  Sum_probs=249.0

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCH---HHHHHHHHHccccCCChhHHHHHHHHHHhcC
Q 011236           75 VIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGL---ESAETYFNSLNDEDKVDKLYGALLNCYVREG  151 (490)
Q Consensus        75 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~---~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g  151 (490)
                      +...+.+.|++++|++.|+...+.|   ++..+..+..++...|+.   ++|...|+...+.  ++..+..|...+...+
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~--~~~A~~~Lg~~~~~~~   83 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADT--SPRAQARLGRLLAAKP   83 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC------------------------------CHHHHHHHHHTC-
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC--CHHHHHHHHHHHHhCC
Confidence            5566778899999999999998887   455555666666777888   8999999998865  5566777777565655


Q ss_pred             -----ChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCc---CcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCCh
Q 011236          152 -----LVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQH---EKIPDVLLDMKENGVPPDNFSYRICINSYGARSEL  223 (490)
Q Consensus       152 -----~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~---~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~  223 (490)
                           +.++|+..|++..+.|   +...+..|...|...+..   .++.+.+......|.   ......+...|...+.+
T Consensus        84 ~~~~~~~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~Lg~~y~~~~~~  157 (452)
T 3e4b_A           84 GATEAEHHEAESLLKKAFANG---EGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGY---PEAGLAQVLLYRTQGTY  157 (452)
T ss_dssp             -CCHHHHHHHHHHHHHHHHTT---CSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTC---TTHHHHHHHHHHHHTCG
T ss_pred             CCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHcCCCc
Confidence                 7789999999999876   344788888888776654   445555655555443   44566677777777755


Q ss_pred             H----HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhc----
Q 011236          224 S----SMENVLQEMESQSHISMDWGTYSTVANYYIIAG---LKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASL----  292 (490)
Q Consensus       224 ~----~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----  292 (490)
                      +    .+..+++... ..+  |+  .+..|...|...|   +.++|+..|++..+.++  ++...+..+...|...    
T Consensus       158 ~~~~~~a~~~~~~a~-~~~--~~--a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~--~~a~~~~~Lg~~y~~g~~~~  230 (452)
T 3e4b_A          158 DQHLDDVERICKAAL-NTT--DI--CYVELATVYQKKQQPEQQAELLKQMEAGVSRGT--VTAQRVDSVARVLGDATLGT  230 (452)
T ss_dssp             GGGHHHHHHHHHHHT-TTC--TT--HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTC--SCHHHHHHHHHHHTCGGGSS
T ss_pred             ccCHHHHHHHHHHHH-cCC--HH--HHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCC--HHHHHHHHHHHHHhCCCCCC
Confidence            4    4444555553 322  33  7778999999999   99999999999988776  5666667788888655    


Q ss_pred             CChhHHHHHHHHHHHhcCCCChhhHHHHHHH-H--HhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC-----C
Q 011236          293 GNKDEMMKFWGLQKIKCKKQLNRDYITMLGS-L--VKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG-----M  364 (490)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-----~  364 (490)
                      +++++|...|++..    ..+...+..+... +  ...+++++|...|++..+.|   +...+..|...|. .|     +
T Consensus       231 ~d~~~A~~~~~~aa----~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d  302 (452)
T 3e4b_A          231 PDEKTAQALLEKIA----PGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPAD  302 (452)
T ss_dssp             CCHHHHHHHHHHHG----GGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCC
T ss_pred             CCHHHHHHHHHHHc----CCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCC
Confidence            79999999999776    2455666667666 4  56899999999999999876   5667777888787 55     9


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc----
Q 011236          365 IEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD----  436 (490)
Q Consensus       365 ~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~----  436 (490)
                      +++|...|++.. .   -++..+..|...|..    ..+.++|..+|+++.+     .|.   ......|...|..    
T Consensus       303 ~~~A~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~-----~g~---~~A~~~Lg~~y~~G~g~  370 (452)
T 3e4b_A          303 AKAAEAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAAR-----NGQ---NSADFAIAQLFSQGKGT  370 (452)
T ss_dssp             HHHHHHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHT-----TTC---TTHHHHHHHHHHSCTTB
T ss_pred             HHHHHHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHh-----hCh---HHHHHHHHHHHHhCCCC
Confidence            999999999888 3   377788888888876    4599999999999988     442   3455566666653    


Q ss_pred             CCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHH
Q 011236          437 NRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESM  481 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m  481 (490)
                      ..+.++|..+++...+.+.. .......+......+  .+|..+.++-
T Consensus       371 ~~d~~~A~~~~~~A~~~g~~~a~~~l~~l~~~~~~~~~~~a~~~~~~~  418 (452)
T 3e4b_A          371 KPDPLNAYVFSQLAKAQDTPEANDLATQLEAPLTPAQRAEGQRLVQQE  418 (452)
T ss_dssp             CCCHHHHHHHHHHHHTTCCHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            56899999999999998876 332222222221112  5566666543

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.73  E-value=1.1e-15  Score=129.84  Aligned_cols=198  Identities=13%  Similarity=0.002  Sum_probs=121.2

Q ss_pred             CCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHH
Q 011236          205 PDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNH  284 (490)
Q Consensus       205 p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  284 (490)
                      ++...+..+...+...|++++|...|++.. +.++ .+...+..+..++...|++++|+..|++.....+  .+...+..
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P--~~~~a~~~   78 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERAL-KENP-QDPEALYWLARTQLKLGLVNPALENGKTLVARTP--RYLGGYMV   78 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHH-TTSS-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--CcHHHHHH
Confidence            455566666666777777777777777766 5444 4566666677777777777777777777666554  45666666


Q ss_pred             HHHHHHhc-----------CChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHH
Q 011236          285 LISHYASL-----------GNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPN  353 (490)
Q Consensus       285 l~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  353 (490)
                      +..++...           |++++|+..+++.....+ .+...+..+..++...|++++|...|++..+..  .+...+.
T Consensus        79 lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~  155 (217)
T 2pl2_A           79 LSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVNP-RYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRS  155 (217)
T ss_dssp             HHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHH
T ss_pred             HHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHH
Confidence            66666666           677777777766666554 455566666666667777777777777766654  4556666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEA  410 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~  410 (490)
                      .+..+|...|++++|...|++..+..+. +...+..+...+...|++++|+..+++.
T Consensus       156 ~la~~~~~~g~~~~A~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          156 ALAELYLSMGRLDEALAQYAKALEQAPK-DLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHTC--------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            6666677777777777777776665443 5566666666677777777776666654

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.72  E-value=8.7e-16  Score=134.45  Aligned_cols=227  Identities=15%  Similarity=0.009  Sum_probs=171.4

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCC--CCC----HHHH
Q 011236          137 DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGV--PPD----NFSY  210 (490)
Q Consensus       137 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~--~p~----~~~~  210 (490)
                      ...|..+...+...|++++|+..|++..+..  ++..+|..+..++...|++++|.+.+++..+...  .|+    ..++
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   82 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSF   82 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHH
Confidence            4567777888888888888888888888776  5778888888888888888888888888766321  112    4677


Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHH
Q 011236          211 RICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYA  290 (490)
Q Consensus       211 ~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  290 (490)
                      ..+...+...|++++|...|+++. ...  |+.       ..+...|++++|...++++....+  .+...+..+...+.
T Consensus        83 ~~l~~~~~~~~~~~~A~~~~~~a~-~~~--~~~-------~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~~~~~~~  150 (258)
T 3uq3_A           83 ARIGNAYHKLGDLKKTIEYYQKSL-TEH--RTA-------DILTKLRNAEKELKKAEAEAYVNP--EKAEEARLEGKEYF  150 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHH-HHC--CCH-------HHHHHHHHHHHHHHHHHHHHHCCH--HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHH-hcC--chh-------HHHHHHhHHHHHHHHHHHHHHcCc--chHHHHHHHHHHHH
Confidence            778888888888888888888887 322  332       346667788888888888776554  46677788888888


Q ss_pred             hcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHH
Q 011236          291 SLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADA  370 (490)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  370 (490)
                      ..|++++|...+++.....+ .+...+..+...+...|++++|...+++..+.. +.+...+..+...|...|++++|..
T Consensus       151 ~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~  228 (258)
T 3uq3_A          151 TKSDWPNAVKAYTEMIKRAP-EDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQIAVKEYASALE  228 (258)
T ss_dssp             HTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-HHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            88888888888888777665 566777888888888888888888888887753 3346677778888888888888888


Q ss_pred             HHHHHHHcC
Q 011236          371 VLKEIVKKG  379 (490)
Q Consensus       371 ~~~~m~~~~  379 (490)
                      .+++..+..
T Consensus       229 ~~~~a~~~~  237 (258)
T 3uq3_A          229 TLDAARTKD  237 (258)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhC
Confidence            888777653

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.71  E-value=1.7e-15  Score=128.65  Aligned_cols=200  Identities=18%  Similarity=0.103  Sum_probs=145.3

Q ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHH
Q 011236          240 SMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYIT  319 (490)
Q Consensus       240 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  319 (490)
                      +++...+..+...+...|++++|+..|++.....+  .+...+..+..++...|++++|...+++.....+ .+...+..
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p--~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~   78 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENP--QDPEALYWLARTQLKLGLVNPALENGKTLVARTP-RYLGGYMV   78 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSS--SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHH
Confidence            35667788888889999999999999998887666  5788888888899999999999999998888765 56677888


Q ss_pred             HHHHHHhc-----------CCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 011236          320 MLGSLVKI-----------GELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS  388 (490)
Q Consensus       320 l~~~~~~~-----------~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~  388 (490)
                      +..++...           |++++|...+++..+.. +-+...+..+...|...|++++|+..|++.++.+  .+...+.
T Consensus        79 lg~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~  155 (217)
T 2pl2_A           79 LSEAYVALYRQAEDRERGKGYLEQALSVLKDAERVN-PRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRS  155 (217)
T ss_dssp             HHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHH
T ss_pred             HHHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHH
Confidence            88888888           88888888888887752 2245667777788888888888888888888776  4777888


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       389 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      .+..+|...|++++|+..|+++++.       .|+ ...+..+...+...|++++|...+++...
T Consensus       156 ~la~~~~~~g~~~~A~~~~~~al~~-------~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~  213 (217)
T 2pl2_A          156 ALAELYLSMGRLDEALAQYAKALEQ-------APKDLDLRVRYASALLLKGKAEEAARAAALEHH  213 (217)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHH-------STTCHHHHHHHHHHHTC----------------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh-------CCCChHHHHHHHHHHHHccCHHHHHHHHHHHhh
Confidence            8888888888888888888888772       243 46677777788888888888887776543

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.70  E-value=4.6e-15  Score=131.09  Aligned_cols=250  Identities=11%  Similarity=-0.024  Sum_probs=166.2

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC--hhhHHHHH
Q 011236          209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD--ALGYNHLI  286 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~  286 (490)
                      .+......+...|++++|...|+++. +... .+...+..+..+|...|++++|+..+++....... ++  ..+|..+.
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l-~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~~~lg   81 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLE-AKKY-NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNA-TKAKSADFEYYG   81 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHH-HTTC-CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCT-TTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHH-HhCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCc-hhHHHHHHHHHH
Confidence            34445566667777777777777776 3332 33446666777777777777777777777662211 22  22367777


Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHH
Q 011236          287 SHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIE  366 (490)
Q Consensus       287 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  366 (490)
                      ..+...|++++|...|++.....+ .+...+..+...+...|++++|...+++..+. .+.+...+..+...+...++++
T Consensus        82 ~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~l~~~~~~~~~~~  159 (272)
T 3u4t_A           82 KILMKKGQDSLAIQQYQAAVDRDT-TRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP-TTTDPKVFYELGQAYYYNKEYV  159 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS-SCCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcccHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc-CCCcHHHHHHHHHHHHHHHHHH
Confidence            777777777777777777776655 45567777777788888888888888777665 2234455555662333445888


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC---HHHHHHHHHHHHHhhhcCcCCCcc------hhhHHHHHHHHHcC
Q 011236          367 KADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN---MEKAFECMKEALAVHEENKFWRPK------PSLVSSILDWLGDN  437 (490)
Q Consensus       367 ~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~p~------~~~~~~l~~~~~~~  437 (490)
                      +|...|+++.+..+. +...+..+...+...|+   +++|...++++++...    -.|+      ...|..+...+...
T Consensus       160 ~A~~~~~~a~~~~p~-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~----~~~~~~~~~~~~~~~~l~~~~~~~  234 (272)
T 3u4t_A          160 KADSSFVKVLELKPN-IYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCA----PGGAKYKDELIEANEYIAYYYTIN  234 (272)
T ss_dssp             HHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHG----GGGGGGHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCcc-chHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHh----cccccchHHHHHHHHHHHHHHHHc
Confidence            888888888876543 56677777777777777   7778888888877331    1122      24667777788888


Q ss_pred             CCHHHHHHHHHHHHhcccc-hhhhHHHHHHHH
Q 011236          438 RDVEEVEAFVSSLKIKVQK-RNMYHALTEAHI  468 (490)
Q Consensus       438 g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~  468 (490)
                      |++++|...++++.+..|. +..+..+.....
T Consensus       235 ~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~  266 (272)
T 3u4t_A          235 RDKVKADAAWKNILALDPTNKKAIDGLKMKLE  266 (272)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCHHHHHHHC----
T ss_pred             CCHHHHHHHHHHHHhcCccHHHHHHHhhhhhc
Confidence            8888888888888888877 666665554443

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.70  E-value=7.1e-15  Score=129.85  Aligned_cols=196  Identities=11%  Similarity=0.035  Sum_probs=86.3

Q ss_pred             hHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCc--chHHHHHHHH
Q 011236          106 DHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSA--LNYNGIMCLY  182 (490)
Q Consensus       106 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~--~~~~~l~~~~  182 (490)
                      ........+...|++++|+..|+...+..| +..+|..+...+...|++++|+..+++..+.+..|+.  .+|..+...+
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~   84 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKIL   84 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHH
Confidence            334444455555555555555555555444 2334555555555555555555555555542211111  1144444445


Q ss_pred             HhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011236          183 TNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKA  262 (490)
Q Consensus       183 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a  262 (490)
                      ...|++++|.+.|++..+... .+..++..+...+...|++++|...|++.. +... .+...+..+...+...+++++|
T Consensus        85 ~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al-~~~~-~~~~~~~~l~~~~~~~~~~~~A  161 (272)
T 3u4t_A           85 MKKGQDSLAIQQYQAAVDRDT-TRLDMYGQIGSYFYNKGNFPLAIQYMEKQI-RPTT-TDPKVFYELGQAYYYNKEYVKA  161 (272)
T ss_dssp             HHTTCHHHHHHHHHHHHHHST-TCTHHHHHHHHHHHHTTCHHHHHHHHGGGC-CSSC-CCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHcccHHHHHHHHHHHHhcCc-ccHHHHHHHHHHHHHccCHHHHHHHHHHHh-hcCC-CcHHHHHHHHHHHHHHHHHHHH
Confidence            555555555555555444321 123344444444444444444444444444 2221 2333333333122222344444


Q ss_pred             HHHHHHHhhhhccCCChhhHHHHHHHHHhcCC---hhHHHHHHHHHH
Q 011236          263 IIYLKKCEDIVSKSKDALGYNHLISHYASLGN---KDEMMKFWGLQK  306 (490)
Q Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~  306 (490)
                      +..|+++.+..+  .+...+..+..++...|+   +++|...+++..
T Consensus       162 ~~~~~~a~~~~p--~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~  206 (272)
T 3u4t_A          162 DSSFVKVLELKP--NIYIGYLWRARANAAQDPDTKQGLAKPYYEKLI  206 (272)
T ss_dssp             HHHHHHHHHHST--TCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHH
T ss_pred             HHHHHHHHHhCc--cchHHHHHHHHHHHHcCcchhhHHHHHHHHHHH
Confidence            444444444332  233334444444444443   444444444333

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.69  E-value=8.5e-15  Score=134.58  Aligned_cols=248  Identities=9%  Similarity=0.047  Sum_probs=200.2

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCC-HHHHHHHHHHHhhhhccCCChhhHHHHH
Q 011236          208 FSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGL-KEKAIIYLKKCEDIVSKSKDALGYNHLI  286 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~~~~~~l~  286 (490)
                      ..|..+...+...|++++|+..|+++. ..+. -+..+|+.+..++...|+ +++|+..|+++....+  .+...|..+.
T Consensus        98 ~a~~~lg~~~~~~g~~~~Al~~~~~al-~l~P-~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P--~~~~a~~~~g  173 (382)
T 2h6f_A           98 DVYDYFRAVLQRDERSERAFKLTRDAI-ELNA-ANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP--KNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHH-HHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT--TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHH-HhCc-cCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCC--CCHHHHHHHH
Confidence            457777778888889999999999887 5554 567788888888889996 9999999999888766  5788888999


Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh-cCCH
Q 011236          287 SHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ-KGMI  365 (490)
Q Consensus       287 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~  365 (490)
                      .++...|++++|+..|++++...+ .+...|..+..++.+.|++++|...++++++... -+...|+.+..++.+ .|..
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~ldP-~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P-~~~~a~~~lg~~l~~l~~~~  251 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILNQDA-KNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISNTTGYN  251 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHccCHHHHHHHHHHHHHhCc-cCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcCcc
Confidence            999999999999999998888776 6778888888899999999999999999888633 366788888888888 5665


Q ss_pred             HHH-----HHHHHHHHHcCCCCCHHHHHHHHHHHhccC--CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCC
Q 011236          366 EKA-----DAVLKEIVKKGKTPTPNSWSIIAAGYADKN--NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNR  438 (490)
Q Consensus       366 ~~A-----~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g  438 (490)
                      ++|     +..|++.++..+. +...|..+...+...|  ++++|++.++++ +      .-..+...+..+...+.+.|
T Consensus       252 ~eA~~~~el~~~~~Al~l~P~-~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~------~~p~~~~al~~La~~~~~~~  323 (382)
T 2h6f_A          252 DRAVLEREVQYTLEMIKLVPH-NESAWNYLKGILQDRGLSKYPNLLNQLLDL-Q------PSHSSPYLIAFLVDIYEDML  323 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-T------TTCCCHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHccCccchHHHHHHHHHh-c------cCCCCHHHHHHHHHHHHHHh
Confidence            777     5888888887665 7788999999898888  688999888887 5      12234467788888887764


Q ss_pred             --------C-HHHHHHHHHHH-Hhcccc-hhhhHHHHHHHHh
Q 011236          439 --------D-VEEVEAFVSSL-KIKVQK-RNMYHALTEAHIR  469 (490)
Q Consensus       439 --------~-~~~a~~~~~~~-~~~~~~-~~~~~~l~~~~~~  469 (490)
                              + .++|.++++++ .+..|. ...|..+...+..
T Consensus       324 ~~~~~~~~~~~~~A~~~~~~l~~~~DP~r~~~w~~~~~~l~~  365 (382)
T 2h6f_A          324 ENQCDNKEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQS  365 (382)
T ss_dssp             HTTCSSHHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHH
Confidence                    2 58999999999 888888 8888888777754

>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=99.69  E-value=1.5e-14  Score=126.13  Aligned_cols=203  Identities=14%  Similarity=-0.012  Sum_probs=118.2

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHH
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGS  323 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  323 (490)
                      ..+..+...+...|++++|...|+++....+  .+...+..+...+...|++++|.+.+++.....+ .+...+..+...
T Consensus        38 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~--~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~~  114 (252)
T 2ho1_A           38 DAYIQLGLGYLQRGNTEQAKVPLRKALEIDP--SSADAHAALAVVFQTEMEPKLADEEYRKALASDS-RNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHTTCTGGGHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHHhcCC--ChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc-CcHHHHHHHHHH
Confidence            4445555555666666666666665555433  3455555666666666666666666665555443 344555556666


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCC-CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHH
Q 011236          324 LVKIGELEEAEKMLEEWELSCYCY-DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEK  402 (490)
Q Consensus       324 ~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  402 (490)
                      +...|++++|.+.++++.+.+..| +...+..+...|...|++++|...++++.+..+. +...+..+...+...|++++
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRN-QPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHcCCHHH
Confidence            666666666666666665522222 3345555666666666666666666666665433 45566666666666666666


Q ss_pred             HHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          403 AFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       403 a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      |..+++++.+      ....+...+..+...+...|++++|.++++++.+..|.
T Consensus       194 A~~~~~~~~~------~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p~  241 (252)
T 2ho1_A          194 ARQYYDLFAQ------GGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYPG  241 (252)
T ss_dssp             HHHHHHHHHT------TSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHH------hCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC
Confidence            6666666655      11133345555666666666666666666666666555

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.68  E-value=3.6e-14  Score=121.24  Aligned_cols=205  Identities=10%  Similarity=-0.044  Sum_probs=133.5

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHH
Q 011236          243 WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLG  322 (490)
Q Consensus       243 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  322 (490)
                      ...+..+...+...|++++|...|+++....+  .+...+..+...+...|++++|...+++.....+ .+...+..+..
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~l~~   84 (225)
T 2vq2_A            8 SNIKTQLAMEYMRGQDYRQATASIEDALKSDP--KNELAWLVRAEIYQYLKVNDKAQESFRQALSIKP-DSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCc--cchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC-CChHHHHHHHH
Confidence            44555666666777777777777776665444  4556666666777777777777777776666544 45556666677


Q ss_pred             HHHhc-CCHHHHHHHHHHHHhcCCCC-CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH
Q 011236          323 SLVKI-GELEEAEKMLEEWELSCYCY-DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM  400 (490)
Q Consensus       323 ~~~~~-~~~~~a~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  400 (490)
                      .+... |++++|...++++.+.+..| +...+..+...|...|++++|...++++.+..+. +...+..+...+...|++
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~  163 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQ-FPPAFKELARTKMLAGQL  163 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHTCH
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CchHHHHHHHHHHHcCCH
Confidence            77777 77777777777766622222 2445666677777777777777777777765433 566677777777777777


Q ss_pred             HHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          401 EKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ++|...++++++..+     ..+...+..+...+...|+.+.|..+++.+.+..|.
T Consensus       164 ~~A~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p~  214 (225)
T 2vq2_A          164 GDADYYFKKYQSRVE-----VLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFPY  214 (225)
T ss_dssp             HHHHHHHHHHHHHHC-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHhCC-----CCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCC
Confidence            777777777766220     023455556666666777777777777777666665

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.68  E-value=3.9e-15  Score=139.70  Aligned_cols=298  Identities=14%  Similarity=0.044  Sum_probs=147.9

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCC----cchHHHHHHHHHhcCCcCcHHHHHHHHHHC----CCCC-CH
Q 011236          137 DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGS----ALNYNGIMCLYTNTGQHEKIPDVLLDMKEN----GVPP-DN  207 (490)
Q Consensus       137 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~~p-~~  207 (490)
                      ...+......+...|++++|...|++..+.+.. +    ..+|..+...+...|++++|...+++....    +-.| ..
T Consensus         9 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   87 (406)
T 3sf4_A            9 CLELALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   87 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHH
Confidence            444555566666666666666666666665322 2    234555555555666666666655554321    1111 12


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC----hhhHH
Q 011236          208 FSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD----ALGYN  283 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~  283 (490)
                      .++..+...+...|++++|...+++..                                    ...+..++    ..++.
T Consensus        88 ~~~~~la~~~~~~g~~~~A~~~~~~al------------------------------------~~~~~~~~~~~~~~~~~  131 (406)
T 3sf4_A           88 KASGNLGNTLKVLGNFDEAIVCCQRHL------------------------------------DISRELNDKVGEARALY  131 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHH------------------------------------HHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHH------------------------------------HHHHhcccccchHHHHH
Confidence            234444444555555555555554443                                    22111011    22344


Q ss_pred             HHHHHHHhcCC--------------------hhHHHHHHHHHHHhcC-----CCChhhHHHHHHHHHhcCCHHHHHHHHH
Q 011236          284 HLISHYASLGN--------------------KDEMMKFWGLQKIKCK-----KQLNRDYITMLGSLVKIGELEEAEKMLE  338 (490)
Q Consensus       284 ~l~~~~~~~~~--------------------~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~  338 (490)
                      .+...|...|+                    +++|...+++......     .....++..+...+...|++++|...++
T Consensus       132 ~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  211 (406)
T 3sf4_A          132 NLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHE  211 (406)
T ss_dssp             HHHHHHHHHHHTCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHH
T ss_pred             HHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHH
Confidence            44444444444                    4455444443332211     0111234455555555566666655555


Q ss_pred             HHHhcCCC-CC----chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHhccCCHHHHHHHHH
Q 011236          339 EWELSCYC-YD----FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PT----PNSWSIIAAGYADKNNMEKAFECMK  408 (490)
Q Consensus       339 ~~~~~~~~-~~----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~~~~  408 (490)
                      +..+.... ++    ..++..+...|...|++++|...+++..+.... ++    ..++..+...|...|++++|...++
T Consensus       212 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  291 (406)
T 3sf4_A          212 QRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHL  291 (406)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHH
Confidence            55432110 01    124555566666666666666666665442111 01    3455666666667777777777776


Q ss_pred             HHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcc------cc-hhhhHHHHHHHHhcC
Q 011236          409 EALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV------QK-RNMYHALTEAHIRSG  471 (490)
Q Consensus       409 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------~~-~~~~~~l~~~~~~~g  471 (490)
                      ++++..+..........++..+...+...|++++|...+++..+..      +. ..++..+...+...|
T Consensus       292 ~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g  361 (406)
T 3sf4_A          292 KHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLG  361 (406)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhh
Confidence            6665332111111113455566666666777777777666654431      11 455666666666555

>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=99.67  E-value=5.4e-12  Score=123.73  Aligned_cols=425  Identities=8%  Similarity=0.017  Sum_probs=296.0

Q ss_pred             CCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcC---HHHHHH
Q 011236           49 PDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRG---LESAET  125 (490)
Q Consensus        49 ~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~A~~  125 (490)
                      +.+.+. .+++-+... +-|...|..++..+.+.+.++.+..+|+.+...- |.....+...+..-.+.++   ++.+..
T Consensus        48 ~~d~i~-~lE~~l~~n-p~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~f-P~~~~lW~~Yi~~E~~~~~~~~~~~v~~  124 (679)
T 4e6h_A           48 ESDVIG-KLNDMIEEQ-PTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDRF-PLMANIWCMRLSLEFDKMEELDAAVIEP  124 (679)
T ss_dssp             CSCHHH-HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTC--CCCHHHHHH
T ss_pred             CHHHHH-HHHHHHHHC-cCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhhCCcchHHHHHH
Confidence            344444 455555554 5699999999999999999999999999999886 6788888888888888898   999999


Q ss_pred             HHHHccccC---CChhHHHHHHHHHHhcCCh--------hHHHHHHHHHHh-cCC-CCC-cchHHHHHHHHHh-------
Q 011236          126 YFNSLNDED---KVDKLYGALLNCYVREGLV--------DESLSLMQKMKE-MGS-FGS-ALNYNGIMCLYTN-------  184 (490)
Q Consensus       126 ~~~~~~~~~---p~~~~~~~li~~~~~~g~~--------~~a~~~~~~m~~-~~~-~p~-~~~~~~l~~~~~~-------  184 (490)
                      +|++.....   |++..|...+....+.++.        +...++|+.... .|. .|+ ...|...+.....       
T Consensus       125 lfeRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~  204 (679)
T 4e6h_A          125 VLARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKF  204 (679)
T ss_dssp             HHHHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHH
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcH
Confidence            999999887   8888999888877666654        334477777654 366 554 3567777765442       


Q ss_pred             --cCCcCcHHHHHHHHHHCCCCCCHHHHHHH---HHHHh----------ccCChHHHHHHHHHHHh-CCC----CC----
Q 011236          185 --TGQHEKIPDVLLDMKENGVPPDNFSYRIC---INSYG----------ARSELSSMENVLQEMES-QSH----IS----  240 (490)
Q Consensus       185 --~~~~~~a~~~~~~m~~~~~~p~~~~~~~l---i~~~~----------~~g~~~~a~~~~~~~~~-~~~----~~----  240 (490)
                        .++.+.+..+|+..+......-..+|...   .....          ...+++.|...+.++.. ..+    ++    
T Consensus       205 eeq~~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~  284 (679)
T 4e6h_A          205 EEQQRVQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLN  284 (679)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSST
T ss_pred             HHHhHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccc
Confidence              33466788899998863222122333222   21110          01123344455544321 011    10    


Q ss_pred             -------C-----C---HHHHHHHHHHHHHcC-------CHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHH
Q 011236          241 -------M-----D---WGTYSTVANYYIIAG-------LKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEM  298 (490)
Q Consensus       241 -------~-----~---~~~~~~li~~~~~~~-------~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  298 (490)
                             |     +   ...|...+.---..+       ..+.+..+|+++....+  .+...|...+..+...|+.++|
T Consensus       285 ~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p--~~~~lW~~ya~~~~~~~~~~~a  362 (679)
T 4e6h_A          285 QATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVC--FAPEIWFNMANYQGEKNTDSTV  362 (679)
T ss_dssp             TCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTT--TCHHHHHHHHHHHHHHSCCTTH
T ss_pred             cchhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHcC--CCHHHHHHHHHHHHhcCcHHHH
Confidence                   1     0   123333333222221       13446678888888666  5788899999988899999999


Q ss_pred             H-HHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC---------CCC------------chhHHHHH
Q 011236          299 M-KFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY---------CYD------------FRVPNIIL  356 (490)
Q Consensus       299 ~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---------~~~------------~~~~~~l~  356 (490)
                      . .+|++.....+ .+...+...+....+.|+++.|.++|+.+.+...         .|+            ..+|...+
T Consensus       363 ~r~il~rAi~~~P-~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~  441 (679)
T 4e6h_A          363 ITKYLKLGQQCIP-NSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYM  441 (679)
T ss_dssp             HHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHH
Confidence            7 99999887654 5666677888888899999999999999886410         132            23677788


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHH
Q 011236          357 LGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK-NNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLG  435 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~  435 (490)
                      ....+.|..+.|..+|.+.++.-..+....|...+..-.+. ++.+.|..+|+.+++..      .-+...+...+....
T Consensus       442 ~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~------p~~~~~w~~y~~fe~  515 (679)
T 4e6h_A          442 NTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYF------ATDGEYINKYLDFLI  515 (679)
T ss_dssp             HHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHH------TTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC------CCchHHHHHHHHHHH
Confidence            88888999999999999998861112334444333333343 55899999999999833      234456678888888


Q ss_pred             cCCCHHHHHHHHHHHHhccc---c-hhhhHHHHHHHHhcC--CcHHHHHHHHHhCC
Q 011236          436 DNRDVEEVEAFVSSLKIKVQ---K-RNMYHALTEAHIRSG--QEVDGLLESMKADD  485 (490)
Q Consensus       436 ~~g~~~~a~~~~~~~~~~~~---~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~  485 (490)
                      ..|+.+.|..+|++.....+   . ...|..++..-.+.|  +.+..+.+++.+.-
T Consensus       516 ~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~  571 (679)
T 4e6h_A          516 YVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKF  571 (679)
T ss_dssp             HHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHS
T ss_pred             hCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            89999999999999999877   3 788999999999999  78999999988754

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.67  E-value=4.2e-15  Score=128.86  Aligned_cols=197  Identities=15%  Similarity=0.104  Sum_probs=82.2

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHH
Q 011236          209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISH  288 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  288 (490)
                      .|..+...+...|++++|...|+++. +... .+...+..+..++...|++++|+..|+++....+  .+..++..+...
T Consensus        25 ~~~~~a~~~~~~~~~~~A~~~~~~~l-~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~la~~  100 (243)
T 2q7f_A           25 TGGQQMGRGSEFGDYEKAAEAFTKAI-EENK-EDAIPYINFANLLSSVNELERALAFYDKALELDS--SAATAYYGAGNV  100 (243)
T ss_dssp             -----------------CCTTHHHHH-TTCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCHHHHHHHHHHHH-HhCc-ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC--cchHHHHHHHHH
Confidence            34444445555555555555555554 3222 3344444455555555555555555555444332  344444445555


Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 011236          289 YASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKA  368 (490)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  368 (490)
                      +...|++++|...+++.....+ .+...+..+...+...|++++|...++++.+. .+.+...+..+...|...|++++|
T Consensus       101 ~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A  178 (243)
T 2q7f_A          101 YVVKEMYKEAKDMFEKALRAGM-ENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL-NENDTEARFQFGMCLANEGMLDEA  178 (243)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHTC-CSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHcCCHHHH
Confidence            5555555555555554444433 33344444444444444444444444444443 112333344444444444444444


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          369 DAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       369 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...++++.+..+. +..++..+...|...|++++|...++++++
T Consensus       179 ~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  221 (243)
T 2q7f_A          179 LSQFAAVTEQDPG-HADAFYNAGVTYAYKENREKALEMLDKAID  221 (243)
T ss_dssp             HHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCcc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHc
Confidence            4444444443222 334444444444444444444444444444

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.67  E-value=3.4e-14  Score=123.92  Aligned_cols=199  Identities=10%  Similarity=-0.108  Sum_probs=127.6

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHH
Q 011236          208 FSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLIS  287 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  287 (490)
                      ..+..+...+...|++++|...|+++. +... .+..++..+..+|...|++++|.+.|+++....+  .+...+..+..
T Consensus        38 ~~~~~~a~~~~~~~~~~~A~~~~~~al-~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~--~~~~~~~~la~  113 (252)
T 2ho1_A           38 DAYIQLGLGYLQRGNTEQAKVPLRKAL-EIDP-SSADAHAALAVVFQTEMEPKLADEEYRKALASDS--RNARVLNNYGG  113 (252)
T ss_dssp             HHHHHHHHHHHHTTCTGGGHHHHHHHH-HHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCChHHHHHHHHHHH-hcCC-ChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc--CcHHHHHHHHH
Confidence            445555666666666666666666665 3322 3455666666666666777777776666665443  35566666666


Q ss_pred             HHHhcCChhHHHHHHHHHHHhcCC-CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHH
Q 011236          288 HYASLGNKDEMMKFWGLQKIKCKK-QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIE  366 (490)
Q Consensus       288 ~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  366 (490)
                      .+...|++++|.+++++....... .+...+..+...+...|++++|...++++.+.. +.+...+..+...|...|+++
T Consensus       114 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~  192 (252)
T 2ho1_A          114 FLYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYV  192 (252)
T ss_dssp             HHHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHH
Confidence            667777777777777665551111 234556666666777777777777777766652 224556666777777777777


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          367 KADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       367 ~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +|...++++.+..+. +...+..+...+...|++++|.++++++.+
T Consensus       193 ~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~  237 (252)
T 2ho1_A          193 PARQYYDLFAQGGGQ-NARSLLLGIRLAKVFEDRDTAASYGLQLKR  237 (252)
T ss_dssp             HHHHHHHHHHTTSCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCcC-cHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            777777777665432 566677777777777777777777777766

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.66  E-value=1.9e-14  Score=132.20  Aligned_cols=247  Identities=9%  Similarity=0.044  Sum_probs=129.3

Q ss_pred             hHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCC-cCcHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 011236          138 KLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQ-HEKIPDVLLDMKENGVPPDNFSYRICINS  216 (490)
Q Consensus       138 ~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~~~~~li~~  216 (490)
                      .+|+.+...+.+.|++++|+..+++....... +..+|+.+..++...|+ +++|+..|++.++... -+...|..+..+
T Consensus        98 ~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~-~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~P-~~~~a~~~~g~~  175 (382)
T 2h6f_A           98 DVYDYFRAVLQRDERSERAFKLTRDAIELNAA-NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRVL  175 (382)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCChHHHHHHHHHHHHhCcc-CHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCC-CCHHHHHHHHHH
Confidence            34555555555555555555555555554333 44455555555555554 5555555555555322 134455555555


Q ss_pred             HhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHh-cCCh
Q 011236          217 YGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYAS-LGNK  295 (490)
Q Consensus       217 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~  295 (490)
                      +...|++++|+..|+++. ..+. -+..+|..+..++...|++++|+..|+++....+  .+...|+.+..++.. .|..
T Consensus       176 ~~~~g~~~eAl~~~~kal-~ldP-~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P--~~~~a~~~lg~~l~~l~~~~  251 (382)
T 2h6f_A          176 VEWLRDPSQELEFIADIL-NQDA-KNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV--RNNSVWNQRYFVISNTTGYN  251 (382)
T ss_dssp             HHHHTCCTTHHHHHHHHH-HHCT-TCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCSC
T ss_pred             HHHccCHHHHHHHHHHHH-HhCc-cCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHhcCcc
Confidence            555555555555555555 3333 3455555555556666666666666666555444  355556666665555 4443


Q ss_pred             hHH-----HHHHHHHHHhcCCCChhhHHHHHHHHHhcC--CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC-----
Q 011236          296 DEM-----MKFWGLQKIKCKKQLNRDYITMLGSLVKIG--ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG-----  363 (490)
Q Consensus       296 ~~a-----~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-----  363 (490)
                      ++|     +..+++.+...+ .+...|..+...+...|  ++++|.+.+.++ +. .+.+...+..+...|.+.|     
T Consensus       252 ~eA~~~~el~~~~~Al~l~P-~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~-~p~~~~al~~La~~~~~~~~~~~~  328 (382)
T 2h6f_A          252 DRAVLEREVQYTLEMIKLVP-HNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QP-SHSSPYLIAFLVDIYEDMLENQCD  328 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHHST-TCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TT-TCCCHHHHHHHHHHHHHHHHTTCS
T ss_pred             hHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHccCccchHHHHHHHHHh-cc-CCCCHHHHHHHHHHHHHHhccccc
Confidence            555     355555555444 44455555555555555  456666666555 22 2223445555666665543     


Q ss_pred             ----CHHHHHHHHHHH-HHcCCCCCHHHHHHHHHHH
Q 011236          364 ----MIEKADAVLKEI-VKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       364 ----~~~~A~~~~~~m-~~~~~~p~~~~~~~l~~~~  394 (490)
                          ..++|..+|+++ .+.++. ....|..+...+
T Consensus       329 ~~~~~~~~A~~~~~~l~~~~DP~-r~~~w~~~~~~l  363 (382)
T 2h6f_A          329 NKEDILNKALELCEILAKEKDTI-RKEYWRYIGRSL  363 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHHTTCGG-GHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHhCch-hHHHHHHHHHHH
Confidence                246666666666 444322 233444444433

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.66  E-value=3.7e-15  Score=131.88  Aligned_cols=196  Identities=10%  Similarity=-0.140  Sum_probs=83.0

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHH
Q 011236          209 SYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISH  288 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  288 (490)
                      ++..+...+...|++++|...|+++. ..+. .+..++..+..+|...|++++|...|+++....+  .+..++..+..+
T Consensus        45 ~~~~l~~~~~~~~~~~~A~~~~~~al-~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~~--~~~~~~~~la~~  120 (275)
T 1xnf_A           45 LLYERGVLYDSLGLRALARNDFSQAL-AIRP-DMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP--TYNYAHLNRGIA  120 (275)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH-HHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHH-HcCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCc--cccHHHHHHHHH
Confidence            34444444444444444444444444 2222 2344444444444444555555544444444332  234444444444


Q ss_pred             HHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 011236          289 YASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKA  368 (490)
Q Consensus       289 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  368 (490)
                      +...|++++|...++++....+  +.......+..+...|++++|...+++.... .+++...+ .++..+...++.++|
T Consensus       121 ~~~~g~~~~A~~~~~~a~~~~~--~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~-~~~~~~~~~~~~~~a  196 (275)
T 1xnf_A          121 LYYGGRDKLAQDDLLAFYQDDP--NDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK-SDKEQWGW-NIVEFYLGNISEQTL  196 (275)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH-SCCCSTHH-HHHHHHTTSSCHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCC--CChHHHHHHHHHHHhcCHHHHHHHHHHHHhc-CCcchHHH-HHHHHHHHhcCHHHH
Confidence            4445555555555444444322  1112222222233344455555555444433 12222222 233344444444444


Q ss_pred             HHHHHHHHHcCCCC---CHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          369 DAVLKEIVKKGKTP---TPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       369 ~~~~~~m~~~~~~p---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...+++..+.....   +..+|..+...|...|++++|...|++++.
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  243 (275)
T 1xnf_A          197 MERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA  243 (275)
T ss_dssp             HHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44444443321110   123444445555555555555555555544

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.66  E-value=1.1e-14  Score=126.12  Aligned_cols=211  Identities=12%  Similarity=-0.020  Sum_probs=115.3

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                      ....|..+...+...|++++|...|+++....+  .+...+..+...+...|++++|...+++.....+ .+...+..+.
T Consensus        22 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~--~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la   98 (243)
T 2q7f_A           22 ASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENK--EDAIPYINFANLLSSVNELERALAFYDKALELDS-SAATAYYGAG   98 (243)
T ss_dssp             --------------------CCTTHHHHHTTCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCc--ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC-cchHHHHHHH
Confidence            344555566666666666666666666665443  3556666666666666666666666666655543 4455566666


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHH
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNME  401 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  401 (490)
                      ..+...|++++|.+.++++.+.. +.+...+..+...|...|++++|...++++.+..+. +...+..+...+...|+++
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~  176 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNEN-DTEARFQFGMCLANEGMLD  176 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHcCCHH
Confidence            66666666666666666666542 234455566666666666666666666666655433 5556666666666666666


Q ss_pred             HHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHH
Q 011236          402 KAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHAL  463 (490)
Q Consensus       402 ~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l  463 (490)
                      +|...++++.+..      ..+..++..+...+...|++++|...++++.+..|. ...+..+
T Consensus       177 ~A~~~~~~~~~~~------~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~  233 (243)
T 2q7f_A          177 EALSQFAAVTEQD------PGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAK  233 (243)
T ss_dssp             HHHHHHHHHHHHC------TTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhC------cccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCcchHHHHHHH
Confidence            6666666666521      123455666666666666666666666666666665 4444433

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.66  E-value=4.8e-15  Score=139.12  Aligned_cols=307  Identities=13%  Similarity=0.040  Sum_probs=190.2

Q ss_pred             CChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC-----hhHHHHHHHHHHhcCChhHHHHHHHHHHhc----CCCC-C
Q 011236          102 FSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV-----DKLYGALLNCYVREGLVDESLSLMQKMKEM----GSFG-S  171 (490)
Q Consensus       102 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~m~~~----~~~p-~  171 (490)
                      .....+......+...|++++|...|+......|+     ..+|..+...+...|++++|...+++....    +..| .
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~   86 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGE   86 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHH
Confidence            34455667778889999999999999999887764     357888999999999999999999987543    2111 2


Q ss_pred             cchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCC-CC----HHHHHHHHHHHhccCC--------------------hHHH
Q 011236          172 ALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVP-PD----NFSYRICINSYGARSE--------------------LSSM  226 (490)
Q Consensus       172 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~-p~----~~~~~~li~~~~~~g~--------------------~~~a  226 (490)
                      ..++..+...+...|++++|...+++..+.... ++    ..++..+...+...|+                    +++|
T Consensus        87 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A  166 (406)
T 3sf4_A           87 AKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAA  166 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHH
Confidence            556888889999999999999999988653110 11    2355566666666666                    5555


Q ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHH
Q 011236          227 ENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQK  306 (490)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  306 (490)
                      ...+++.. .                            ++....  ... ....++..+...+...|++++|...+++..
T Consensus       167 ~~~~~~al-~----------------------------~~~~~~--~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al  214 (406)
T 3sf4_A          167 VDFYEENL-S----------------------------LVTALG--DRA-AQGRAFGNLGNTHYLLGNFRDAVIAHEQRL  214 (406)
T ss_dssp             HHHHHHHH-H----------------------------HHHHTT--CHH-HHHHHHHHHHHHHHHHTBHHHHHHHHHHHH
T ss_pred             HHHHHHHH-H----------------------------HHHhcc--CcH-HHHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            55554433 1                            000000  000 112344445555555555555555555444


Q ss_pred             HhcC-CCC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC----C-CchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          307 IKCK-KQL----NRDYITMLGSLVKIGELEEAEKMLEEWELSCYC----Y-DFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       307 ~~~~-~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      .... .++    ..++..+...+...|++++|...+++..+....    + ...++..+...|...|++++|...+++..
T Consensus       215 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~  294 (406)
T 3sf4_A          215 LIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHL  294 (406)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHH
Confidence            3322 111    124555566666666666666666655432110    0 13456667777778888888888877776


Q ss_pred             HcCCC-CC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCH
Q 011236          377 KKGKT-PT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDV  440 (490)
Q Consensus       377 ~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  440 (490)
                      +.... ++    ..++..+...|...|++++|...++++++..+..........++..+...+...|+.
T Consensus       295 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  363 (406)
T 3sf4_A          295 AIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLS  363 (406)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHh
Confidence            53111 11    456778888888889999999998888775432211122234566666666666654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.65  E-value=6.9e-14  Score=119.50  Aligned_cols=202  Identities=12%  Similarity=-0.032  Sum_probs=152.6

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHH
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHL  285 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  285 (490)
                      +...+..+...+...|++++|.+.|+++. +... .+...+..+..+|...|++++|...++++....+  .+..++..+
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~-~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~--~~~~~~~~l   82 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDAL-KSDP-KNELAWLVRAEIYQYLKVNDKAQESFRQALSIKP--DSAEINNNY   82 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHH-HhCc-cchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCC--CChHHHHHH
Confidence            44566777777888888888888888776 4333 4567777788888888888888888888777554  567778888


Q ss_pred             HHHHHhc-CChhHHHHHHHHHHHhcCC-CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC
Q 011236          286 ISHYASL-GNKDEMMKFWGLQKIKCKK-QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG  363 (490)
Q Consensus       286 ~~~~~~~-~~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  363 (490)
                      ...+... |++++|...++.+...... .+...+..+...+...|++++|...++++.+.. +.+...+..+...|...|
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~  161 (225)
T 2vq2_A           83 GWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAG  161 (225)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcC
Confidence            8888888 8888888888877762111 234667778888888888888888888887753 334667778888888888


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          364 MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       364 ~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ++++|...++++.+..+..+...+..+...+...|+.+.+..+++.+..
T Consensus       162 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  210 (225)
T 2vq2_A          162 QLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQA  210 (225)
T ss_dssp             CHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHH
Confidence            8888888888888765423677777777788888888888888888876

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.65  E-value=7.4e-14  Score=123.43  Aligned_cols=248  Identities=13%  Similarity=-0.017  Sum_probs=194.9

Q ss_pred             HhccCChHHHHHHHHHHHhCCCC---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcC
Q 011236          217 YGARSELSSMENVLQEMESQSHI---SMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG  293 (490)
Q Consensus       217 ~~~~g~~~~a~~~~~~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  293 (490)
                      ....|++++|+..|+++. +...   +.+..++..+..++...|++++|...|+++....+  .+..+|..+...+...|
T Consensus        15 ~~~~~~~~~A~~~~~~~~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~--~~~~~~~~la~~~~~~~   91 (275)
T 1xnf_A           15 LQPTLQQEVILARMEQIL-ASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRP--DMPEVFNYLGIYLTQAG   91 (275)
T ss_dssp             CCCCHHHHHHHHHHHHHH-TSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHTT
T ss_pred             cCccchHHHHHHHHHHHH-hcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcCC--CcHHHHHHHHHHHHHcc
Confidence            345688999999999998 5432   12467788899999999999999999999998765  57889999999999999


Q ss_pred             ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHH
Q 011236          294 NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLK  373 (490)
Q Consensus       294 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  373 (490)
                      ++++|...|++.....+ .+...+..+...+...|++++|...++++.+.  .|+.......+..+...|++++|...++
T Consensus        92 ~~~~A~~~~~~al~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~  168 (275)
T 1xnf_A           92 NFDAAYEAFDSVLELDP-TYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLK  168 (275)
T ss_dssp             CHHHHHHHHHHHHHHCT-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhcCc-cccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHH
Confidence            99999999999988765 56788999999999999999999999999985  4555555555566677899999999998


Q ss_pred             HHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          374 EIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       374 ~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      +....... +...+ .++..+...++.++|...++++....+   ...|+ ...+..+...+.+.|++++|...++++.+
T Consensus       169 ~~~~~~~~-~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  243 (275)
T 1xnf_A          169 QHFEKSDK-EQWGW-NIVEFYLGNISEQTLMERLKADATDNT---SLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVA  243 (275)
T ss_dssp             HHHHHSCC-CSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHH---HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHhcCCc-chHHH-HHHHHHHHhcCHHHHHHHHHHHhcccc---cccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            88876433 44444 477778888889999999999876221   11112 47888999999999999999999999999


Q ss_pred             cccc-hhhhHHHHHHHHhcC--CcHHHHH
Q 011236          453 KVQK-RNMYHALTEAHIRSG--QEVDGLL  478 (490)
Q Consensus       453 ~~~~-~~~~~~l~~~~~~~g--~~a~~~~  478 (490)
                      ..|. ...+   ..++...|  ++|++.+
T Consensus       244 ~~p~~~~~~---~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          244 NNVHNFVEH---RYALLELSLLGQDQDDL  269 (275)
T ss_dssp             TCCTTCHHH---HHHHHHHHHHHHC----
T ss_pred             CCchhHHHH---HHHHHHHHHHHhhHHHH
Confidence            8875 3333   44555555  5555443

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.64  E-value=1.5e-14  Score=136.06  Aligned_cols=283  Identities=12%  Similarity=0.015  Sum_probs=188.3

Q ss_pred             chHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCH----HHHHHHHHHHhccCChHHHHHHHHHHHhC---C-CCCCCHH
Q 011236          173 LNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDN----FSYRICINSYGARSELSSMENVLQEMESQ---S-HISMDWG  244 (490)
Q Consensus       173 ~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~g~~~~a~~~~~~~~~~---~-~~~~~~~  244 (490)
                      ..+..+...+...|++++|...|++..+.+.. +.    ..+..+...+...|++++|...+++....   . +......
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  127 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAK  127 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHH
Confidence            34555666777888888888888888775322 22    46777778888888888888888877521   1 1113345


Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC----CChhhHHHHHHHHHhcCC-----------------hhHHHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS----KDALGYNHLISHYASLGN-----------------KDEMMKFWG  303 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~~  303 (490)
                      ++..+...|...|++++|...+++........    ....++..+...|...|+                 +++|...++
T Consensus       128 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~  207 (411)
T 4a1s_A          128 SSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQ  207 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHH
Confidence            66777888888888888888888876542110    234567777788888888                 788888777


Q ss_pred             HHHHhcC-----CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC-CC----chhHHHHHHHHHhcCCHHHHHHHHH
Q 011236          304 LQKIKCK-----KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYC-YD----FRVPNIILLGYSQKGMIEKADAVLK  373 (490)
Q Consensus       304 ~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~g~~~~A~~~~~  373 (490)
                      +......     .....++..+...+...|++++|...+++..+.... ++    ..++..+...|...|++++|...++
T Consensus       208 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  287 (411)
T 4a1s_A          208 ENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYK  287 (411)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence            6554321     112235677777788888888888888877654211 11    1256677777888888888888887


Q ss_pred             HHHHcCCC-CC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHH
Q 011236          374 EIVKKGKT-PT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVS  448 (490)
Q Consensus       374 ~m~~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  448 (490)
                      +..+.... .+    ..++..+...|...|++++|..++++++...+..........++..+...+...|++++|...++
T Consensus       288 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  367 (411)
T 4a1s_A          288 RTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAE  367 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHH
Confidence            77653211 11    35677777788888888888888888887443221111112466677777888888888888888


Q ss_pred             HHHhcccc
Q 011236          449 SLKIKVQK  456 (490)
Q Consensus       449 ~~~~~~~~  456 (490)
                      +..+....
T Consensus       368 ~al~~~~~  375 (411)
T 4a1s_A          368 QHLQLAXX  375 (411)
T ss_dssp             HHHHHCCH
T ss_pred             HHHHHHhh
Confidence            87776554

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.63  E-value=8.6e-15  Score=137.75  Aligned_cols=275  Identities=10%  Similarity=0.012  Sum_probs=214.8

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCc----chHHHHHHHHHhcCCcCcHHHHHHHHHHC----CC-CCCH
Q 011236          137 DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSA----LNYNGIMCLYTNTGQHEKIPDVLLDMKEN----GV-PPDN  207 (490)
Q Consensus       137 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~----~~~~~l~~~~~~~~~~~~a~~~~~~m~~~----~~-~p~~  207 (490)
                      ...+..+...+...|++++|+..|+++.+.+.. +.    ..|..+...+...|++++|...+++..+.    +- +...
T Consensus        48 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  126 (411)
T 4a1s_A           48 CLELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEA  126 (411)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHH
Confidence            344566778889999999999999999987433 33    46888999999999999999999988653    11 2234


Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHhC----CCCCCCHHHHHHHHHHHHHcCC-----------------HHHHHHHH
Q 011236          208 FSYRICINSYGARSELSSMENVLQEMESQ----SHISMDWGTYSTVANYYIIAGL-----------------KEKAIIYL  266 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~----~~~~~~~~~~~~li~~~~~~~~-----------------~~~a~~~~  266 (490)
                      .++..+...+...|++++|...+++....    .+......++..+...|...|+                 +++|+..+
T Consensus       127 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~  206 (411)
T 4a1s_A          127 KSSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFY  206 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHH
Confidence            57888889999999999999999987621    1111235577889999999999                 99999999


Q ss_pred             HHHhhhhccC----CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC-CC----hhhHHHHHHHHHhcCCHHHHHHHH
Q 011236          267 KKCEDIVSKS----KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK-QL----NRDYITMLGSLVKIGELEEAEKML  337 (490)
Q Consensus       267 ~~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~  337 (490)
                      ++........    ....++..+...|...|++++|...+++....... ++    ...+..+...+...|++++|...+
T Consensus       207 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  286 (411)
T 4a1s_A          207 QENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHY  286 (411)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence            9876532210    23357888899999999999999999988776541 12    126788999999999999999999


Q ss_pred             HHHHhcCCCC-----CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHhccCCHHHHHHHH
Q 011236          338 EEWELSCYCY-----DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PT----PNSWSIIAAGYADKNNMEKAFECM  407 (490)
Q Consensus       338 ~~~~~~~~~~-----~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~~~  407 (490)
                      ++..+.....     ...++..+...|...|++++|...+++..+.... ++    ..++..+...|...|++++|..++
T Consensus       287 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  366 (411)
T 4a1s_A          287 KRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYA  366 (411)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHH
Confidence            9887652211     1456778889999999999999999998764211 12    347889999999999999999999


Q ss_pred             HHHHH
Q 011236          408 KEALA  412 (490)
Q Consensus       408 ~~~~~  412 (490)
                      +++++
T Consensus       367 ~~al~  371 (411)
T 4a1s_A          367 EQHLQ  371 (411)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            99998

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.63  E-value=1.9e-14  Score=136.47  Aligned_cols=379  Identities=15%  Similarity=0.064  Sum_probs=249.4

Q ss_pred             HHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCh---hHHHHHHHHHHhCCCCCChhhHHHHHHHHH
Q 011236           39 LYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRF---KHALQVSEWMSGQGLAFSVHDHAVQLDLIG  115 (490)
Q Consensus        39 l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  115 (490)
                      +.....+.|+.++++. ++++....|.   ...+..+...+...|+.   ++|++.|++..+.    ++..+..+...+.
T Consensus         9 la~~~~~~g~~~~A~~-~~~~aa~~g~---~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~----~~~A~~~Lg~~~~   80 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQ-NYQQLAELGY---SEAQVGLADIQVGTRDPAQIKQAEATYRAAADT----SPRAQARLGRLLA   80 (452)
T ss_dssp             HHHHHHHHHHHHHHHH-HHHHHHHHTC---CTGGGTCC--------------------------------CHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHH-HHHHHHHCCC---HHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhC----CHHHHHHHHHHHH
Confidence            4445556677777777 6766666653   34445555556667777   8999999988855    4555666666444


Q ss_pred             hhc-----CHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChh---HHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCC
Q 011236          116 KVR-----GLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVD---ESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQ  187 (490)
Q Consensus       116 ~~~-----~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~---~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  187 (490)
                      ..+     ++++|...|+.....++ ..++..|...|...+..+   ++.+.+......|   +...+..|...|...+.
T Consensus        81 ~~~~~~~~~~~~A~~~~~~Aa~~g~-~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg~~y~~~~~  156 (452)
T 3e4b_A           81 AKPGATEAEHHEAESLLKKAFANGE-GNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQVLLYRTQGT  156 (452)
T ss_dssp             TC--CCHHHHHHHHHHHHHHHHTTC-SSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHHHHHHHHTC
T ss_pred             hCCCCCCcCHHHHHHHHHHHHHCCC-HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCC
Confidence            444     78899999999888663 236777888887766544   4555555555554   56778888888888887


Q ss_pred             cCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccC---ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc----CCHH
Q 011236          188 HEKIPDVLLDMKENGVPPDNFSYRICINSYGARS---ELSSMENVLQEMESQSHISMDWGTYSTVANYYIIA----GLKE  260 (490)
Q Consensus       188 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~----~~~~  260 (490)
                      ++++........+.-...+...+..|...|...|   +.++|.+.|++.. +.+. ++...+..+...|...    ++++
T Consensus       157 ~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa-~~g~-~~a~~~~~Lg~~y~~g~~~~~d~~  234 (452)
T 3e4b_A          157 YDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGV-SRGT-VTAQRVDSVARVLGDATLGTPDEK  234 (452)
T ss_dssp             GGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-HTTC-SCHHHHHHHHHHHTCGGGSSCCHH
T ss_pred             cccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHH-HCCC-HHHHHHHHHHHHHhCCCCCCCCHH
Confidence            7776665444433222234447888888888899   9999999999998 6666 6666666677777665    7999


Q ss_pred             HHHHHHHHHhhhhccCCChhhHHHHHHH-H--HhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcC-----CHHH
Q 011236          261 KAIIYLKKCEDIVSKSKDALGYNHLISH-Y--ASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG-----ELEE  332 (490)
Q Consensus       261 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-----~~~~  332 (490)
                      +|+..|++..    + .+...+..+... +  ...+++++|...|++....+   +...+..+...|. .|     ++++
T Consensus       235 ~A~~~~~~aa----~-g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~  305 (452)
T 3e4b_A          235 TAQALLEKIA----P-GYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKA  305 (452)
T ss_dssp             HHHHHHHHHG----G-GSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHH
T ss_pred             HHHHHHHHHc----C-CCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHH
Confidence            9999999987    2 466677777777 4  56899999999999877654   5677777777777 55     9999


Q ss_pred             HHHHHHHHHhcCCCCCchhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHH
Q 011236          333 AEKMLEEWELSCYCYDFRVPNIILLGYSQ----KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAF  404 (490)
Q Consensus       333 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~  404 (490)
                      |...|++.. .   -+...+..|...|..    ..++++|...|++..+.|   +......|...|..    ..+..+|.
T Consensus       306 A~~~~~~Aa-~---g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~G~g~~~d~~~A~  378 (452)
T 3e4b_A          306 AEAHFEKAV-G---REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNG---QNSADFAIAQLFSQGKGTKPDPLNAY  378 (452)
T ss_dssp             HHHHHHTTT-T---TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTT---CTTHHHHHHHHHHSCTTBCCCHHHHH
T ss_pred             HHHHHHHHh-C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhC---hHHHHHHHHHHHHhCCCCCCCHHHHH
Confidence            999999887 3   355667777777776    348999999999999876   34556677777764    46899999


Q ss_pred             HHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          405 ECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       405 ~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      .+|+.+.+     .|. ++.......+......++.++|..+.++..+.
T Consensus       379 ~~~~~A~~-----~g~-~~a~~~l~~l~~~~~~~~~~~a~~~~~~~~~~  421 (452)
T 3e4b_A          379 VFSQLAKA-----QDT-PEANDLATQLEAPLTPAQRAEGQRLVQQELAA  421 (452)
T ss_dssp             HHHHHHHT-----TCC-HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-----CCC-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHh
Confidence            99999988     453 22322222233333445667777777765554

>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=99.63  E-value=6.5e-13  Score=117.27  Aligned_cols=226  Identities=11%  Similarity=-0.022  Sum_probs=153.1

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHhhhhccCCChhh
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII----AGLKEKAIIYLKKCEDIVSKSKDALG  281 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~  281 (490)
                      +..++..+...+...|++++|...|++.. +.   -+..++..+...|..    .+++++|...|++..+.+    +...
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~-~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~----~~~a   76 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKAC-DL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN----YSNG   76 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT----CHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHH-HC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC----CHHH
Confidence            34455566666666777777777777766 32   334556666667777    777777777777665432    4556


Q ss_pred             HHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCchhHH
Q 011236          282 YNHLISHYAS----LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVK----IGELEEAEKMLEEWELSCYCYDFRVPN  353 (490)
Q Consensus       282 ~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  353 (490)
                      +..+...|..    .+++++|...|++....+   +...+..+...|..    .+++++|...+++..+.+   +...+.
T Consensus        77 ~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~  150 (273)
T 1ouv_A           77 CHLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCT  150 (273)
T ss_dssp             HHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             HHHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHH
Confidence            6666667766    777777777777666542   55666667777776    777777777777777654   445566


Q ss_pred             HHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHHHHHHHHHHhhhcCcCCCcchh
Q 011236          354 IILLGYSQ----KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAFECMKEALAVHEENKFWRPKPS  425 (490)
Q Consensus       354 ~l~~~~~~----~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~p~~~  425 (490)
                      .+...|..    .+++++|...|++..+.+   +...+..+...|..    .+++++|+..|+++.+     .+  | ..
T Consensus       151 ~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~-----~~--~-~~  219 (273)
T 1ouv_A          151 ILGSLYDAGRGTPKDLKKALASYDKACDLK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACE-----LE--N-GG  219 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHH-----TT--C-HH
T ss_pred             HHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHh-----CC--C-HH
Confidence            66666766    777777877777777663   45667777777777    7778888888877776     22  2 45


Q ss_pred             hHHHHHHHHHc----CCCHHHHHHHHHHHHhcccc
Q 011236          426 LVSSILDWLGD----NRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       426 ~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+..+...+..    .+++++|.+.+++..+.+|.
T Consensus       220 a~~~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~~~  254 (273)
T 1ouv_A          220 GCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGAK  254 (273)
T ss_dssp             HHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             HHHHHHHHHHcCCCcccCHHHHHHHHHHHHHcCCH
Confidence            66666777776    77778888888777777665

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.63  E-value=1.7e-14  Score=131.39  Aligned_cols=283  Identities=14%  Similarity=0.067  Sum_probs=146.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCC----cchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHH
Q 011236          140 YGALLNCYVREGLVDESLSLMQKMKEMGSFGS----ALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICIN  215 (490)
Q Consensus       140 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~  215 (490)
                      +......+...|++++|...|+++.+.... +    ...+..+...+...|++++|.+.+++..+..             
T Consensus         8 l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-------------   73 (338)
T 3ro2_A            8 LALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLA-------------   73 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-------------
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh-------------
Confidence            334445555666666666666666554221 1    2344455555555555555555555443210             


Q ss_pred             HHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC----hhhHHHHHHHHHh
Q 011236          216 SYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD----ALGYNHLISHYAS  291 (490)
Q Consensus       216 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~  291 (490)
                                        ....+.+....++..+...|...|++++|...+++........++    ..++..+...+..
T Consensus        74 ------------------~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~  135 (338)
T 3ro2_A           74 ------------------RTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHA  135 (338)
T ss_dssp             ------------------HHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             ------------------hcccccHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHH
Confidence                              000000011233444444555555555555555544332221111    1244445555555


Q ss_pred             cCC--------------------hhHHHHHHHHHHHhcC-----CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC
Q 011236          292 LGN--------------------KDEMMKFWGLQKIKCK-----KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYC  346 (490)
Q Consensus       292 ~~~--------------------~~~a~~~~~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  346 (490)
                      .|+                    +++|...+++......     ......+..+...+...|++++|...+++..+....
T Consensus       136 ~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~  215 (338)
T 3ro2_A          136 KGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKE  215 (338)
T ss_dssp             HHHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             cCcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHh
Confidence            555                    5555555544332211     011234555566666666666666666665532110


Q ss_pred             -C----CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhc
Q 011236          347 -Y----DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEE  416 (490)
Q Consensus       347 -~----~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  416 (490)
                       +    ...++..+...|...|++++|...+++..+.... ++    ..++..+...|...|++++|...++++++..+.
T Consensus       216 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~  295 (338)
T 3ro2_A          216 FGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQE  295 (338)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             cCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHh
Confidence             0    1225566666777777777777777766543111 11    345667777777888888888888877764322


Q ss_pred             CcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Q 011236          417 NKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV  454 (490)
Q Consensus       417 ~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  454 (490)
                      .........++..+...+.+.|++++|...++++.+..
T Consensus       296 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  333 (338)
T 3ro2_A          296 LKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEIS  333 (338)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC-
T ss_pred             cCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHH
Confidence            11111123466677777778888888888887776543

>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=99.63  E-value=1.3e-12  Score=115.40  Aligned_cols=223  Identities=11%  Similarity=-0.047  Sum_probs=194.8

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHh----cCChhHHHHHHHHHHHhcCCCChhhH
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYAS----LGNKDEMMKFWGLQKIKCKKQLNRDY  317 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~  317 (490)
                      +..++..+...|...|++++|+..|++..+   + .+..++..+...|..    .+++++|...|++....+   +...+
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~---~-~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~   77 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACD---L-KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGC   77 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---T-TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHH---C-CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            566778899999999999999999999877   2 456788889999999    999999999999887764   67888


Q ss_pred             HHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 011236          318 ITMLGSLVK----IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ----KGMIEKADAVLKEIVKKGKTPTPNSWSI  389 (490)
Q Consensus       318 ~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~~p~~~~~~~  389 (490)
                      ..+...|..    .+++++|...+++..+.+   +...+..+...|..    .+++++|...|++..+.+   +...+..
T Consensus        78 ~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~  151 (273)
T 1ouv_A           78 HLLGNLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTI  151 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHH
Confidence            899999999    999999999999999874   66788889999999    999999999999999976   6778888


Q ss_pred             HHHHHhc----cCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc----CCCHHHHHHHHHHHHhcccchhhhH
Q 011236          390 IAAGYAD----KNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD----NRDVEEVEAFVSSLKIKVQKRNMYH  461 (490)
Q Consensus       390 l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~  461 (490)
                      +...|..    .+++++|+..|+++.+     .+   +...+..+...+..    .+++++|...+++..+.++ +..+.
T Consensus       152 lg~~~~~~~~~~~~~~~A~~~~~~a~~-----~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~-~~a~~  222 (273)
T 1ouv_A          152 LGSLYDAGRGTPKDLKKALASYDKACD-----LK---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN-GGGCF  222 (273)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHH-----TT---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC-HHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHHHHHH-----CC---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC-HHHHH
Confidence            8888888    9999999999999998     32   45677888888988    9999999999999998866 67788


Q ss_pred             HHHHHHHh----cC--CcHHHHHHHHHhCCC
Q 011236          462 ALTEAHIR----SG--QEVDGLLESMKADDI  486 (490)
Q Consensus       462 ~l~~~~~~----~g--~~a~~~~~~m~~~~~  486 (490)
                      .+...|.+    .+  ++|.+++++..+.|.
T Consensus       223 ~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          223 NLGAMQYNGEGVTRNEKQAIENFKKGCKLGA  253 (273)
T ss_dssp             HHHHHHHTTSSSSCCSTTHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCCcccCHHHHHHHHHHHHHcCC
Confidence            88999987    66  899999999887653

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.61  E-value=5.7e-14  Score=127.94  Aligned_cols=275  Identities=15%  Similarity=0.026  Sum_probs=208.4

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC----CChh
Q 011236          209 SYRICINSYGARSELSSMENVLQEMESQSHISMD----WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS----KDAL  280 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~  280 (490)
                      .+......+...|++++|...|+++. +.+. .+    ...+..+...|...|++++|...+++........    ....
T Consensus         7 ~l~~~g~~~~~~g~~~~A~~~~~~al-~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~   84 (338)
T 3ro2_A            7 ELALEGERLCKSGDCRAGVSFFEAAV-QVGT-EDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAK   84 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH-HHCC-SCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHH-hhCc-ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHH
Confidence            44455677888999999999999987 4332 23    3677788899999999999999998876532110    2356


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHhcC-CCC----hhhHHHHHHHHHhcCC--------------------HHHHHH
Q 011236          281 GYNHLISHYASLGNKDEMMKFWGLQKIKCK-KQL----NRDYITMLGSLVKIGE--------------------LEEAEK  335 (490)
Q Consensus       281 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~----~~~~~~l~~~~~~~~~--------------------~~~a~~  335 (490)
                      ++..+...+...|++++|...+++...... .++    ..++..+...+...|+                    +++|..
T Consensus        85 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~  164 (338)
T 3ro2_A           85 ASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVD  164 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHH
Confidence            788899999999999999999998776543 122    3377888899999999                    999999


Q ss_pred             HHHHHHhc----CCCC-CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHhccCCHHHHHH
Q 011236          336 MLEEWELS----CYCY-DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PT----PNSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       336 ~~~~~~~~----~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      .+++....    +..+ ...++..+...|...|++++|...+++..+.... ++    ..++..+...+...|++++|..
T Consensus       165 ~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  244 (338)
T 3ro2_A          165 LYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASE  244 (338)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            99876543    1111 2346778888899999999999999988753111 12    2378888999999999999999


Q ss_pred             HHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-------hhhhHHHHHHHHhcC--CcHHH
Q 011236          406 CMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-------RNMYHALTEAHIRSG--QEVDG  476 (490)
Q Consensus       406 ~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-------~~~~~~l~~~~~~~g--~~a~~  476 (490)
                      .+++++...+..........++..+...+...|++++|...++++.+..+.       ..++..+...|.+.|  ++|..
T Consensus       245 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  324 (338)
T 3ro2_A          245 YYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMH  324 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHH
Confidence            999998855322111112467788889999999999999999988765332       558889999999999  89999


Q ss_pred             HHHHHHhCC
Q 011236          477 LLESMKADD  485 (490)
Q Consensus       477 ~~~~m~~~~  485 (490)
                      ++++..+..
T Consensus       325 ~~~~a~~~~  333 (338)
T 3ro2_A          325 FAEKHLEIS  333 (338)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHHH
Confidence            999887653

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.60  E-value=4.5e-13  Score=110.58  Aligned_cols=166  Identities=16%  Similarity=0.078  Sum_probs=122.4

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                      +...|..+...|...|++++|+..|++..+..+  .+..++..+..+|...|++++|...+.......+ .+...+..+.
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p--~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~   80 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADP--NNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDT-TSAEAYYILG   80 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC-CCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCc-hhHHHHHHHH
Confidence            456677777778888888888888887777655  4667777777777788888888887776666654 5556666677


Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHH
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNME  401 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~  401 (490)
                      ..+...++++.+...+.+..+. .+.+...+..+...|.+.|++++|+..|++..+..+. +..+|..+..+|.+.|+++
T Consensus        81 ~~~~~~~~~~~a~~~~~~a~~~-~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~-~~~~~~~lg~~~~~~g~~~  158 (184)
T 3vtx_A           81 SANFMIDEKQAAIDALQRAIAL-NTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPG-FIRAYQSIGLAYEGKGLRD  158 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh-CccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcch-hhhHHHHHHHHHHHCCCHH
Confidence            7777777788787777777765 2335566777777777788888888888877776554 6677777777888888888


Q ss_pred             HHHHHHHHHHH
Q 011236          402 KAFECMKEALA  412 (490)
Q Consensus       402 ~a~~~~~~~~~  412 (490)
                      +|++.|+++++
T Consensus       159 ~A~~~~~~al~  169 (184)
T 3vtx_A          159 EAVKYFKKALE  169 (184)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            88888888777

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.57  E-value=2.4e-12  Score=115.71  Aligned_cols=222  Identities=10%  Similarity=-0.025  Sum_probs=141.4

Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH-------HcCCH-------HHHHHHHHHHhhhhccCCChhhHHHHHHHH
Q 011236          224 SSMENVLQEMESQSHISMDWGTYSTVANYYI-------IAGLK-------EKAIIYLKKCEDIVSKSKDALGYNHLISHY  289 (490)
Q Consensus       224 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~-------~~~~~-------~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  289 (490)
                      ++|..+|++.. ...+ .+...|..++..+.       ..|++       ++|..+|++......+ .+...|..++..+
T Consensus        33 ~~a~~~~~~al-~~~p-~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p-~~~~~~~~~~~~~  109 (308)
T 2ond_A           33 KRVMFAYEQCL-LVLG-HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLK-KNMLLYFAYADYE  109 (308)
T ss_dssp             HHHHHHHHHHH-HHHT-TCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HHcC-CCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCc-ccHHHHHHHHHHH
Confidence            45666666665 3332 44555555555554       23664       6777777777663222 4556677777777


Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCChh-hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHH-hcCCHHH
Q 011236          290 ASLGNKDEMMKFWGLQKIKCKKQLNR-DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYS-QKGMIEK  367 (490)
Q Consensus       290 ~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~  367 (490)
                      ...|++++|..+|++.....+ .+.. .|..++..+.+.|++++|..+|++..+.. +.+...|........ ..|++++
T Consensus       110 ~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~  187 (308)
T 2ond_A          110 ESRMKYEKVHSIYNRLLAIED-IDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSV  187 (308)
T ss_dssp             HHTTCHHHHHHHHHHHHTSSS-SCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHH
T ss_pred             HhcCCHHHHHHHHHHHHhccc-cCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHcCCHHH
Confidence            777777777777776666433 2222 67777777777777777777777777652 223334433322221 2577778


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCc-CCCcc--hhhHHHHHHHHHcCCCHHHHH
Q 011236          368 ADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENK-FWRPK--PSLVSSILDWLGDNRDVEEVE  444 (490)
Q Consensus       368 A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~p~--~~~~~~l~~~~~~~g~~~~a~  444 (490)
                      |..+|++.++..+. +...|..++..+.+.|+.++|..+|++++.     . .+.|+  ...|..++....+.|+.+.|.
T Consensus       188 A~~~~~~al~~~p~-~~~~~~~~~~~~~~~g~~~~A~~~~~~al~-----~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~  261 (308)
T 2ond_A          188 AFKIFELGLKKYGD-IPEYVLAYIDYLSHLNEDNNTRVLFERVLT-----SGSLPPEKSGEIWARFLAFESNIGDLASIL  261 (308)
T ss_dssp             HHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-----SSSSCGGGCHHHHHHHHHHHHHHSCHHHHH
T ss_pred             HHHHHHHHHHhCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-----ccCCCHHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            88887777776443 667777777777777888888888887776     2 23443  356677777777777888888


Q ss_pred             HHHHHHHhcccc
Q 011236          445 AFVSSLKIKVQK  456 (490)
Q Consensus       445 ~~~~~~~~~~~~  456 (490)
                      .+++++.+..|.
T Consensus       262 ~~~~~a~~~~p~  273 (308)
T 2ond_A          262 KVEKRRFTAFRE  273 (308)
T ss_dssp             HHHHHHHHHTTT
T ss_pred             HHHHHHHHHccc
Confidence            777777777765

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.56  E-value=1.6e-13  Score=131.02  Aligned_cols=207  Identities=11%  Similarity=-0.032  Sum_probs=147.3

Q ss_pred             HHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCCh-hHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHH
Q 011236          259 KEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNK-DEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKML  337 (490)
Q Consensus       259 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  337 (490)
                      +++++..++......+  .+...+..+..++...|++ ++|++.|++.....+ .+...|..+..+|...|++++|.+.|
T Consensus        84 ~~~al~~l~~~~~~~~--~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~  160 (474)
T 4abn_A           84 MEKTLQQMEEVLGSAQ--VEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEP-ELVEAWNQLGEVYWKKGDVTSAHTCF  160 (474)
T ss_dssp             HHHHHHHHHHHHTTCC--CCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCc--hhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            4455555555444332  4566677777777777777 777777777766654 45667777777777777777777777


Q ss_pred             HHHHhcCCCCCchhHHHHHHHHHhc---------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc--------CCH
Q 011236          338 EEWELSCYCYDFRVPNIILLGYSQK---------GMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK--------NNM  400 (490)
Q Consensus       338 ~~~~~~~~~~~~~~~~~l~~~~~~~---------g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~--------~~~  400 (490)
                      ++..+.  .|+...+..+...|...         |++++|...|++..+..+. +...|..+..+|...        |++
T Consensus       161 ~~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~~~~~~~~~g~~  237 (474)
T 4abn_A          161 SGALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVL-DGRSWYILGNAYLSLYFNTGQNPKIS  237 (474)
T ss_dssp             HHHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHhhccccchH
Confidence            777764  35556677777777777         7788888888887776544 677777777777777        778


Q ss_pred             HHHHHHHHHHHHhhhcCcCCCc----chhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--Cc
Q 011236          401 EKAFECMKEALAVHEENKFWRP----KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QE  473 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~~~~p----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~  473 (490)
                      ++|+..|+++++       +.|    +...|..+..++...|++++|...|+++.+..|. ...+..+..++...|  ++
T Consensus       238 ~~A~~~~~~al~-------~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~e  310 (474)
T 4abn_A          238 QQALSAYAQAEK-------VDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTS  310 (474)
T ss_dssp             HHHHHHHHHHHH-------HCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-------hCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHH
Confidence            888888888877       234    4567777778888888888888888888887777 777777777777777  55


Q ss_pred             HHHHH
Q 011236          474 VDGLL  478 (490)
Q Consensus       474 a~~~~  478 (490)
                      |++.+
T Consensus       311 Ai~~~  315 (474)
T 4abn_A          311 LLESK  315 (474)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            55443

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.55  E-value=1.3e-12  Score=121.56  Aligned_cols=232  Identities=8%  Similarity=0.035  Sum_probs=168.9

Q ss_pred             HHHHHhccCChHHHHHHHHHHHhCC-CCCC----CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCC-----ChhhH
Q 011236          213 CINSYGARSELSSMENVLQEMESQS-HISM----DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSK-----DALGY  282 (490)
Q Consensus       213 li~~~~~~g~~~~a~~~~~~~~~~~-~~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~  282 (490)
                      ....+...|++++|...|++.. +. .-.+    ...++..+..+|...|++++|+..+++........+     ...++
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al-~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  187 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAE-SKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCH  187 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHH-TTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHH-HHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHH
Confidence            5566778899999999999887 32 1112    246777888899999999999999988876544312     23577


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHHhcCC-CCh----hhHHHHHHHHHhcCCHHHHHHHHHHHHhc----CC-CCCchhH
Q 011236          283 NHLISHYASLGNKDEMMKFWGLQKIKCKK-QLN----RDYITMLGSLVKIGELEEAEKMLEEWELS----CY-CYDFRVP  352 (490)
Q Consensus       283 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~-~~~~~~~  352 (490)
                      +.+...|...|++++|...+++....... ++.    .++..+...|...|++++|...+++..+.    +. +....++
T Consensus       188 ~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  267 (383)
T 3ulq_A          188 SLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAY  267 (383)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHH
Confidence            88888899999999999999877765331 111    36778888899999999999999888762    22 3345567


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcC----CCCCHHHHHHHHHHHhccCC---HHHHHHHHHHHHHhhhcCcCCCcc-h
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKG----KTPTPNSWSIIAAGYADKNN---MEKAFECMKEALAVHEENKFWRPK-P  424 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~----~~p~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~p~-~  424 (490)
                      ..+...|.+.|++++|...+++..+..    -+.....+..+...+...|+   .++|+.++++.        +..|+ .
T Consensus       268 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~--------~~~~~~~  339 (383)
T 3ulq_A          268 FLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK--------MLYADLE  339 (383)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT--------TCHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC--------cCHHHHH
Confidence            888888999999999999988876531    11112335677788888888   66777776664        22233 3


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      ..+..+...|...|++++|...+++..+.
T Consensus       340 ~~~~~la~~y~~~g~~~~A~~~~~~al~~  368 (383)
T 3ulq_A          340 DFAIDVAKYYHERKNFQKASAYFLKVEQV  368 (383)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            56778888899999999999999887654

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.55  E-value=6.1e-12  Score=113.03  Aligned_cols=218  Identities=10%  Similarity=0.010  Sum_probs=101.5

Q ss_pred             hHHHHHHHHHHhcCCCCCcchHHHHHHHHHh-------cCCc-------CcHHHHHHHHHHCCCCC-CHHHHHHHHHHHh
Q 011236          154 DESLSLMQKMKEMGSFGSALNYNGIMCLYTN-------TGQH-------EKIPDVLLDMKENGVPP-DNFSYRICINSYG  218 (490)
Q Consensus       154 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~-------~~~~-------~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~  218 (490)
                      ++|..+|++.....+. ++..|..++..+..       .|++       ++|..+|++.++. +.| +...|..++..+.
T Consensus        33 ~~a~~~~~~al~~~p~-~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~-~~p~~~~~~~~~~~~~~  110 (308)
T 2ond_A           33 KRVMFAYEQCLLVLGH-HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST-LLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTT-TTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHH-hCcccHHHHHHHHHHHH
Confidence            4555555555554222 44455555544432       3443       4555555555542 112 3334555555555


Q ss_pred             ccCChHHHHHHHHHHHhCCCCCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHH-hcCChh
Q 011236          219 ARSELSSMENVLQEMESQSHISMDWG-TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYA-SLGNKD  296 (490)
Q Consensus       219 ~~g~~~~a~~~~~~~~~~~~~~~~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~  296 (490)
                      +.|++++|..+|+++. +... .+.. +|..++..+.+.|++++|..+|++..+..+  .+...|........ ..|+.+
T Consensus       111 ~~~~~~~A~~~~~~al-~~~p-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p--~~~~~~~~~a~~~~~~~~~~~  186 (308)
T 2ond_A          111 SRMKYEKVHSIYNRLL-AIED-IDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDAR--TRHHVYVTAALMEYYCSKDKS  186 (308)
T ss_dssp             HTTCHHHHHHHHHHHH-TSSS-SCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTT--CCTHHHHHHHHHHHHTSCCHH
T ss_pred             hcCCHHHHHHHHHHHH-hccc-cCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHHHHHcCCHH
Confidence            5555555555555555 3221 1122 455555555555555555555555554333  22333332222211 135555


Q ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcC-CCC--CchhHHHHHHHHHhcCCHHHHHHHHH
Q 011236          297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSC-YCY--DFRVPNIILLGYSQKGMIEKADAVLK  373 (490)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~--~~~~~~~l~~~~~~~g~~~~A~~~~~  373 (490)
                      +|..+|+......+ .+...|..++..+.+.|++++|..+|++..... ++|  ....|..++..+.+.|+.+.|..+++
T Consensus       187 ~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~  265 (308)
T 2ond_A          187 VAFKIFELGLKKYG-DIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEK  265 (308)
T ss_dssp             HHHHHHHHHHHHHT-TCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            55555555544433 334444555555555555555555555555431 222  22344444555555555555555555


Q ss_pred             HHHHc
Q 011236          374 EIVKK  378 (490)
Q Consensus       374 ~m~~~  378 (490)
                      ++.+.
T Consensus       266 ~a~~~  270 (308)
T 2ond_A          266 RRFTA  270 (308)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.54  E-value=1.5e-12  Score=107.31  Aligned_cols=171  Identities=11%  Similarity=0.038  Sum_probs=149.4

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHH
Q 011236          277 KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIIL  356 (490)
Q Consensus       277 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  356 (490)
                      .+...|..+...|...|++++|++.|++.....+ .+...+..+..++.+.|++++|...+....... +.+...+..+.
T Consensus         3 e~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~   80 (184)
T 3vtx_A            3 ETTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADP-NNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILG   80 (184)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHH
Confidence            4677899999999999999999999999988876 677889999999999999999999999998863 33566777788


Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc
Q 011236          357 LGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD  436 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~  436 (490)
                      ..+...++++.|...+.+..+..+. +...+..+...|.+.|++++|++.|+++++..|      .+..++..+..++.+
T Consensus        81 ~~~~~~~~~~~a~~~~~~a~~~~~~-~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p------~~~~~~~~lg~~~~~  153 (184)
T 3vtx_A           81 SANFMIDEKQAAIDALQRAIALNTV-YADAYYKLGLVYDSMGEHDKAIEAYEKTISIKP------GFIRAYQSIGLAYEG  153 (184)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT------TCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCcc-chHHHHHHHHHHHHhCCchhHHHHHHHHHHhcc------hhhhHHHHHHHHHHH
Confidence            8899999999999999999987655 788899999999999999999999999998331      244788899999999


Q ss_pred             CCCHHHHHHHHHHHHhcccc
Q 011236          437 NRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .|++++|.+.|+++.+..|.
T Consensus       154 ~g~~~~A~~~~~~al~~~p~  173 (184)
T 3vtx_A          154 KGLRDEAVKYFKKALEKEEK  173 (184)
T ss_dssp             TTCHHHHHHHHHHHHHTTHH
T ss_pred             CCCHHHHHHHHHHHHhCCcc
Confidence            99999999999999988876

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.53  E-value=2.7e-12  Score=119.35  Aligned_cols=233  Identities=13%  Similarity=0.023  Sum_probs=179.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCC----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC------hhhHH
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSK----DALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL------NRDYI  318 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~  318 (490)
                      ....+...|++++|+..|++........+    ...++..+...|...|++++|...+.+.........      ..++.
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            56678899999999999999876422212    346788999999999999999999998877544222      24688


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCC-----chhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CC-CCCHHHHH
Q 011236          319 TMLGSLVKIGELEEAEKMLEEWELSCYCYD-----FRVPNIILLGYSQKGMIEKADAVLKEIVKK----GK-TPTPNSWS  388 (490)
Q Consensus       319 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~----~~-~p~~~~~~  388 (490)
                      .+...|...|++++|...+++..+.....+     ..++..+...|...|++++|...+++..+.    +. +....++.
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  268 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYF  268 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHH
Confidence            889999999999999999998876421111     237788999999999999999999998872    22 22456799


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCC---HHHHHHHHHHHHhcccc-hhhhHHHH
Q 011236          389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRD---VEEVEAFVSSLKIKVQK-RNMYHALT  464 (490)
Q Consensus       389 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~~~-~~~~~~l~  464 (490)
                      .+...|.+.|++++|...++++++..+.. +-......+..+...+...|+   .++|..++++.. ..+. ...+..+.
T Consensus       269 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~-~~~~~~~~~~~la  346 (383)
T 3ulq_A          269 LITQIHYKLGKIDKAHEYHSKGMAYSQKA-GDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKM-LYADLEDFAIDVA  346 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHH-TCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCc-CHHHHHHHHHHHH
Confidence            99999999999999999999998844211 111112345677888889999   778888887762 2233 77889999


Q ss_pred             HHHHhcC--CcHHHHHHHHHh
Q 011236          465 EAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       465 ~~~~~~g--~~a~~~~~~m~~  483 (490)
                      ..|...|  ++|...+++..+
T Consensus       347 ~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          347 KYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            9999999  899999988764

>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=99.52  E-value=1e-10  Score=114.72  Aligned_cols=393  Identities=7%  Similarity=-0.033  Sum_probs=272.6

Q ss_pred             hhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCC---hhHHHHHH
Q 011236           85 FKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGL---VDESLSLM  160 (490)
Q Consensus        85 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~---~~~a~~~~  160 (490)
                      ..+.+..|+..+..+ +.+...+..++..+.+.+.++.+..+|+.+....| ....|...+..-.+.|+   ++.+..+|
T Consensus        48 ~~d~i~~lE~~l~~n-p~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lf  126 (679)
T 4e6h_A           48 ESDVIGKLNDMIEEQ-PTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDRFPLMANIWCMRLSLEFDKMEELDAAVIEPVL  126 (679)
T ss_dssp             CSCHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTC--CCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHC-cCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhhCCcchHHHHHHHH
Confidence            455566677777666 57999999999999999999999999999999887 57889999999889999   99999999


Q ss_pred             HHHHhcC-CCCCcchHHHHHHHHHhcCCc--------CcHHHHHHHHHH-CCC-CCC-HHHHHHHHHHHhc---------
Q 011236          161 QKMKEMG-SFGSALNYNGIMCLYTNTGQH--------EKIPDVLLDMKE-NGV-PPD-NFSYRICINSYGA---------  219 (490)
Q Consensus       161 ~~m~~~~-~~p~~~~~~~l~~~~~~~~~~--------~~a~~~~~~m~~-~~~-~p~-~~~~~~li~~~~~---------  219 (490)
                      ++..... ..|++..|..-+....+.++.        +.+.++|+..+. .|. .|+ ...|...+.....         
T Consensus       127 eRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~ee  206 (679)
T 4e6h_A          127 ARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEE  206 (679)
T ss_dssp             HHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHH
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHH
Confidence            9998874 247888888887776666554        234477777654 466 554 4677777765432         


Q ss_pred             cCChHHHHHHHHHHHhCCCCCCCHHHH---HHHHHHH----------HHcCCHHHHHHHHHHHhhhh------ccC----
Q 011236          220 RSELSSMENVLQEMESQSHISMDWGTY---STVANYY----------IIAGLKEKAIIYLKKCEDIV------SKS----  276 (490)
Q Consensus       220 ~g~~~~a~~~~~~~~~~~~~~~~~~~~---~~li~~~----------~~~~~~~~a~~~~~~~~~~~------~~~----  276 (490)
                      .++++.+..+|+++. ......-..+|   ..+...+          -...+++.|...+.++....      .+.    
T Consensus       207 q~~~~~~R~iy~raL-~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~  285 (679)
T 4e6h_A          207 QQRVQYIRKLYKTLL-CQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQ  285 (679)
T ss_dssp             HHHHHHHHHHHHHHT-TSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTT
T ss_pred             HhHHHHHHHHHHHHH-hCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhcccccccc
Confidence            345678899999997 42211112233   2222111          01123444555555432210      000    


Q ss_pred             ------C--C------hhhHHHHHHHHHhcC-------ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHH-
Q 011236          277 ------K--D------ALGYNHLISHYASLG-------NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAE-  334 (490)
Q Consensus       277 ------~--~------~~~~~~l~~~~~~~~-------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~-  334 (490)
                            |  +      ...|...+..--..+       ..+.+..+|++.+...+ -....|...+.-+...|+.++|. 
T Consensus       286 ~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p-~~~~lW~~ya~~~~~~~~~~~a~r  364 (679)
T 4e6h_A          286 ATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVC-FAPEIWFNMANYQGEKNTDSTVIT  364 (679)
T ss_dssp             CCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTT-TCHHHHHHHHHHHHHHSCCTTHHH
T ss_pred             chhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHcC-CCHHHHHHHHHHHHhcCcHHHHHH
Confidence                  0  1      134555554433322       12345678888888766 57788888888888899999996 


Q ss_pred             HHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC---------CCC------------HHHHHHHHHH
Q 011236          335 KMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK---------TPT------------PNSWSIIAAG  393 (490)
Q Consensus       335 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~---------~p~------------~~~~~~l~~~  393 (490)
                      .+|+..... ++.+...|-..+...-+.|++++|..+|+++++...         .|+            ..+|...+..
T Consensus       365 ~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~  443 (679)
T 4e6h_A          365 KYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNT  443 (679)
T ss_dssp             HHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHH
Confidence            999999875 445666677788888899999999999999986410         132            3468888888


Q ss_pred             HhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcC-CCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC
Q 011236          394 YADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDN-RDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG  471 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~-g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g  471 (490)
                      ..+.|+.+.|..+|.++++     .--.+....|...+..-.+. ++.+.|.++|+...+..|. +..|...+......|
T Consensus       444 erR~~~l~~AR~vf~~A~~-----~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~  518 (679)
T 4e6h_A          444 MKRIQGLAASRKIFGKCRR-----LKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVN  518 (679)
T ss_dssp             HHHHHCHHHHHHHHHHHHH-----TGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT
T ss_pred             HHHcCCHHHHHHHHHHHHH-----hcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCC
Confidence            8889999999999999998     20111233444333333344 5599999999999999888 888888998888888


Q ss_pred             --CcHHHHHHHHHhCCC
Q 011236          472 --QEVDGLLESMKADDI  486 (490)
Q Consensus       472 --~~a~~~~~~m~~~~~  486 (490)
                        +.|..+|++......
T Consensus       519 ~~~~AR~lferal~~~~  535 (679)
T 4e6h_A          519 EESQVKSLFESSIDKIS  535 (679)
T ss_dssp             CHHHHHHHHHHHTTTSS
T ss_pred             CHHHHHHHHHHHHHhcC
Confidence              899999999877643

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.51  E-value=1.3e-11  Score=114.47  Aligned_cols=233  Identities=11%  Similarity=0.029  Sum_probs=169.5

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHhCCC-CCCC----HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCC-----Chhh
Q 011236          212 ICINSYGARSELSSMENVLQEMESQSH-ISMD----WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSK-----DALG  281 (490)
Q Consensus       212 ~li~~~~~~g~~~~a~~~~~~~~~~~~-~~~~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~  281 (490)
                      .....+...|++++|...|++.. ... -.++    ..++..+..+|...|+++.|...+++........+     ...+
T Consensus       106 ~~g~~~~~~g~~~~A~~~~~~al-~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  184 (378)
T 3q15_A          106 FRGMYEFDQKEYVEAIGYYREAE-KELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQS  184 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH-TTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHH-HHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHH
Confidence            34455678899999999999887 321 1122    45677888899999999999999988776433212     2356


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcC-CC----ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc----CCCCCchhH
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCK-KQ----LNRDYITMLGSLVKIGELEEAEKMLEEWELS----CYCYDFRVP  352 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~~~  352 (490)
                      ++.+..+|...|++++|.+.+++...... .+    ...++..+...|...|++++|...+++..+.    +.+....++
T Consensus       185 ~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  264 (378)
T 3q15_A          185 LFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVL  264 (378)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHH
Confidence            77888899999999999999987776432 11    2246778888899999999999999988761    222336677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCC---C-CHHHHHHHHHHHhccCC---HHHHHHHHHHHHHhhhcCcCCCcc-h
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKGKT---P-TPNSWSIIAAGYADKNN---MEKAFECMKEALAVHEENKFWRPK-P  424 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~---p-~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~p~-~  424 (490)
                      ..+...|.+.|++++|...+++..+....   | ....+..+...|...++   ..+|+.++++.        +..|+ .
T Consensus       265 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~--------~~~~~~~  336 (378)
T 3q15_A          265 FGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK--------NLHAYIE  336 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT--------TCHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC--------CChhHHH
Confidence            88888999999999999999998774221   1 23346666677777888   77777777662        22233 3


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      ..+..+...|...|++++|...|++..+.
T Consensus       337 ~~~~~la~~y~~~g~~~~A~~~~~~al~~  365 (378)
T 3q15_A          337 ACARSAAAVFESSCHFEQAAAFYRKVLKA  365 (378)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            56778888999999999999999887654

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.51  E-value=1.6e-11  Score=113.70  Aligned_cols=273  Identities=12%  Similarity=0.001  Sum_probs=123.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcc----hHHHHHHHHHhcCCcCcHHHHHHHHHHCCC-CCCH----HHH
Q 011236          140 YGALLNCYVREGLVDESLSLMQKMKEMGSFGSAL----NYNGIMCLYTNTGQHEKIPDVLLDMKENGV-PPDN----FSY  210 (490)
Q Consensus       140 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~----~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~-~p~~----~~~  210 (490)
                      .......+...|++++|...+++........+..    +++.+...+...|++++|.+.+++..+... .++.    .++
T Consensus        17 ~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   96 (373)
T 1hz4_A           17 NALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSL   96 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            3344455566777777777777766653221111    344455556666666666666666543110 0111    223


Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHh---CCCCC--C-CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC--C-Chhh
Q 011236          211 RICINSYGARSELSSMENVLQEMES---QSHIS--M-DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS--K-DALG  281 (490)
Q Consensus       211 ~~li~~~~~~g~~~~a~~~~~~~~~---~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~--~-~~~~  281 (490)
                      ..+...+...|++++|...+++...   ..+..  | ....+..+...+...|++++|...+++........  + ...+
T Consensus        97 ~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  176 (373)
T 1hz4_A           97 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQC  176 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHH
Confidence            4445555566666666666655541   11111  1 12334445555556666666666665554432210  0 1123


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCCh-hhHH-----HHHHHHHhcCCHHHHHHHHHHHHhcCCCCC---chhH
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLN-RDYI-----TMLGSLVKIGELEEAEKMLEEWELSCYCYD---FRVP  352 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~  352 (490)
                      +..+...+...|++++|...+++.......++. ..+.     ..+..+...|++++|...+++.......+.   ...+
T Consensus       177 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  256 (373)
T 1hz4_A          177 LAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQW  256 (373)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHH
Confidence            444455555555555555555554433221111 1111     112224455555555555554443211100   0122


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHc----CCCCCH-HHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKK----GKTPTP-NSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~----~~~p~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ..+...+...|++++|...+++....    |..++. .++..+..++...|+.++|...+++++.
T Consensus       257 ~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          257 RNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            33444444555555555555444332    111111 1333444444455555555555555544

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.50  E-value=6.7e-13  Score=126.66  Aligned_cols=212  Identities=9%  Similarity=-0.026  Sum_probs=126.5

Q ss_pred             CHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCCh-hHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHH
Q 011236          119 GLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLV-DESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLL  196 (490)
Q Consensus       119 ~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~-~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~  196 (490)
                      .++.+...++......| +...|..+...+...|++ ++|++.|++..+.... +...|..+..+|...|++++|.+.|+
T Consensus        83 ~~~~al~~l~~~~~~~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~  161 (474)
T 4abn_A           83 EMEKTLQQMEEVLGSAQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPE-LVEAWNQLGEVYWKKGDVTSAHTCFS  161 (474)
T ss_dssp             HHHHHHHHHHHHHTTCCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            35556666665555544 466666667777777777 7777777776665433 45566666666666666666666666


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHhcc---------CChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHc--------CCH
Q 011236          197 DMKENGVPPDNFSYRICINSYGAR---------SELSSMENVLQEMESQSHISMDWGTYSTVANYYIIA--------GLK  259 (490)
Q Consensus       197 ~m~~~~~~p~~~~~~~li~~~~~~---------g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~--------~~~  259 (490)
                      +..+.  .|+...+..+..++...         |++++|...|++.. +... .+...|..+..+|...        |++
T Consensus       162 ~al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al-~~~p-~~~~~~~~lg~~~~~~~~~~~~~~g~~  237 (474)
T 4abn_A          162 GALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAV-QMDV-LDGRSWYILGNAYLSLYFNTGQNPKIS  237 (474)
T ss_dssp             HHHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHH-HHCT-TCHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHHHHHhhccccchH
Confidence            66654  34555666666666666         66666666666665 3332 3455566666666666        666


Q ss_pred             HHHHHHHHHHhhhhcc-CCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011236          260 EKAIIYLKKCEDIVSK-SKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM  336 (490)
Q Consensus       260 ~~a~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  336 (490)
                      ++|+..|++.....+. ..+...|..+..+|...|++++|...|++.....+ .+...+..+..++...|++++|.+.
T Consensus       238 ~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~a~~~l~~~~~~lg~~~eAi~~  314 (474)
T 4abn_A          238 QQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDP-AWPEPQQREQQLLEFLSRLTSLLES  314 (474)
T ss_dssp             HHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666666554320 01445566666666666666666666665555544 3444555555555555555555543

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.49  E-value=2.4e-13  Score=122.45  Aligned_cols=131  Identities=13%  Similarity=0.028  Sum_probs=56.8

Q ss_pred             HHHHHHHHHhccCChHHHHHHHHHHHhCC-------CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhh-------c
Q 011236          209 SYRICINSYGARSELSSMENVLQEMESQS-------HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIV-------S  274 (490)
Q Consensus       209 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~-------~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-------~  274 (490)
                      ++..+...+...|++++|..+|+++. +.       ..+....++..+...|...|++++|...+++.....       .
T Consensus        29 ~~~~l~~~~~~~g~~~~A~~~~~~a~-~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  107 (311)
T 3nf1_A           29 TLHNLVIQYASQGRYEVAVPLCKQAL-EDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDH  107 (311)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH-HHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH-HHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            44444555555555555555555544 21       111223344444555555555555555555444321       0


Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhc-----C--CCChhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          275 KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKC-----K--KQLNRDYITMLGSLVKIGELEEAEKMLEEWE  341 (490)
Q Consensus       275 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-----~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  341 (490)
                      + ....++..+...|...|++++|...+++.....     .  ......+..+...+...|++++|.+.++++.
T Consensus       108 ~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~  180 (311)
T 3nf1_A          108 P-AVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRAL  180 (311)
T ss_dssp             H-HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             h-HHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            1 123344444444555555555555554444331     0  0112233444444444444444444444443

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.48  E-value=8.4e-14  Score=125.43  Aligned_cols=239  Identities=14%  Similarity=0.103  Sum_probs=119.6

Q ss_pred             ChhHHHHHHHHHHhcCChhHHHHHHHHHHhc-------CCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHC------C
Q 011236          136 VDKLYGALLNCYVREGLVDESLSLMQKMKEM-------GSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKEN------G  202 (490)
Q Consensus       136 ~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~-------~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~------~  202 (490)
                      +..++..+...+...|++++|..+++++.+.       ..+....++..+...+...|++++|...+++..+.      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            3566777777888888888888888777653       12223444555666666666666666666655432      1


Q ss_pred             C-CCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhh-------c
Q 011236          203 V-PPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIV-------S  274 (490)
Q Consensus       203 ~-~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-------~  274 (490)
                      - +....++..+...+...|++++|...|+++.                                    ...       .
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~------------------------------------~~~~~~~~~~~  149 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRAL------------------------------------EIREKVLGKDH  149 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHH------------------------------------HHHHHHHCTTC
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHH------------------------------------HHHHHhcCCCC
Confidence            1 1122334444444444555555555444443                                    321       0


Q ss_pred             cCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhc------CC-CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc----
Q 011236          275 KSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKC------KK-QLNRDYITMLGSLVKIGELEEAEKMLEEWELS----  343 (490)
Q Consensus       275 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----  343 (490)
                      + .....+..+...+...|++++|..++++.....      .. ....++..+...+...|++++|...++++.+.    
T Consensus       150 ~-~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~  228 (311)
T 3nf1_A          150 P-DVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHER  228 (311)
T ss_dssp             H-HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             h-HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence            1 123344555555555555555555555544431      01 11234555555556666666666666555532    


Q ss_pred             ---CCCCCch-h------HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          344 ---CYCYDFR-V------PNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       344 ---~~~~~~~-~------~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                         ...+... .      +..+...+...+.+.++...++........ +..++..+...|.+.|++++|..+++++++
T Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          229 EFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPT-VTTTLKNLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             HHC------CCHHHHHHHHHHC-------CCSCCCC---------CHH-HHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCch-HHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence               0111111 1      111222233345555566666666554222 456788888888888888888888888877

>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=99.46  E-value=1.6e-11  Score=101.00  Aligned_cols=165  Identities=16%  Similarity=0.083  Sum_probs=113.1

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHH
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGS  323 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  323 (490)
                      ..+..+...+...|++++|...++++....+  .+...+..+...+...|++++|...+++.....+ .+...+..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~   85 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDADA--FDVDVALHLGIAYVKTGAVDRGTELLERSLADAP-DNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTTS--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc--cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHH
Confidence            3455566666677777777777776665444  4556666667777777777777777776666544 455666667777


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHH
Q 011236          324 LVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKA  403 (490)
Q Consensus       324 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  403 (490)
                      +...|++++|.+.++++.+. .+.+...+..+...|...|++++|...++++.+..+. +...+..+...+...|++++|
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A  163 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEA-NPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPN-EGKVHRAIAFSYEQMGRHEEA  163 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhcCHHHHHHHHHHHHhc-CcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHcCCHHHH
Confidence            77777777777777777665 2335556667777777777777787777777776533 566777777777788888888


Q ss_pred             HHHHHHHHHh
Q 011236          404 FECMKEALAV  413 (490)
Q Consensus       404 ~~~~~~~~~~  413 (490)
                      ...++++++.
T Consensus       164 ~~~~~~~~~~  173 (186)
T 3as5_A          164 LPHFKKANEL  173 (186)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHc
Confidence            8888777763

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.44  E-value=5.4e-11  Score=110.32  Aligned_cols=233  Identities=11%  Similarity=0.010  Sum_probs=176.8

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCC----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC-C-----ChhhH
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSK----DALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK-Q-----LNRDY  317 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~-----~~~~~  317 (490)
                      .....+...|++++|+..|++........+    ...++..+...|...|+++.|...+.+....... +     ...++
T Consensus       106 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          106 FRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            355667889999999999999876533212    2467888999999999999999999987765431 1     23467


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcC----CC-CCchhHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCCCCHHHH
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSC----YC-YDFRVPNIILLGYSQKGMIEKADAVLKEIVK-----KGKTPTPNSW  387 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~----~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~-----~~~~p~~~~~  387 (490)
                      ..+...|...|++++|.+.+++..+..    .. ....++..+...|...|++++|...+++..+     ..+. ...++
T Consensus       186 ~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~-~~~~~  264 (378)
T 3q15_A          186 FVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDL-LPKVL  264 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGG-HHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChh-HHHHH
Confidence            889999999999999999999887631    11 1234677889999999999999999999987     4433 36788


Q ss_pred             HHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCC---HHHHHHHHHHHHhcccc-hhhhHHH
Q 011236          388 SIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRD---VEEVEAFVSSLKIKVQK-RNMYHAL  463 (490)
Q Consensus       388 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~~~-~~~~~~l  463 (490)
                      ..+...|.+.|++++|...++++++..... +-......+..+...+...|+   ..+|..++++.. ..+. ...+..+
T Consensus       265 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~-~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~-~~~~~~~~~~~l  342 (378)
T 3q15_A          265 FGLSWTLCKAGQTQKAFQFIEEGLDHITAR-SHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKN-LHAYIEACARSA  342 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCTT-CCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHc-CCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCC-ChhHHHHHHHHH
Confidence            999999999999999999999999844211 111222455666667778888   777777777632 2223 7788899


Q ss_pred             HHHHHhcC--CcHHHHHHHHHh
Q 011236          464 TEAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       464 ~~~~~~~g--~~a~~~~~~m~~  483 (490)
                      ...|...|  ++|...+++..+
T Consensus       343 a~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          343 AAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            99999999  889988887653

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.42  E-value=2.2e-10  Score=105.97  Aligned_cols=306  Identities=10%  Similarity=0.005  Sum_probs=215.6

Q ss_pred             HHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHH----HHHHHHHHHhccCChHHHHHHHHHHHh---CCCCC-CCHHHH
Q 011236          175 YNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNF----SYRICINSYGARSELSSMENVLQEMES---QSHIS-MDWGTY  246 (490)
Q Consensus       175 ~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~----~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~~-~~~~~~  246 (490)
                      +......+...|++++|...+++........+..    ++..+...+...|++++|...+++...   ..+.. ....++
T Consensus        17 ~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   96 (373)
T 1hz4_A           17 NALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSL   96 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            3444556678899999999999988754322322    456677788889999999999998762   11210 012335


Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHhhhhccC--C----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCC----Chhh
Q 011236          247 STVANYYIIAGLKEKAIIYLKKCEDIVSKS--K----DALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQ----LNRD  316 (490)
Q Consensus       247 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~--~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~  316 (490)
                      ..+...+...|++++|...+++........  +    ....+..+...+...|++++|...+++........    ...+
T Consensus        97 ~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  176 (373)
T 1hz4_A           97 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQC  176 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHH
Confidence            667888999999999999999987644210  1    23456678888899999999999999887765422    1245


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc-hhHH-----HHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHH
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDF-RVPN-----IILLGYSQKGMIEKADAVLKEIVKKGKTPT---PNSW  387 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~-----~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~---~~~~  387 (490)
                      +..+...+...|++++|...+++.......++. ..+.     ..+..+...|++++|...+++.......+.   ...+
T Consensus       177 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  256 (373)
T 1hz4_A          177 LAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQW  256 (373)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHH
Confidence            777888899999999999999988765222222 1222     233447789999999999988876543221   2357


Q ss_pred             HHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccchhhhHHHHHH
Q 011236          388 SIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEA  466 (490)
Q Consensus       388 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~  466 (490)
                      ..+...+...|++++|...++++....+. .+..++. ..+..+..++...|+.++|...+++.....+...    .+..
T Consensus       257 ~~la~~~~~~g~~~~A~~~l~~a~~~~~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~~~~g----~~~~  331 (373)
T 1hz4_A          257 RNIARAQILLGEFEPAEIVLEELNENARS-LRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANRTG----FISH  331 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHC----CCHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHh-CcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhcccc----HHHH
Confidence            78888999999999999999999885432 1222233 3666777888899999999999999887655421    3344


Q ss_pred             HHhcCCcHHHHHHHHHhCC
Q 011236          467 HIRSGQEVDGLLESMKADD  485 (490)
Q Consensus       467 ~~~~g~~a~~~~~~m~~~~  485 (490)
                      +...|+....+++++....
T Consensus       332 ~~~~g~~~~~ll~~~~~~~  350 (373)
T 1hz4_A          332 FVIEGEAMAQQLRQLIQLN  350 (373)
T ss_dssp             HHTTHHHHHHHHHHHHHTT
T ss_pred             HHHccHHHHHHHHHHHhCC
Confidence            5566666677777776544

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.40  E-value=5.8e-11  Score=101.52  Aligned_cols=207  Identities=11%  Similarity=0.040  Sum_probs=133.7

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHH
Q 011236          241 MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITM  320 (490)
Q Consensus       241 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  320 (490)
                      .++..+......+...|++++|+..|++.....+. ++...+..+..++...|++++|+..+++.....+ .+...+..+
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l   82 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNN-QDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNY-NLANAYIGK   82 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTT-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC-SHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCC-CCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCc-chHHHHHHH
Confidence            34566777777788888888888888877776654 4556666677777788888888888877766554 455667777


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCc-------hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHH
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYCYDF-------RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT---PNSWSII  390 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~---~~~~~~l  390 (490)
                      ...+...|++++|...+++..+.. +.+.       ..|..+...+...|++++|...|++.++  ..|+   ...|..+
T Consensus        83 ~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~l  159 (228)
T 4i17_A           83 SAAYRDMKNNQEYIATLTEGIKAV-PGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATD--VTSKKWKTDALYSL  159 (228)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SSCHHHHHHHHHHH
T ss_pred             HHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHh--cCCCcccHHHHHHH
Confidence            777777888888888887777652 2233       3456666667777777777777777654  5665   2355556


Q ss_pred             HHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHH
Q 011236          391 AAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTE  465 (490)
Q Consensus       391 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~  465 (490)
                      ...|...     +..+++++....      ..+...|....  ....+.+++|...+++..+..|. ..+...+..
T Consensus       160 ~~~~~~~-----~~~~~~~a~~~~------~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~p~~~~~~~~l~~  222 (228)
T 4i17_A          160 GVLFYNN-----GADVLRKATPLA------SSNKEKYASEK--AKADAAFKKAVDYLGEAVTLSPNRTEIKQMQDQ  222 (228)
T ss_dssp             HHHHHHH-----HHHHHHHHGGGT------TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHH-----HHHHHHHHHhcc------cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHH
Confidence            6665443     333444444411      11223333222  22345578899999998888887 665555543

>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=99.40  E-value=5.7e-11  Score=97.67  Aligned_cols=166  Identities=14%  Similarity=0.030  Sum_probs=131.6

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHH
Q 011236          208 FSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLIS  287 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  287 (490)
                      ..+..+...+...|++++|...++++. .... .+..++..+...+...|++++|...++++....+  .+...+..+..
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~a~   84 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVY-DADA-FDVDVALHLGIAYVKTGAVDRGTELLERSLADAP--DNVKVATVLGL   84 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTC-CTTS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHH-HhCc-cChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC--CCHHHHHHHHH
Confidence            456667777888888888888888876 4443 5677788888888888888888888888877654  56777888888


Q ss_pred             HHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHH
Q 011236          288 HYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEK  367 (490)
Q Consensus       288 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  367 (490)
                      .+...|++++|...+++.....+ .+...+..+...+...|++++|...++++.+.. +.+...+..+...|...|++++
T Consensus        85 ~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~  162 (186)
T 3as5_A           85 TYVQVQKYDLAVPLLIKVAEANP-INFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEE  162 (186)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHhcCc-HhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHH
Confidence            88888888888888888777655 566778888888888888888888888888763 3356677888888888899999


Q ss_pred             HHHHHHHHHHcC
Q 011236          368 ADAVLKEIVKKG  379 (490)
Q Consensus       368 A~~~~~~m~~~~  379 (490)
                      |...++++.+..
T Consensus       163 A~~~~~~~~~~~  174 (186)
T 3as5_A          163 ALPHFKKANELD  174 (186)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcC
Confidence            988888887653

>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=99.38  E-value=2.9e-11  Score=120.07  Aligned_cols=167  Identities=15%  Similarity=0.071  Sum_probs=130.6

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHH
Q 011236          243 WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLG  322 (490)
Q Consensus       243 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  322 (490)
                      ..+|+.|..+|.+.|++++|++.|++..+..+  .+..+|..+..+|.+.|++++|+..|++.+...+ .+...|..+..
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P--~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~P-~~~~a~~nLg~   85 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEVFP--EFAAAHSNLASVLQQQGKLQEALMHYKEAIRISP-TFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHH
Confidence            56777788888888888888888888777655  4677788888888888888888888887777665 56677888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHH
Q 011236          323 SLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEK  402 (490)
Q Consensus       323 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~  402 (490)
                      +|.+.|++++|.+.|++..+.. +-+...|+.+...|.+.|++++|+..|++.++..+. +...|..+...+...|++++
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l~-P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~-~~~a~~~L~~~l~~~g~~~~  163 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQIN-PAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPD-FPDAYCNLAHCLQIVCDWTD  163 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHTTCCTT
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-ChHHHhhhhhHHHhcccHHH
Confidence            8888888888888888887752 224567788888888888888888888888887654 67778888888888888888


Q ss_pred             HHHHHHHHHHhh
Q 011236          403 AFECMKEALAVH  414 (490)
Q Consensus       403 a~~~~~~~~~~~  414 (490)
                      |.+.++++++..
T Consensus       164 A~~~~~kal~l~  175 (723)
T 4gyw_A          164 YDERMKKLVSIV  175 (723)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC
Confidence            888888877644

>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=99.37  E-value=3.3e-11  Score=119.65  Aligned_cols=169  Identities=15%  Similarity=0.072  Sum_probs=137.8

Q ss_pred             ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHH
Q 011236          278 DALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILL  357 (490)
Q Consensus       278 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  357 (490)
                      +..+|+.+...|.+.|++++|++.|++.+...+ -+..++..+..+|.+.|++++|.+.|++..+.. +-+...|..+..
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P-~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg~   85 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVFP-EFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            457788888888899999999999988887765 567788888888888899999999888888752 224667888888


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHc
Q 011236          358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGD  436 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~  436 (490)
                      +|.+.|++++|++.|++.++.++. +...|..+...|.+.|++++|++.|+++++       +.|+. ..+..+..++..
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l~P~-~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~-------l~P~~~~a~~~L~~~l~~  157 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQINPA-FADAHSNLASIHKDSGNIPEAIASYRTALK-------LKPDFPDAYCNLAHCLQI  157 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCSCCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCCCChHHHhhhhhHHHh
Confidence            888889999999888888887655 677888888888888999999999988888       34554 678888888888


Q ss_pred             CCCHHHHHHHHHHHHhcccc
Q 011236          437 NRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .|++++|.+.++++.+..+.
T Consensus       158 ~g~~~~A~~~~~kal~l~~~  177 (723)
T 4gyw_A          158 VCDWTDYDERMKKLVSIVAD  177 (723)
T ss_dssp             TTCCTTHHHHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhChh
Confidence            88888888888888776554

>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=99.34  E-value=1.6e-10  Score=98.74  Aligned_cols=150  Identities=8%  Similarity=-0.058  Sum_probs=79.0

Q ss_pred             CcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHH
Q 011236          171 SALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVA  250 (490)
Q Consensus       171 ~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li  250 (490)
                      |+..+......+...|++++|...|++..+...+++...+..+..++...|++++|...|++.. +.+. .+..++..+.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al-~~~p-~~~~~~~~l~   83 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAI-KKNY-NLANAYIGKS   83 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HTTC-SHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHH-HhCc-chHHHHHHHH
Confidence            3445555555566666666666666666554332444555455555666666666666666655 3332 2344555555


Q ss_pred             HHHHHcCCHHHHHHHHHHHhhhhccCCCh-------hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCC--ChhhHHHHH
Q 011236          251 NYYIIAGLKEKAIIYLKKCEDIVSKSKDA-------LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQ--LNRDYITML  321 (490)
Q Consensus       251 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~  321 (490)
                      .+|...|++++|+..|++.....+  .+.       ..|..+...+...|++++|...|++.....+ .  +...+..+.
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~~~l~  160 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAVP--GNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTS-KKWKTDALYSLG  160 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHST--TCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSC-HHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHHCC--CcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCC-CcccHHHHHHHH
Confidence            666666666666666666555443  233       3345555555555555555555555444322 2  233444444


Q ss_pred             HHHH
Q 011236          322 GSLV  325 (490)
Q Consensus       322 ~~~~  325 (490)
                      .++.
T Consensus       161 ~~~~  164 (228)
T 4i17_A          161 VLFY  164 (228)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>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=99.33  E-value=4.1e-11  Score=106.00  Aligned_cols=227  Identities=13%  Similarity=0.056  Sum_probs=140.5

Q ss_pred             hcCCcCcHHHHHHHHHHC-------CCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhC------CCCCCCHHHHHHHH
Q 011236          184 NTGQHEKIPDVLLDMKEN-------GVPPDNFSYRICINSYGARSELSSMENVLQEMESQ------SHISMDWGTYSTVA  250 (490)
Q Consensus       184 ~~~~~~~a~~~~~~m~~~-------~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~------~~~~~~~~~~~~li  250 (490)
                      ..|++++|...|++..+.       +.+....++..+...+...|++++|...++++...      .+.+....++..+.
T Consensus        13 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~   92 (283)
T 3edt_B           13 GLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLA   92 (283)
T ss_dssp             CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHH
Confidence            456777777777666541       11223456777778888888888888888777621      11223356677788


Q ss_pred             HHHHHcCCHHHHHHHHHHHhhhh-------ccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhc------CC-CChhh
Q 011236          251 NYYIIAGLKEKAIIYLKKCEDIV-------SKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKC------KK-QLNRD  316 (490)
Q Consensus       251 ~~~~~~~~~~~a~~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~------~~-~~~~~  316 (490)
                      .+|...|++++|...|++.....       .+ ....++..+...|...|++++|...+++.....      .. ....+
T Consensus        93 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           93 VLYGKRGKYKEAEPLCKRALEIREKVLGKFHP-DVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCH-HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHcCCCCh-HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            88888888888888888776542       11 345677788888888888888888888776651      11 23456


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhc-------CCCCCc-hhHHHHHHHHHhcCCHHHH------HHHHHHHHHcCCCC
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELS-------CYCYDF-RVPNIILLGYSQKGMIEKA------DAVLKEIVKKGKTP  382 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~-~~~~~l~~~~~~~g~~~~A------~~~~~~m~~~~~~p  382 (490)
                      +..+...+...|++++|...+++..+.       ...+.. ..+..+...+...+....+      ...++..... ...
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVD-SPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCCC-CHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCCC-CHH
Confidence            777888888888888888888877653       112222 2333333333333322222      2222111111 011


Q ss_pred             CHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          383 TPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       383 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...++..+...|...|++++|..+++++++
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            234677778888888888888888888765

>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=99.33  E-value=4.4e-11  Score=105.77  Aligned_cols=235  Identities=13%  Similarity=0.029  Sum_probs=155.6

Q ss_pred             hccCChHHHHHHHHHHHh------CCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhh------ccCCChhhHHHH
Q 011236          218 GARSELSSMENVLQEMES------QSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIV------SKSKDALGYNHL  285 (490)
Q Consensus       218 ~~~g~~~~a~~~~~~~~~------~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~~l  285 (490)
                      ...|++++|+..|++...      ..+.+....++..+...|...|++++|+..++++....      .......++..+
T Consensus        12 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l   91 (283)
T 3edt_B           12 SGLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNL   91 (283)
T ss_dssp             -CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            356777777777766652      22332456778889999999999999999999987652      110345788899


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhc-----C--CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc------CCCC-Cchh
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKC-----K--KQLNRDYITMLGSLVKIGELEEAEKMLEEWELS------CYCY-DFRV  351 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~-----~--~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~-~~~~  351 (490)
                      ...|...|++++|...+++.....     .  .....++..+...+...|++++|...++++.+.      +..| ...+
T Consensus        92 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  171 (283)
T 3edt_B           92 AVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKT  171 (283)
T ss_dssp             HHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            999999999999999999877652     1  133467888889999999999999999988765      1122 3456


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHc-------CCCCC-HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKK-------GKTPT-PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK  423 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~-------~~~p~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~  423 (490)
                      +..+...|...|++++|...+++..+.       ...+. ...|..+...+...+....+.. +..+...........|+
T Consensus       172 ~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  250 (283)
T 3edt_B          172 KNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAP-YGEYGSWYKACKVDSPT  250 (283)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC-------------CCCCCCHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHH-HHHHHHHHHhcCCCCHH
Confidence            778888999999999999999988764       11222 2234444433333332222221 22222111000112232


Q ss_pred             -hhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          424 -PSLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       424 -~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                       ..++..+...+...|++++|..++++..+.
T Consensus       251 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          251 VNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence             357778888999999999999999887653

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.30  E-value=1.1e-09  Score=95.43  Aligned_cols=176  Identities=10%  Similarity=0.009  Sum_probs=103.9

Q ss_pred             HHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-CCCchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          298 MMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY-CYDFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       298 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      |+..+++....+ .++..++..+..++...|++++|.+++.+.+..+. .-+...+..++..|.+.|+.+.|.+.+++|.
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            555565554443 24445555666777777777777777777655433 1244556666777777777777777777776


Q ss_pred             HcCCCC-----CHHHHHHHHHH--Hhc--cCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHH
Q 011236          377 KKGKTP-----TPNSWSIIAAG--YAD--KNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFV  447 (490)
Q Consensus       377 ~~~~~p-----~~~~~~~l~~~--~~~--~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~  447 (490)
                      +.  .|     +..+...+..+  ...  .+++++|..+|+++.+       -.|+..+...++.++.+.|++++|++.+
T Consensus       164 ~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~-------~~p~~~~~~lLln~~~~~g~~~eAe~~L  234 (310)
T 3mv2_B          164 NA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQ-------TFPTWKTQLGLLNLHLQQRNIAEAQGIV  234 (310)
T ss_dssp             HH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHT-------TSCSHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             hc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHH-------hCCCcccHHHHHHHHHHcCCHHHHHHHH
Confidence            64  33     23444444444  222  2367777777777655       2244223333334666777777777777


Q ss_pred             HHHHhc----------ccc-hhhhHHHHHHHHhcCCcHHHHHHHHHh
Q 011236          448 SSLKIK----------VQK-RNMYHALTEAHIRSGQEVDGLLESMKA  483 (490)
Q Consensus       448 ~~~~~~----------~~~-~~~~~~l~~~~~~~g~~a~~~~~~m~~  483 (490)
                      +.+.+.          .|. +.++..+|......|++|.++++++.+
T Consensus       235 ~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk~a~~l~~qL~~  281 (310)
T 3mv2_B          235 ELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGLDTEDLTNQLVK  281 (310)
T ss_dssp             HHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTCTTHHHHHHHHH
T ss_pred             HHHHHhcccccccccCCCCCHHHHHHHHHHHHHhChHHHHHHHHHHH
Confidence            765554          244 666655555555566667777777766

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.28  E-value=4.3e-10  Score=100.00  Aligned_cols=246  Identities=10%  Similarity=-0.025  Sum_probs=171.1

Q ss_pred             CcHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc-C-ChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Q 011236          189 EKIPDVLLDMKENGVPPDNFSYRICINSYGAR-S-ELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYL  266 (490)
Q Consensus       189 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-g-~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  266 (490)
                      .+|.+++.+..+. .++....+ .+   +... + ++++|...|++.                ...|...|++++|...|
T Consensus         2 ~~a~~~~~~a~k~-~~~~~~~~-~~---~~~~~~~~~~~A~~~~~~a----------------~~~~~~~g~~~~A~~~~   60 (292)
T 1qqe_A            2 SDPVELLKRAEKK-GVPSSGFM-KL---FSGSDSYKFEEAADLCVQA----------------ATIYRLRKELNLAGDSF   60 (292)
T ss_dssp             CCHHHHHHHHHHH-SSCCCTHH-HH---HSCCSHHHHHHHHHHHHHH----------------HHHHHHTTCTHHHHHHH
T ss_pred             CcHHHHHHHHHHH-hCcCCCcc-hh---cCCCCCccHHHHHHHHHHH----------------HHHHHHcCCHHHHHHHH
Confidence            4677777777664 32222222 22   2211 2 488888888776                33577889999999999


Q ss_pred             HHHhhhhccC---C-ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC-CC----hhhHHHHHHHHHhc-CCHHHHHHH
Q 011236          267 KKCEDIVSKS---K-DALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK-QL----NRDYITMLGSLVKI-GELEEAEKM  336 (490)
Q Consensus       267 ~~~~~~~~~~---~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~-~~~~~a~~~  336 (490)
                      .+........   + ...+|+.+..+|...|++++|+..+++....... .+    ..++..+..+|... |++++|...
T Consensus        61 ~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~  140 (292)
T 1qqe_A           61 LKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDC  140 (292)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHH
Confidence            8876543210   1 2468889999999999999999999987765431 11    34688889999996 999999999


Q ss_pred             HHHHHhcCCCCC-----chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH------HHHHHHHHHHhccCCHHHHHH
Q 011236          337 LEEWELSCYCYD-----FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTP------NSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       337 ~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~------~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      +++..+.....+     ..+++.+...|.+.|++++|+..|++..+..+....      ..|..+..++...|++++|..
T Consensus       141 ~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~  220 (292)
T 1qqe_A          141 YELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAAR  220 (292)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            999876421111     346788899999999999999999999987554322      157788888999999999999


Q ss_pred             HHHHHHHhhhcCcCCCcchhhHHHHHHHHH--cCCCHHHHHHHHHHHHhcccc
Q 011236          406 CMKEALAVHEENKFWRPKPSLVSSILDWLG--DNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       406 ~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~--~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .|+++++..|+... ......+..++.++.  ..+++++|...|+++....|.
T Consensus       221 ~~~~al~l~p~~~~-~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l~~~  272 (292)
T 1qqe_A          221 TLQEGQSEDPNFAD-SRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKW  272 (292)
T ss_dssp             HHHGGGCC----------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCHH
T ss_pred             HHHHHHhhCCCCCC-cHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCccHHH
Confidence            99999873321110 001123455666665  567799999999887776665

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.23  E-value=6.4e-09  Score=90.68  Aligned_cols=181  Identities=9%  Similarity=-0.078  Sum_probs=103.3

Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 011236          226 MENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQ  305 (490)
Q Consensus       226 a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  305 (490)
                      |+..|++.. ..+ .++..++..+..++...|++++|++++.+....++...+...+..++..+.+.|+.+.|.+.++.|
T Consensus        85 a~~~l~~l~-~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~  162 (310)
T 3mv2_B           85 NIEELENLL-KDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNY  162 (310)
T ss_dssp             CCHHHHHTT-TTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHH-hcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            556666665 333 244445556667777777777777777765444431034556666777777777777777777766


Q ss_pred             HHhcC---CCChhhHHHHHHHH--HhcC--CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHc
Q 011236          306 KIKCK---KQLNRDYITMLGSL--VKIG--ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       306 ~~~~~---~~~~~~~~~l~~~~--~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      ....+   ..+..+...++.++  ...|  ++.+|..+|+++.+.  .|+..+...++.++.+.|++++|.+.++.+.+.
T Consensus       163 ~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~  240 (310)
T 3mv2_B          163 TNAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSD  240 (310)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSH
T ss_pred             HhcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            55421   00244444454442  2223  677777777776554  233222233444677777777777777765543


Q ss_pred             C---------CCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          379 G---------KTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       379 ~---------~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .         -+-|+.++..+|......|+  +|.++++++.+
T Consensus       241 ~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~  281 (310)
T 3mv2_B          241 YYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVK  281 (310)
T ss_dssp             HHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHH
T ss_pred             cccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHH
Confidence            1         01255556455554445555  66777777766

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.21  E-value=9.2e-10  Score=96.20  Aligned_cols=185  Identities=8%  Similarity=-0.063  Sum_probs=96.9

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC---HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC-hhhH
Q 011236          207 NFSYRICINSYGARSELSSMENVLQEMESQSHISMD---WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD-ALGY  282 (490)
Q Consensus       207 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~  282 (490)
                      ...+-.+...+.+.|++++|...|+++. ...+ .+   ...+..+..+|...|++++|+..|++.....+..+. ..++
T Consensus        15 ~~~~~~~a~~~~~~g~~~~A~~~~~~~l-~~~p-~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           15 PQEAFERAMEFYNQGKYDRAIEYFKAVF-TYGR-THEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHG-GGCS-CSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHH-HhCC-CCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            3444445555555666666666666655 3221 11   344555555666666666666666665554332111 2344


Q ss_pred             HHHHHHHHh--------cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHH
Q 011236          283 NHLISHYAS--------LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNI  354 (490)
Q Consensus       283 ~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  354 (490)
                      ..+..++..        .|++++|...|++.....+ .+......+...              ..+...    -...+..
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~a~~~~--------------~~~~~~----~~~~~~~  153 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYP-NHELVDDATQKI--------------RELRAK----LARKQYE  153 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCT-TCTTHHHHHHHH--------------HHHHHH----HHHHHHH
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCc-CchhHHHHHHHH--------------HHHHHH----HHHHHHH
Confidence            445555555        5555555555555555443 111111111100              000000    0001345


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHhcc----------CCHHHHHHHHHHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVKKGKTP--TPNSWSIIAAGYADK----------NNMEKAFECMKEALA  412 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~~~~~p--~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~  412 (490)
                      +...|.+.|++++|...|+++++..+..  ....+..+..+|...          |++++|...|+++++
T Consensus       154 la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~  223 (261)
T 3qky_A          154 AARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQ  223 (261)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHH
Confidence            6677778888888888888887764331  234566666777655          777888888888877

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.18  E-value=2e-09  Score=82.98  Aligned_cols=125  Identities=14%  Similarity=0.180  Sum_probs=50.8

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC
Q 011236          285 LISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM  364 (490)
Q Consensus       285 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  364 (490)
                      +...+...|++++|..+++.+....+ .+...+..+...+...|++++|...++++.+.+ +.+...+..+...+...|+
T Consensus         7 l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~   84 (136)
T 2fo7_A            7 LGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGD   84 (136)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHcCcHHHHHHHHHHHHHcCC-cchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHHhcC
Confidence            33333344444444444443333322 223333333344444444444444444443321 1122333344444444444


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          365 IEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       365 ~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +++|...++++.+..+. +..++..+...+...|++++|...+++++.
T Consensus        85 ~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           85 YDEAIEYYQKALELDPR-SAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            44444444444443221 333444444444444444444444444443

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.18  E-value=3.2e-09  Score=94.37  Aligned_cols=238  Identities=12%  Similarity=0.067  Sum_probs=167.3

Q ss_pred             hHHHHHHHHHHhcCCCCCcchHHHHHHHHHhc--C-CcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHH
Q 011236          154 DESLSLMQKMKEMGSFGSALNYNGIMCLYTNT--G-QHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVL  230 (490)
Q Consensus       154 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~--~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  230 (490)
                      .+|.+++.+.... .++....| .+   + +.  + ++++|...|++.               ...|...|++++|...|
T Consensus         2 ~~a~~~~~~a~k~-~~~~~~~~-~~---~-~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~   60 (292)
T 1qqe_A            2 SDPVELLKRAEKK-GVPSSGFM-KL---F-SGSDSYKFEEAADLCVQA---------------ATIYRLRKELNLAGDSF   60 (292)
T ss_dssp             CCHHHHHHHHHHH-SSCCCTHH-HH---H-SCCSHHHHHHHHHHHHHH---------------HHHHHHTTCTHHHHHHH
T ss_pred             CcHHHHHHHHHHH-hCcCCCcc-hh---c-CCCCCccHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHH
Confidence            3567777777665 22222222 22   2 32  2 477888877776               34577889999999999


Q ss_pred             HHHHh---CCCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC----hhhHHHHHHHHHhc-CChhHHHHH
Q 011236          231 QEMES---QSHISM-DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD----ALGYNHLISHYASL-GNKDEMMKF  301 (490)
Q Consensus       231 ~~~~~---~~~~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~-~~~~~a~~~  301 (490)
                      ++...   +.+-.+ ...+|+.+..+|...|++++|+..|++.....+...+    ..+++.+...|... |++++|+..
T Consensus        61 ~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~  140 (292)
T 1qqe_A           61 LKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDC  140 (292)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHH
Confidence            88761   122212 2568889999999999999999999988765443122    35788899999996 999999999


Q ss_pred             HHHHHHhcCCC-C----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCch------hHHHHHHHHHhcCCHHHHHH
Q 011236          302 WGLQKIKCKKQ-L----NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFR------VPNIILLGYSQKGMIEKADA  370 (490)
Q Consensus       302 ~~~~~~~~~~~-~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~------~~~~l~~~~~~~g~~~~A~~  370 (490)
                      |++.....+.. +    ..++..+...+.+.|++++|...+++..+........      .+..+..++...|++++|..
T Consensus       141 ~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~  220 (292)
T 1qqe_A          141 YELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAAR  220 (292)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            99887765411 1    3468889999999999999999999999864433221      46677888999999999999


Q ss_pred             HHHHHHHcCCC-CC---HHHHHHHHHHHh--ccCCHHHHHHHHHHHHH
Q 011236          371 VLKEIVKKGKT-PT---PNSWSIIAAGYA--DKNNMEKAFECMKEALA  412 (490)
Q Consensus       371 ~~~~m~~~~~~-p~---~~~~~~l~~~~~--~~~~~~~a~~~~~~~~~  412 (490)
                      .|++..+..+. ++   ...+..++.+|.  ..+++++|+..|+++..
T Consensus       221 ~~~~al~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~  268 (292)
T 1qqe_A          221 TLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMR  268 (292)
T ss_dssp             HHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSC
T ss_pred             HHHHHHhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCc
Confidence            99998764322 11   113455566664  45778888888877654

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=99.18  E-value=2.5e-09  Score=82.45  Aligned_cols=131  Identities=15%  Similarity=0.159  Sum_probs=86.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSL  324 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  324 (490)
                      .+..+...+...|++++|..+++++....+  .+...+..+...+...|++++|...++++....+ .+...+..+...+
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~--~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~   79 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDP--RSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP-RSAEAWYNLGNAY   79 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCC--cchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCC-CchHHHHHHHHHH
Confidence            345566667777777777777777665443  4556666666777777777777777776665544 4455666667777


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011236          325 VKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG  379 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  379 (490)
                      ...|++++|.+.++++.+.. +.+...+..+...+.+.|++++|...++++.+.+
T Consensus        80 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  133 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD  133 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHS
T ss_pred             HHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHHccC
Confidence            77777777777777776652 2345566667777777777777777777776643

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.17  E-value=1.6e-09  Score=90.86  Aligned_cols=159  Identities=15%  Similarity=0.047  Sum_probs=80.0

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHH----------------HHHHHHhcCChhHHHHHHHHHHHhcCC
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNH----------------LISHYASLGNKDEMMKFWGLQKIKCKK  311 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~----------------l~~~~~~~~~~~~a~~~~~~~~~~~~~  311 (490)
                      .....+...|++++|+..|++.....+  .+...|..                +..+|...|++++|...|++.....+ 
T Consensus         9 ~~g~~~~~~g~~~~A~~~~~~al~~~p--~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-   85 (208)
T 3urz_A            9 QKVSAAIEAGQNGQAVSYFRQTIALNI--DRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKAP-   85 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCH--HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCC--CChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCC-
Confidence            344455666777777777776665443  23334433                55555566666666666665555544 


Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC--HHHHHHHHHHHHHcCCCCCHHHHHH
Q 011236          312 QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM--IEKADAVLKEIVKKGKTPTPNSWSI  389 (490)
Q Consensus       312 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~--~~~A~~~~~~m~~~~~~p~~~~~~~  389 (490)
                      .+...+..+..++...|++++|...|++..+.. +.+...+..+...|...|+  .+.+...++....  +.|....+..
T Consensus        86 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~a~~~  162 (208)
T 3urz_A           86 NNVDCLEACAEMQVCRGQEKDALRMYEKILQLE-ADNLAANIFLGNYYYLTAEQEKKKLETDYKKLSS--PTKMQYARYR  162 (208)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHHHHHHHHHHC---C--CCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC--CCchhHHHHH
Confidence            445555555556666666666666666655542 1234445555555444332  2233333333321  1112222333


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHH
Q 011236          390 IAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       390 l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...++...|++++|...|+++++
T Consensus       163 ~g~~~~~~~~~~~A~~~~~~al~  185 (208)
T 3urz_A          163 DGLSKLFTTRYEKARNSLQKVIL  185 (208)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHTT
T ss_pred             HHHHHHHccCHHHHHHHHHHHHH
Confidence            34444455566666666666655

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.17  E-value=2.3e-09  Score=93.60  Aligned_cols=208  Identities=11%  Similarity=-0.085  Sum_probs=138.8

Q ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC-CCC-hhhH
Q 011236          241 MDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD-ALGYNHLISHYASLGNKDEMMKFWGLQKIKCK-KQL-NRDY  317 (490)
Q Consensus       241 ~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~-~~~~  317 (490)
                      .+...+-.+...+.+.|++++|+..|+++....+..+. ...+..+..+|...|++++|...|+......+ .|. ...+
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            34566666777888888888888888888776542111 56777788888888888888888888877755 222 3456


Q ss_pred             HHHHHHHHh--------cCCHHHHHHHHHHHHhcCCCCC-chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHH
Q 011236          318 ITMLGSLVK--------IGELEEAEKMLEEWELSCYCYD-FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWS  388 (490)
Q Consensus       318 ~~l~~~~~~--------~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~  388 (490)
                      ..+..++..        .|++++|...|+++.+.  .|+ ......+.              .+..+...    -...+.
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~--------------~~~~~~~~----~~~~~~  152 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR--YPNHELVDDATQ--------------KIRELRAK----LARKQY  152 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH--CTTCTTHHHHHH--------------HHHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHH--CcCchhHHHHHH--------------HHHHHHHH----HHHHHH
Confidence            667777777        78888888888887775  232 22222111              11111110    011256


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcC----------CCHHHHHHHHHHHHhcccc--
Q 011236          389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDN----------RDVEEVEAFVSSLKIKVQK--  456 (490)
Q Consensus       389 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~----------g~~~~a~~~~~~~~~~~~~--  456 (490)
                      .+...|.+.|++++|+..|+++++..|   .-......+..+..++...          |++++|...++++.+..|.  
T Consensus       153 ~la~~~~~~g~~~~A~~~~~~~l~~~p---~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~  229 (261)
T 3qky_A          153 EAARLYERRELYEAAAVTYEAVFDAYP---DTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDSP  229 (261)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCT---TSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTCT
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHCC---CCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCCh
Confidence            778889999999999999999998432   1111235677777888765          8999999999999998887  


Q ss_pred             --hhhhHHHHHHHHhcC
Q 011236          457 --RNMYHALTEAHIRSG  471 (490)
Q Consensus       457 --~~~~~~l~~~~~~~g  471 (490)
                        ......+...+.+.+
T Consensus       230 ~~~~a~~~l~~~~~~~~  246 (261)
T 3qky_A          230 LLRTAEELYTRARQRLT  246 (261)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence              344455555544444

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.15  E-value=9.8e-10  Score=109.62  Aligned_cols=172  Identities=9%  Similarity=-0.074  Sum_probs=109.9

Q ss_pred             HHcCCHHHHHHHHHHHh--------hhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHH
Q 011236          254 IIAGLKEKAIIYLKKCE--------DIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLV  325 (490)
Q Consensus       254 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  325 (490)
                      ...|++++|++.+++..        ...+  .+...+..+..++...|++++|...|++.....+ .+...+..+..++.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p--~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~  478 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFS--ESVELPLMEVRALLDLGDVAKATRKLDDLAERVG-WRWRLVWYRAVAEL  478 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCT--TCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-CCHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccc--cchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCc-chHHHHHHHHHHHH
Confidence            55667777777777665        3222  4556666667777777777777777776666654 45566666777777


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHH
Q 011236          326 KIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       326 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      ..|++++|...|++..+.. +-+...+..+..+|.+.|++++ ...|++.++.++. +...|..+..++.+.|++++|++
T Consensus       479 ~~g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~  555 (681)
T 2pzi_A          479 LTGDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDG-VISAAFGLARARSAEGDRVGAVR  555 (681)
T ss_dssp             HHTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCc-hHHHHHHHHHHHHHcCCHHHHHH
Confidence            7777777777777776652 2245566667777777777777 7777777766544 56667777777777777777777


Q ss_pred             HHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCC
Q 011236          406 CMKEALAVHEENKFWRPKP-SLVSSILDWLGDNR  438 (490)
Q Consensus       406 ~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g  438 (490)
                      .|+++++       +.|+. ..+..+..++...|
T Consensus       556 ~~~~al~-------l~P~~~~a~~~~~~~~~~~~  582 (681)
T 2pzi_A          556 TLDEVPP-------TSRHFTTARLTSAVTLLSGR  582 (681)
T ss_dssp             HHHTSCT-------TSTTHHHHHHHHHHHTC---
T ss_pred             HHHhhcc-------cCcccHHHHHHHHHHHHccC
Confidence            7777655       33543 45555555554433

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=99.14  E-value=2e-08  Score=95.64  Aligned_cols=200  Identities=13%  Similarity=0.013  Sum_probs=117.7

Q ss_pred             HHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          260 EKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEE  339 (490)
Q Consensus       260 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  339 (490)
                      +.+..+|+++....+  .+...|...+..+...|+.+.|..+|++.... + .+...+..    |....+.++.   ++.
T Consensus       196 ~Rv~~~ye~al~~~p--~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~-P-~~~~l~~~----y~~~~e~~~~---~~~  264 (493)
T 2uy1_A          196 SRMHFIHNYILDSFY--YAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM-S-DGMFLSLY----YGLVMDEEAV---YGD  264 (493)
T ss_dssp             HHHHHHHHHHHHHTT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C-CSSHHHHH----HHHHTTCTHH---HHH
T ss_pred             HHHHHHHHHHHHcCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-C-CcHHHHHH----HHhhcchhHH---HHH
Confidence            446677887776555  45677777777777888888888888887777 3 23222221    2221111111   222


Q ss_pred             HHhcC------------CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc-cCCHHHHHHH
Q 011236          340 WELSC------------YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD-KNNMEKAFEC  406 (490)
Q Consensus       340 ~~~~~------------~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~-~~~~~~a~~~  406 (490)
                      +.+.-            ......+|...+..+.+.+..+.|..+|++. .. ...+...|......-.. .++.+.|..+
T Consensus       265 l~~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~-~~~~~~v~i~~A~lE~~~~~d~~~ar~i  342 (493)
T 2uy1_A          265 LKRKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GN-EGVGPHVFIYCAFIEYYATGSRATPYNI  342 (493)
T ss_dssp             HHHHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TT-SCCCHHHHHHHHHHHHHHHCCSHHHHHH
T ss_pred             HHHHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hC-CCCChHHHHHHHHHHHHHCCChHHHHHH
Confidence            22110            0011234566666666677788888888888 32 22244444432222222 2368888888


Q ss_pred             HHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccchhhhHHHHHHHHhcC--CcHHHHHHHHH
Q 011236          407 MKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKRNMYHALTEAHIRSG--QEVDGLLESMK  482 (490)
Q Consensus       407 ~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~~~~m~  482 (490)
                      |+.+++..       |+ +..+...+....+.|+.+.|..+|+++.+   ....|...+..=...|  +.+..+++++.
T Consensus       343 fe~al~~~-------~~~~~~~~~yid~e~~~~~~~~aR~l~er~~k---~~~lw~~~~~fE~~~G~~~~~r~v~~~~~  411 (493)
T 2uy1_A          343 FSSGLLKH-------PDSTLLKEEFFLFLLRIGDEENARALFKRLEK---TSRMWDSMIEYEFMVGSMELFRELVDQKM  411 (493)
T ss_dssp             HHHHHHHC-------TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSCC---BHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            88888722       32 34455566666777888888888888621   1667777777666677  55666676665

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.13  E-value=2.6e-09  Score=89.66  Aligned_cols=168  Identities=8%  Similarity=-0.087  Sum_probs=130.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHH----------------HHHHHHhcCCHHHHHHHHHHHHhc
Q 011236          280 LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYIT----------------MLGSLVKIGELEEAEKMLEEWELS  343 (490)
Q Consensus       280 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~----------------l~~~~~~~~~~~~a~~~~~~~~~~  343 (490)
                      ..+......+...|++++|...|+......+ .+...+..                +..++.+.|++++|...+++..+.
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~   83 (208)
T 3urz_A            5 DEMLQKVSAAIEAGQNGQAVSYFRQTIALNI-DRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQK   83 (208)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCH-HHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            3344556677889999999999998888765 44556666                889999999999999999999986


Q ss_pred             CCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC--HHHHHHHHHHHHHhhhcCcCCC
Q 011236          344 CYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN--MEKAFECMKEALAVHEENKFWR  421 (490)
Q Consensus       344 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~  421 (490)
                      . +-+...+..+...|...|++++|...|++.++..+. +..+|..+...|...|+  ...+...++....       ..
T Consensus        84 ~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~~-------~~  154 (208)
T 3urz_A           84 A-PNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEAD-NLAANIFLGNYYYLTAEQEKKKLETDYKKLSS-------PT  154 (208)
T ss_dssp             C-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHC---C-------CC
T ss_pred             C-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC-------CC
Confidence            3 336778899999999999999999999999998765 78889999988876654  3445556655543       22


Q ss_pred             cchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccch
Q 011236          422 PKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQKR  457 (490)
Q Consensus       422 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  457 (490)
                      |....+.....++...|++++|...|+++.+..|..
T Consensus       155 ~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~  190 (208)
T 3urz_A          155 KMQYARYRDGLSKLFTTRYEKARNSLQKVILRFPST  190 (208)
T ss_dssp             HHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCH
T ss_pred             chhHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCH
Confidence            333344555666777899999999999999998873

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.13  E-value=6.8e-08  Score=85.13  Aligned_cols=218  Identities=8%  Similarity=0.009  Sum_probs=140.0

Q ss_pred             ChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhc--CHHHHHHHHHHccccCC-ChhHHHHHHHHH----Hhc---CCh
Q 011236           84 RFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVR--GLESAETYFNSLNDEDK-VDKLYGALLNCY----VRE---GLV  153 (490)
Q Consensus        84 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~A~~~~~~~~~~~p-~~~~~~~li~~~----~~~---g~~  153 (490)
                      ..++|+++++.++..+ |-....++.--.++...|  ++++++.+++.+....| +..+|+.--..+    ...   +++
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            3457888888888876 345555666666666677  88888888888888776 566676654444    444   678


Q ss_pred             hHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcC--cHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC------hHH
Q 011236          154 DESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHE--KIPDVLLDMKENGVPPDNFSYRICINSYGARSE------LSS  225 (490)
Q Consensus       154 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~--~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~------~~~  225 (490)
                      ++++.+++.+.+...+ |..+|+--.-.+.+.|.++  ++++.++.+.+.++. |...|+.-.......+.      +++
T Consensus       127 ~~EL~~~~~~l~~~pk-ny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~~-N~sAW~~R~~ll~~l~~~~~~~~~~e  204 (306)
T 3dra_A          127 YREFDILEAMLSSDPK-NHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDLK-NNSAWSHRFFLLFSKKHLATDNTIDE  204 (306)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHSSGGGCCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccccchhhhHHH
Confidence            8888888888877655 7777777666677777777  777788887775442 55566555444444444      566


Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHH-HHHHHHHHhhhh--ccCCChhhHHHHHHHHHhcCChhHHHHHH
Q 011236          226 MENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEK-AIIYLKKCEDIV--SKSKDALGYNHLISHYASLGNKDEMMKFW  302 (490)
Q Consensus       226 a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~-a~~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  302 (490)
                      +++.++++. ..++ -|...|+.+...+.+.|+... +..+..++...+  .+ .+...+..+...|.+.|+.++|.+++
T Consensus       205 El~~~~~aI-~~~p-~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~-~s~~al~~la~~~~~~~~~~~A~~~~  281 (306)
T 3dra_A          205 ELNYVKDKI-VKCP-QNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQV-TSSFALETLAKIYTQQKKYNESRTVY  281 (306)
T ss_dssp             HHHHHHHHH-HHCS-SCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEE-SCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHH-HhCC-CCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCC-CCHHHHHHHHHHHHccCCHHHHHHHH
Confidence            666666665 4444 556666666666666665333 334555444332  12 45566666666666666666666666


Q ss_pred             HHHHH
Q 011236          303 GLQKI  307 (490)
Q Consensus       303 ~~~~~  307 (490)
                      +.+..
T Consensus       282 ~~l~~  286 (306)
T 3dra_A          282 DLLKS  286 (306)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            65544

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.11  E-value=2.7e-10  Score=90.02  Aligned_cols=142  Identities=14%  Similarity=0.100  Sum_probs=97.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM  400 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  400 (490)
                      ...+...|++++|...++...... +-+...+..+...|.+.|++++|...|++.++..+. +..+|..+..+|.+.|++
T Consensus         4 G~~~~~~~~~e~ai~~~~~a~~~~-p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~   81 (150)
T 4ga2_A            4 GSMRRSKADVERYIASVQGSTPSP-RQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQER-DPKAHRFLGLLYELEENT   81 (150)
T ss_dssp             ---CCCHHHHHHHHHHHHHHSCSH-HHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcChHHHHHHHHHHhcccC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCch
Confidence            334455667777777777765531 112344556777778888888888888888777655 677788888888888888


Q ss_pred             HHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHH-HHHHHHhcccc-hhhhHHHHHHHHhcC
Q 011236          401 EKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEA-FVSSLKIKVQK-RNMYHALTEAHIRSG  471 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~-~~~~~~~~~~~-~~~~~~l~~~~~~~g  471 (490)
                      ++|+..|+++++       +.|+ ...+..+...+.+.|++++|.+ +++++.+..|. +.+|......+...|
T Consensus        82 ~~A~~~~~~al~-------~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G  148 (150)
T 4ga2_A           82 DKAVECYRRSVE-------LNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEG  148 (150)
T ss_dssp             HHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhC
Confidence            888888888877       3354 3667777777777777765544 45777777777 777777777776666

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=99.10  E-value=4.2e-09  Score=105.08  Aligned_cols=175  Identities=11%  Similarity=-0.082  Sum_probs=147.1

Q ss_pred             hccCChHHHHHHHHHHHhC-------CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHH
Q 011236          218 GARSELSSMENVLQEMESQ-------SHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYA  290 (490)
Q Consensus       218 ~~~g~~~~a~~~~~~~~~~-------~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  290 (490)
                      ...|++++|++.+++.. +       ..-+.+...+..+..+|...|++++|+..|+++.+..+  .+...|..+..++.
T Consensus       402 ~~~~~~~~A~~~~~~al-~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p--~~~~a~~~lg~~~~  478 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAAR-HGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAERVG--WRWRLVWYRAVAEL  478 (681)
T ss_dssp             TTTCCHHHHHHHHHHHH-TC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC--CCHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhh-hhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCc--chHHHHHHHHHHHH
Confidence            77899999999999986 1       22235567888899999999999999999999998776  68889999999999


Q ss_pred             hcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHH
Q 011236          291 SLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADA  370 (490)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  370 (490)
                      ..|++++|...|++.....+ .+...+..+..++.+.|++++ .+.|++..+.. +.+...|..+..+|.+.|++++|..
T Consensus       479 ~~g~~~~A~~~~~~al~l~P-~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~  555 (681)
T 2pzi_A          479 LTGDYDSATKHFTEVLDTFP-GELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVR  555 (681)
T ss_dssp             HHTCHHHHHHHHHHHHHHST-TCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHH
Confidence            99999999999999988876 677888999999999999999 99999998863 3356788899999999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          371 VLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       371 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      .|++..+.++. +...|..+..++...++
T Consensus       556 ~~~~al~l~P~-~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          556 TLDEVPPTSRH-FTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHTSCTTSTT-HHHHHHHHHHHTC----
T ss_pred             HHHhhcccCcc-cHHHHHHHHHHHHccCC
Confidence            99999886543 46778888888877665

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.10  E-value=1.3e-08  Score=86.49  Aligned_cols=194  Identities=8%  Similarity=-0.097  Sum_probs=118.8

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC-hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCCh--hhHH
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD-ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLN--RDYI  318 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~  318 (490)
                      +...+..+...+...|++++|+..|+++....+..+. ...+..+..++.+.|++++|+..|++.....+....  ..+.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            3455666778899999999999999998876553121 356778888999999999999999988887663221  2444


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHH------------
Q 011236          319 TMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNS------------  386 (490)
Q Consensus       319 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~------------  386 (490)
                      .+..++...+..     .+            ..|..+...+...|++++|...|+++++..+. +...            
T Consensus        83 ~~g~~~~~~~~~-----~~------------~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~-~~~a~~a~~~l~~~~~  144 (225)
T 2yhc_A           83 MRGLTNMALDDS-----AL------------QGFFGVDRSDRDPQQARAAFSDFSKLVRGYPN-SQYTTDATKRLVFLKD  144 (225)
T ss_dssp             HHHHHHHHHHC-------------------------------CCHHHHHHHHHHHHHHTTCTT-CTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhh-----hh------------hhhhccchhhcCcHHHHHHHHHHHHHHHHCcC-ChhHHHHHHHHHHHHH
Confidence            455555442110     00            00111112222334444444444444443221 1111            


Q ss_pred             -----HHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          387 -----WSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       387 -----~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                           ...+...|.+.|++++|+..|+++++..|   +.......+..+..++.+.|++++|.+.++.+...+|.
T Consensus       145 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p---~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~  216 (225)
T 2yhc_A          145 RLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYP---DTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSN  216 (225)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST---TSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSC
T ss_pred             HHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCc---CCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCC
Confidence                 13456677888888888888888887332   11111246777888888888888888888888887776

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.10  E-value=8.7e-08  Score=84.44  Aligned_cols=232  Identities=6%  Similarity=-0.094  Sum_probs=145.0

Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC--CHHHHHHHHHHHhhhhccCCChhhHHHHHHHH----Hhc---CC
Q 011236          224 SSMENVLQEMESQSHISMDWGTYSTVANYYIIAG--LKEKAIIYLKKCEDIVSKSKDALGYNHLISHY----ASL---GN  294 (490)
Q Consensus       224 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~---~~  294 (490)
                      ++|+.+++.+. ..++ -...+|+.--.++...|  ++++++..++.+....+  .+..+|+.-...+    ...   ++
T Consensus        50 ~~aL~~t~~~L-~~nP-~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nP--k~y~aW~~R~~iL~~~~~~l~~~~~  125 (306)
T 3dra_A           50 ERALHITELGI-NELA-SHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNE--KNYQIWNYRQLIIGQIMELNNNDFD  125 (306)
T ss_dssp             HHHHHHHHHHH-HHCT-TCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCT--TCCHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHHHHHHH-HHCc-HHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCc--ccHHHHHHHHHHHHHHHHhccccCC
Confidence            45666666655 3333 33444555555555555  66666666666666554  3444554444333    333   56


Q ss_pred             hhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHH--HHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC------HH
Q 011236          295 KDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELE--EAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM------IE  366 (490)
Q Consensus       295 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~------~~  366 (490)
                      +++++.+++.+....+ -+..+|+.-...+.+.|.++  ++.+.++++.+..+ -|...|+.-...+.+.++      ++
T Consensus       126 ~~~EL~~~~~~l~~~p-kny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~~~~~~  203 (306)
T 3dra_A          126 PYREFDILEAMLSSDP-KNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLATDNTID  203 (306)
T ss_dssp             THHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCCHHHHH
T ss_pred             HHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccchhhhHH
Confidence            6666666666666554 55556665555555666665  66677777666532 245555555555555554      78


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHH-HHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHH
Q 011236          367 KADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEK-AFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEA  445 (490)
Q Consensus       367 ~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~  445 (490)
                      ++++.+++++...+. |...|+.+...+.+.|+... +..+..+..+..   ..-..++..+..+...+.+.|+.++|.+
T Consensus       204 eEl~~~~~aI~~~p~-n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~---~~~~~s~~al~~la~~~~~~~~~~~A~~  279 (306)
T 3dra_A          204 EELNYVKDKIVKCPQ-NPSTWNYLLGIHERFDRSITQLEEFSLQFVDLE---KDQVTSSFALETLAKIYTQQKKYNESRT  279 (306)
T ss_dssp             HHHHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGG---GTEESCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhCCC-CccHHHHHHHHHHhcCCChHHHHHHHHHHHhcc---CCCCCCHHHHHHHHHHHHccCCHHHHHH
Confidence            888888888888766 88888888888877777444 445665555411   0112455778888888888888899999


Q ss_pred             HHHHHHh-cccc-hhhhHHHHH
Q 011236          446 FVSSLKI-KVQK-RNMYHALTE  465 (490)
Q Consensus       446 ~~~~~~~-~~~~-~~~~~~l~~  465 (490)
                      +++.+.+ .+|. ...|+..+.
T Consensus       280 ~~~~l~~~~Dpir~~yW~~~~~  301 (306)
T 3dra_A          280 VYDLLKSKYNPIRSNFWDYQIS  301 (306)
T ss_dssp             HHHHHHHTTCGGGHHHHHHHHH
T ss_pred             HHHHHHhccChHHHHHHHHHHh
Confidence            9988886 5776 666766554

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=99.08  E-value=1.2e-09  Score=86.30  Aligned_cols=143  Identities=6%  Similarity=-0.134  Sum_probs=86.7

Q ss_pred             HHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCH
Q 011236          251 NYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGEL  330 (490)
Q Consensus       251 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  330 (490)
                      ..+...|++++|+..+.......+  .+...+..+...|.+.|++++|.+.|++.+...+ .+..+|..+..++.+.|++
T Consensus         5 ~~~~~~~~~e~ai~~~~~a~~~~p--~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~~~~   81 (150)
T 4ga2_A            5 SMRRSKADVERYIASVQGSTPSPR--QKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQE-RDPKAHRFLGLLYELEENT   81 (150)
T ss_dssp             --CCCHHHHHHHHHHHHHHSCSHH--HHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcChHHHHHHHHHHhcccCc--ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCch
Confidence            344455666666666666655443  3445555666667777777777777776666654 4566666677777777777


Q ss_pred             HHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHH-HHHHHHcCCCCCHHHHHHHHHHHhccC
Q 011236          331 EEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAV-LKEIVKKGKTPTPNSWSIIAAGYADKN  398 (490)
Q Consensus       331 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~-~~~m~~~~~~p~~~~~~~l~~~~~~~~  398 (490)
                      ++|...|++..+.. +-+...+..+...|.+.|++++|... +++.++..+. ++.+|......+...|
T Consensus        82 ~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~-~~~~~~l~~~ll~~~G  148 (150)
T 4ga2_A           82 DKAVECYRRSVELN-PTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPG-SPAVYKLKEQLLDCEG  148 (150)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHhC
Confidence            77777777766642 22445666666667777776554443 4666665443 5556665555555554

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.07  E-value=3.1e-09  Score=86.58  Aligned_cols=162  Identities=11%  Similarity=-0.021  Sum_probs=105.3

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHH-H
Q 011236          246 YSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGS-L  324 (490)
Q Consensus       246 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~  324 (490)
                      +..+...+...|++++|+..|++.....+  .+...+..+..++...|++++|...++......+  +...+..+... +
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~~~P--~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~~~~~~~~~~~   84 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSDELQ--SRGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNSYKSLIAKLEL   84 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCHHHH--TSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCC--CcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChHHHHHHHHHHH
Confidence            34456677777888888888877776655  5667777777777788888888887776655443  33322222111 1


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC-CHHHHHHHHHHHhccCCHHHH
Q 011236          325 VKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTP-TPNSWSIIAAGYADKNNMEKA  403 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p-~~~~~~~l~~~~~~~~~~~~a  403 (490)
                      ...++...+...+++..+.. +.+...+..+...+...|++++|...|+++.+..+.+ +...+..+...+...|+.++|
T Consensus        85 ~~~~~~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A  163 (176)
T 2r5s_A           85 HQQAAESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAI  163 (176)
T ss_dssp             HHHHTSCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHH
T ss_pred             HhhcccchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcH
Confidence            12222334566777776642 2245667777777788888888888888777765443 345677777777778888888


Q ss_pred             HHHHHHHHH
Q 011236          404 FECMKEALA  412 (490)
Q Consensus       404 ~~~~~~~~~  412 (490)
                      ...|++++.
T Consensus       164 ~~~y~~al~  172 (176)
T 2r5s_A          164 ASKYRRQLY  172 (176)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            877777654

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.04  E-value=5.5e-08  Score=82.63  Aligned_cols=187  Identities=5%  Similarity=-0.092  Sum_probs=123.9

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCC-C-CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh-hhH
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEMESQSHIS-M-DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA-LGY  282 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~  282 (490)
                      +...+..+...+...|++++|...|+++. ...+. + ....+..+..+|.+.|++++|+..|+++.+..+..+.. .++
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~-~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~   81 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALD-NRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVM   81 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHH-HHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHH
Confidence            34455667788899999999999999998 43221 2 24677789999999999999999999999876642221 245


Q ss_pred             HHHHHHHHh------------------cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 011236          283 NHLISHYAS------------------LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSC  344 (490)
Q Consensus       283 ~~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  344 (490)
                      ..+..++..                  .|++++|...|++.....+ .+..........          ..+...+.   
T Consensus        82 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P-~~~~a~~a~~~l----------~~~~~~~~---  147 (225)
T 2yhc_A           82 YMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYP-NSQYTTDATKRL----------VFLKDRLA---  147 (225)
T ss_dssp             HHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCT-TCTTHHHHHHHH----------HHHHHHHH---
T ss_pred             HHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCc-CChhHHHHHHHH----------HHHHHHHH---
Confidence            555555544                  3455666666665555443 111121111100          00000000   


Q ss_pred             CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          345 YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT--PNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       345 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                           .....+...|.+.|++++|...|+++++..+...  ...+..+..+|.+.|+.++|.+.++.+..
T Consensus       148 -----~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~  212 (225)
T 2yhc_A          148 -----KYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA  212 (225)
T ss_dssp             -----HHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHh
Confidence                 0112456678899999999999999998754311  24688889999999999999999998887

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.04  E-value=5.9e-09  Score=102.16  Aligned_cols=152  Identities=9%  Similarity=-0.044  Sum_probs=98.5

Q ss_pred             cCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHH
Q 011236          256 AGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEK  335 (490)
Q Consensus       256 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  335 (490)
                      .|++++|+..|++..+..+  .+...+..+...+...|++++|.+.+++.....+ .+...+..+..++...|++++|.+
T Consensus         2 ~g~~~~A~~~~~~al~~~p--~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~   78 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRP--QDFVAWLMLADAELGMGDTTAGEMAVQRGLALHP-GHPEAVARLGRVRWTQQRHAEAAV   78 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTST-TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHH
Confidence            4677788888887766554  4667777777788888888888888887766654 456677777777778888888888


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc---CCHHHHHHHHHHHHH
Q 011236          336 MLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK---NNMEKAFECMKEALA  412 (490)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~  412 (490)
                      .+++..+.. +.+...+..+...|.+.|++++|...+++..+..+. +...+..+...+...   |+.++|.+.++++++
T Consensus        79 ~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~  156 (568)
T 2vsy_A           79 LLQQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPE-EPYITAQLLNWRRRLCDWRALDVLSAQVRAAVA  156 (568)
T ss_dssp             HHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHH
T ss_pred             HHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhhccccHHHHHHHHHHHHh
Confidence            888777752 234566777777777888888888888877776544 566777777777777   778888888887777

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.03  E-value=7.5e-09  Score=91.59  Aligned_cols=162  Identities=7%  Similarity=-0.087  Sum_probs=82.8

Q ss_pred             hhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchH-HHHHHH
Q 011236          104 VHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNY-NGIMCL  181 (490)
Q Consensus       104 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~-~~l~~~  181 (490)
                      ...+..+...+...|++++|...|++.....| +..++..+...+.+.|++++|...++++....  |+.... ......
T Consensus       117 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~--p~~~~~~~~~~~~  194 (287)
T 3qou_A          117 EELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQD--QDTRYQGLVAQIE  194 (287)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGG--CSHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhh--cchHHHHHHHHHH
Confidence            34444444555555555555555555555554 34555555555555666666665555554442  222211 111222


Q ss_pred             HHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCC-CCHHHHHHHHHHHHHcCCHH
Q 011236          182 YTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHIS-MDWGTYSTVANYYIIAGLKE  260 (490)
Q Consensus       182 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~~~~~~li~~~~~~~~~~  260 (490)
                      +...++.+.|...+++..+... .+...+..+...+...|++++|...|+++. +.+.. .+...+..++..|...|+.+
T Consensus       195 l~~~~~~~~a~~~l~~al~~~P-~~~~~~~~la~~l~~~g~~~~A~~~l~~~l-~~~p~~~~~~a~~~l~~~~~~~g~~~  272 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAENP-EDAALATQLALQLHQVGRNEEALELLFGHL-RXDLTAADGQTRXTFQEILAALGTGD  272 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCTTGGGGHHHHHHHHHHHHHCTTC
T ss_pred             HHhhcccCccHHHHHHHHhcCC-ccHHHHHHHHHHHHHcccHHHHHHHHHHHH-hcccccccchHHHHHHHHHHHcCCCC
Confidence            4444555555555555555321 244455555566666666666666666555 22221 12445555666666666666


Q ss_pred             HHHHHHHHH
Q 011236          261 KAIIYLKKC  269 (490)
Q Consensus       261 ~a~~~~~~~  269 (490)
                      +|...|++.
T Consensus       273 ~a~~~~r~a  281 (287)
T 3qou_A          273 ALASXYRRQ  281 (287)
T ss_dssp             HHHHHHHHH
T ss_pred             cHHHHHHHH
Confidence            666555554

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=99.02  E-value=3.6e-09  Score=86.19  Aligned_cols=162  Identities=12%  Similarity=0.046  Sum_probs=110.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHH-
Q 011236          280 LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLG-  358 (490)
Q Consensus       280 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-  358 (490)
                      ..+......+...|++++|...|++.....+ .+...+..+...+...|++++|...++.+....  |+...+..+... 
T Consensus         7 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~   83 (176)
T 2r5s_A            7 EQLLKQVSELLQQGEHAQALNVIQTLSDELQ-SRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLE   83 (176)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHTSCHHHH-TSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHH
Confidence            3455666777788888888888887776655 566777888888888888888888888876642  333332222211 


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc---hhhHHHHHHHHH
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK---PSLVSSILDWLG  435 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~---~~~~~~l~~~~~  435 (490)
                      +...+...+|...+++..+..+. +...+..+...+...|++++|...|+++++       ..|+   ...+..+...+.
T Consensus        84 ~~~~~~~~~a~~~~~~al~~~P~-~~~~~~~la~~~~~~g~~~~A~~~~~~~l~-------~~p~~~~~~a~~~l~~~~~  155 (176)
T 2r5s_A           84 LHQQAAESPELKRLEQELAANPD-NFELACELAVQYNQVGRDEEALELLWNILK-------VNLGAQDGEVKKTFMDILS  155 (176)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT-------TCTTTTTTHHHHHHHHHHH
T ss_pred             HHhhcccchHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcccHHHHHHHHHHHHH-------hCcccChHHHHHHHHHHHH
Confidence            12222334567777777776544 677778888888888888888888888877       2343   346777777788


Q ss_pred             cCCCHHHHHHHHHHHHh
Q 011236          436 DNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       436 ~~g~~~~a~~~~~~~~~  452 (490)
                      ..|+.++|...|++...
T Consensus       156 ~~g~~~~A~~~y~~al~  172 (176)
T 2r5s_A          156 ALGQGNAIASKYRRQLY  172 (176)
T ss_dssp             HHCSSCHHHHHHHHHHH
T ss_pred             HhCCCCcHHHHHHHHHH
Confidence            88888888877776543

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=99.02  E-value=1.7e-08  Score=90.43  Aligned_cols=232  Identities=10%  Similarity=-0.005  Sum_probs=156.7

Q ss_pred             cCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011236          185 TGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAII  264 (490)
Q Consensus       185 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  264 (490)
                      .|++++|.+++++..+... ..         .+...++++.|...|.+.                ...|...|++++|..
T Consensus         4 ~~~~~eA~~~~~~a~k~~~-~~---------~~~~~~~~~~A~~~~~~a----------------~~~~~~~g~~~~A~~   57 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLK-TS---------FMKWKPDYDSAASEYAKA----------------AVAFKNAKQLEQAKD   57 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-CC---------SSSCSCCHHHHHHHHHHH----------------HHHHHHTTCHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHcc-cc---------ccCCCCCHHHHHHHHHHH----------------HHHHHHcCCHHHHHH
Confidence            4566777777777655311 10         011146777777776654                456778899999999


Q ss_pred             HHHHHhhhhccCCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC---CC--hhhHHHHHHHHHhcCCHHHHHH
Q 011236          265 YLKKCEDIVSKSKD----ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK---QL--NRDYITMLGSLVKIGELEEAEK  335 (490)
Q Consensus       265 ~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~--~~~~~~l~~~~~~~~~~~~a~~  335 (490)
                      .|.+.........+    ..+|+.+...|...|++++|+..|++.......   +.  ..++..+...|.. |++++|..
T Consensus        58 ~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~  136 (307)
T 2ifu_A           58 AYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVH  136 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHH
Confidence            99887654432112    357888888999999999999999877665321   11  3567788888888 99999999


Q ss_pred             HHHHHHhcCCCC-----CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC----CCC-HHHHHHHHHHHhccCCHHHHHH
Q 011236          336 MLEEWELSCYCY-----DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK----TPT-PNSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       336 ~~~~~~~~~~~~-----~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~----~p~-~~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      .+++..+.....     ...+++.+...|.+.|++++|+..|++..+...    .+. ...+..++.++...|++++|..
T Consensus       137 ~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~  216 (307)
T 2ifu_A          137 LYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQK  216 (307)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            999887642111     135677888899999999999999998876421    111 2356677778888899999999


Q ss_pred             HHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHH
Q 011236          406 CMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAF  446 (490)
Q Consensus       406 ~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  446 (490)
                      .|++++ ..|.... .........++.++ ..|+.+.+..+
T Consensus       217 ~~~~al-~~p~~~~-~~e~~~l~~l~~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          217 CVRESY-SIPGFSG-SEDCAALEDLLQAY-DEQDEEQLLRV  254 (307)
T ss_dssp             HHHHHT-TSTTSTT-SHHHHHHHHHHHHH-HTTCHHHHHHH
T ss_pred             HHHHHh-CCCCCCC-CHHHHHHHHHHHHH-HhcCHHHHHHH
Confidence            999987 5532111 11123455566655 56777766663

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.01  E-value=1.3e-08  Score=90.08  Aligned_cols=161  Identities=11%  Similarity=0.038  Sum_probs=68.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHH-HHHHHH
Q 011236          281 GYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPN-IILLGY  359 (490)
Q Consensus       281 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~  359 (490)
                      .+..+...+...|++++|...|++.....+ .+...+..+...+.+.|++++|...++++...  .|+..... .....+
T Consensus       119 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~P-~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~~l  195 (287)
T 3qou_A          119 LXAQQAMQLMQESNYTDALPLLXDAWQLSN-QNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQIEL  195 (287)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHTT-SCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHHHHhCC-cchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHHHH
Confidence            333444444444444444444444444433 33344444444444444444444444444332  12211111 111123


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCC
Q 011236          360 SQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRD  439 (490)
Q Consensus       360 ~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  439 (490)
                      .+.++.++|...+++..+..+. +...+..+...+...|++++|+..|+++++..|+    ..+...+..++..+...|+
T Consensus       196 ~~~~~~~~a~~~l~~al~~~P~-~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~----~~~~~a~~~l~~~~~~~g~  270 (287)
T 3qou_A          196 LXQAADTPEIQQLQQQVAENPE-DAALATQLALQLHQVGRNEEALELLFGHLRXDLT----AADGQTRXTFQEILAALGT  270 (287)
T ss_dssp             HHHHTSCHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT----GGGGHHHHHHHHHHHHHCT
T ss_pred             HhhcccCccHHHHHHHHhcCCc-cHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccc----cccchHHHHHHHHHHHcCC
Confidence            3344444445555554444332 4444555555555555555555555555441110    0112344444445555555


Q ss_pred             HHHHHHHHHH
Q 011236          440 VEEVEAFVSS  449 (490)
Q Consensus       440 ~~~a~~~~~~  449 (490)
                      .++|...+++
T Consensus       271 ~~~a~~~~r~  280 (287)
T 3qou_A          271 GDALASXYRR  280 (287)
T ss_dssp             TCHHHHHHHH
T ss_pred             CCcHHHHHHH
Confidence            5554444443

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=99.01  E-value=1.5e-08  Score=90.74  Aligned_cols=219  Identities=8%  Similarity=-0.049  Sum_probs=155.0

Q ss_pred             cCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHH
Q 011236          220 RSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMM  299 (490)
Q Consensus       220 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~  299 (490)
                      .|++++|.+++++.. +... ..      +   +...++++.|...|.+.                ...|...|++++|.
T Consensus         4 ~~~~~eA~~~~~~a~-k~~~-~~------~---~~~~~~~~~A~~~~~~a----------------~~~~~~~g~~~~A~   56 (307)
T 2ifu_A            4 AQKISEAHEHIAKAE-KYLK-TS------F---MKWKPDYDSAASEYAKA----------------AVAFKNAKQLEQAK   56 (307)
T ss_dssp             HHHHHHHHHHHHHHH-HHHC-CC------S---SSCSCCHHHHHHHHHHH----------------HHHHHHTTCHHHHH
T ss_pred             cchHHHHHHHHHHHH-HHcc-cc------c---cCCCCCHHHHHHHHHHH----------------HHHHHHcCCHHHHH
Confidence            567778888887765 2111 11      0   11146777777776653                45677889999999


Q ss_pred             HHHHHHHHhcCC-CC----hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC---C--CchhHHHHHHHHHhcCCHHHHH
Q 011236          300 KFWGLQKIKCKK-QL----NRDYITMLGSLVKIGELEEAEKMLEEWELSCYC---Y--DFRVPNIILLGYSQKGMIEKAD  369 (490)
Q Consensus       300 ~~~~~~~~~~~~-~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~--~~~~~~~l~~~~~~~g~~~~A~  369 (490)
                      ..|.+....... .+    ..+|..+...|.+.|++++|...+++..+.-..   +  -..+++.+...|.. |++++|+
T Consensus        57 ~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~  135 (307)
T 2ifu_A           57 DAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAV  135 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHH
Confidence            999877665431 11    347888899999999999999999987654111   1  13467778888988 9999999


Q ss_pred             HHHHHHHHcCCCC-C----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHH
Q 011236          370 AVLKEIVKKGKTP-T----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEV  443 (490)
Q Consensus       370 ~~~~~m~~~~~~p-~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a  443 (490)
                      ..|++.++..... +    ..++..+...|.+.|++++|+..|++++...++... .+.. ..+..+...+...|++++|
T Consensus       136 ~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~-~~~~~~~~~~~g~~~~~~g~~~~A  214 (307)
T 2ifu_A          136 HLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMEN-YPTCYKKCIAQVLVQLHRADYVAA  214 (307)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC-HHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCC-hhHHHHHHHHHHHHHHHcCCHHHH
Confidence            9999987642211 1    457889999999999999999999999985542221 2222 3666777788888999999


Q ss_pred             HHHHHHHHhcccc------hhhhHHHHHHHH
Q 011236          444 EAFVSSLKIKVQK------RNMYHALTEAHI  468 (490)
Q Consensus       444 ~~~~~~~~~~~~~------~~~~~~l~~~~~  468 (490)
                      ...|++.. ..|.      ......++.++.
T Consensus       215 ~~~~~~al-~~p~~~~~~e~~~l~~l~~~~~  244 (307)
T 2ifu_A          215 QKCVRESY-SIPGFSGSEDCAALEDLLQAYD  244 (307)
T ss_dssp             HHHHHHHT-TSTTSTTSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-CCCCCCCCHHHHHHHHHHHHHH
Confidence            99999998 7765      233555666664

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=99.00  E-value=1.4e-07  Score=83.86  Aligned_cols=169  Identities=11%  Similarity=-0.028  Sum_probs=118.5

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcC-CCChh----hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCc-----hhHH
Q 011236          284 HLISHYASLGNKDEMMKFWGLQKIKCK-KQLNR----DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDF-----RVPN  353 (490)
Q Consensus       284 ~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~  353 (490)
                      ..+..+...|++++|..+++....... .|+..    .+..+...+...|++++|...++++.+.....+.     .+++
T Consensus        80 ~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~  159 (293)
T 3u3w_A           80 DQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIEN  159 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHH
Confidence            345667778888888888887766433 12211    2334666667778888888888888874322222     2578


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHc-----CCCCC-HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKK-----GKTPT-PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLV  427 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~-----~~~p~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~  427 (490)
                      .+...|...|++++|...|+++.+.     +..+. ..+|..+...|.+.|++++|...++++++..+.......-..+|
T Consensus       160 ~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~  239 (293)
T 3u3w_A          160 AIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLY  239 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence            8888899999999999998888741     11112 23788888999999999999999999887554332222225678


Q ss_pred             HHHHHHHHcCC-CHHHHHHHHHHHHh
Q 011236          428 SSILDWLGDNR-DVEEVEAFVSSLKI  452 (490)
Q Consensus       428 ~~l~~~~~~~g-~~~~a~~~~~~~~~  452 (490)
                      ..+..++.+.| ++++|...++++..
T Consensus       240 ~~lg~~~~~~g~~~~~A~~~~~~Al~  265 (293)
T 3u3w_A          240 YQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            88888999999 46999988887765

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=99.00  E-value=1.5e-08  Score=99.34  Aligned_cols=154  Identities=8%  Similarity=-0.055  Sum_probs=102.5

Q ss_pred             cCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHH
Q 011236          185 TGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAII  264 (490)
Q Consensus       185 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~  264 (490)
                      .|++++|.+.|++..+... .+...+..+...+...|++++|.+.|++.. +.+. .+...+..+..+|...|++++|.+
T Consensus         2 ~g~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al-~~~p-~~~~~~~~lg~~~~~~g~~~~A~~   78 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRP-QDFVAWLMLADAELGMGDTTAGEMAVQRGL-ALHP-GHPEAVARLGRVRWTQQRHAEAAV   78 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHH-TTST-TCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHHCCCHHHHHH
Confidence            4677888888887766422 346677777788888888888888888887 5544 456777778888888888888888


Q ss_pred             HHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc---CCHHHHHHHHHHHH
Q 011236          265 YLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI---GELEEAEKMLEEWE  341 (490)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~  341 (490)
                      .|++..+..+  .+...+..+..+|...|++++|.+.|++.....+ .+...+..+...+...   |+.++|.+.+++..
T Consensus        79 ~~~~al~~~p--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al  155 (568)
T 2vsy_A           79 LLQQASDAAP--EHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLP-EEPYITAQLLNWRRRLCDWRALDVLSAQVRAAV  155 (568)
T ss_dssp             HHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHH
T ss_pred             HHHHHHhcCC--CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Confidence            8888777654  4667778888888888888888888887777655 5566777777777777   88888888888877


Q ss_pred             hcC
Q 011236          342 LSC  344 (490)
Q Consensus       342 ~~~  344 (490)
                      +.+
T Consensus       156 ~~~  158 (568)
T 2vsy_A          156 AQG  158 (568)
T ss_dssp             HHT
T ss_pred             hcC
Confidence            763

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.99  E-value=2.4e-07  Score=88.28  Aligned_cols=340  Identities=11%  Similarity=-0.016  Sum_probs=192.4

Q ss_pred             hhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCC-hhHHHHHHHHH
Q 011236           85 FKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGL-VDESLSLMQKM  163 (490)
Q Consensus        85 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~-~~~a~~~~~~m  163 (490)
                      +..|..+|+.+...-  |.              |+++.+..+|+.....-|+...|...+....+.++ .+....+|+..
T Consensus        11 i~~aR~vyer~l~~~--P~--------------~~~e~~~~iferal~~~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~a   74 (493)
T 2uy1_A           11 LSSPSAIMEHARRLY--MS--------------KDYRSLESLFGRCLKKSYNLDLWMLYIEYVRKVSQKKFKLYEVYEFT   74 (493)
T ss_dssp             -CCHHHHHHHHHHHH--HT--------------TCHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHC----CTHHHHHHH
T ss_pred             hHHHHHHHHHHHHHC--CC--------------CCHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCchHHHHHHHHHHH
Confidence            666666666666543  11              77888888888777766777777777776666553 34455666665


Q ss_pred             Hhc-CCCC-CcchHHHHHHHHH----hcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCC
Q 011236          164 KEM-GSFG-SALNYNGIMCLYT----NTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQS  237 (490)
Q Consensus       164 ~~~-~~~p-~~~~~~~l~~~~~----~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~  237 (490)
                      ... |..| +...|...+..+.    ..++.+.+.++|+..+......-...|...... .+..+...+..++.+.    
T Consensus        75 l~~vg~d~~s~~iW~~Yi~f~~~~~~~~~~~~~vR~iy~rAL~~P~~~~~~lw~~Y~~f-E~~~~~~~~~~~~~~~----  149 (493)
T 2uy1_A           75 LGQFENYWDSYGLYKEYIEEEGKIEDEQTRIEKIRNGYMRALQTPMGSLSELWKDFENF-ELELNKITGKKIVGDT----  149 (493)
T ss_dssp             HHHSTTCTTCHHHHHHHHHHTSSCSSHHHHHHHHHHHHHHHHTSCCTTHHHHHHHHHHH-HHHHCHHHHHHHHHHH----
T ss_pred             HHHcCCCcccHHHHHHHHHHHHhchhhhHHHHHHHHHHHHHHhChhhhHHHHHHHHHHH-HHHhccccHHHHHHHH----
Confidence            543 3222 4445555554433    124455666666666652111001111111111 1111111122221111    


Q ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcC-C------hhHHHHHHHHHHHhcC
Q 011236          238 HISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG-N------KDEMMKFWGLQKIKCK  310 (490)
Q Consensus       238 ~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~------~~~a~~~~~~~~~~~~  310 (490)
                                        .+.+..|..+++.+...... .+...|...+..-...+ .      .+.+..+|++++...+
T Consensus       150 ------------------~~~y~~ar~~y~~~~~~~~~-~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~~p  210 (493)
T 2uy1_A          150 ------------------LPIFQSSFQRYQQIQPLIRG-WSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDSFY  210 (493)
T ss_dssp             ------------------HHHHHHHHHHHHHHHHHHHT-CSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             ------------------hHHHHHHHHHHHHHHHHHhh-ccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHcCC
Confidence                              12344555556655543332 34456666555533221 1      3456788998888765


Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC---------CC
Q 011236          311 KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG---------KT  381 (490)
Q Consensus       311 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~---------~~  381 (490)
                       .....|...+.-+.+.|+.+.|..+++.....  +.+...+.    .|....+.++.   ++.+.+.-         ..
T Consensus       211 -~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~--P~~~~l~~----~y~~~~e~~~~---~~~l~~~~~~~~~~~~~~~  280 (493)
T 2uy1_A          211 -YAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM--SDGMFLSL----YYGLVMDEEAV---YGDLKRKYSMGEAESAEKV  280 (493)
T ss_dssp             -TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSSHHHH----HHHHHTTCTHH---HHHHHHHTC----------
T ss_pred             -CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC--CCcHHHHH----HHHhhcchhHH---HHHHHHHHHhhccchhhhh
Confidence             55778888888888999999999999999987  33333332    23332222222   33332210         00


Q ss_pred             C---CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc-CCCHHHHHHHHHHHHhcccc-
Q 011236          382 P---TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD-NRDVEEVEAFVSSLKIKVQK-  456 (490)
Q Consensus       382 p---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~-~g~~~~a~~~~~~~~~~~~~-  456 (490)
                      +   ....|...+....+.++.+.|..+|+++ . .   .+  .+...|......-.. .++.+.|..+|+...+..|. 
T Consensus       281 ~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~-~---~~--~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~  353 (493)
T 2uy1_A          281 FSKELDLLRINHLNYVLKKRGLELFRKLFIEL-G-N---EG--VGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDS  353 (493)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-T-T---SC--CCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTC
T ss_pred             cccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-h-C---CC--CChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCC
Confidence            1   1245777777777788899999999999 4 1   22  233444332222222 33699999999999998877 


Q ss_pred             hhhhHHHHHHHHhcC--CcHHHHHHHH
Q 011236          457 RNMYHALTEAHIRSG--QEVDGLLESM  481 (490)
Q Consensus       457 ~~~~~~l~~~~~~~g--~~a~~~~~~m  481 (490)
                      +..|...++...+.|  +.|..+|++.
T Consensus       354 ~~~~~~yid~e~~~~~~~~aR~l~er~  380 (493)
T 2uy1_A          354 TLLKEEFFLFLLRIGDEENARALFKRL  380 (493)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            777777888777888  7788887764

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.92  E-value=2.2e-07  Score=82.52  Aligned_cols=211  Identities=6%  Similarity=-0.153  Sum_probs=140.7

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHH---HHHHHHHHHHHcCCHHHHHHHHHHHh
Q 011236          194 VLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWG---TYSTVANYYIIAGLKEKAIIYLKKCE  270 (490)
Q Consensus       194 ~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~~~  270 (490)
                      .+..+......|+..+...+...+.-.-  +   .++.    .. ...+..   .+...+..+...|++++|..++++..
T Consensus        33 ~~s~~e~g~~~~~~~~l~~i~~~l~~~~--~---~~~~----~~-~~~~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l  102 (293)
T 3u3w_A           33 EVSRIESGAVYPSMDILQGIAAKLQIPI--I---HFYE----VL-IYSDIERKKQFKDQVIMLCKQKRYKEIYNKVWNEL  102 (293)
T ss_dssp             HHHHHHTTSCCCCHHHHHHHHHHHTCCT--H---HHHH----TT-TSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHhCcCH--H---HHhC----CC-CCCcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence            3444444334577766666666554221  1   1111    11 112222   23334677888899999999998887


Q ss_pred             hhhccCCCh----hhHHHHHHHHHhcCChhHHHHHHHHHHHhcC-CCCh----hhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          271 DIVSKSKDA----LGYNHLISHYASLGNKDEMMKFWGLQKIKCK-KQLN----RDYITMLGSLVKIGELEEAEKMLEEWE  341 (490)
Q Consensus       271 ~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~  341 (490)
                      ......++.    ..+..+...+...|++++|+..+++...... .++.    .+++.+...|...|++++|...++++.
T Consensus       103 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al  182 (293)
T 3u3w_A          103 KKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQIL  182 (293)
T ss_dssp             TTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             ccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            644321221    1233466677778899999999998887433 2222    268888899999999999999999887


Q ss_pred             hc-----CCCC-CchhHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCCC-HHHHHHHHHHHhccCC-HHHHHHHHHH
Q 011236          342 LS-----CYCY-DFRVPNIILLGYSQKGMIEKADAVLKEIVKK----GKTPT-PNSWSIIAAGYADKNN-MEKAFECMKE  409 (490)
Q Consensus       342 ~~-----~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~----~~~p~-~~~~~~l~~~~~~~~~-~~~a~~~~~~  409 (490)
                      +.     +..+ ...++..+...|.+.|++++|...+++.++.    +..+. ..+|..+..+|.+.|+ +++|.+.+++
T Consensus       183 ~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~  262 (293)
T 3u3w_A          183 KQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKK  262 (293)
T ss_dssp             HHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHH
Confidence            42     1111 1236788899999999999999999988753    22222 5689999999999995 6999999999


Q ss_pred             HHHhh
Q 011236          410 ALAVH  414 (490)
Q Consensus       410 ~~~~~  414 (490)
                      ++...
T Consensus       263 Al~i~  267 (293)
T 3u3w_A          263 ASFFF  267 (293)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98733

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.89  E-value=4.2e-08  Score=74.57  Aligned_cols=107  Identities=13%  Similarity=0.008  Sum_probs=66.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSS  429 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~  429 (490)
                      .+......|.+.|++++|+..|++.++..+. +..+|..+..+|.+.|++++|+..++++++.       .|+ ...|..
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~-------~p~~~~a~~~   86 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKRDPE-NAILYSNRAACLTKLMEFQRALDDCDTCIRL-------DSKFIKGYIR   86 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHhhHHHhhccHHHHHHHHHHHHHh-------hhhhhHHHHH
Confidence            3444555666666666666666666665543 5666666666666666666666666666662       233 355666


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHH
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTE  465 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~  465 (490)
                      +..++...|++++|.+.|++..+..|. ...+..|..
T Consensus        87 lg~~~~~~~~~~~A~~~~~~al~l~P~~~~a~~~l~~  123 (126)
T 4gco_A           87 KAACLVAMREWSKAQRAYEDALQVDPSNEEAREGVRN  123 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCcCCHHHHHHHHH
Confidence            666666666666666666666666666 555554443

>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=98.89  E-value=7.9e-08  Score=80.73  Aligned_cols=160  Identities=12%  Similarity=0.061  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcC----CcCcHHHHHHHHHHCCCCCCHHHHHHHH
Q 011236          139 LYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTG----QHEKIPDVLLDMKENGVPPDNFSYRICI  214 (490)
Q Consensus       139 ~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~----~~~~a~~~~~~m~~~~~~p~~~~~~~li  214 (490)
                      ++..|...|...+++++|+..|++..+.|   ++..+..|...|.. +    ++++|.+.|++..+.|   +...+..|.
T Consensus        20 a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~~~Lg   92 (212)
T 3rjv_A           20 AQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGEIVLA   92 (212)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHHHHHH
Confidence            33444444444444444444444444432   33333444444433 3    4444444444444332   233333444


Q ss_pred             HHHhc----cCChHHHHHHHHHHHhCCCCC-CCHHHHHHHHHHHHH----cCCHHHHHHHHHHHhhhhccCCChhhHHHH
Q 011236          215 NSYGA----RSELSSMENVLQEMESQSHIS-MDWGTYSTVANYYII----AGLKEKAIIYLKKCEDIVSKSKDALGYNHL  285 (490)
Q Consensus       215 ~~~~~----~g~~~~a~~~~~~~~~~~~~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  285 (490)
                      ..|..    .+++++|...|++.. +.+.. .....+..|...|..    .+++++|+..|++....+   .+...+..|
T Consensus        93 ~~y~~g~g~~~d~~~A~~~~~~A~-~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~---~~~~a~~~L  168 (212)
T 3rjv_A           93 RVLVNRQAGATDVAHAITLLQDAA-RDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSLS---RTGYAEYWA  168 (212)
T ss_dssp             HHHTCGGGSSCCHHHHHHHHHHHT-SSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHTS---CTTHHHHHH
T ss_pred             HHHHcCCCCccCHHHHHHHHHHHH-HcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHcC---CCHHHHHHH
Confidence            44433    445555555555544 33210 013444444444444    445555555555544331   222334444


Q ss_pred             HHHHHhc-C-----ChhHHHHHHHHHHHhc
Q 011236          286 ISHYASL-G-----NKDEMMKFWGLQKIKC  309 (490)
Q Consensus       286 ~~~~~~~-~-----~~~~a~~~~~~~~~~~  309 (490)
                      ...|... |     +.++|...|+.....+
T Consensus       169 g~~y~~g~gg~~~~d~~~A~~~~~~A~~~g  198 (212)
T 3rjv_A          169 GMMFQQGEKGFIEPNKQKALHWLNVSCLEG  198 (212)
T ss_dssp             HHHHHHCBTTTBCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHcCCCCCCCCCHHHHHHHHHHHHHcC
Confidence            4444322 1     4555555555444443

>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=98.89  E-value=1.3e-07  Score=79.44  Aligned_cols=125  Identities=17%  Similarity=-0.040  Sum_probs=66.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ  361 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (490)
                      +..+...+...|++++|...|++..    .|+...+..+...+...|++++|...+++..+.. +.+...+..+..+|..
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~   83 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQ   83 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHH
Confidence            3444555555566666666555432    2344555555555555555555555555555542 2234445555555555


Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCH----------------HHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          362 KGMIEKADAVLKEIVKKGKTPTP----------------NSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~~~~p~~----------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .|++++|...|++..+.... +.                ..+..+..+|...|++++|...|+++++
T Consensus        84 ~~~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  149 (213)
T 1hh8_A           84 TEKYDLAIKDLKEALIQLRG-NQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  149 (213)
T ss_dssp             TTCHHHHHHHHHHHHHTTTT-CSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHHhCCC-ccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            55555555555555554322 11                4455555555555555555555555554

>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=98.88  E-value=3.4e-07  Score=76.84  Aligned_cols=177  Identities=8%  Similarity=0.003  Sum_probs=112.1

Q ss_pred             HHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcC----CHHHHHHHH
Q 011236          262 AIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIG----ELEEAEKML  337 (490)
Q Consensus       262 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~a~~~~  337 (490)
                      |.+.|++..+.    .+..++..+...|...+++++|...|++....   .+...+..+...|.. +    ++++|...|
T Consensus         5 A~~~~~~aa~~----g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---g~~~a~~~lg~~y~~-~g~~~~~~~A~~~~   76 (212)
T 3rjv_A            5 PGSQYQQQAEA----GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQ---GDGDALALLAQLKIR-NPQQADYPQARQLA   76 (212)
T ss_dssp             TTHHHHHHHHT----TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHT---TCHHHHHHHHHHTTS-STTSCCHHHHHHHH
T ss_pred             HHHHHHHHHHC----CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHc---CCHHHHHHHHHHHHc-CCCCCCHHHHHHHH
Confidence            44445544432    34455666666666666666676666665543   244555555555555 5    677777777


Q ss_pred             HHHHhcCCCCCchhHHHHHHHHHh----cCCHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHHhc----cCCHHHHHHHHH
Q 011236          338 EEWELSCYCYDFRVPNIILLGYSQ----KGMIEKADAVLKEIVKKGKT-PTPNSWSIIAAGYAD----KNNMEKAFECMK  408 (490)
Q Consensus       338 ~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~~-p~~~~~~~l~~~~~~----~~~~~~a~~~~~  408 (490)
                      ++..+.|   +...+..|...|..    .+++++|...|++..+.|.. .++..+..|...|..    .+++++|+.+|+
T Consensus        77 ~~A~~~g---~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~  153 (212)
T 3rjv_A           77 EKAVEAG---SKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFK  153 (212)
T ss_dssp             HHHHHTT---CHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHH
T ss_pred             HHHHHCC---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            7776543   34455666666665    67788888888877776531 025667777777777    677888888888


Q ss_pred             HHHHhhhcCcCCCcchhhHHHHHHHHHcC-C-----CHHHHHHHHHHHHhcccc
Q 011236          409 EALAVHEENKFWRPKPSLVSSILDWLGDN-R-----DVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       409 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~-g-----~~~~a~~~~~~~~~~~~~  456 (490)
                      ++.+     .  ..+...+..|...|... |     +.++|..+|++..+.+..
T Consensus       154 ~A~~-----~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~~  200 (212)
T 3rjv_A          154 GSSS-----L--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGFD  200 (212)
T ss_dssp             HHHH-----T--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTCH
T ss_pred             HHHH-----c--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCCH
Confidence            8877     2  23445566666666542 2     788888888887776654

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.87  E-value=6.3e-07  Score=79.49  Aligned_cols=174  Identities=11%  Similarity=-0.025  Sum_probs=120.1

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCCh-----hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC---CC--
Q 011236          279 ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLN-----RDYITMLGSLVKIGELEEAEKMLEEWELSCYC---YD--  348 (490)
Q Consensus       279 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~--  348 (490)
                      ...+...+..+...|++++|.+.+............     ..+..+...+...|++++|...+++..+....   +.  
T Consensus        75 ~~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~  154 (293)
T 2qfc_A           75 KKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQN  154 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHH
Confidence            344556667777888888888888766665432111     22344556667788899999988888754221   11  


Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHHHHHH---cCCC-C--CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc
Q 011236          349 FRVPNIILLGYSQKGMIEKADAVLKEIVK---KGKT-P--TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP  422 (490)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~A~~~~~~m~~---~~~~-p--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p  422 (490)
                      ..+++.+...|...|++++|...|++..+   .... +  ...+|..+...|...|++++|+.+++++++..........
T Consensus       155 ~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~  234 (293)
T 2qfc_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHH
Confidence            33677888889999999999999988873   2111 1  1257888888999999999999999998874422111111


Q ss_pred             chhhHHHHHHHHHcCCCHHHH-HHHHHHHHh
Q 011236          423 KPSLVSSILDWLGDNRDVEEV-EAFVSSLKI  452 (490)
Q Consensus       423 ~~~~~~~l~~~~~~~g~~~~a-~~~~~~~~~  452 (490)
                      -..+|..+...+.+.|++++| ...+++...
T Consensus       235 ~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            246788888899999999999 777776654

>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=98.87  E-value=3.7e-06  Score=74.54  Aligned_cols=198  Identities=10%  Similarity=0.011  Sum_probs=125.8

Q ss_pred             HHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcC--ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCC-HHHHHH
Q 011236          259 KEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG--NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGE-LEEAEK  335 (490)
Q Consensus       259 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~a~~  335 (490)
                      +++++.+++.+....+  .+..+|+.-...+...+  .+++++.+++.+....+ -+...|+.-...+...|. ++++.+
T Consensus        90 l~~EL~~~~~~L~~~P--Kny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dp-rNy~AW~~R~~vl~~l~~~~~eel~  166 (331)
T 3dss_A           90 VKAELGFLESCLRVNP--KSYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEELA  166 (331)
T ss_dssp             HHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCC--CCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHhCcCHHHHHH
Confidence            4556666666665444  45566665555555555  35666666666666554 555555555555555565 466666


Q ss_pred             HHHHHHhcCCCCCchhHHHHHHHHHhc--------------CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc----
Q 011236          336 MLEEWELSCYCYDFRVPNIILLGYSQK--------------GMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK----  397 (490)
Q Consensus       336 ~~~~~~~~~~~~~~~~~~~l~~~~~~~--------------g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~----  397 (490)
                      .++.+.+.. +-|...|+.....+.+.              +.++++++.+.+.+...+. |...|+-+-..+.+.    
T Consensus       167 ~~~~~I~~~-p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~P~-d~SaW~Y~r~ll~~~~~~~  244 (331)
T 3dss_A          167 FTDSLITRN-FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDPN-DQSAWFYHRWLLGAGSGRC  244 (331)
T ss_dssp             HHHHHHHHC-SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHSSSCGG
T ss_pred             HHHHHHHHC-CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhccCcc
Confidence            666666652 22444555444444433              4578888999998888766 888887666555554    


Q ss_pred             -------CCHHHHHHHHHHHHHhhhcCcCCCcch-hhHH---HHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHH
Q 011236          398 -------NNMEKAFECMKEALAVHEENKFWRPKP-SLVS---SILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTE  465 (490)
Q Consensus       398 -------~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~---~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~  465 (490)
                             +.++++++.++++++..       |+. ..+.   .+..+....|..+++...+.++.+.+|. ..-|..+..
T Consensus       245 ~~~~~~~~~l~~el~~~~elle~~-------pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~Dp~r~~~y~d~~~  317 (331)
T 3dss_A          245 ELSVEKSTVLQSELESCKELQELE-------PENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDLRS  317 (331)
T ss_dssp             GCCHHHHHHHHHHHHHHHHHHHHC-------TTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHCGGGHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHHHHhhC-------cccchHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCcchhhHHHHHHH
Confidence                   45789999999999843       554 1222   2222333568888999999999999998 777777665


Q ss_pred             HHH
Q 011236          466 AHI  468 (490)
Q Consensus       466 ~~~  468 (490)
                      .+.
T Consensus       318 ~~~  320 (331)
T 3dss_A          318 KFL  320 (331)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.87  E-value=3.3e-08  Score=82.40  Aligned_cols=102  Identities=9%  Similarity=-0.010  Sum_probs=47.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCC--CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKK----GKTP--TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP  424 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~----~~~p--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~  424 (490)
                      ++..+...|...|++++|...+++..+.    +..|  ....+..+...+...|++++|...+++++...........-.
T Consensus        68 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  147 (203)
T 3gw4_A           68 ALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIA  147 (203)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHH
Confidence            3444455555555555555555554432    1010  122345555555556666666666655554221111111111


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      .++..+...+...|++++|...+++..+
T Consensus       148 ~~~~~la~~~~~~g~~~~A~~~~~~al~  175 (203)
T 3gw4_A          148 CAFRGLGDLAQQEKNLLEAQQHWLRARD  175 (203)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            2344555555566666666665555444

>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=98.85  E-value=1.2e-06  Score=78.02  Aligned_cols=174  Identities=10%  Similarity=0.014  Sum_probs=115.4

Q ss_pred             HhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhc-CHHHHHHHHHHccccCC-ChhHHHHHHHHHHhc-C-ChhH
Q 011236           80 RSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVR-GLESAETYFNSLNDEDK-VDKLYGALLNCYVRE-G-LVDE  155 (490)
Q Consensus        80 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~-g-~~~~  155 (490)
                      .+.+..++|+++++.++..+ +-+...++.--.++...| .+++++.+++.+....| +..+|+.-...+.+. + ++++
T Consensus        65 ~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~~~  143 (349)
T 3q7a_A           65 AKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDPVS  143 (349)
T ss_dssp             HTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCCHH
T ss_pred             HhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCChHH
Confidence            34445568888888888887 345556666666666677 58888888888888877 677788777766666 6 7888


Q ss_pred             HHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcC--------cHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC-----
Q 011236          156 SLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHE--------KIPDVLLDMKENGVPPDNFSYRICINSYGARSE-----  222 (490)
Q Consensus       156 a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~--------~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~-----  222 (490)
                      ++++++.+.+...+ |..+|+--.-.+.+.|.++        ++++.++++.+..+ -|...|+.....+.+.+.     
T Consensus       144 EL~~~~k~L~~dpk-Ny~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~~lL~~l~~~~~~~  221 (349)
T 3q7a_A          144 EIEYIHGSLLPDPK-NYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRWYLRVSRPGAETSS  221 (349)
T ss_dssp             HHHHHHHHTSSCTT-CHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHTTSTTCCCCH
T ss_pred             HHHHHHHHHHhCCC-CHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccccch
Confidence            88888888887655 6777766555555555555        67777777776543 355666666666555554     


Q ss_pred             --hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCC
Q 011236          223 --LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGL  258 (490)
Q Consensus       223 --~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~  258 (490)
                        ++++++.++++. ..++ -|...|+.+-..+.+.|.
T Consensus       222 ~~~~eELe~~~~aI-~~~P-~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          222 RSLQDELIYILKSI-HLIP-HNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             HHHHHHHHHHHHHH-HHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHH-HhCC-CCHHHHHHHHHHHHhcCC
Confidence              456666666655 3343 455555555555544443

>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=98.82  E-value=4.3e-07  Score=76.20  Aligned_cols=125  Identities=16%  Similarity=-0.009  Sum_probs=70.4

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI  327 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  327 (490)
                      .+...+...|++++|+..|++..    . ++...+..+..++...|++++|...|++.....+ .+...+..+..++...
T Consensus        11 ~~g~~~~~~~~~~~A~~~~~~a~----~-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~-~~~~~~~~lg~~~~~~   84 (213)
T 1hh8_A           11 NEGVLAADKKDWKGALDAFSAVQ----D-PHSRICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQRGMLYYQT   84 (213)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHTSS----S-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHc----C-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-cchHHHHHHHHHHHHc
Confidence            34445555555555555555542    2 4455555555555555666666655555555443 3445555555555566


Q ss_pred             CCHHHHHHHHHHHHhcCCCCCc----------------hhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011236          328 GELEEAEKMLEEWELSCYCYDF----------------RVPNIILLGYSQKGMIEKADAVLKEIVKKG  379 (490)
Q Consensus       328 ~~~~~a~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  379 (490)
                      |++++|...+++..+... .+.                ..+..+..+|.+.|++++|...|++..+..
T Consensus        85 ~~~~~A~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           85 EKYDLAIKDLKEALIQLR-GNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             TCHHHHHHHHHHHHHTTT-TCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             ccHHHHHHHHHHHHHhCC-CccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            666666666655555311 111                455666666777777777777777776654

>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=98.81  E-value=2.5e-06  Score=75.98  Aligned_cols=220  Identities=7%  Similarity=-0.024  Sum_probs=116.8

Q ss_pred             CChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcC-CcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhcc-C-ChHHHH
Q 011236          151 GLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTG-QHEKIPDVLLDMKENGVPPDNFSYRICINSYGAR-S-ELSSME  227 (490)
Q Consensus       151 g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-g-~~~~a~  227 (490)
                      +..++|+++++++...++. +..+|+.--..+...| .+++++++++.+.....+ +..+|+.-..++... + ++++++
T Consensus        68 e~se~AL~lt~~~L~~nP~-~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPK-ny~aW~hR~wlL~~l~~~~~~~EL  145 (349)
T 3q7a_A           68 EKSERALELTEIIVRMNPA-HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLK-SYQVWHHRLLLLDRISPQDPVSEI  145 (349)
T ss_dssp             CCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCC-CHHHHHHHHHHHHHHCCSCCHHHH
T ss_pred             CCCHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHhcCCChHHHH
Confidence            3344555555555555433 3444554444444445 355566666555554321 333444333333333 3 556666


Q ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHH--------HHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCC-----
Q 011236          228 NVLQEMESQSHISMDWGTYSTVANYYIIAGLKE--------KAIIYLKKCEDIVSKSKDALGYNHLISHYASLGN-----  294 (490)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~--------~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-----  294 (490)
                      ++++++. +.+. -+-.+|+.-..++.+.|.++        ++++.++++.+..+  .|..+|+.....+.+.++     
T Consensus       146 ~~~~k~L-~~dp-kNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp--~N~SAW~~R~~lL~~l~~~~~~~  221 (349)
T 3q7a_A          146 EYIHGSL-LPDP-KNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG--RNNSAWGWRWYLRVSRPGAETSS  221 (349)
T ss_dssp             HHHHHHT-SSCT-TCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHTTSTTCCCCH
T ss_pred             HHHHHHH-HhCC-CCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC--CCHHHHHHHHHHHHhccccccch
Confidence            6666666 4444 45555555444444444444        67777777776555  567777777766666665     


Q ss_pred             --hhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCH--------------------HHHHHHHHHHHhcC-----CCC
Q 011236          295 --KDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGEL--------------------EEAEKMLEEWELSC-----YCY  347 (490)
Q Consensus       295 --~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------------------~~a~~~~~~~~~~~-----~~~  347 (490)
                        ++++++.+++.+...+ -|...|+.+-..+.+.|..                    ........++...+     ..+
T Consensus       222 ~~~~eELe~~~~aI~~~P-~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  300 (349)
T 3q7a_A          222 RSLQDELIYILKSIHLIP-HNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLP  300 (349)
T ss_dssp             HHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSC
T ss_pred             HHHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCC
Confidence              5667777776666655 5666666655555554432                    12222222222111     023


Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 011236          348 DFRVPNIILLGYSQKGMIEKADAVLKEIVK  377 (490)
Q Consensus       348 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  377 (490)
                      +......|++.|...|+.++|.++++.+.+
T Consensus       301 s~~al~~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          301 VPLALEYLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            444556666666666777777777766654

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.80  E-value=2e-07  Score=70.47  Aligned_cols=113  Identities=12%  Similarity=0.137  Sum_probs=63.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                      ..+..+...+...|++++|...++++.+..+. +..++..+...+...|++++|..+++++....      ..+..++..
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~------~~~~~~~~~   82 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-NAEAWYNLGNAYYKQGDYDEAIEYYQKALELD------PNNAEAWYN   82 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC------TTCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC------CccHHHHHH
Confidence            34455555556666666666666665554322 45555566666666666666666666665511      123345555


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHh
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIR  469 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~  469 (490)
                      +...+...|++++|...++++.+..|. ...+..+...+..
T Consensus        83 la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  123 (125)
T 1na0_A           83 LGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQK  123 (125)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHh
Confidence            556666666666666666666665555 5555555554443

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.79  E-value=2.1e-07  Score=70.61  Aligned_cols=96  Identities=11%  Similarity=-0.036  Sum_probs=67.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011236          315 RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       315 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~  394 (490)
                      ..+......|.+.|++++|.+.|++..+.. +.+...|..+..+|.+.|++++|+..|++.++.++. +...|..+..+|
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~   91 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSK-FIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhh-hhHHHHHHHHHH
Confidence            345556666777777777777777776652 335566677777777777777777777777776544 566777777777


Q ss_pred             hccCCHHHHHHHHHHHHH
Q 011236          395 ADKNNMEKAFECMKEALA  412 (490)
Q Consensus       395 ~~~~~~~~a~~~~~~~~~  412 (490)
                      ...|++++|++.|+++++
T Consensus        92 ~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           92 VAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHH
Confidence            777777777777777777

>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=98.79  E-value=5.3e-08  Score=85.78  Aligned_cols=194  Identities=12%  Similarity=-0.012  Sum_probs=127.4

Q ss_pred             CHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHH
Q 011236           68 SELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNC  146 (490)
Q Consensus        68 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~  146 (490)
                      +...+..+...+...|++++|+..|+...+.. +.++..+..+..++.+.|++++|...++......| +..++..+..+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~   81 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQC   81 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            55677788888889999999999999988876 45778888888899999999999999999888887 57788889999


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHH
Q 011236          147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSM  226 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a  226 (490)
                      +...|++++|+..|++..+.+.. +...+...+....+..   +. .-+......-.+.+......+...  ..|+.++|
T Consensus        82 ~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~~~~~~~~~~---~~-~~~~~~~~~~~~~~~~i~~~l~~l--~~~~~~~A  154 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYSLAKE-QRLNFGDDIPSALRIA---KK-KRWNSIEERRIHQESELHSYLTRL--IAAERERE  154 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHH-TTCCCCSHHHHHHHHH---HH-HHHHHHHHTCCCCCCHHHHHHHHH--HHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhCcc-chhhHHHHHHHHHHHH---HH-HHHHHHHHHHHhhhHHHHHHHHHH--HHHHHHHH
Confidence            99999999999999888765321 1111111111111111   11 112222333344444444433332  25788888


Q ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHHHHHHc-CCHHHHHHHHHHHhh
Q 011236          227 ENVLQEMESQSHISMDWGTYSTVANYYIIA-GLKEKAIIYLKKCED  271 (490)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~~-~~~~~a~~~~~~~~~  271 (490)
                      .+.+++.. +.+. .+......+...+.+. +.+++|.++|.++.+
T Consensus       155 ~~~~~~al-~~~p-~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          155 LEECQRNH-EGHE-DDGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HTTTSGGG-TTTS-CHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHhhh-cccc-chhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            88887776 4432 2233333344444444 567788888887655

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.79  E-value=1.2e-07  Score=74.29  Aligned_cols=95  Identities=17%  Similarity=0.099  Sum_probs=50.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHh
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYA  395 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~  395 (490)
                      .+..+...+.+.|++++|...|+++.... +.+...|..+..+|...|++++|+..|++..+..+. ++..|..+..+|.
T Consensus        38 ~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~-~~~~~~~lg~~~~  115 (151)
T 3gyz_A           38 DIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKN-DYTPVFHTGQCQL  115 (151)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSS-CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCC-CcHHHHHHHHHHH
Confidence            34444555555555555555555555541 223444555555555555555555555555554433 4445555555555


Q ss_pred             ccCCHHHHHHHHHHHHH
Q 011236          396 DKNNMEKAFECMKEALA  412 (490)
Q Consensus       396 ~~~~~~~a~~~~~~~~~  412 (490)
                      ..|++++|...|+++++
T Consensus       116 ~lg~~~eA~~~~~~al~  132 (151)
T 3gyz_A          116 RLKAPLKAKECFELVIQ  132 (151)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            55555555555555555

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.78  E-value=1.1e-07  Score=74.68  Aligned_cols=101  Identities=13%  Similarity=0.006  Sum_probs=90.0

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhh
Q 011236          348 DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSL  426 (490)
Q Consensus       348 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~  426 (490)
                      +...+..+...+.+.|++++|...|+++++..+. +...|..+..+|...|++++|+..|+++++.       .|+ +..
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~-~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l-------~P~~~~~  106 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFY-NVDYIMGLAAIYQIKEQFQQAADLYAVAFAL-------GKNDYTP  106 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------SSSCCHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHccHHHHHHHHHHHHhh-------CCCCcHH
Confidence            3446777888899999999999999999998765 8889999999999999999999999999983       354 478


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          427 VSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       427 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      |..+..++...|++++|...|+++.+..|+
T Consensus       107 ~~~lg~~~~~lg~~~eA~~~~~~al~l~~~  136 (151)
T 3gyz_A          107 VFHTGQCQLRLKAPLKAKECFELVIQHSND  136 (151)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            889999999999999999999999998876

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.77  E-value=2.1e-07  Score=71.32  Aligned_cols=115  Identities=12%  Similarity=-0.005  Sum_probs=71.6

Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHH
Q 011236          349 FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVS  428 (490)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~  428 (490)
                      ...+..+...+.+.|++++|...|++..+..+. +...+..+...+...|++++|...++++++..      ..+...+.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~------~~~~~~~~   88 (133)
T 2lni_A           16 ALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPK-DAKLYSNRAACYTKLLEFQLALKDCEECIQLE------PTFIKGYT   88 (133)
T ss_dssp             HHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTT-CHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC------TTCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC-cHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC------CCchHHHH
Confidence            344555666666666777777666666665433 55666666666667777777777777766622      12345566


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhc
Q 011236          429 SILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRS  470 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~  470 (490)
                      .+...+...|++++|.+.+++..+..|. ...+..+...+...
T Consensus        89 ~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  131 (133)
T 2lni_A           89 RKAAALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQ  131 (133)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHh
Confidence            6666666777777777777766666666 55666665555443

>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=98.77  E-value=3.8e-07  Score=73.02  Aligned_cols=130  Identities=8%  Similarity=-0.101  Sum_probs=74.7

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHH
Q 011236          280 LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGY  359 (490)
Q Consensus       280 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  359 (490)
                      ..+..+...+...|++++|...|+......+ .+...+..+...+...|++++|...+++..+.. +.+...+..+...+
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~   91 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELNP-SNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            3455555556666666666666665555443 345555666666666666666666666665542 22444556666666


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH--HHHhccCCHHHHHHHHHHHHH
Q 011236          360 SQKGMIEKADAVLKEIVKKGKTPTPNSWSIIA--AGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       360 ~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...|++++|...|++..+..+. +...+..+.  ..+...|++++|+..+.....
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~p~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVKPH-DKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            6666666666666666665433 344443222  235556666666666665544

>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=98.76  E-value=4.8e-07  Score=72.39  Aligned_cols=129  Identities=16%  Similarity=0.006  Sum_probs=84.0

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHH
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGS  323 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  323 (490)
                      ..+..+...+...|++++|...|++.....+  .+..++..+..++...|++++|...+++.....+ .+...+..+..+
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~--~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~a~~   90 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELNP--SNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHST--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhCC--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHH
Confidence            3455566667777777777777777666544  4566677777777777777777777776666654 455667777777


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCchhHHH--HHHHHHhcCCHHHHHHHHHHHH
Q 011236          324 LVKIGELEEAEKMLEEWELSCYCYDFRVPNI--ILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       324 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~--l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      +...|++++|...+++..+... .+...+..  .+..+...|++++|...+....
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~~p-~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKVKP-HDKDAKMKYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHST-TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHHHHHHHcccchH
Confidence            7777777777777777776522 23333322  3333566677777777776654

>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=98.76  E-value=1.3e-07  Score=76.96  Aligned_cols=119  Identities=8%  Similarity=0.003  Sum_probs=70.7

Q ss_pred             hcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHH-HHhcCCH--HH
Q 011236          291 SLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLG-YSQKGMI--EK  367 (490)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~--~~  367 (490)
                      ..|++++|...++......+ .+...+..+...|...|++++|...+++..+.. +.+...+..+... |...|++  ++
T Consensus        22 ~~~~~~~A~~~~~~al~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~   99 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRANP-QNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQ   99 (177)
T ss_dssp             -----CCCCHHHHHHHHHCC-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHH
T ss_pred             hccCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHH
Confidence            34566666666665555544 445566666666666666666666666666542 2244455555555 5566666  77


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          368 ADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       368 A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      |...++++.+..+. +...+..+...|...|++++|...|+++++
T Consensus       100 A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          100 TRAMIDKALALDSN-EITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCC-cHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            77777766665433 456666666667777777777777777666

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.75  E-value=2.6e-07  Score=76.82  Aligned_cols=121  Identities=12%  Similarity=0.057  Sum_probs=58.3

Q ss_pred             ccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC----CChhhHHHHHHHHHhcCC
Q 011236          219 ARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS----KDALGYNHLISHYASLGN  294 (490)
Q Consensus       219 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~~l~~~~~~~~~  294 (490)
                      ..|++++|.++++.+. . .......++..+...+...|++++|...+++........    ....++..+...+...|+
T Consensus         4 ~~g~~~~A~~~~~~~~-~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            4 EAHDYALAERQAQALL-A-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ---CHHHHHHHHHHHH-T-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             ccccHHHHHHHHHHhc-C-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            4566666666444443 2 222344555666666666666666666666655421110    123445555555666666


Q ss_pred             hhHHHHHHHHHHHhcC-CC-C----hhhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          295 KDEMMKFWGLQKIKCK-KQ-L----NRDYITMLGSLVKIGELEEAEKMLEEWE  341 (490)
Q Consensus       295 ~~~a~~~~~~~~~~~~-~~-~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~  341 (490)
                      +++|...+++...... .+ +    ...+..+...+...|++++|...+++..
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  134 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSL  134 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            6666666554443311 01 1    1224444444445555555555554443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.75  E-value=1.2e-06  Score=77.59  Aligned_cols=168  Identities=5%  Similarity=-0.154  Sum_probs=119.5

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC---CC--hh
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKD----ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKK---QL--NR  315 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~~--~~  315 (490)
                      .+...+..+...|++++|.+.+.+........++    ...+..+...+...|++++|+..+++.......   +.  ..
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            3444667778888888888888776654332011    122344556677788999999988877654321   11  34


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcC-CCCC-----chhHHHHHHHHHhcCCHHHHHHHHHHHHHcC----CCC-CH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSC-YCYD-----FRVPNIILLGYSQKGMIEKADAVLKEIVKKG----KTP-TP  384 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~----~~p-~~  384 (490)
                      +++.+...|...|++++|...+++..+.- ..|+     ..++..+...|...|++++|...+++.++..    ... -.
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            77888889999999999999998887320 1122     2577888899999999999999999886532    111 15


Q ss_pred             HHHHHHHHHHhccCCHHHH-HHHHHHHHH
Q 011236          385 NSWSIIAAGYADKNNMEKA-FECMKEALA  412 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a-~~~~~~~~~  412 (490)
                      .+|..+...|.+.|++++| ...+++++.
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            6788999999999999999 788888876

>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=98.74  E-value=3.5e-07  Score=69.60  Aligned_cols=106  Identities=10%  Similarity=0.043  Sum_probs=65.9

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSS  429 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~  429 (490)
                      .+..+...+.+.|++++|+..|++.++..+. +...|..+..+|.+.|++++|++.++++++..|+.....+.. .+|..
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~-~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELDPS-NITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            3445666677777777777777777766544 566677777777777777777777777766443221111111 35556


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccch
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQKR  457 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~~  457 (490)
                      +..++...|++++|.+.|++..+..|.+
T Consensus        89 lg~~~~~~~~~~~A~~~~~kal~~~~~~  116 (127)
T 4gcn_A           89 AGNAFQKQNDLSLAVQWFHRSLSEFRDP  116 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSCCH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhhCcCH
Confidence            6666677777777777777766655543

>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=98.74  E-value=5.2e-08  Score=85.82  Aligned_cols=195  Identities=9%  Similarity=-0.041  Sum_probs=114.3

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHH
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHL  285 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l  285 (490)
                      +...+..+...+...|++++|...|++.. .... .+...|..+..+|...|++++|+..+++.....+  .+...+..+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al-~~~p-~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~l   78 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAI-TRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALELDG--QSVKAHFFL   78 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCT--TCHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC--CCHHHHHHH
Confidence            44556667777777778888888777776 3333 3566777777778888888888888877776554  466777777


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCH
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMI  365 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  365 (490)
                      ..++...|++++|...|+......+ .+...+...+....+.   ..+. -+........+.+......+.. + ..|+.
T Consensus        79 g~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~~~i~~~l~~-l-~~~~~  151 (281)
T 2c2l_A           79 GQCQLEMESYDEAIANLQRAYSLAK-EQRLNFGDDIPSALRI---AKKK-RWNSIEERRIHQESELHSYLTR-L-IAAER  151 (281)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHH-HTTCCCCSHHHHHHHH---HHHH-HHHHHHHTCCCCCCHHHHHHHH-H-HHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCc-cchhhHHHHHHHHHHH---HHHH-HHHHHHHHHHhhhHHHHHHHHH-H-HHHHH
Confidence            7778888888888888777666543 1111111111111111   1111 1122222324444444443322 2 26788


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc-CCHHHHHHHHHHHHH
Q 011236          366 EKADAVLKEIVKKGKTPTPNSWSIIAAGYADK-NNMEKAFECMKEALA  412 (490)
Q Consensus       366 ~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~  412 (490)
                      ++|.+.++...+..+. +......+...+.+. +.+++|.++|.++.+
T Consensus       152 ~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          152 ERELEECQRNHEGHED-DGHIRAQQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             HHHHTTTSGGGTTTSC-HHHHTHHHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHhhhccccc-hhhhhhHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            8888888777765321 333334444444444 567788888877755

>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=98.72  E-value=4.1e-08  Score=88.95  Aligned_cols=132  Identities=6%  Similarity=-0.130  Sum_probs=86.3

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC--------------hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcC
Q 011236          279 ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL--------------NRDYITMLGSLVKIGELEEAEKMLEEWELSC  344 (490)
Q Consensus       279 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  344 (490)
                      ...+..+...+.+.|++++|...|++.....+...              ...|..+..++.+.|++++|...+++..+..
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  226 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD  226 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            33444444555555555555555554444433111              3567777777777888888888887777752


Q ss_pred             CCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHH-HHHHHHHHH
Q 011236          345 YCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKA-FECMKEALA  412 (490)
Q Consensus       345 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a-~~~~~~~~~  412 (490)
                       +.+...+..+..+|...|++++|...|++.++..+. +...+..+...+.+.|+.++| ...++.|..
T Consensus       227 -p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~~  293 (336)
T 1p5q_A          227 -SNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPN-NKAAKTQLAVCQQRIRRQLAREKKLYANMFE  293 (336)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             335666777777788888888888888888776544 666777777777777777777 456666654

>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=9.6e-08  Score=74.97  Aligned_cols=98  Identities=11%  Similarity=0.053  Sum_probs=51.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSS  429 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~  429 (490)
                      .+..+...+.+.|++++|...|++....++. +...|..+..+|...|++++|+..|++++..       .| +...+..
T Consensus        23 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l-------~p~~~~~~~~   94 (148)
T 2vgx_A           23 QLYSLAFNQYQSGXYEDAHXVFQALCVLDHY-DSRFFLGLGACRQAMGQYDLAIHSYSYGAVM-------DIXEPRFPFH   94 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------STTCTHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHcCcc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-------CCCCchHHHH
Confidence            3444445555555555555555555554433 4555555555555555555555555555551       12 2244455


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      +..++...|++++|...|++..+..|.
T Consensus        95 lg~~~~~~g~~~~A~~~~~~al~~~p~  121 (148)
T 2vgx_A           95 AAECLLQXGELAEAESGLFLAQELIAN  121 (148)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence            555555555555555555555554443

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.71  E-value=6.1e-07  Score=67.66  Aligned_cols=96  Identities=13%  Similarity=0.093  Sum_probs=45.1

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHH
Q 011236          281 GYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYS  360 (490)
Q Consensus       281 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  360 (490)
                      .+..+...+...|++++|...++++....+ .+...+..+...+...|++++|...++++.+.. +.+..++..+...|.
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~   88 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDP-NNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCc-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHH
Confidence            344444444444555555554444444332 233444444444445555555555555444431 223334444555555


Q ss_pred             hcCCHHHHHHHHHHHHHc
Q 011236          361 QKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       361 ~~g~~~~A~~~~~~m~~~  378 (490)
                      ..|++++|...++++.+.
T Consensus        89 ~~~~~~~A~~~~~~~~~~  106 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALEL  106 (125)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHHh
Confidence            555555555555555544

>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=98.69  E-value=4.1e-08  Score=88.92  Aligned_cols=152  Identities=9%  Similarity=-0.030  Sum_probs=119.0

Q ss_pred             cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC--------------chhHHHHHH
Q 011236          292 LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD--------------FRVPNIILL  357 (490)
Q Consensus       292 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--------------~~~~~~l~~  357 (490)
                      .+++++|...|+......+ .+...+..+...+.+.|++++|...|++..+......              ...|..+..
T Consensus       126 L~~~~~A~~~~~~a~~~~p-~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~  204 (336)
T 1p5q_A          126 LKSFEKAKESWEMNSEEKL-EQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAM  204 (336)
T ss_dssp             EEEEECCCCGGGCCHHHHH-HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHH
T ss_pred             EeecccccchhcCCHHHHH-HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHH
Confidence            3455566665554333322 3456788899999999999999999999998633221              378888999


Q ss_pred             HHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHc
Q 011236          358 GYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGD  436 (490)
Q Consensus       358 ~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~  436 (490)
                      +|.+.|++++|+..+++.++..+. +...|..+..+|...|++++|+..|+++++.       .|+ ...+..+..++.+
T Consensus       205 ~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l-------~P~~~~a~~~l~~~~~~  276 (336)
T 1p5q_A          205 CHLKLQAFSAAIESCNKALELDSN-NEKGLSRRGEAHLAVNDFELARADFQKVLQL-------YPNNKAAKTQLAVCQQR  276 (336)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CSSCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-------CCCCHHHHHHHHHHHHH
Confidence            999999999999999999998655 7889999999999999999999999999983       344 4678888888888


Q ss_pred             CCCHHHH-HHHHHHHHh
Q 011236          437 NRDVEEV-EAFVSSLKI  452 (490)
Q Consensus       437 ~g~~~~a-~~~~~~~~~  452 (490)
                      .|+.++| ...++.|..
T Consensus       277 ~~~~~~a~~~~~~~~~~  293 (336)
T 1p5q_A          277 IRRQLAREKKLYANMFE  293 (336)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            9999888 446665544

>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=98.69  E-value=3.6e-07  Score=74.23  Aligned_cols=120  Identities=8%  Similarity=0.073  Sum_probs=67.9

Q ss_pred             ccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHH-HHhcCCh--
Q 011236          219 ARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISH-YASLGNK--  295 (490)
Q Consensus       219 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~~--  295 (490)
                      ..|++++|...+++.. .... .+...+..+..+|...|++++|+..|++.....+  .+...+..+..+ +...|++  
T Consensus        22 ~~~~~~~A~~~~~~al-~~~p-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~la~~l~~~~~~~~~   97 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKI-RANP-QNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRG--ENAELYAALATVLYYQASQHMT   97 (177)
T ss_dssp             -----CCCCHHHHHHH-HHCC-SCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHC--SCHHHHHHHHHHHHHHTTTCCC
T ss_pred             hccCHHHHHHHHHHHH-HhCC-CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC--CCHHHHHHHHHHHHHhcCCcch
Confidence            4555666666666554 3222 3455566666666666666666666666665544  355555555555 5566665  


Q ss_pred             hHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc
Q 011236          296 DEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELS  343 (490)
Q Consensus       296 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  343 (490)
                      ++|...++......+ .+...+..+...+...|++++|...++++.+.
T Consensus        98 ~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           98 AQTRAMIDKALALDS-NEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            666666666655544 34455556666666666666666666666654

>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=98.68  E-value=1e-07  Score=74.74  Aligned_cols=100  Identities=12%  Similarity=-0.068  Sum_probs=70.1

Q ss_pred             ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011236          313 LNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAA  392 (490)
Q Consensus       313 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~  392 (490)
                      +...+..+...+...|++++|...|+...... +.+...|..+..+|...|++++|...|++.+..++. +...|..+..
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~-~~~~~~~lg~   97 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIX-EPRFPFHAAE   97 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CchHHHHHHH
Confidence            33455566667777777777777777776652 235566677777777777777777777777776544 5667777777


Q ss_pred             HHhccCCHHHHHHHHHHHHHhh
Q 011236          393 GYADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       393 ~~~~~~~~~~a~~~~~~~~~~~  414 (490)
                      +|...|++++|...|+++++..
T Consensus        98 ~~~~~g~~~~A~~~~~~al~~~  119 (148)
T 2vgx_A           98 CLLQXGELAEAESGLFLAQELI  119 (148)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC
Confidence            7777788888888887777733

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.68  E-value=5.8e-07  Score=68.43  Aligned_cols=113  Identities=12%  Similarity=-0.016  Sum_probs=54.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSI  430 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l  430 (490)
                      .+..+...+...|++++|...+++..+..+. +...+..+...+...|++++|...+++++...      ..+...+..+
T Consensus        14 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~------~~~~~~~~~~   86 (131)
T 2vyi_A           14 RLKTEGNEQMKVENFEAAVHFYGKAIELNPA-NAVYFCNRAAAYSKLGNYAGAVQDCERAICID------PAYSKAYGRM   86 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC------TTCHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC------ccCHHHHHHH
Confidence            3344444445555555555555555444322 34445555555555555555555555555411      1123444444


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhc
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRS  470 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~  470 (490)
                      ...+...|++++|...+++..+..|. ...+..+..++.+.
T Consensus        87 ~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~  127 (131)
T 2vyi_A           87 GLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKL  127 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHH
Confidence            45555555555555555555555444 44444444444443

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.67  E-value=9.4e-07  Score=67.57  Aligned_cols=97  Identities=13%  Similarity=-0.015  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHH
Q 011236          243 WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLG  322 (490)
Q Consensus       243 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  322 (490)
                      ...+..+...+...|++++|...|++.....+  .+...+..+..++...|++++|...+++.....+ .+...+..+..
T Consensus        16 ~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~--~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~la~   92 (133)
T 2lni_A           16 ALMVKNKGNECFQKGDYPQAMKHYTEAIKRNP--KDAKLYSNRAACYTKLLEFQLALKDCEECIQLEP-TFIKGYTRKAA   92 (133)
T ss_dssp             HHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCT--TCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCC--CcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CchHHHHHHHH
Confidence            33444444444444444444444444443322  2334444444444444444444444444444332 23334444444


Q ss_pred             HHHhcCCHHHHHHHHHHHHh
Q 011236          323 SLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       323 ~~~~~~~~~~a~~~~~~~~~  342 (490)
                      ++.+.|++++|.+.+++..+
T Consensus        93 ~~~~~~~~~~A~~~~~~~~~  112 (133)
T 2lni_A           93 ALEAMKDYTKAMDVYQKALD  112 (133)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHH
Confidence            44444444444444444443

>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=98.66  E-value=4.9e-07  Score=68.63  Aligned_cols=94  Identities=14%  Similarity=0.059  Sum_probs=44.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHH
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSIL  431 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~  431 (490)
                      ..+...+.+.|++++|...|++.++..+. +...|..+..+|.+.|++++|+..++++++.       .|+ ...+..+.
T Consensus         8 ~~~g~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~-------~p~~~~~~~~lg   79 (126)
T 3upv_A            8 RLEGKEYFTKSDWPNAVKAYTEMIKRAPE-DARGYSNRAAALAKLMSFPEAIADCNKAIEK-------DPNFVRAYIRKA   79 (126)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------CTTCHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHHHhCCC-ChHHHHHHHHHHHHhcCHHHHHHHHHHHHHh-------CCCcHHHHHHHH
Confidence            33444444455555555555555444332 4444555555555555555555555555441       122 23444444


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhcc
Q 011236          432 DWLGDNRDVEEVEAFVSSLKIKV  454 (490)
Q Consensus       432 ~~~~~~g~~~~a~~~~~~~~~~~  454 (490)
                      .++...|++++|...+++..+..
T Consensus        80 ~~~~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           80 TAQIAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCHHHHHHHHHHHHHhC
Confidence            45555555555555555554444

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.66  E-value=6.9e-07  Score=68.02  Aligned_cols=116  Identities=11%  Similarity=-0.062  Sum_probs=58.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHH
Q 011236          280 LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGY  359 (490)
Q Consensus       280 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  359 (490)
                      ..+..+...+...|++++|...+++.....+ .+...+..+...+...|++++|...+++..+.. +.+...+..+...|
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~   90 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELNP-ANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLAL   90 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHH
Confidence            3444455555555555555555555444433 334445555555555555555555555555431 22334455555555


Q ss_pred             HhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC
Q 011236          360 SQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKN  398 (490)
Q Consensus       360 ~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~  398 (490)
                      ...|++++|...|++..+..+. +...+..+...+...|
T Consensus        91 ~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~l~~~~~~~~  128 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKALELDPD-NETYKSNLKIAELKLR  128 (131)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHT
T ss_pred             HHhCCHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHh
Confidence            5555555555555555554332 4444444544444444

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.65  E-value=1.7e-07  Score=80.56  Aligned_cols=187  Identities=11%  Similarity=-0.011  Sum_probs=89.0

Q ss_pred             hhcCHHHHHHHHHHccccCC-ChhHHHHH-------HHHHHhcCChhHHHHHHHHHHhcCCCCCcc--------------
Q 011236          116 KVRGLESAETYFNSLNDEDK-VDKLYGAL-------LNCYVREGLVDESLSLMQKMKEMGSFGSAL--------------  173 (490)
Q Consensus       116 ~~~~~~~A~~~~~~~~~~~p-~~~~~~~l-------i~~~~~~g~~~~a~~~~~~m~~~~~~p~~~--------------  173 (490)
                      ..++...|.+.|.++...+| ....|..+       ...+.+.++..+++..+..-.+  +.|+..              
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            46778888888888887777 36677766       3455555555555444443333  222110              


Q ss_pred             --------hHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC--H
Q 011236          174 --------NYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMD--W  243 (490)
Q Consensus       174 --------~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~  243 (490)
                              .+-.+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+... ... .|.  .
T Consensus        96 ~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~-~~~-d~~~~~  171 (282)
T 4f3v_A           96 YPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAG-KWP-DKFLAG  171 (282)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGG-GCS-CHHHHH
T ss_pred             cccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhh-ccC-CcccHH
Confidence                    11223334445555555555555544422  222233333344555555555555554333 111 010  1


Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCC--ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhc
Q 011236          244 GTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSK--DALGYNHLISHYASLGNKDEMMKFWGLQKIKC  309 (490)
Q Consensus       244 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  309 (490)
                      ..+..+..++...|++++|+..|++....... |  ..........++.+.|+.++|..+|+++....
T Consensus       172 ~a~~~LG~al~~LG~~~eAl~~l~~a~~g~~~-P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~  238 (282)
T 4f3v_A          172 AAGVAHGVAAANLALFTEAERRLTEANDSPAG-EACARAIAWYLAMARRSQGNESAAVALLEWLQTTH  238 (282)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTSTTT-TTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCC-ccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            23344455555555555555555554422110 1  22233444444555555555555555554443

>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=98.62  E-value=1.2e-06  Score=65.17  Aligned_cols=107  Identities=17%  Similarity=0.008  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSI  430 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l  430 (490)
                      .+..+...+...|++++|...|++..+..+. +...+..+...+...|++++|...++++.+..      +.+...+..+
T Consensus         6 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~------~~~~~~~~~~   78 (118)
T 1elw_A            6 ELKEKGNKALSVGNIDDALQCYSEAIKLDPH-NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK------PDWGKGYSRK   78 (118)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC------TTCHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC------cccHHHHHHH
Confidence            3444555555566666666666655554332 45555555556666666666666666665511      1123455555


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHH
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALT  464 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~  464 (490)
                      ..++...|++++|...+++..+..|. ...+..+.
T Consensus        79 a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~  113 (118)
T 1elw_A           79 AAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQ  113 (118)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            55566666666666666666655555 44444433

>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=98.62  E-value=1.4e-06  Score=66.09  Aligned_cols=98  Identities=12%  Similarity=-0.034  Sum_probs=76.2

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011236          315 RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       315 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~  394 (490)
                      ..+..+...+.+.|++++|...|++..+.. +.+...|..+..+|.+.|++++|+..+++.++.++. +...|..+..++
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~   82 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN-FVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHH
Confidence            456666777778888888888888877752 335667778888888888888888888888887654 677888888888


Q ss_pred             hccCCHHHHHHHHHHHHHhh
Q 011236          395 ADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       395 ~~~~~~~~a~~~~~~~~~~~  414 (490)
                      ...|++++|...|+++++..
T Consensus        83 ~~~~~~~~A~~~~~~al~~~  102 (126)
T 3upv_A           83 IAVKEYASALETLDAARTKD  102 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHhC
Confidence            88888888888888888743

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.61  E-value=3e-07  Score=79.10  Aligned_cols=131  Identities=11%  Similarity=-0.036  Sum_probs=76.8

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC--HHHHHHHHHHHh
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT--PNSWSIIAAGYA  395 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~--~~~~~~l~~~~~  395 (490)
                      ..+...+...|++++|.++|+.+...+  |+......+...+.+.+++++|+..|+...... .|.  ...+..+..++.
T Consensus       106 LayA~~L~~~g~y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~a~~~LG~al~  182 (282)
T 4f3v_A          106 MGFAACEAAQGNYADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGAAGVAHGVAAA  182 (282)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHHHHHHHHHHHH
Confidence            344555666777777777776665532  222244444556667777777777776443321 110  225666666777


Q ss_pred             ccCCHHHHHHHHHHHHHhhhcCcCCCcc--hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          396 DKNNMEKAFECMKEALAVHEENKFWRPK--PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       396 ~~~~~~~a~~~~~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..|++++|+..|+++..     ....|.  .........++.+.|+.++|..+|+++....|.
T Consensus       183 ~LG~~~eAl~~l~~a~~-----g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~  240 (282)
T 4f3v_A          183 NLALFTEAERRLTEAND-----SPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE  240 (282)
T ss_dssp             HTTCHHHHHHHHHHHHT-----STTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC
T ss_pred             HCCCHHHHHHHHHHHhc-----CCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc
Confidence            77777777777777664     222132  234555556666777777777777777766665

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.60  E-value=9.5e-07  Score=68.69  Aligned_cols=94  Identities=15%  Similarity=0.001  Sum_probs=44.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      +..+...+.+.|++++|...|+...... +.+...|..+..+|.+.|++++|...|++.++.++. +...|..+..+|..
T Consensus        21 ~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~   98 (142)
T 2xcb_A           21 LYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDIN-EPRFPFHAAECHLQ   98 (142)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCC-CcHHHHHHHHHHHH
Confidence            3334444444555555555555544431 123334444444455555555555555555444332 34444444455555


Q ss_pred             cCCHHHHHHHHHHHHH
Q 011236          397 KNNMEKAFECMKEALA  412 (490)
Q Consensus       397 ~~~~~~a~~~~~~~~~  412 (490)
                      .|++++|...|+++++
T Consensus        99 ~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           99 LGDLDGAESGFYSARA  114 (142)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            5555555555555444

>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=98.60  E-value=2.2e-05  Score=69.59  Aligned_cols=218  Identities=11%  Similarity=-0.012  Sum_probs=152.9

Q ss_pred             HcCCHH-HHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCC----------hhHHHHHHHHHHHhcCCCChhhHHHHHHH
Q 011236          255 IAGLKE-KAIIYLKKCEDIVSKSKDALGYNHLISHYASLGN----------KDEMMKFWGLQKIKCKKQLNRDYITMLGS  323 (490)
Q Consensus       255 ~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  323 (490)
                      +.|.++ +|+..++.+....+  .+..+|+.--..+...+.          +++++.+++.+....+ -+..+|+.-...
T Consensus        41 ~~~e~s~eaL~~t~~~L~~nP--~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~P-Kny~aW~hR~wl  117 (331)
T 3dss_A           41 QAGELDESVLELTSQILGANP--DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNP-KSYGTWHHRCWL  117 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTCT--TCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHCc--hhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCC-CCHHHHHHHHHH
Confidence            344433 56666666666554  344445443333332222          5788899998888776 677788877777


Q ss_pred             HHhcC--CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC-HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc---
Q 011236          324 LVKIG--ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM-IEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK---  397 (490)
Q Consensus       324 ~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~---  397 (490)
                      +.+.+  +++++..+++.+.+.. +-|...|+.-...+...|. ++++++.++++++.++. |...|+.....+.+.   
T Consensus       118 L~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~-N~SAW~~R~~ll~~l~~~  195 (331)
T 3dss_A          118 LSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFS-NYSSWHYRSCLLPQLHPQ  195 (331)
T ss_dssp             HHHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSC-CHHHHHHHHHHHHHHSCC
T ss_pred             HhccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHhhhc
Confidence            77777  4899999999999873 3477788877777788888 69999999999999877 888888777766554   


Q ss_pred             -----------CCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcC-----------CCHHHHHHHHHHHHhcc
Q 011236          398 -----------NNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDN-----------RDVEEVEAFVSSLKIKV  454 (490)
Q Consensus       398 -----------~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~-----------g~~~~a~~~~~~~~~~~  454 (490)
                                 +.++++++++++++.       ..|+. ..|+-+-..+.+.           +.++++.+.++++.+..
T Consensus       196 ~~~~~~~~~~~~~~~eEle~~~~ai~-------~~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~  268 (331)
T 3dss_A          196 PDSGPQGRLPENVLLKELELVQNAFF-------TDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELE  268 (331)
T ss_dssp             C------CCCHHHHHHHHHHHHHHHH-------HSTTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cccccccccchHHHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhC
Confidence                       458899999999998       33544 5565554555544           45789999999999999


Q ss_pred             cc-hhhhHHHHH---HHHhcC--CcHHHHHHHHHhC
Q 011236          455 QK-RNMYHALTE---AHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       455 ~~-~~~~~~l~~---~~~~~g--~~a~~~~~~m~~~  484 (490)
                      |. .-.+..++.   +....|  +++..++.++.+.
T Consensus       269 pd~~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          269 PENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             cccchHHHHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence            88 333333322   222344  6788888888763

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.59  E-value=1.3e-06  Score=64.41  Aligned_cols=101  Identities=11%  Similarity=0.092  Sum_probs=76.5

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc---ch
Q 011236          348 DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP---KP  424 (490)
Q Consensus       348 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p---~~  424 (490)
                      +...+..+...+...|++++|...+++..+..+. +...|..+...+...|++++|...++++++.       .|   +.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~-------~~~~~~~   76 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPE-ESKYWLMKGKALYNLERYEEAVDCYNYVINV-------IEDEYNK   76 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-------SCCTTCH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcC-CHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-------CcccchH
Confidence            4456677777788888888888888888776544 6677778888888888888888888888772       23   35


Q ss_pred             hhHHHHHHHHHcC-CCHHHHHHHHHHHHhcccc
Q 011236          425 SLVSSILDWLGDN-RDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       425 ~~~~~l~~~~~~~-g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..+..+...+... |++++|.+.+++.....|.
T Consensus        77 ~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~p~  109 (112)
T 2kck_A           77 DVWAAKADALRYIEGKEVEAEIAEARAKLEHHH  109 (112)
T ss_dssp             HHHHHHHHHHTTCSSCSHHHHHHHHHHGGGCCC
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHhhcccC
Confidence            6777777888888 8888888888888777664

>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=98.58  E-value=9.2e-08  Score=79.43  Aligned_cols=128  Identities=11%  Similarity=-0.041  Sum_probs=83.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC---------------CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhc
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKTP---------------TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEE  416 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p---------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  416 (490)
                      +..+...+...|++++|...|++.++....-               ...+|..+..+|...|++++|+..++++++..  
T Consensus        41 ~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~--  118 (198)
T 2fbn_A           41 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID--  118 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC--
Confidence            3334444555555555555555555432210               13678888888999999999999999998832  


Q ss_pred             CcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHH-HHHHHHHhCC
Q 011236          417 NKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVD-GLLESMKADD  485 (490)
Q Consensus       417 ~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~-~~~~~m~~~~  485 (490)
                          ..+...+..+..++...|++++|...|++..+..|. ..++..+...+...+  +++. ..+..|...+
T Consensus       119 ----p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          119 ----KNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             ----TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHC-------------
T ss_pred             ----cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence                134577888888889999999999999999988888 888888888888777  4444 5556665544

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.57  E-value=2.5e-05  Score=73.37  Aligned_cols=200  Identities=9%  Similarity=0.025  Sum_probs=132.2

Q ss_pred             HHHhccCChHHHHHHHHHHHhCCCCCCC---------------HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh
Q 011236          215 NSYGARSELSSMENVLQEMESQSHISMD---------------WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA  279 (490)
Q Consensus       215 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~---------------~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  279 (490)
                      ..+.+.|++++|++.|..+.....-..+               ...+..+...|...|++++|.+.+..+.......++.
T Consensus        12 ~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~   91 (434)
T 4b4t_Q           12 RRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKS   91 (434)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccch
Confidence            3455667777777777766522111111               1235668888899999999998888876543321222


Q ss_pred             ----hhHHHHHHHHHhcCChhHHHHHHHHHHHhcC----C-CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC---
Q 011236          280 ----LGYNHLISHYASLGNKDEMMKFWGLQKIKCK----K-QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY---  347 (490)
Q Consensus       280 ----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~----~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~---  347 (490)
                          .+.+.+...+...|+.+.+..++........    . .-..++..+...+...|++++|..+++++...-...   
T Consensus        92 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~  171 (434)
T 4b4t_Q           92 KTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDK  171 (434)
T ss_dssp             HHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCS
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccc
Confidence                2233344444557888888888886654322    1 123467788888999999999999998876542111   


Q ss_pred             --CchhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CC-CC-C--HHHHHHHHHHHhccCCHHHHHHHHHHHHHhh
Q 011236          348 --DFRVPNIILLGYSQKGMIEKADAVLKEIVKK--GK-TP-T--PNSWSIIAAGYADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       348 --~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~--~~-~p-~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  414 (490)
                        ...++..++..|...|++++|..++++....  .. .| .  ...+..+...+...+++++|...|.++.+..
T Consensus       172 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~~~  246 (434)
T 4b4t_Q          172 PSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFESY  246 (434)
T ss_dssp             THHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh
Confidence              1346778888899999999999998887642  11 11 1  2456777778888999999999888887633

>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=98.57  E-value=1.8e-07  Score=77.70  Aligned_cols=149  Identities=6%  Similarity=-0.118  Sum_probs=78.2

Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC---------------hhh
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL---------------NRD  316 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---------------~~~  316 (490)
                      .....|+++++.+.++.-.....  .....+..+...+...|++++|...|++.....+...               ...
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~   90 (198)
T 2fbn_A           13 GRENLYFQGAKKSIYDYTDEEKV--QSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISC   90 (198)
T ss_dssp             ---------CCCSGGGCCHHHHH--HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHH
T ss_pred             hhhhhhhccccCchhhCCHHHHH--HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHH
Confidence            33444455555444443222111  2334455556666666666666666666555433111               245


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      +..+..++...|++++|...++...+. .+.+...+..+..+|...|++++|...|++..+..+. +...+..+..++..
T Consensus        91 ~~~la~~~~~~~~~~~A~~~~~~al~~-~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~  168 (198)
T 2fbn_A           91 NLNLATCYNKNKDYPKAIDHASKVLKI-DKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPN-NLDIRNSYELCVNK  168 (198)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHh-CcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHH
Confidence            566666666677777777777766665 2234455666666677777777777777776665433 45556666665555


Q ss_pred             cCCHHHHH
Q 011236          397 KNNMEKAF  404 (490)
Q Consensus       397 ~~~~~~a~  404 (490)
                      .++.+++.
T Consensus       169 ~~~~~~~~  176 (198)
T 2fbn_A          169 LKEARKKD  176 (198)
T ss_dssp             HHHHHC--
T ss_pred             HHHHHHHH
Confidence            55554444

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.56  E-value=1.2e-06  Score=70.05  Aligned_cols=97  Identities=13%  Similarity=0.042  Sum_probs=58.5

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011236          314 NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG  393 (490)
Q Consensus       314 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~  393 (490)
                      ...+..+...+.+.|++++|...|++..+.. +.+...|..+..+|.+.|++++|+..|++.++..+. +...|..+..+
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~   88 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPK-YSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence            3445556666666666666666666666542 224455566666666666666666666666665433 45566666666


Q ss_pred             HhccCCHHHHHHHHHHHHH
Q 011236          394 YADKNNMEKAFECMKEALA  412 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~  412 (490)
                      |...|++++|...|+++++
T Consensus        89 ~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHH
Confidence            6666666666666666665

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.55  E-value=6.7e-06  Score=77.39  Aligned_cols=203  Identities=11%  Similarity=-0.009  Sum_probs=146.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCCh---------------hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCC-C
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKDA---------------LGYNHLISHYASLGNKDEMMKFWGLQKIKCKK-Q  312 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~---------------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-~  312 (490)
                      -...+.+.|++++|++.|..+.+..+...+.               ..+..+...|...|++++|.+++......... +
T Consensus        10 ~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~   89 (434)
T 4b4t_Q           10 EARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFA   89 (434)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence            3566788999999999999987754431111               23778899999999999999999977664432 2


Q ss_pred             Chh----hHHHHHHHHHhcCCHHHHHHHHHHHHhc----CCCCC-chhHHHHHHHHHhcCCHHHHHHHHHHHHHc--CC-
Q 011236          313 LNR----DYITMLGSLVKIGELEEAEKMLEEWELS----CYCYD-FRVPNIILLGYSQKGMIEKADAVLKEIVKK--GK-  380 (490)
Q Consensus       313 ~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~--~~-  380 (490)
                      +..    ..+.+...+...|+.+.+..++......    +..+. ..++..+...|...|++++|..+++++...  +. 
T Consensus        90 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~  169 (434)
T 4b4t_Q           90 KSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD  169 (434)
T ss_dssp             HHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS
T ss_pred             chHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc
Confidence            221    2333344445678999999999887643    22222 346778899999999999999999988653  11 


Q ss_pred             -CC-CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc--hhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          381 -TP-TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK--PSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       381 -~p-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                       .| ...+|..++..|...|++++|..++++++...+... ..|.  ...+..+...+...|++++|...|.+..+
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~-~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIY-CPTQTVAELDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCC-CchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence             11 234788999999999999999999999987443111 1111  24566777788899999999988877654

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.54  E-value=1.7e-06  Score=65.74  Aligned_cols=106  Identities=13%  Similarity=0.101  Sum_probs=73.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC--CC----HHHHHH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT--PT----PNSWSI  389 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~--p~----~~~~~~  389 (490)
                      .+..+...+.+.|++++|...|++.++.. +.+...|+.+..+|.+.|++++|+..+++.++.++.  ++    ..+|..
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~   88 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSR   88 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHH
Confidence            45566777777777777777777777652 234556777777778888888888877777664321  11    235777


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          390 IAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       390 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                      +..++...|++++|++.|++++.       ..|++.+...
T Consensus        89 lg~~~~~~~~~~~A~~~~~kal~-------~~~~~~~~~~  121 (127)
T 4gcn_A           89 AGNAFQKQNDLSLAVQWFHRSLS-------EFRDPELVKK  121 (127)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH-------HSCCHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHh-------hCcCHHHHHH
Confidence            78888889999999999999887       3466655443

>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=98.54  E-value=3.6e-06  Score=64.74  Aligned_cols=102  Identities=10%  Similarity=-0.033  Sum_probs=69.6

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011236          312 QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIA  391 (490)
Q Consensus       312 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~  391 (490)
                      .+...+..+...+...|++++|...|+...... +.+...+..+..+|...|++++|...+++..+.++. +...|..+.
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCch-hHHHHHHHH
Confidence            345566666667777777777777777766652 224556666777777777777777777777776544 566777777


Q ss_pred             HHHhccCCHHHHHHHHHHHHHhhh
Q 011236          392 AGYADKNNMEKAFECMKEALAVHE  415 (490)
Q Consensus       392 ~~~~~~~~~~~a~~~~~~~~~~~~  415 (490)
                      .++...|++++|...|+++++..|
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~~p  108 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSLAK  108 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHCh
Confidence            777777777777777777776443

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.52  E-value=1.7e-06  Score=67.25  Aligned_cols=99  Identities=10%  Similarity=0.030  Sum_probs=60.8

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSI  430 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l  430 (490)
                      .+..+...+.+.|++++|...|++....++. +...|..+..+|...|++++|+..|++++...|      .+...+..+
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p------~~~~~~~~l   92 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLDHY-DARYFLGLGACRQSLGLYEQALQSYSYGALMDI------NEPRFPFHA   92 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT------TCTHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC------CCcHHHHHH
Confidence            3444555566666666666666666665443 556666666666666666666666666666221      223455566


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..++...|++++|...|++..+..|.
T Consensus        93 g~~~~~~g~~~~A~~~~~~al~~~p~  118 (142)
T 2xcb_A           93 AECHLQLGDLDGAESGFYSARALAAA  118 (142)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            66666666666666666666666554

>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=98.51  E-value=5.8e-06  Score=61.40  Aligned_cols=95  Identities=13%  Similarity=-0.075  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ  361 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  361 (490)
                      +..+...+...|++++|...++......+ .+...+..+...+...|++++|...+++..+.. +.+...+..+..+|..
T Consensus         7 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~   84 (118)
T 1elw_A            7 LKEKGNKALSVGNIDDALQCYSEAIKLDP-HNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEF   84 (118)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHHHHHHCC-CcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHH
Confidence            33344444444444444444444443332 233344444444444444444444444444431 1123344444444445


Q ss_pred             cCCHHHHHHHHHHHHHc
Q 011236          362 KGMIEKADAVLKEIVKK  378 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~  378 (490)
                      .|++++|...+++..+.
T Consensus        85 ~~~~~~A~~~~~~~~~~  101 (118)
T 1elw_A           85 LNRFEEAKRTYEEGLKH  101 (118)
T ss_dssp             TTCHHHHHHHHHHHHTT
T ss_pred             HhhHHHHHHHHHHHHHc
Confidence            55555555555544443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.49  E-value=1.6e-06  Score=68.76  Aligned_cols=102  Identities=16%  Similarity=0.060  Sum_probs=56.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchh
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS  425 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~  425 (490)
                      ++..+...|...|++++|...+++..+.... ++    ...+..+...+...|++++|...++++++.............
T Consensus        51 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  130 (164)
T 3ro3_A           51 AYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGR  130 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHH
Confidence            4445555556666666666666555432100 01    334566666667777777777777776653321111111124


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          426 LVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       426 ~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      .+..+...+...|++++|.+.+++..+
T Consensus       131 ~~~~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A          131 ACWSLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            555666667777777777777766554

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.48  E-value=5.6e-06  Score=64.20  Aligned_cols=114  Identities=12%  Similarity=0.017  Sum_probs=82.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCC------C-----chhHHHHHHHHHhcCCHHHHHHHHHHHHHc-------C
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSCYCY------D-----FRVPNIILLGYSQKGMIEKADAVLKEIVKK-------G  379 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~------~-----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~-------~  379 (490)
                      ......+.+.|++++|...|++.++.....      +     ...|..+..++.+.|++++|+..+++.++.       +
T Consensus        15 ~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~   94 (159)
T 2hr2_A           15 LSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELN   94 (159)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTT
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCC
Confidence            334444445555555555555554431110      1     227888888889999999999999988886       5


Q ss_pred             CCCCHHHH----HHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHH
Q 011236          380 KTPTPNSW----SIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILD  432 (490)
Q Consensus       380 ~~p~~~~~----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~  432 (490)
                      +. +...|    .....++...|++++|+..|++++++.|+..++.+........+.
T Consensus        95 pd-~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~~~~~~~~~~~~~  150 (159)
T 2hr2_A           95 QD-EGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMMEVAI  150 (159)
T ss_dssp             ST-HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHHHHH
T ss_pred             Cc-hHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHH
Confidence            43 55678    899999999999999999999999999988898887766655554

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.47  E-value=1.3e-06  Score=65.76  Aligned_cols=97  Identities=11%  Similarity=0.133  Sum_probs=55.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSI  430 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l  430 (490)
                      +..+...+.+.|++++|...|++.++..+. +...|..+..++...|++++|+..|+++++       +.|+ ...+..+
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~-------l~P~~~~~~~~l   91 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARM-------LDPKDIAVHAAL   91 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------hCCCCHHHHHHH
Confidence            334455566666666666666666665443 555666666666666666666666666665       2232 3455556


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..++...|++++|...++++.+..|.
T Consensus        92 a~~~~~~g~~~~A~~~~~~al~~~P~  117 (121)
T 1hxi_A           92 AVSHTNEHNANAALASLRAWLLSQPQ  117 (121)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCcC
Confidence            66666666666666666666655443

>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=98.47  E-value=3.5e-06  Score=64.03  Aligned_cols=104  Identities=14%  Similarity=0.021  Sum_probs=48.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSI  430 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l  430 (490)
                      +..+...+...|++++|...|++..+..+. +...+..+...+...|++++|...+++++...+......+. ..++..+
T Consensus         7 ~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~l   85 (131)
T 1elr_A            7 EKELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (131)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHHHH
Confidence            334444455555555555555555444322 44445555555555555555555555555432211000000 3344444


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ...+...|++++|...++++.+..|.
T Consensus        86 a~~~~~~~~~~~A~~~~~~~~~~~~~  111 (131)
T 1elr_A           86 GNSYFKEEKYKDAIHFYNKSLAEHRT  111 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhCCC
Confidence            55555555555555555555544433

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.44  E-value=4.7e-06  Score=65.00  Aligned_cols=97  Identities=11%  Similarity=-0.128  Sum_probs=46.6

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc-chh
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP-KPS  425 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~  425 (490)
                      .+..+...+...|++++|...|++..+..  |+    ...|..+...|...|++++|+..++++++.       .| +..
T Consensus        30 ~~~~~a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-------~~~~~~  100 (148)
T 2dba_A           30 QLRKEGNELFKCGDYGGALAAYTQALGLD--ATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK-------DGGDVK  100 (148)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHTSC--CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------TSCCHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHc--ccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh-------CccCHH
Confidence            34444444455555555555555554432  22    344444555555555555555555555441       12 233


Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          426 LVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       426 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+..+..++...|++++|...+++..+..|.
T Consensus       101 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~  131 (148)
T 2dba_A          101 ALYRRSQALEKLGRLDQAVLDLQRCVSLEPK  131 (148)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC
Confidence            4444444555555555555555555554444

>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=98.43  E-value=1.9e-06  Score=65.58  Aligned_cols=110  Identities=13%  Similarity=0.141  Sum_probs=77.2

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC--CC----HHHHH
Q 011236          315 RDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT--PT----PNSWS  388 (490)
Q Consensus       315 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~--p~----~~~~~  388 (490)
                      ..+..+...+...|++++|...+++..+.. +.+...+..+...|...|++++|...+++..+..+.  ++    ..+|.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            445666677777777777777777777652 335566777777788888888888888877765332  12    66788


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHH
Q 011236          389 IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILD  432 (490)
Q Consensus       389 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~  432 (490)
                      .+...+...|++++|...|+++++       ..|+......+..
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~~~l~~  120 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLA-------EHRTPDVLKKCQQ  120 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH-------HCCCHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHH-------hCCCHHHHHHHHH
Confidence            888888889999999999988887       3355555444443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.43  E-value=3.8e-06  Score=67.05  Aligned_cols=100  Identities=14%  Similarity=-0.041  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHH
Q 011236          207 NFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLI  286 (490)
Q Consensus       207 ~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  286 (490)
                      ...+..+...+...|++++|+..|++.. +... .+...|..+..+|...|++++|+..|++.....+  .+...|..+.
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al-~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p--~~~~~~~~lg   86 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQAL-SIAP-ANPIYLSNRAAAYSASGQHEKAAEDAELATVVDP--KYSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHST-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-cCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC--CCHHHHHHHH
Confidence            3455556666666677777777776665 3332 3556666666677777777777777776666544  4566666666


Q ss_pred             HHHHhcCChhHHHHHHHHHHHhcC
Q 011236          287 SHYASLGNKDEMMKFWGLQKIKCK  310 (490)
Q Consensus       287 ~~~~~~~~~~~a~~~~~~~~~~~~  310 (490)
                      .+|...|++++|...|++.....+
T Consensus        87 ~~~~~~g~~~~A~~~~~~al~~~p  110 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGIEAEG  110 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHccCHHHHHHHHHHHHHhCC
Confidence            777777777777777766666554

>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=98.39  E-value=8.7e-06  Score=62.55  Aligned_cols=98  Identities=9%  Similarity=-0.050  Sum_probs=50.3

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                      +...+..+...+...|++++|+..|+......+  .+...|..+..++...|++++|...++......+ .+...+..+.
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~   84 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNP--LVAVYYTNRALCYLKMQQPEQALADCRRALELDG-QSVKAHFFLG   84 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCc--CcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCc-hhHHHHHHHH
Confidence            344444555555555555555555555544433  3444555555555555555555555555544433 3444455555


Q ss_pred             HHHHhcCCHHHHHHHHHHHHh
Q 011236          322 GSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      .++...|++++|...+++..+
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHH
Confidence            555555555555555555444

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.38  E-value=3.9e-06  Score=61.72  Aligned_cols=95  Identities=12%  Similarity=-0.080  Sum_probs=39.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC--CchhHHHHHHHH
Q 011236          282 YNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY--DFRVPNIILLGY  359 (490)
Q Consensus       282 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~  359 (490)
                      +..+...+...|++++|...+++.....+ .+...+..+...+...|++++|...+++..+.. +.  +...+..+...|
T Consensus         9 ~~~~~~~~~~~~~~~~A~~~~~~a~~~~~-~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~   86 (112)
T 2kck_A            9 YYLEGVLQYDAGNYTESIDLFEKAIQLDP-EESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADAL   86 (112)
T ss_dssp             GGGHHHHHHSSCCHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhCc-CCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHHH
Confidence            33344444444444444444444433332 233334444444444444444444444444331 11  233344444444


Q ss_pred             Hhc-CCHHHHHHHHHHHHHc
Q 011236          360 SQK-GMIEKADAVLKEIVKK  378 (490)
Q Consensus       360 ~~~-g~~~~A~~~~~~m~~~  378 (490)
                      ... |++++|.+.+++..+.
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           87 RYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             TTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHhCCHHHHHHHHHHHhhc
Confidence            444 4444444444444443

>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=3.6e-06  Score=63.22  Aligned_cols=94  Identities=14%  Similarity=-0.007  Sum_probs=62.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      +..+...+.+.|++++|...+++..+.. +.+...|..+..++...|++++|+..|++.++..+. +...+..+..++..
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~-~~~~~~~la~~~~~   97 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence            4445556666777777777777766642 224556666666677777777777777777666544 55666677777777


Q ss_pred             cCCHHHHHHHHHHHHH
Q 011236          397 KNNMEKAFECMKEALA  412 (490)
Q Consensus       397 ~~~~~~a~~~~~~~~~  412 (490)
                      .|++++|+..++++++
T Consensus        98 ~g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           98 EHNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHHC
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            7777777777777665

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.37  E-value=1.8e-05  Score=61.61  Aligned_cols=96  Identities=8%  Similarity=-0.054  Sum_probs=61.8

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC----chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHH
Q 011236          314 NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD----FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSI  389 (490)
Q Consensus       314 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~  389 (490)
                      ...+..+...+...|++++|...|++..+.  .|+    ...+..+...|...|++++|...+++..+..+. +...|..
T Consensus        28 ~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~  104 (148)
T 2dba_A           28 VEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGG-DVKALYR  104 (148)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSC-CHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCcc-CHHHHHH
Confidence            344555566666666666666666666653  233    455666666677777777777777776665433 5566666


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHH
Q 011236          390 IAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       390 l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +..++...|++++|...|+++++
T Consensus       105 ~a~~~~~~~~~~~A~~~~~~al~  127 (148)
T 2dba_A          105 RSQALEKLGRLDQAVLDLQRCVS  127 (148)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH
Confidence            77777777777777777777766

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.36  E-value=3.1e-06  Score=67.08  Aligned_cols=135  Identities=15%  Similarity=-0.005  Sum_probs=101.1

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP  424 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~  424 (490)
                      .++..+...|...|++++|...+++..+.... ++    ..++..+...+...|++++|...++++++..+.........
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   89 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEA   89 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHH
Confidence            35666777788888888888888877653211 12    14788889999999999999999999988553222211224


Q ss_pred             hhHHHHHHHHHcCCCHHHHHHHHHHHHhccc-----c--hhhhHHHHHHHHhcC--CcHHHHHHHHHhC
Q 011236          425 SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ-----K--RNMYHALTEAHIRSG--QEVDGLLESMKAD  484 (490)
Q Consensus       425 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-----~--~~~~~~l~~~~~~~g--~~a~~~~~~m~~~  484 (490)
                      ..+..+...+...|++++|...+++..+...     .  ...+..+...+...|  ++|.+.+++..+.
T Consensus        90 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~  158 (164)
T 3ro3_A           90 QSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEI  158 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            5677888899999999999999998765421     1  677888999999999  8899999877643

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.36  E-value=1.3e-05  Score=60.73  Aligned_cols=91  Identities=10%  Similarity=0.091  Sum_probs=41.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCCc---hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHH
Q 011236          320 MLGSLVKIGELEEAEKMLEEWELSCYCYDF---RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPT---PNSWSIIAAG  393 (490)
Q Consensus       320 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~---~~~~~~l~~~  393 (490)
                      +...+...|++++|...++.+.+... .+.   ..+..+..+|.+.|++++|...|+++.+..+. +   ...+..+..+
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~la~~   85 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELYP-NGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPT-HDKAAGGLLKLGLS   85 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCS-SSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-STTHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHCC-CCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHH
Confidence            33444445555555555555544311 111   23444444455555555555555555444322 2   3344444445


Q ss_pred             HhccCCHHHHHHHHHHHHH
Q 011236          394 YADKNNMEKAFECMKEALA  412 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~  412 (490)
                      +...|++++|...|++++.
T Consensus        86 ~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            5555555555555555544

>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=98.34  E-value=2.6e-06  Score=80.96  Aligned_cols=88  Identities=16%  Similarity=0.070  Sum_probs=42.2

Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHH
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELE  331 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  331 (490)
                      .+.+.|++++|++.|++..+..+  .+..+|..+..+|.+.|++++|+..+++.....+ .+...+..+..+|...|+++
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~p--~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p-~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELNP--SNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT-TCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhCC--ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHH
Confidence            34444555555555555444333  3344455555555555555555555554444332 33344444444455555555


Q ss_pred             HHHHHHHHHHh
Q 011236          332 EAEKMLEEWEL  342 (490)
Q Consensus       332 ~a~~~~~~~~~  342 (490)
                      +|.+.+++..+
T Consensus        92 eA~~~~~~al~  102 (477)
T 1wao_1           92 AALRDYETVVK  102 (477)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55555554444

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.33  E-value=3.2e-06  Score=67.37  Aligned_cols=65  Identities=12%  Similarity=0.038  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..|..+..+|.+.|++++|+..++++++.       .|+ ...|..+..++...|++++|...|++..+..|.
T Consensus        64 ~~~~nla~~~~~~~~~~~A~~~~~~al~~-------~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~  129 (162)
T 3rkv_A           64 PLYANMSQCYLNIGDLHEAEETSSEVLKR-------EETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPA  129 (162)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHH-------STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGG
T ss_pred             HHHHHHHHHHHhcCcHHHHHHHHHHHHhc-------CCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCC
Confidence            34555555555555555555555555551       122 244555555555555555555555555555554

>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=98.32  E-value=9.2e-07  Score=83.70  Aligned_cols=88  Identities=11%  Similarity=0.003  Sum_probs=61.8

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHH
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVS  428 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~  428 (490)
                      ..|..+..+|.+.|++++|+..+++.++..+. +...|..+..+|...|++++|+..|+++++       +.|+. ..+.
T Consensus       318 ~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~~g~a~~~~g~~~~A~~~~~~al~-------l~P~~~~a~~  389 (457)
T 1kt0_A          318 AAFLNLAMCYLKLREYTKAVECCDKALGLDSA-NEKGLYRRGEAQLLMNEFESAKGDFEKVLE-------VNPQNKAARL  389 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT-------TC----CHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHccCHHHHHHHHHHHHH-------hCCCCHHHHH
Confidence            56667777777888888888888887776544 677777777888888888888888888776       33433 5666


Q ss_pred             HHHHHHHcCCCHHHHHH
Q 011236          429 SILDWLGDNRDVEEVEA  445 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~  445 (490)
                      .+..++.+.|+.+++.+
T Consensus       390 ~l~~~~~~~~~~~~a~~  406 (457)
T 1kt0_A          390 QISMCQKKAKEHNERDR  406 (457)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            66667777777666653

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.29  E-value=2.8e-05  Score=58.91  Aligned_cols=94  Identities=9%  Similarity=0.064  Sum_probs=52.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCH---HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc----hhhH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVKKGKTPTP---NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK----PSLV  427 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~----~~~~  427 (490)
                      +...+...|++++|...|+++.+..+. +.   ..+..+..++...|++++|...|++++...       |+    ...+
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~p~-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~-------p~~~~~~~~~   79 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELYPN-GVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY-------PTHDKAAGGL   79 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCSS-STTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-------TTSTTHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHCCC-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC-------CCCcccHHHH
Confidence            444555566666666666666554332 22   345555566666666666666666665522       22    3345


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          428 SSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       428 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..+..++...|++++|...|+++.+..|.
T Consensus        80 ~~la~~~~~~g~~~~A~~~~~~~~~~~p~  108 (129)
T 2xev_A           80 LKLGLSQYGEGKNTEAQQTLQQVATQYPG  108 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCCC
Confidence            55555566666666666666666665554

>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=98.28  E-value=7.6e-06  Score=77.38  Aligned_cols=94  Identities=12%  Similarity=0.071  Sum_probs=75.8

Q ss_pred             HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHH
Q 011236          384 PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHA  462 (490)
Q Consensus       384 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~  462 (490)
                      ..+|..+..+|.+.|++++|+..++++++..+      .+...|..+..+|...|++++|...|+++.+..|. ..++..
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p------~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~  390 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLDS------ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQ  390 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCC------ccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            56889999999999999999999999998332      24578899999999999999999999999999999 889999


Q ss_pred             HHHHHHhcC--CcH-HHHHHHHHh
Q 011236          463 LTEAHIRSG--QEV-DGLLESMKA  483 (490)
Q Consensus       463 l~~~~~~~g--~~a-~~~~~~m~~  483 (490)
                      +..++.+.|  +++ ..++++|..
T Consensus       391 l~~~~~~~~~~~~a~~~~~~~~f~  414 (457)
T 1kt0_A          391 ISMCQKKAKEHNERDRRIYANMFK  414 (457)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999888  333 345555543

>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=98.25  E-value=5.1e-06  Score=78.98  Aligned_cols=113  Identities=8%  Similarity=-0.069  Sum_probs=49.6

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcC
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDN  437 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~  437 (490)
                      +.+.|++++|...+++.++..+. +..+|..+..+|.+.|++++|++.++++++       +.|+ ...+..+..++...
T Consensus        16 ~~~~g~~~~A~~~~~~Al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~-------l~p~~~~~~~~lg~~~~~~   87 (477)
T 1wao_1           16 YFKAKDYENAIKFYSQAIELNPS-NAIYYGNRSLAYLRTECYGYALGDATRAIE-------LDKKYIKGYYRRAASNMAL   87 (477)
T ss_dssp             TTTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------SCTTCHHHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHc
Confidence            33444555555555544444322 344444555555555555555555555544       1122 23444444445555


Q ss_pred             CCHHHHHHHHHHHHhcccc-hhhhHHHHHH--HHhcC--CcHHHHHH
Q 011236          438 RDVEEVEAFVSSLKIKVQK-RNMYHALTEA--HIRSG--QEVDGLLE  479 (490)
Q Consensus       438 g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~--~~~~g--~~a~~~~~  479 (490)
                      |++++|.+.++++.+..|. ...+..+..+  +.+.|  ++|++.++
T Consensus        88 g~~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           88 GKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            5555555555555444444 3444444333  34334  44444444

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.21  E-value=2.5e-05  Score=62.09  Aligned_cols=63  Identities=17%  Similarity=0.141  Sum_probs=53.9

Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          349 FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...|..+..+|.+.|++++|+..+++.++.++. +...|..+..+|...|++++|...|++++.
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKREET-NEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCc-chHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence            456777888888999999999999998887654 778888899999999999999999999888

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.17  E-value=4.7e-06  Score=62.17  Aligned_cols=88  Identities=15%  Similarity=-0.013  Sum_probs=45.0

Q ss_pred             cCCcCcHHHHHHHHHHCCC--CCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHH
Q 011236          185 TGQHEKIPDVLLDMKENGV--PPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKA  262 (490)
Q Consensus       185 ~~~~~~a~~~~~~m~~~~~--~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a  262 (490)
                      .|++++|...|++..+.+.  +.+...+..+..++...|++++|...|++.. +.++ -+..++..+..++...|++++|
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al-~~~p-~~~~~~~~l~~~~~~~g~~~~A   80 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGV-KQFP-NHQALRVFYAMVLYNLGRYEQG   80 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHCT-TCHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HhCC-CchHHHHHHHHHHHHcCCHHHH
Confidence            3555666666666555321  1123345555555666666666666666655 3332 3345555555666666666666


Q ss_pred             HHHHHHHhhhhc
Q 011236          263 IIYLKKCEDIVS  274 (490)
Q Consensus       263 ~~~~~~~~~~~~  274 (490)
                      +..|++.....+
T Consensus        81 ~~~~~~al~~~p   92 (117)
T 3k9i_A           81 VELLLKIIAETS   92 (117)
T ss_dssp             HHHHHHHHHHHC
T ss_pred             HHHHHHHHHhCC
Confidence            666665555443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.17  E-value=5.1e-06  Score=61.98  Aligned_cols=88  Identities=9%  Similarity=-0.104  Sum_probs=58.7

Q ss_pred             cCChHHHHHHHHHHHhCCC--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhH
Q 011236          220 RSELSSMENVLQEMESQSH--ISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE  297 (490)
Q Consensus       220 ~g~~~~a~~~~~~~~~~~~--~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  297 (490)
                      .|++++|+..|++.. +.+  -+.+..++..+..+|...|++++|+..|++..+..+  .+...+..+..++...|++++
T Consensus         3 ~g~~~~A~~~~~~al-~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~l~~~~~~~g~~~~   79 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAI-ASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFP--NHQALRVFYAMVLYNLGRYEQ   79 (117)
T ss_dssp             ----CCCHHHHHHHH-SSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHTCHHH
T ss_pred             CCcHHHHHHHHHHHH-HcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--CchHHHHHHHHHHHHcCCHHH
Confidence            567777777777777 543  113355666777777777777777777777776655  456677777777777777777


Q ss_pred             HHHHHHHHHHhcC
Q 011236          298 MMKFWGLQKIKCK  310 (490)
Q Consensus       298 a~~~~~~~~~~~~  310 (490)
                      |...+++.....+
T Consensus        80 A~~~~~~al~~~p   92 (117)
T 3k9i_A           80 GVELLLKIIAETS   92 (117)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhCC
Confidence            7777777666654

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.15  E-value=2.7e-05  Score=60.34  Aligned_cols=106  Identities=12%  Similarity=-0.013  Sum_probs=85.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCC------CH-----HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcC
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTP------TP-----NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKF  419 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p------~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  419 (490)
                      .+......+.+.|++++|+..|++.++..+..      +.     ..|..+..++.+.|++++|+..++++++.....-.
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e   92 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGE   92 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhcccc
Confidence            34556677889999999999999999875431      22     38999999999999999999999999984111112


Q ss_pred             CCcch-hhH----HHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          420 WRPKP-SLV----SSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       420 ~~p~~-~~~----~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      +.|+. ..|    .....++...|++++|...|++..+..|.
T Consensus        93 ~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~  134 (159)
T 2hr2_A           93 LNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEE  134 (159)
T ss_dssp             TTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            25765 677    88899999999999999999999988765

>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=98.10  E-value=4.3e-05  Score=69.89  Aligned_cols=136  Identities=10%  Similarity=-0.056  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSL  324 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  324 (490)
                      .+..+...+.+.|++++|+..|++.......  ..           .....++       ..... ..+...|..+..+|
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~--~~-----------~~~~~~~-------~~~~~-~~~~~~~~nla~~~  283 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEG--SR-----------AAAEDAD-------GAKLQ-PVALSCVLNIGACK  283 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH--HH-----------HHSCHHH-------HGGGH-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhc--Cc-----------cccChHH-------HHHHH-HHHHHHHHHHHHHH
Confidence            3555667777777777777777776652211  00           0000000       00000 02233444455555


Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHH
Q 011236          325 VKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKA  403 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a  403 (490)
                      .+.|++++|...+++..+.. +.+...+..+..+|...|++++|+..|++..+..+. +...+..+...+...++.+++
T Consensus       284 ~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~-~~~~~~~l~~~~~~~~~~~~a  360 (370)
T 1ihg_A          284 LKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE-DKAIQAELLKVKQKIKAQKDK  360 (370)
T ss_dssp             HHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccCHHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHHHHHH
Confidence            55555555555555555431 123344455555555555555555555555554332 444445555555544444444

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.09  E-value=2.4e-05  Score=73.93  Aligned_cols=129  Identities=13%  Similarity=-0.001  Sum_probs=60.5

Q ss_pred             HHhcCCHHHHHHHHHHHHhcC---CCC----CchhHHHHHHHHHhcCCHHHHHHHHHHHHH-----cCCC-CCHH-HHHH
Q 011236          324 LVKIGELEEAEKMLEEWELSC---YCY----DFRVPNIILLGYSQKGMIEKADAVLKEIVK-----KGKT-PTPN-SWSI  389 (490)
Q Consensus       324 ~~~~~~~~~a~~~~~~~~~~~---~~~----~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~-----~~~~-p~~~-~~~~  389 (490)
                      +...|++++|..++++.++..   +.+    ...+++.|...|...|++++|..++++.++     .|.. |+.. +++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            344555666655555544321   111    123455555555555566665555555443     2322 1121 3555


Q ss_pred             HHHHHhccCCHHHHHHHHHHHHHhhhcCcCC-Ccch-hhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          390 IAAGYADKNNMEKAFECMKEALAVHEENKFW-RPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       390 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      |...|...|++++|..+++++++......|- .|+. .+...+..++...|.+++|+.++.++++
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555555555555555555544333331 1111 2223333444445555555555555543

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.09  E-value=9.3e-06  Score=73.42  Aligned_cols=151  Identities=8%  Similarity=0.001  Sum_probs=65.4

Q ss_pred             hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHH
Q 011236          279 ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLG  358 (490)
Q Consensus       279 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  358 (490)
                      ...+..+...+.+.|++++|...|++.....+  +...       +...++.+++...+.          ...|..+..+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p--~~~~-------~~~~~~~~~~~~~l~----------~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMG--DDFM-------FQLYGKYQDMALAVK----------NPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSC--HHHH-------HTCCHHHHHHHHHHH----------THHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhc--cchh-------hhhcccHHHHHHHHH----------HHHHHHHHHH
Confidence            34455566666666777777776666555432  2111       112222222221110          1255666666


Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHH-HHc
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDW-LGD  436 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~-~~~  436 (490)
                      |.+.|++++|+..+++.++..+. +...|..+..+|...|++++|...|+++++       +.|+. ..+..+... ...
T Consensus       240 ~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~a~~~~g~~~~A~~~l~~al~-------l~p~~~~a~~~L~~l~~~~  311 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTEEEK-NPKALFRRGKAKAELGQMDSARDDFRKAQK-------YAPDDKAIRRELRALAEQE  311 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH-------HCCCCHHHHHHHHHHHHHH
Confidence            77777777777777777665433 566677777777777777777777777655       23433 233333332 123


Q ss_pred             CCCHHHHHHHHHHHHhcccc
Q 011236          437 NRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+..+.+...|.+|....|.
T Consensus       312 ~~~~~~a~~~~~~~l~~~p~  331 (338)
T 2if4_A          312 KALYQKQKEMYKGIFKGKDE  331 (338)
T ss_dssp             --------------------
T ss_pred             HHHHHHHHHHHHHhhCCCCC
Confidence            34555666666666555443

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.08  E-value=0.00027  Score=68.41  Aligned_cols=168  Identities=6%  Similarity=-0.091  Sum_probs=118.1

Q ss_pred             hhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCC----------HHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC-
Q 011236          295 KDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGE----------LEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG-  363 (490)
Q Consensus       295 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-  363 (490)
                      .++|++.++.+....+ -+...|+.--.++...|+          ++++.+.++.+.+.. +-+..+|+.-...+.+.| 
T Consensus        45 ~eeal~~~~~~l~~nP-~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           45 DESVLELTSQILGANP-DFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             SHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHHHHHHHCc-hhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccc
Confidence            3456677776666554 444455555555555555          777888888887763 335667777777777777 


Q ss_pred             -CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcC----
Q 011236          364 -MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKN-NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDN----  437 (490)
Q Consensus       364 -~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~----  437 (490)
                       ++++++..++++.+.++. |..+|+.-...+.+.| .++++++.++++++.+      .-|...|......+.+.    
T Consensus       123 ~~~~~el~~~~k~l~~d~~-N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~------p~n~saW~~r~~ll~~l~~~~  195 (567)
T 1dce_A          123 PNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN------FSNYSSWHYRSCLLPQLHPQP  195 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT------CCCHHHHHHHHHHHHHHSCCC
T ss_pred             ccHHHHHHHHHHHHhhccc-cccHHHHHHHHHHHcCCChHHHHHHHHHHHHHC------CCCccHHHHHHHHHHhhcccc
Confidence             668888888888888766 7888888777777777 7888888888887722      12345566555554442    


Q ss_pred             ----------CCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC
Q 011236          438 ----------RDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG  471 (490)
Q Consensus       438 ----------g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g  471 (490)
                                +.++++.+.++++....|. ..+|..+...+.+.+
T Consensus       196 ~~~~~~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~  240 (567)
T 1dce_A          196 DSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAE  240 (567)
T ss_dssp             CSSSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCC
T ss_pred             cccccccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCC
Confidence                      5578899999999988888 889998888887776

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=98.08  E-value=0.00014  Score=70.51  Aligned_cols=172  Identities=6%  Similarity=-0.032  Sum_probs=89.8

Q ss_pred             hHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcC----------HHHHHHHHHHccccCC-ChhHHHHHHHHHHhcC--C
Q 011236           86 KHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRG----------LESAETYFNSLNDEDK-VDKLYGALLNCYVREG--L  152 (490)
Q Consensus        86 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~----------~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g--~  152 (490)
                      ++|++.++.+...+ +-....+..--.++...|+          +++++..++.+...+| +..+|+.-...+.+.|  +
T Consensus        46 eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~l~~~~  124 (567)
T 1dce_A           46 ESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLPEPN  124 (567)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCSSCC
T ss_pred             HHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHccccc
Confidence            34555555555554 2333334333333333444          4555555555555444 3444554444444444  3


Q ss_pred             hhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHH
Q 011236          153 VDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQE  232 (490)
Q Consensus       153 ~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~  232 (490)
                      ++++++.++++.+.... |..+|+.-...+.+.|.                                  .++++.+.+++
T Consensus       125 ~~~el~~~~k~l~~d~~-N~~aW~~R~~~l~~l~~----------------------------------~~~~el~~~~~  169 (567)
T 1dce_A          125 WARELELCARFLEADER-NFHCWDYRRFVAAQAAV----------------------------------APAEELAFTDS  169 (567)
T ss_dssp             HHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCC----------------------------------CHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhhccc-cccHHHHHHHHHHHcCC----------------------------------ChHHHHHHHHH
Confidence            35555555555544333 44444444333333330                                  44555555555


Q ss_pred             HHhCCCCCCCHHHHHHHHHHHHHc--------------CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhH
Q 011236          233 MESQSHISMDWGTYSTVANYYIIA--------------GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE  297 (490)
Q Consensus       233 ~~~~~~~~~~~~~~~~li~~~~~~--------------~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  297 (490)
                      +. +.++ -+..+|+.....+.+.              +.++++++.+++.....+  .|..+|..+-..+.+.++.++
T Consensus       170 ~I-~~~p-~n~saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~ai~~~P--~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          170 LI-TRNF-SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTDP--NDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             TT-TTTC-CCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHHHHHCS--SCSHHHHHHHHHHSCCCCCSC
T ss_pred             HH-HHCC-CCccHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHHHhhCC--CCccHHHHHHHHHhcCCCccc
Confidence            55 4444 4445555444444432              456788888888877665  577888888777777666443

>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=98.08  E-value=4.5e-05  Score=69.74  Aligned_cols=139  Identities=11%  Similarity=0.023  Sum_probs=102.0

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHH
Q 011236          281 GYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYS  360 (490)
Q Consensus       281 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  360 (490)
                      .+..+...+.+.|++++|+..|++.+.....  ..          .....+++.       +. .+.+..+|..+..+|.
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~--~~----------~~~~~~~~~-------~~-~~~~~~~~~nla~~~~  284 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEG--SR----------AAAEDADGA-------KL-QPVALSCVLNIGACKL  284 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH--HH----------HHSCHHHHG-------GG-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhc--Cc----------cccChHHHH-------HH-HHHHHHHHHHHHHHHH
Confidence            4666777788888888888888876653220  00          001111111       11 1224567888999999


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCH
Q 011236          361 QKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDV  440 (490)
Q Consensus       361 ~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  440 (490)
                      +.|++++|+..+++.++..+. +...|..+..+|...|++++|+..|+++++..|+      +...+..+..++...++.
T Consensus       285 ~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~------~~~~~~~l~~~~~~~~~~  357 (370)
T 1ihg_A          285 KMSDWQGAVDSCLEALEIDPS-NTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE------DKAIQAELLKVKQKIKAQ  357 (370)
T ss_dssp             HTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT------CHHHHHHHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCC------CHHHHHHHHHHHHHHHHH
Confidence            999999999999999997654 7889999999999999999999999999996653      356677777888888888


Q ss_pred             HHHHHH
Q 011236          441 EEVEAF  446 (490)
Q Consensus       441 ~~a~~~  446 (490)
                      +++.+.
T Consensus       358 ~~a~k~  363 (370)
T 1ihg_A          358 KDKEKA  363 (370)
T ss_dssp             HHHHHC
T ss_pred             HHHHHH
Confidence            877653

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.03  E-value=1.3e-05  Score=72.50  Aligned_cols=145  Identities=13%  Similarity=0.006  Sum_probs=84.5

Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011236          314 NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG  393 (490)
Q Consensus       314 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~  393 (490)
                      ...+..+...+.+.|++++|...|++....  .|+..       .+...|+.+++...+.          ...|..+..+
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~-------~~~~~~~~~~~~~~l~----------~~~~~nla~~  239 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDF-------MFQLYGKYQDMALAVK----------NPCHLNIAAC  239 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHH-------HHTCCHHHHHHHHHHH----------THHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccch-------hhhhcccHHHHHHHHH----------HHHHHHHHHH
Confidence            345667777777888888888888887764  23321       1223334444433221          1378899999


Q ss_pred             HhccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC
Q 011236          394 YADKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG  471 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g  471 (490)
                      |.+.|++++|+..++++++.       .| +...|..+..+|...|++++|...|+++.+..|. ..++..+........
T Consensus       240 ~~~~g~~~~A~~~~~~al~~-------~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~  312 (338)
T 2if4_A          240 LIKLKRYDEAIGHCNIVLTE-------EEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEK  312 (338)
T ss_dssp             HHTTTCCHHHHHHHHHHHHH-------CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------
T ss_pred             HHHcCCHHHHHHHHHHHHHh-------CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999983       34 4578999999999999999999999999999888 777777776644443


Q ss_pred             ---CcHHHHHHHHHhC
Q 011236          472 ---QEVDGLLESMKAD  484 (490)
Q Consensus       472 ---~~a~~~~~~m~~~  484 (490)
                         +.+..+|++|...
T Consensus       313 ~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          313 ALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             ----------------
T ss_pred             HHHHHHHHHHHHhhCC
Confidence               7788888888754

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.97  E-value=3.6e-05  Score=72.69  Aligned_cols=125  Identities=14%  Similarity=-0.015  Sum_probs=88.9

Q ss_pred             HHHhcCChhHHHHHHHHHHHhcC------CC-ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhc---CCC---CC-chhHH
Q 011236          288 HYASLGNKDEMMKFWGLQKIKCK------KQ-LNRDYITMLGSLVKIGELEEAEKMLEEWELS---CYC---YD-FRVPN  353 (490)
Q Consensus       288 ~~~~~~~~~~a~~~~~~~~~~~~------~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~---~~-~~~~~  353 (490)
                      .+...|++++|+.++++.+....      .| ...+++.|..+|...|++++|..++++.++.   -+.   |+ ..+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            45578899999988887766432      12 2246788888888999999999988877643   122   22 34678


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHH-----cCCC-CCHH-HHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVK-----KGKT-PTPN-SWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~-----~~~~-p~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .|...|...|++++|..++++..+     .|.. |+.. +.+.+..++...+.+++|..++.++.+
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888889999999999998888764     3543 2222 345566677778888888888888876

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.89  E-value=5.5e-05  Score=55.98  Aligned_cols=78  Identities=13%  Similarity=0.122  Sum_probs=46.5

Q ss_pred             HHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          333 AEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       333 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +...+++..+.. +.+...+..+...|...|++++|...|++.++..+. +...|..+..+|...|++++|...|+++++
T Consensus         4 a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A            4 ITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPT-YSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            455555555532 224455566666666666666666666666665433 455666666666666666666666666665

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.89  E-value=6.7e-06  Score=60.43  Aligned_cols=62  Identities=11%  Similarity=0.128  Sum_probs=39.2

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          350 RVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       350 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ..+..+...+...|++++|...|++.++..+. +...|..+..++...|++++|+..++++++
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   66 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQPQ-NPVGYSNKAMALIKLGEYTQAIQMCQQGLR   66 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            34555566666666666666666666665433 555666666666666666666666666665

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.87  E-value=0.00013  Score=53.90  Aligned_cols=78  Identities=13%  Similarity=0.101  Sum_probs=39.9

Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHH
Q 011236          226 MENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQ  305 (490)
Q Consensus       226 a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  305 (490)
                      |...|++.. ..+. .+...+..+..+|...|++++|+..|++.....+  .+...|..+..++...|++++|...|++.
T Consensus         4 a~~~~~~al-~~~p-~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p--~~~~~~~~la~~~~~~g~~~~A~~~~~~a   79 (115)
T 2kat_A            4 ITERLEAML-AQGT-DNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDP--TYSVAWKWLGKTLQGQGDRAGARQAWESG   79 (115)
T ss_dssp             HHHHHHHHH-TTTC-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHH-HhCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCC--CcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            444455444 3332 3444555555555555555555555555554433  34445555555555555555555555544


Q ss_pred             HH
Q 011236          306 KI  307 (490)
Q Consensus       306 ~~  307 (490)
                      ..
T Consensus        80 l~   81 (115)
T 2kat_A           80 LA   81 (115)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=97.84  E-value=5.5e-05  Score=58.49  Aligned_cols=98  Identities=15%  Similarity=0.022  Sum_probs=65.8

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC----------HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          327 IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM----------IEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       327 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----------~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      .+.+++|.+.++...+.. +.+...|+.+..++...++          +++|+..|++.++.++. +...|..+..+|..
T Consensus        15 ~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~-~~~A~~~LG~ay~~   92 (158)
T 1zu2_A           15 ILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNAYTS   92 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcC-cHHHHHHHHHHHHH
Confidence            344555555555555542 2244455555555555444          56888888888887665 67788888888887


Q ss_pred             cC-----------CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHH
Q 011236          397 KN-----------NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDW  433 (490)
Q Consensus       397 ~~-----------~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~  433 (490)
                      .|           ++++|++.|+++++       +.|+...|...+..
T Consensus        93 lg~l~P~~~~a~g~~~eA~~~~~kAl~-------l~P~~~~y~~al~~  133 (158)
T 1zu2_A           93 FAFLTPDETEAKHNFDLATQFFQQAVD-------EQPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHHHHHHH
T ss_pred             hcccCcchhhhhccHHHHHHHHHHHHH-------hCCCCHHHHHHHHH
Confidence            64           89999999999998       55776666555443

>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=97.82  E-value=3.6e-05  Score=59.55  Aligned_cols=97  Identities=12%  Similarity=0.100  Sum_probs=80.5

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH----------HHHHHHHHHHHHhhhcCcCCCcch-hhH
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM----------EKAFECMKEALAVHEENKFWRPKP-SLV  427 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~----------~~a~~~~~~~~~~~~~~~~~~p~~-~~~  427 (490)
                      ..+.+++++|.+.++..++..+. +...|..+..++...+++          ++|+..|+++++       +.|+. ..|
T Consensus        12 ~~r~~~feeA~~~~~~Ai~l~P~-~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~-------ldP~~~~A~   83 (158)
T 1zu2_A           12 FDRILLFEQIRQDAENTYKSNPL-DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL-------IDPKKDEAV   83 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHH-------hCcCcHHHH
Confidence            45667899999999999998766 889999999999888764          599999999998       44655 789


Q ss_pred             HHHHHHHHcCC-----------CHHHHHHHHHHHHhcccchhhhHHH
Q 011236          428 SSILDWLGDNR-----------DVEEVEAFVSSLKIKVQKRNMYHAL  463 (490)
Q Consensus       428 ~~l~~~~~~~g-----------~~~~a~~~~~~~~~~~~~~~~~~~l  463 (490)
                      ..+..+|...|           ++++|.+.|+++.+..|....|...
T Consensus        84 ~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~a  130 (158)
T 1zu2_A           84 WCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKS  130 (158)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            99999998774           8999999999999999984444333

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.82  E-value=0.00016  Score=50.55  Aligned_cols=83  Identities=13%  Similarity=0.203  Sum_probs=66.1

Q ss_pred             CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhH
Q 011236          383 TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYH  461 (490)
Q Consensus       383 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~  461 (490)
                      +...+..+...+...|++++|...++++++..      +.+...+..+...+...|++++|...+++..+..|. ...+.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~   81 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELD------PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQ   81 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC------TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC------CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCHHHHH
Confidence            34567788888888999999999999988722      124567788888888999999999999999888888 88888


Q ss_pred             HHHHHHHhcC
Q 011236          462 ALTEAHIRSG  471 (490)
Q Consensus       462 ~l~~~~~~~g  471 (490)
                      .+..++.+.|
T Consensus        82 ~l~~~~~~~g   91 (91)
T 1na3_A           82 NLGNAKQKQG   91 (91)
T ss_dssp             HHHHHHHHHC
T ss_pred             HHHHHHHhcC
Confidence            8887776554

>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=97.80  E-value=0.00077  Score=51.61  Aligned_cols=111  Identities=10%  Similarity=-0.080  Sum_probs=64.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHH
Q 011236          329 ELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAF  404 (490)
Q Consensus       329 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~  404 (490)
                      ++++|.+.|++..+.|.   ....  |...|...+.+++|...|++..+.|   +...+..|...|..    .+++++|+
T Consensus        10 d~~~A~~~~~~aa~~g~---~~a~--lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A           10 DLKKAIQYYVKACELNE---MFGC--LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTTC---TTHH--HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCCC---Hhhh--HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            45566666666665541   1122  4555555556666666666666653   55556666666655    56666666


Q ss_pred             HHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc----CCCHHHHHHHHHHHHhccc
Q 011236          405 ECMKEALAVHEENKFWRPKPSLVSSILDWLGD----NRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       405 ~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~  455 (490)
                      .+|+++.+     .   -+...+..|...|..    .++.++|..+|++..+.+.
T Consensus        82 ~~~~~Aa~-----~---g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           82 QYYSKACG-----L---NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHH-----T---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHc-----C---CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            66666665     2   234445555555555    5666666666666666554

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.75  E-value=2.4e-05  Score=57.34  Aligned_cols=65  Identities=6%  Similarity=-0.093  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC
Q 011236           70 LELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK  135 (490)
Q Consensus        70 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p  135 (490)
                      ..+..+...+...|++++|++.|++..+.. +.++..+..+..++...|++++|+..|+......|
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p   69 (111)
T 2l6j_A            5 EKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTS   69 (111)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC
Confidence            344444455555555555555555555443 23344444444444455555555555554444443

>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=97.70  E-value=0.00086  Score=51.33  Aligned_cols=108  Identities=8%  Similarity=-0.068  Sum_probs=67.2

Q ss_pred             ChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh----cCCHHHHH
Q 011236          294 NKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ----KGMIEKAD  369 (490)
Q Consensus       294 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~  369 (490)
                      ++++|...|++....+. +...    +...|...+.+++|.+.|++..+.|   +...+..|...|..    .+++++|.
T Consensus        10 d~~~A~~~~~~aa~~g~-~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~   81 (138)
T 1klx_A           10 DLKKAIQYYVKACELNE-MFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   81 (138)
T ss_dssp             HHHHHHHHHHHHHHTTC-TTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHcCCC-Hhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHHH
Confidence            45566666665555442 3222    5555555556666666666666653   34555566666666    66777777


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHHHHHHHHHH
Q 011236          370 AVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAFECMKEALA  412 (490)
Q Consensus       370 ~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~  412 (490)
                      ..|++..+.|   ++..+..|...|..    .++.++|..+|+++.+
T Consensus        82 ~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~  125 (138)
T 1klx_A           82 QYYSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACR  125 (138)
T ss_dssp             HHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHH
Confidence            7777777654   55666666666666    6777777777777766

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.68  E-value=0.00057  Score=47.57  Aligned_cols=62  Identities=21%  Similarity=0.329  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIK  308 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  308 (490)
                      .+..+...+...|++++|+..|++.....+  .+...+..+..++...|++++|...+++....
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~   72 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELDP--NNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL   72 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            344444444455555555555554444332  23444444444455555555555555444443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.68  E-value=0.00031  Score=50.33  Aligned_cols=64  Identities=11%  Similarity=0.133  Sum_probs=42.4

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          348 DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       348 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +...+..+...|.+.|++++|+..|++.++.++. +...|..+..+|...|++++|.+.|+++++
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPD-YVGTYYHLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3445566666667777777777777777666544 455666677777777777777777776665

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.62  E-value=0.00047  Score=49.35  Aligned_cols=65  Identities=15%  Similarity=0.084  Sum_probs=39.6

Q ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 011236          242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIK  308 (490)
Q Consensus       242 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  308 (490)
                      +...+..+..+|...|++++|+..|++..+..+  .+...|..+..+|...|++++|...|++....
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p--~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDP--DYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHST--TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC--CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            345555566666666666666666666665544  34556666666666666666666666655443

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.55  E-value=0.003  Score=56.26  Aligned_cols=74  Identities=12%  Similarity=0.063  Sum_probs=53.5

Q ss_pred             CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchh
Q 011236          346 CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS  425 (490)
Q Consensus       346 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~  425 (490)
                      +.+..+|..+...+...|++++|...+++++..+  |+...|..+...+.-.|++++|.+.++++..       +.|...
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~Alr-------L~P~~~  344 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFN-------LRPGAN  344 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HSCSHH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-------cCCCcC
Confidence            4455666666666666788888888888888775  5776777777777788888888888888877       446666


Q ss_pred             hHH
Q 011236          426 LVS  428 (490)
Q Consensus       426 ~~~  428 (490)
                      +|.
T Consensus       345 t~~  347 (372)
T 3ly7_A          345 TLY  347 (372)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            554

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=97.38  E-value=0.0032  Score=56.09  Aligned_cols=72  Identities=7%  Similarity=-0.050  Sum_probs=45.6

Q ss_pred             CCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHH
Q 011236          170 GSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTY  246 (490)
Q Consensus       170 p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  246 (490)
                      .+..+|..+...+...|++++|...+++....+  |+...|..+...+.-.|++++|.+.|++.. ..  .|...+|
T Consensus       275 ~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~Al-rL--~P~~~t~  346 (372)
T 3ly7_A          275 NLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAF-NL--RPGANTL  346 (372)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HH--SCSHHHH
T ss_pred             cCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-hc--CCCcChH
Confidence            355566666555555677777777777776654  566666666666677777777777777665 32  2444454

>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=97.27  E-value=0.0019  Score=60.01  Aligned_cols=96  Identities=7%  Similarity=-0.134  Sum_probs=57.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcC---CCCC----HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcC-CCcch-hhH
Q 011236          357 LGYSQKGMIEKADAVLKEIVKKG---KTPT----PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKF-WRPKP-SLV  427 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~~---~~p~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~p~~-~~~  427 (490)
                      ..+.+.|++++|+.++++..+..   +.|+    ..+++.+...|...|++++|+.++++++.......| -.|+. .++
T Consensus       295 e~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l  374 (429)
T 3qwp_A          295 EELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQV  374 (429)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHH
T ss_pred             HHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHH
Confidence            33455667777777777665431   1111    235677777777777777777777777664432222 22333 456


Q ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          428 SSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       428 ~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      +.|...|...|++++|+.+++++.+
T Consensus       375 ~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          375 MKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            6777777777777777777766544

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.26  E-value=0.00055  Score=48.71  Aligned_cols=56  Identities=18%  Similarity=0.326  Sum_probs=33.1

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCCCHH-HHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          356 LLGYSQKGMIEKADAVLKEIVKKGKTPTPN-SWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       356 ~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...+.+.|++++|...|++..+..+. +.. .|..+..+|...|++++|...|+++++
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTEPV-GKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCSS-THHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            34455566666666666666655433 444 566666666666666666666666665

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=97.26  E-value=0.00091  Score=62.06  Aligned_cols=93  Identities=5%  Similarity=-0.138  Sum_probs=69.4

Q ss_pred             hcCCHHHHHHHHHHHHHc-----CCC-CC-HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcC-CCcch-hhHHHHH
Q 011236          361 QKGMIEKADAVLKEIVKK-----GKT-PT-PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKF-WRPKP-SLVSSIL  431 (490)
Q Consensus       361 ~~g~~~~A~~~~~~m~~~-----~~~-p~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~p~~-~~~~~l~  431 (490)
                      ..|++++|+.++++.++.     |.. |+ ..+++.|..+|...|++++|..+++++++......| -.|+. .+++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            357888898888887652     221 22 357888999999999999999999998875543334 23444 5788889


Q ss_pred             HHHHcCCCHHHHHHHHHHHHhc
Q 011236          432 DWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       432 ~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      ..|...|++++|+.+++++.+.
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~i  411 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIAI  411 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHH
Confidence            9999999999999998877653

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.14  E-value=0.0017  Score=46.06  Aligned_cols=59  Identities=19%  Similarity=0.186  Sum_probs=37.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCch-hHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYCYDFR-VPNIILLGYSQKGMIEKADAVLKEIVKKGK  380 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  380 (490)
                      ...+.+.|++++|...+++..+.. +.+.. .+..+..+|...|++++|...|++.++.++
T Consensus         7 a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p   66 (99)
T 2kc7_A            7 IKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNP   66 (99)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC
Confidence            445556677777777777766642 22344 566666667777777777777777766543

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=97.13  E-value=0.00045  Score=62.91  Aligned_cols=249  Identities=12%  Similarity=0.107  Sum_probs=141.8

Q ss_pred             hhccCCCCcccHHHhhccCCCCCCChHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhH
Q 011236           28 YRAVKPVARNNLYSRISPLGDPDVSLTPVLDQWVLEGQKISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDH  107 (490)
Q Consensus        28 ~~~~~~~~~~~l~~~l~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  107 (490)
                      .+...|.-|..|-.+....++..+++...++       .-|+..|..++....+.|.+++-+..+....+..  -++..-
T Consensus        49 ~~~n~p~VWs~LgkAqL~~~~v~eAIdsyIk-------A~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~--ke~~ID  119 (624)
T 3lvg_A           49 ERCNEPAVWSQLAKAQLQKGMVKEAIDSYIK-------ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVE  119 (624)
T ss_dssp             SSCCCCCCSSSHHHHTTTSSSCTTTTTSSCC-------CSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTC--CSTTTT
T ss_pred             HHhCCccHHHHHHHHHHccCchHHHHHHHHh-------CCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHh--cccccH
Confidence            3344677788888888888887777763332       3467778888888888888888888877666553  355666


Q ss_pred             HHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcC--------------------
Q 011236          108 AVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMG--------------------  167 (490)
Q Consensus       108 ~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~--------------------  167 (490)
                      +.++-+|++.+++.+-.+++.     +||..-...+.+-|...|.++.|.-+|..+....                    
T Consensus       120 teLi~ayAk~~rL~elEefl~-----~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaAr  194 (624)
T 3lvg_A          120 TELIFALAKTNRLAELEEFIN-----GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGAR  194 (624)
T ss_dssp             HHHHHHHHTSCSSSTTTSTTS-----CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTT
T ss_pred             HHHHHHHHhhCcHHHHHHHHc-----CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHH
Confidence            677778888887655443321     2444444555556666666666655554432110                    


Q ss_pred             CCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHH
Q 011236          168 SFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYS  247 (490)
Q Consensus       168 ~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  247 (490)
                      -.-++.||-.+-.+|...+.+.-|.-+--.++-.   ||  ....++..|-..|.+++-+.+++.-. ... ......|+
T Consensus       195 KAns~ktWKeV~~ACvd~~EfrLAqicGLniIvh---ad--eL~elv~~YE~~G~f~ELIsLlEagl-glE-rAHmGmFT  267 (624)
T 3lvg_A          195 KANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVH---AD--ELEELINYYQDRGYFEELITMLEAAL-GLE-RAHMGMFT  267 (624)
T ss_dssp             TCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCC---SS--CCSGGGSSSSTTCCCTTSTTTHHHHT-TST-TCCHHHHH
T ss_pred             hcCChhHHHHHHHHHhCchHHHHHHHhcchhccc---HH--HHHHHHHHHHhCCCHHHHHHHHHHHh-CCC-chhHHHHH
Confidence            1236677888888888777777666554444321   11  12234555666666666666666554 211 13445555


Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhcc-C-----CChhhHHHHHHHHHhcCChhHH
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSK-S-----KDALGYNHLISHYASLGNKDEM  298 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~-~-----~~~~~~~~l~~~~~~~~~~~~a  298 (490)
                      -|.-.|++- .+++..+.++........ +     .....|..++-.|++-.+++.|
T Consensus       268 ELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA  323 (624)
T 3lvg_A          268 ELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNA  323 (624)
T ss_dssp             HHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHH
Confidence            555555544 334444433332221111 0     1233455555555555555544

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.09  E-value=0.0094  Score=60.86  Aligned_cols=28  Identities=7%  Similarity=0.046  Sum_probs=13.7

Q ss_pred             CHHHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          206 DNFSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       206 ~~~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      +...|..+...+.+.|+++.|++.|.++
T Consensus       680 ~~~~W~~la~~al~~~~~~~A~~~y~~~  707 (814)
T 3mkq_A          680 AEMKWRALGDASLQRFNFKLAIEAFTNA  707 (814)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cHhHHHHHHHHHHHcCCHHHHHHHHHHc
Confidence            3344444555555555555555555444

>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=97.05  E-value=0.0027  Score=58.93  Aligned_cols=103  Identities=12%  Similarity=0.011  Sum_probs=76.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcC---CCCC----chhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----CC-CCCH-HH
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSC---YCYD----FRVPNIILLGYSQKGMIEKADAVLKEIVKK-----GK-TPTP-NS  386 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~---~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~-----~~-~p~~-~~  386 (490)
                      +..+.+.|++++|..++++..+..   +.|+    ..+++.+...|...|++++|+.++++.++.     |. .|+. .+
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            444567889999999999887542   2222    347888999999999999999999988642     32 2332 46


Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchh
Q 011236          387 WSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS  425 (490)
Q Consensus       387 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~  425 (490)
                      ++.|...|...|++++|..+++++++......|  |+..
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG--~~Hp  410 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHG--REHS  410 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTC--TTSH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcC--CCCh
Confidence            899999999999999999999999885543334  5543

>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=96.95  E-value=0.0034  Score=58.24  Aligned_cols=88  Identities=8%  Similarity=-0.096  Sum_probs=69.6

Q ss_pred             ccCCHHHHHHHHHHHHHhhhcCcC-CCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhc-----ccc----hhhhHHHH
Q 011236          396 DKNNMEKAFECMKEALAVHEENKF-WRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIK-----VQK----RNMYHALT  464 (490)
Q Consensus       396 ~~~~~~~a~~~~~~~~~~~~~~~~-~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-----~~~----~~~~~~l~  464 (490)
                      ..|++++|..+++++++......| -.|+. .+++.+..+|...|++++|+.+++++.+.     |+.    ...++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            458999999999999885532233 12333 67889999999999999999999987653     333    77899999


Q ss_pred             HHHHhcC--CcHHHHHHHHHh
Q 011236          465 EAHIRSG--QEVDGLLESMKA  483 (490)
Q Consensus       465 ~~~~~~g--~~a~~~~~~m~~  483 (490)
                      ..|...|  ++|..++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            9999999  889999887653

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.86  E-value=0.011  Score=41.21  Aligned_cols=65  Identities=9%  Similarity=-0.032  Sum_probs=41.4

Q ss_pred             CCchhHHHHHHHHHhcCC---HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          347 YDFRVPNIILLGYSQKGM---IEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       347 ~~~~~~~~l~~~~~~~g~---~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .+...+..+..++...++   .++|..++++.++.++. ++.....+...+.+.|++++|+..|+++++
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~-~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~   71 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPY-NEAALSLIANDHFISFRFQEAIDTWVLLLD   71 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            344555555555543333   56777777777766554 666666666777777777777777777766

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.70  E-value=0.026  Score=40.34  Aligned_cols=79  Identities=11%  Similarity=-0.001  Sum_probs=53.9

Q ss_pred             CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcC-CCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhh
Q 011236          383 TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKF-WRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMY  460 (490)
Q Consensus       383 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~  460 (490)
                      +..-+..+...+.+.+++..|...|+.+++..+.... -.+....+..+..++.+.|+++.|...++++.+..|. ..+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~~~~~~   83 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRAN   83 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHH
Confidence            4445566777778888888888888887774432211 1234467777778888888888888888888877777 4443


Q ss_pred             H
Q 011236          461 H  461 (490)
Q Consensus       461 ~  461 (490)
                      +
T Consensus        84 ~   84 (104)
T 2v5f_A           84 G   84 (104)
T ss_dssp             H
T ss_pred             h
Confidence            3

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=96.65  E-value=0.013  Score=40.95  Aligned_cols=66  Identities=5%  Similarity=-0.029  Sum_probs=37.2

Q ss_pred             CChhhHHHHHHHHHhhcC---HHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcC
Q 011236          102 FSVHDHAVQLDLIGKVRG---LESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMG  167 (490)
Q Consensus       102 ~~~~~~~~l~~~~~~~~~---~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~  167 (490)
                      .++..+..+..++...++   .++|..+|++....+| ++.+...+...+.+.|++++|+..|+++.+..
T Consensus         4 ~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~   73 (93)
T 3bee_A            4 VTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSN   73 (93)
T ss_dssp             CCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            344455555554443333   4566666666666555 35555555666666666666666666666553

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.62  E-value=0.037  Score=42.27  Aligned_cols=83  Identities=13%  Similarity=0.041  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC---CHHHHHHHHHHHHHhhhcCcCCCc--chhhHHHHHHHHHcCCCHH
Q 011236          367 KADAVLKEIVKKGKTPTPNSWSIIAAGYADKN---NMEKAFECMKEALAVHEENKFWRP--KPSLVSSILDWLGDNRDVE  441 (490)
Q Consensus       367 ~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~p--~~~~~~~l~~~~~~~g~~~  441 (490)
                      .+.+-|.+..+.|. ++..+...+..++++.+   +.++++.+|++..+     .. .|  +...+..+.-++.+.|+++
T Consensus        16 ~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~-----~~-~p~~~rd~lY~LAv~~~kl~~Y~   88 (152)
T 1pc2_A           16 KFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLP-----KG-SKEEQRDYVFYLAVGNYRLKEYE   88 (152)
T ss_dssp             HHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHH-----HS-CHHHHHHHHHHHHHHHHHTSCHH
T ss_pred             HHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHh-----cC-CccchHHHHHHHHHHHHHccCHH
Confidence            34444444444433 35555555555555555   34455555555554     11 12  1233344444555555555


Q ss_pred             HHHHHHHHHHhcccc
Q 011236          442 EVEAFVSSLKIKVQK  456 (490)
Q Consensus       442 ~a~~~~~~~~~~~~~  456 (490)
                      +|.+.++.+.+..|.
T Consensus        89 ~A~~y~~~lL~ieP~  103 (152)
T 1pc2_A           89 KALKYVRGLLQTEPQ  103 (152)
T ss_dssp             HHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHhcCCC
Confidence            555555555555554

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.58  E-value=0.015  Score=44.37  Aligned_cols=81  Identities=19%  Similarity=0.136  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC---CHHHHHHHHHHHHHcCCCC--CHHHHHHHHHHHhccCCHHHHH
Q 011236          330 LEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG---MIEKADAVLKEIVKKGKTP--TPNSWSIIAAGYADKNNMEKAF  404 (490)
Q Consensus       330 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~m~~~~~~p--~~~~~~~l~~~~~~~~~~~~a~  404 (490)
                      ...+++-|.+..+.|. ++..+...+..++++.+   +++++..+|+...+.+ .|  +...+-.+.-+|.+.|++++|.
T Consensus        14 l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHH
Confidence            3445555555555443 45556566666777766   5557777777776654 12  3445556666677777777777


Q ss_pred             HHHHHHHH
Q 011236          405 ECMKEALA  412 (490)
Q Consensus       405 ~~~~~~~~  412 (490)
                      ++++.+++
T Consensus        92 ~y~~~lL~   99 (152)
T 1pc2_A           92 KYVRGLLQ   99 (152)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHh
Confidence            77777777

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.45  E-value=0.2  Score=50.90  Aligned_cols=154  Identities=11%  Similarity=0.058  Sum_probs=96.7

Q ss_pred             HHHhcCChhHHHH-HHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHH
Q 011236           78 QLRSRKRFKHALQ-VSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDES  156 (490)
Q Consensus        78 ~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a  156 (490)
                      .....+++++|.+ ++..     + ++......++..+.+.|..+.|.++.+.     |.     .-.......|++++|
T Consensus       608 ~~~~~~~~~~a~~~~l~~-----i-~~~~~~~~~~~~l~~~~~~~~a~~~~~~-----~~-----~~f~~~l~~~~~~~A  671 (814)
T 3mkq_A          608 TLTLRGEIEEAIENVLPN-----V-EGKDSLTKIARFLEGQEYYEEALNISPD-----QD-----QKFELALKVGQLTLA  671 (814)
T ss_dssp             HHHHTTCHHHHHHHTGGG-----C-CCHHHHHHHHHHHHHTTCHHHHHHHCCC-----HH-----HHHHHHHHHTCHHHH
T ss_pred             HHHHhCCHHHHHHHHHhc-----C-CchHHHHHHHHHHHhCCChHHheecCCC-----cc-----hheehhhhcCCHHHH
Confidence            3345788888866 4411     1 1133346677777888888888876531     11     113345667888888


Q ss_pred             HHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhC
Q 011236          157 LSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQ  236 (490)
Q Consensus       157 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~  236 (490)
                      .++.+.+      .+...|..|...+.+.++++.|.++|..+..         |..+...+...|+.+...++-+... .
T Consensus       672 ~~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~-~  735 (814)
T 3mkq_A          672 RDLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAE-T  735 (814)
T ss_dssp             HHHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHH-H
T ss_pred             HHHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHH-H
Confidence            8876433      2667888888888888888888888887743         3345555555677776666555554 3


Q ss_pred             CCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 011236          237 SHISMDWGTYSTVANYYIIAGLKEKAIIYLKKC  269 (490)
Q Consensus       237 ~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~  269 (490)
                      .|-      ++....+|.+.|++++|++++.++
T Consensus       736 ~~~------~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          736 TGK------FNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             TTC------HHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             cCc------hHHHHHHHHHcCCHHHHHHHHHHc
Confidence            332      333445566677777777766653

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=96.04  E-value=8e-06  Score=73.99  Aligned_cols=113  Identities=5%  Similarity=-0.033  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHh
Q 011236           70 LELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVR  149 (490)
Q Consensus        70 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~  149 (490)
                      ..|..|..+....++..+|++-|   ++.   -++..|..++..+.+.|.+++-..++....+...++.+=+.|+-+|++
T Consensus        55 ~VWs~LgkAqL~~~~v~eAIdsy---IkA---~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~~IDteLi~ayAk  128 (624)
T 3lvg_A           55 AVWSQLAKAQLQKGMVKEAIDSY---IKA---DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAK  128 (624)
T ss_dssp             CCSSSHHHHTTTSSSCTTTTTSS---CCC---SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCSTTTTHHHHHHHHT
T ss_pred             cHHHHHHHHHHccCchHHHHHHH---HhC---CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccHHHHHHHHHh
Confidence            34444444444444444443322   111   244444444445545555555444444444333333333444445555


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHH
Q 011236          150 EGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVL  195 (490)
Q Consensus       150 ~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~  195 (490)
                      .++..+-.+++.       .||..-...+.+-|...|.++.|.-+|
T Consensus       129 ~~rL~elEefl~-------~~N~A~iq~VGDrcf~e~lYeAAKily  167 (624)
T 3lvg_A          129 TNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLY  167 (624)
T ss_dssp             SCSSSTTTSTTS-------CCSSSCTHHHHHHHHHSCCSTTSSTTG
T ss_pred             hCcHHHHHHHHc-------CCCcccHHHHHHHHHHccCHHHHHHHH
Confidence            444433322221       134444444444444444444444444

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=96.02  E-value=0.15  Score=38.36  Aligned_cols=113  Identities=12%  Similarity=0.123  Sum_probs=62.9

Q ss_pred             CChhhHHHHHHHHHhcCCh------hHHHHHHHHHHHhcCCCChh-hHHHHHH------HHHhcCCHHHHHHHHHHHHhc
Q 011236          277 KDALGYNHLISHYASLGNK------DEMMKFWGLQKIKCKKQLNR-DYITMLG------SLVKIGELEEAEKMLEEWELS  343 (490)
Q Consensus       277 ~~~~~~~~l~~~~~~~~~~------~~a~~~~~~~~~~~~~~~~~-~~~~l~~------~~~~~~~~~~a~~~~~~~~~~  343 (490)
                      .|..+|-..+...-+.|++      ++..++|++....-+ |+.. .+...+.      .+...++.++|.++|+.+++.
T Consensus        11 ~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~~P-p~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           11 NNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALP-PDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHHSC-GGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHcCC-ccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            3445555555555555555      566666666655544 3321 1111111      112336778888888887665


Q ss_pred             CCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Q 011236          344 CYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAA  392 (490)
Q Consensus       344 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~  392 (490)
                      .-.. ...|.....--.+.|++.+|.+++.+.+..+++| .......+.
T Consensus        90 hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~-~~~le~a~~  136 (161)
T 4h7y_A           90 CKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP-LEMLEIALR  136 (161)
T ss_dssp             CTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC-HHHHHHHHH
T ss_pred             hHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc-HHHHHHHHH
Confidence            2222 4455555555567888888888888888877664 333343333

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.00  E-value=0.069  Score=38.08  Aligned_cols=61  Identities=7%  Similarity=-0.012  Sum_probs=35.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHcC------CCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          352 PNIILLGYSQKGMIEKADAVLKEIVKKG------KTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       352 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~------~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +..+...+.+.|+++.|...|+...+.-      -.+....+..+..++.+.|++++|..++++++.
T Consensus         8 c~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~   74 (104)
T 2v5f_A            8 CFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLE   74 (104)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHh
Confidence            3445555556666666666665554421      112345566666777777777777777777766

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.95  E-value=0.087  Score=41.32  Aligned_cols=27  Identities=19%  Similarity=0.148  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          207 NFSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       207 ~~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      ...|..|.......|+++-|++.|.+.
T Consensus        34 ~~~Wk~Lg~~AL~~gn~~lAe~cy~~~   60 (177)
T 3mkq_B           34 SITWERLIQEALAQGNASLAEMIYQTQ   60 (177)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHh
Confidence            444555555555555555555555444

>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=95.83  E-value=0.041  Score=46.97  Aligned_cols=91  Identities=10%  Similarity=0.037  Sum_probs=62.3

Q ss_pred             HHHHHHHHHHccccCCC---hhHHHHHHHHHHhc-----CChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhc-CCcCc
Q 011236          120 LESAETYFNSLNDEDKV---DKLYGALLNCYVRE-----GLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNT-GQHEK  190 (490)
Q Consensus       120 ~~~A~~~~~~~~~~~p~---~~~~~~li~~~~~~-----g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~-~~~~~  190 (490)
                      ...|...+++..+.+|+   ...|..+...|.+.     |+.++|.+.|++..+.+..-+..++......++.. |+.++
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            35677777777777765   45677777777773     77888888888877765433466777777777764 77777


Q ss_pred             HHHHHHHHHHCCCC--CCHHHH
Q 011236          191 IPDVLLDMKENGVP--PDNFSY  210 (490)
Q Consensus       191 a~~~~~~m~~~~~~--p~~~~~  210 (490)
                      +.+.+++.++....  |+....
T Consensus       259 a~~~L~kAL~a~p~~~P~~~la  280 (301)
T 3u64_A          259 FDEALDRALAIDPESVPHNKLL  280 (301)
T ss_dssp             HHHHHHHHHHCCGGGCSSCHHH
T ss_pred             HHHHHHHHHcCCCCCCCChhHH
Confidence            77777777776554  554333

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.82  E-value=0.5  Score=37.07  Aligned_cols=99  Identities=11%  Similarity=0.070  Sum_probs=46.0

Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHH
Q 011236          290 ASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKAD  369 (490)
Q Consensus       290 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  369 (490)
                      ...|+++.|.++.+.+      .+...|..|.......|+++-|++.|.....         +..+.-.|.-.|+.++-.
T Consensus        16 L~lg~l~~A~e~a~~l------~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~   80 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLS   80 (177)
T ss_dssp             HHTTCHHHHHHHHHHH------CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHH
T ss_pred             HhcCCHHHHHHHHHHh------CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHH
Confidence            3445555555554422      2344555555555555555555555554322         233444444455554444


Q ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHH
Q 011236          370 AVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKE  409 (490)
Q Consensus       370 ~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~  409 (490)
                      ++-+.....|      -++.....+...|+++++.++|.+
T Consensus        81 kla~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~  114 (177)
T 3mkq_B           81 KMQNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAE  114 (177)
T ss_dssp             HHHHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHH
Confidence            4333333322      133444444455555555555544

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.75  E-value=2  Score=43.53  Aligned_cols=154  Identities=13%  Similarity=0.042  Sum_probs=62.0

Q ss_pred             HhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhh--HHHHHHHHHhcCC
Q 011236          217 YGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALG--YNHLISHYASLGN  294 (490)
Q Consensus       217 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~~~  294 (490)
                      +.-.|+-+....++..+.+..  .-++.-...+.-++...|+.+.+..+.+.+.....  |....  -.++..+|+..|+
T Consensus       500 ~vGTgn~~ai~~LL~~~~e~~--~e~vrR~aalgLGll~~g~~e~~~~li~~L~~~~d--p~vRygaa~alglAyaGTGn  575 (963)
T 4ady_A          500 MLGTGKPEAIHDMFTYSQETQ--HGNITRGLAVGLALINYGRQELADDLITKMLASDE--SLLRYGGAFTIALAYAGTGN  575 (963)
T ss_dssp             HTTCCCHHHHHHHHHHHHHCS--CHHHHHHHHHHHHHHTTTCGGGGHHHHHHHHHCSC--HHHHHHHHHHHHHHTTTSCC
T ss_pred             hcccCCHHHHHHHHHHHhccC--cHHHHHHHHHHHHhhhCCChHHHHHHHHHHHhCCC--HHHHHHHHHHHHHHhcCCCC
Confidence            344555555555555544111  01111112222233345565555555555543211  11111  1123344555566


Q ss_pred             hhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCH-HHHHHHHH
Q 011236          295 KDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMI-EKADAVLK  373 (490)
Q Consensus       295 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~-~~A~~~~~  373 (490)
                      .....+++..+... ...+......+.-++...|+.+.+.++++.+.+. ..|.+..-..+.-+....|.. .++..++.
T Consensus       576 ~~aIq~LL~~~~~d-~~d~VRraAViaLGlI~~g~~e~v~rlv~~L~~~-~d~~VR~gAalALGli~aGn~~~~aid~L~  653 (963)
T 4ady_A          576 NSAVKRLLHVAVSD-SNDDVRRAAVIALGFVLLRDYTTVPRIVQLLSKS-HNAHVRCGTAFALGIACAGKGLQSAIDVLD  653 (963)
T ss_dssp             HHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTSSSCSSHHHHTTTGGGC-SCHHHHHHHHHHHHHHTSSSCCHHHHHHHH
T ss_pred             HHHHHHHHHHhccC-CcHHHHHHHHHHHHhhccCCHHHHHHHHHHHHhc-CCHHHHHHHHHHHHHhccCCCcHHHHHHHH
Confidence            55555555544332 1122222222222333344444445555444333 233333333333333333332 34555555


Q ss_pred             HHH
Q 011236          374 EIV  376 (490)
Q Consensus       374 ~m~  376 (490)
                      .+.
T Consensus       654 ~L~  656 (963)
T 4ady_A          654 PLT  656 (963)
T ss_dssp             HHH
T ss_pred             HHc
Confidence            554

>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=95.70  E-value=0.09  Score=44.93  Aligned_cols=87  Identities=15%  Similarity=0.124  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHhhhhccCCChhhHHHHHHHHHh-----cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhc-CCHHHH
Q 011236          260 EKAIIYLKKCEDIVSKSKDALGYNHLISHYAS-----LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKI-GELEEA  333 (490)
Q Consensus       260 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~a  333 (490)
                      ..|...+++..+..+.-.+...|..+...|..     -|+.++|.+.|++.+...+..+..++......++.. |+.+++
T Consensus       180 ~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a  259 (301)
T 3u64_A          180 HAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGF  259 (301)
T ss_dssp             HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHH
Confidence            34445555544433211134456666666666     366666666666666665433455556666666653 666666


Q ss_pred             HHHHHHHHhcCCC
Q 011236          334 EKMLEEWELSCYC  346 (490)
Q Consensus       334 ~~~~~~~~~~~~~  346 (490)
                      .+.+++.......
T Consensus       260 ~~~L~kAL~a~p~  272 (301)
T 3u64_A          260 DEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHCCGG
T ss_pred             HHHHHHHHcCCCC
Confidence            6666666665444

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.66  E-value=2.2  Score=43.28  Aligned_cols=254  Identities=16%  Similarity=0.036  Sum_probs=132.8

Q ss_pred             HHhccCChHHHHHHHHHHHhCCCCCCC--HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhc-------cCCChhhHHHHH
Q 011236          216 SYGARSELSSMENVLQEMESQSHISMD--WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVS-------KSKDALGYNHLI  286 (490)
Q Consensus       216 ~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~-------~~~~~~~~~~l~  286 (490)
                      +....|+.++++.+++... ..+-..+  ...=..+.-+....|..+++..++........       . +....-.++.
T Consensus       383 GlIh~g~~~~gl~~L~~yL-~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~-~~ir~gAaLG  460 (963)
T 4ady_A          383 GVIHKGNLLEGKKVMAPYL-PGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDV-DVLLHGASLG  460 (963)
T ss_dssp             HHHTSSCTTTHHHHHTTTS-TTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHH-HHHHHHHHHH
T ss_pred             hhhccCchHHHHHHHHHhc-cccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCcccccccccc-HHHHHHHHHH
Confidence            4556788888888877665 2110122  22333444556666766677777766554322       0 1111122232


Q ss_pred             HHHHhcCC-hhHHHHHHHHHHHhcCCCChh--hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC
Q 011236          287 SHYASLGN-KDEMMKFWGLQKIKCKKQLNR--DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG  363 (490)
Q Consensus       287 ~~~~~~~~-~~~a~~~~~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  363 (490)
                      -+.+-.|. -+++.+.+..+..... +...  .-.++...++-.|+.+....++..+.+. ..-+..-...+.-++...|
T Consensus       461 LGla~~GS~~eev~e~L~~~L~dd~-~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~-~~e~vrR~aalgLGll~~g  538 (963)
T 4ady_A          461 IGLAAMGSANIEVYEALKEVLYNDS-ATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQET-QHGNITRGLAVGLALINYG  538 (963)
T ss_dssp             HHHHSTTCCCHHHHHHHHHHHHTCC-HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHC-SCHHHHHHHHHHHHHHTTT
T ss_pred             HHHHhcCCCCHHHHHHHHHHHhcCC-HHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhcc-CcHHHHHHHHHHHHhhhCC
Confidence            23333332 2455666655555332 1111  1223344455678888888888877653 2212222333444455778


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHH-HH---HHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCC
Q 011236          364 MIEKADAVLKEIVKKGKTPTPNS-WS---IIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRD  439 (490)
Q Consensus       364 ~~~~A~~~~~~m~~~~~~p~~~~-~~---~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  439 (490)
                      +.+.+..+++.+...   .++.+ |.   .+.-+|+..|+.....++++.+..      ....+..-...+.-++...|+
T Consensus       539 ~~e~~~~li~~L~~~---~dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~------d~~d~VRraAViaLGlI~~g~  609 (963)
T 4ady_A          539 RQELADDLITKMLAS---DESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVS------DSNDDVRRAAVIALGFVLLRD  609 (963)
T ss_dssp             CGGGGHHHHHHHHHC---SCHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH------CSCHHHHHHHHHHHHHHTSSS
T ss_pred             ChHHHHHHHHHHHhC---CCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcc------CCcHHHHHHHHHHHHhhccCC
Confidence            888888888888764   24433 22   344567788887777778888876      222222222233334444566


Q ss_pred             HHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC---CcHHHHHHHHH
Q 011236          440 VEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG---QEVDGLLESMK  482 (490)
Q Consensus       440 ~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g---~~a~~~~~~m~  482 (490)
                      .+.+.++++.+.+.+.+ .+.-..+.-+....|   .+|++.+..+.
T Consensus       610 ~e~v~rlv~~L~~~~d~~VR~gAalALGli~aGn~~~~aid~L~~L~  656 (963)
T 4ady_A          610 YTTVPRIVQLLSKSHNAHVRCGTAFALGIACAGKGLQSAIDVLDPLT  656 (963)
T ss_dssp             CSSHHHHTTTGGGCSCHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhccCCCcHHHHHHHHHHc
Confidence            66666666655544333 333333333333343   56777777665

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=95.59  E-value=0.25  Score=37.24  Aligned_cols=103  Identities=9%  Similarity=0.072  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHHHHcCCH------HHHHHHHHHHhhhhccCCChhhHHHHHHH------HHhcCChhHHHHHHHHHHHhcC
Q 011236          243 WGTYSTVANYYIIAGLK------EKAIIYLKKCEDIVSKSKDALGYNHLISH------YASLGNKDEMMKFWGLQKIKCK  310 (490)
Q Consensus       243 ~~~~~~li~~~~~~~~~------~~a~~~~~~~~~~~~~~~~~~~~~~l~~~------~~~~~~~~~a~~~~~~~~~~~~  310 (490)
                      ..+|-..+...-+.|+.      ++..++|++.....++ .....|...+..      +...++.++|.++|+.+...+.
T Consensus        13 yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~~Pp-~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~hK   91 (161)
T 4h7y_A           13 PEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPP-DKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCK   91 (161)
T ss_dssp             HHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHHSCG-GGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHcCCc-cccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhH
Confidence            44444445555555555      5666666666654442 111111111111      1234788888888888877644


Q ss_pred             CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC
Q 011236          311 KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY  347 (490)
Q Consensus       311 ~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~  347 (490)
                      .. ...|.....--.+.|++..|.+++......+..|
T Consensus        92 kF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~  127 (161)
T 4h7y_A           92 KF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVP  127 (161)
T ss_dssp             TB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBC
T ss_pred             HH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCc
Confidence            33 5566666666677888999999988888876554

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.39  E-value=0.38  Score=35.24  Aligned_cols=88  Identities=11%  Similarity=-0.017  Sum_probs=53.7

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHH---HHHHHHHHHHhhhcCcCCCc--chhhHHHHHHHHHc
Q 011236          362 KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEK---AFECMKEALAVHEENKFWRP--KPSLVSSILDWLGD  436 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~p--~~~~~~~l~~~~~~  436 (490)
                      ......+.+-|.+....|. |+..+--.+..++.+..+...   ++.++++...     .+ .|  .......+.-++.+
T Consensus        14 ~~~l~~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~-----~~-~p~~~Rd~lY~LAvg~yk   86 (126)
T 1nzn_A           14 VEDLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLP-----KG-SKEEQRDYVFYLAVGNYR   86 (126)
T ss_dssp             HHHHHHHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTT-----TS-CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHh-----cC-CcchHHHHHHHHHHHHHH
Confidence            3344455555555555444 566666666777777766554   6677776655     21 23  22334455557777


Q ss_pred             CCCHHHHHHHHHHHHhcccc
Q 011236          437 NRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .|+++.|.+.++.+.+..|.
T Consensus        87 lg~Y~~A~~~~~~lL~~eP~  106 (126)
T 1nzn_A           87 LKEYEKALKYVRGLLQTEPQ  106 (126)
T ss_dssp             TTCHHHHHHHHHHHHHHCTT
T ss_pred             hhhHHHHHHHHHHHHHhCCC
Confidence            77888888777777777775

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.15  E-value=2  Score=39.85  Aligned_cols=164  Identities=7%  Similarity=-0.007  Sum_probs=83.9

Q ss_pred             HHHHHHHHhcCCcCcHHHHHHHHHHC--CCCCC---HHHHHHHHHHHhccCChHHHHHHHHHHHh---CCCCCCC--HHH
Q 011236          176 NGIMCLYTNTGQHEKIPDVLLDMKEN--GVPPD---NFSYRICINSYGARSELSSMENVLQEMES---QSHISMD--WGT  245 (490)
Q Consensus       176 ~~l~~~~~~~~~~~~a~~~~~~m~~~--~~~p~---~~~~~~li~~~~~~g~~~~a~~~~~~~~~---~~~~~~~--~~~  245 (490)
                      ..|...+...|++.+|.+++..+...  |....   ...+...++.|...+++..|..++.++..   .....|+  ...
T Consensus       141 ~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~  220 (445)
T 4b4t_P          141 KDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEY  220 (445)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHH
Confidence            34566666777777777777766432  21111   13455566777778888888777776531   1111122  234


Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHH----HHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHH
Q 011236          246 YSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHL----ISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITML  321 (490)
Q Consensus       246 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l----~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  321 (490)
                      |...+..+...+++.+|-+.|.++........|...+..+    +.+..-.+....-..++.........++...|..++
T Consensus       221 ~~~~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L~  300 (445)
T 4b4t_P          221 YNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQNDNNLKKLESQESLV  300 (445)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHHSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhcccccccHHHHHHH
Confidence            4556667777788888777777665432211233222221    112222222222223333233333335556677777


Q ss_pred             HHHHhc--CCHHHHHHHHHH
Q 011236          322 GSLVKI--GELEEAEKMLEE  339 (490)
Q Consensus       322 ~~~~~~--~~~~~a~~~~~~  339 (490)
                      .+|...  .+++...+.|..
T Consensus       301 k~f~~~~L~~~~~~~~~~~~  320 (445)
T 4b4t_P          301 KLFTTNELMRWPIVQKTYEP  320 (445)
T ss_dssp             HHHHHCCSSSHHHHHHHTCS
T ss_pred             HHHHhchHhhhHHHHHHHHH
Confidence            777553  345555554443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.87  E-value=0.81  Score=33.77  Aligned_cols=57  Identities=19%  Similarity=0.143  Sum_probs=22.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      -++.+...|+-+.-.+++..+.. +.+|++...-.+..+|.+.|+..+|.+++.++.+
T Consensus        97 ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~  153 (172)
T 1wy6_A           97 ALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACK  153 (172)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence            33333444444444444433222 1223333344444444444444444444444443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.85  E-value=0.82  Score=33.74  Aligned_cols=139  Identities=13%  Similarity=-0.004  Sum_probs=84.5

Q ss_pred             hcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHH
Q 011236          291 SLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADA  370 (490)
Q Consensus       291 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  370 (490)
                      -.|..++..++..+....   .+..-|+-+|.-....-+-+-..++++.+-+.   .|.          ..+|++.....
T Consensus        19 ldG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGki---FDi----------s~C~NlKrVi~   82 (172)
T 1wy6_A           19 LDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSY---FDL----------DKCQNLKSVVE   82 (172)
T ss_dssp             HTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGG---SCG----------GGCSCTHHHHH
T ss_pred             HhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhh---cCc----------HhhhcHHHHHH
Confidence            356666677766655544   23444555554444455555555555544322   222          12344443333


Q ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHH
Q 011236          371 VLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       371 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  450 (490)
                      .+-.+-     .+.......+..+..+|.-+.-.+++.+.+.      ...|++.....+..+|.+.|+..+|.+++.++
T Consensus        83 C~~~~n-----~~se~vd~ALd~lv~~~KkDqLdki~~~~l~------n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~A  151 (172)
T 1wy6_A           83 CGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILK------NNEVSASILVAIANALRRVGDERDATTLLIEA  151 (172)
T ss_dssp             HHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--------CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHhc-----chHHHHHHHHHHHHHhccHhHHHHHHHHHhc------cCCCChHHHHHHHHHHHHhcchhhHHHHHHHH
Confidence            332221     1334455566777788888888888877543      45688888888999999999999999999998


Q ss_pred             Hhcccc
Q 011236          451 KIKVQK  456 (490)
Q Consensus       451 ~~~~~~  456 (490)
                      .+.|.+
T Consensus       152 C~kG~k  157 (172)
T 1wy6_A          152 CKKGEK  157 (172)
T ss_dssp             HHTTCH
T ss_pred             HHhhhH
Confidence            888765

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=94.80  E-value=0.11  Score=38.11  Aligned_cols=80  Identities=16%  Similarity=0.122  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHH---HHHHHHHHHHcC-CCCCHHHHHHHHHHHhccCCHHHHHHHH
Q 011236          332 EAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEK---ADAVLKEIVKKG-KTPTPNSWSIIAAGYADKNNMEKAFECM  407 (490)
Q Consensus       332 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~---A~~~~~~m~~~~-~~p~~~~~~~l~~~~~~~~~~~~a~~~~  407 (490)
                      .+.+-+......|. ++..+-..+..++.+......   ++.+++.+...+ +.-.....-.|.-++.+.|++++|.+++
T Consensus        19 ~~~~~y~~e~~~~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~   97 (126)
T 1nzn_A           19 KFEKKFQSEKAAGS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYV   97 (126)
T ss_dssp             HHHHHHHHHHHHSC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHhccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            33444443333332 333443344445555444333   555555554432 1002223334445555666666666666


Q ss_pred             HHHHH
Q 011236          408 KEALA  412 (490)
Q Consensus       408 ~~~~~  412 (490)
                      +.+++
T Consensus        98 ~~lL~  102 (126)
T 1nzn_A           98 RGLLQ  102 (126)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66655

>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=94.76  E-value=3.3  Score=40.22  Aligned_cols=115  Identities=7%  Similarity=-0.047  Sum_probs=58.0

Q ss_pred             CHHHHHHHHHHHHhcCCCCCchhHHH----HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHH
Q 011236          329 ELEEAEKMLEEWELSCYCYDFRVPNI----ILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAF  404 (490)
Q Consensus       329 ~~~~a~~~~~~~~~~~~~~~~~~~~~----l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~  404 (490)
                      +.+.|...+....+.. ..+......    +.......+...++...+.......  ++.......+....+.|+++.|.
T Consensus       229 d~~~A~~~~~~~~~~~-~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~e~~~r~Alr~~d~~~a~  305 (618)
T 1qsa_A          229 DAENARLMIPSLAQAQ-QLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGTGDRRGLN  305 (618)
T ss_dssp             CHHHHHHHHHHHHHHT-TCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CHHHHHHHHHhhhhcc-CCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhccccC--CChHHHHHHHHHHHHCCCHHHHH
Confidence            5667777776665432 222222222    2222223342445555555544332  23333334444444567777777


Q ss_pred             HHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHh
Q 011236          405 ECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       405 ~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      ..|+.|..      ..........-+.+++...|+.++|..+|+.+..
T Consensus       306 ~~~~~l~~------~~~~~~r~~YW~~ra~~~~g~~~~a~~~~~~~a~  347 (618)
T 1qsa_A          306 TWLARLPM------EAKEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (618)
T ss_dssp             HHHHHSCT------TGGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHccc------cccccHhHHHHHHHHHHHcCCHHHHHHHHHHHhc
Confidence            77766543      1111233344455566667777777777777654

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=94.56  E-value=0.16  Score=46.47  Aligned_cols=79  Identities=11%  Similarity=0.071  Sum_probs=63.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHH
Q 011236          353 NIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILD  432 (490)
Q Consensus       353 ~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~  432 (490)
                      ..++..+...|++++|...+..+....+- +...|..++.++.+.|+..+|++.|+...+...++.|+.|+..+-...-.
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~~P~-~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~l~~~  253 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFEHPY-REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRALNER  253 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            45677788899999999998888877654 77889999999999999999999998887766666789998876544433

>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=94.07  E-value=0.95  Score=31.29  Aligned_cols=64  Identities=13%  Similarity=0.142  Sum_probs=45.6

Q ss_pred             CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHH
Q 011236          399 NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAH  467 (490)
Q Consensus       399 ~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~  467 (490)
                      +.-+..+-++.+..     ..+.|++....+.+++|.+..++..|.++|+-++..... ..+|..+++-+
T Consensus        25 D~~e~rrglN~l~~-----~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~~~~iY~~~lqEl   89 (109)
T 1v54_E           25 DAWELRKGMNTLVG-----YDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQEL   89 (109)
T ss_dssp             CHHHHHHHHHHHTT-----SSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhc-----cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCchhhHHHHHHHH
Confidence            45556666666665     667788888888888888888888888888877766555 55666666543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=94.02  E-value=1.2  Score=44.16  Aligned_cols=51  Identities=22%  Similarity=0.186  Sum_probs=32.6

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHH
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEA  410 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~  410 (490)
                      +...|+++.|+.+-++....-+. +..+|..|..+|...|+++.|+-.++.+
T Consensus       347 Ll~K~~~elAL~~Ak~AV~~aPs-eF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          347 LLNRGDYELALGVSNTSTELALD-SFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCSS-CHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             HhccCcHHHHHHHHHHHHhcCch-hhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence            44566677777777666665332 4566777777777777777776666554

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.79  E-value=4.2  Score=37.72  Aligned_cols=95  Identities=15%  Similarity=0.143  Sum_probs=60.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC-----chhHHHHHHHHHhcCCHHHHHHHHHHHHH----cCCCCCH--HH
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSCYCYD-----FRVPNIILLGYSQKGMIEKADAVLKEIVK----KGKTPTP--NS  386 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~----~~~~p~~--~~  386 (490)
                      ..|...+...|++.+|..++..+...-...+     ...+...++.|...+++.+|..+++++..    ....|+.  ..
T Consensus       141 ~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~  220 (445)
T 4b4t_P          141 KDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLEY  220 (445)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHH
Confidence            4566777777888888888877754312111     23455666777788888888887777642    2222222  24


Q ss_pred             HHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          387 WSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       387 ~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      |...+..+...+++.+|.+.|.++.+
T Consensus       221 ~~~~~~~~~~e~~y~~a~~~y~e~~~  246 (445)
T 4b4t_P          221 YNLLVKISLHKREYLEVAQYLQEIYQ  246 (445)
T ss_dssp             HHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            56666677778888888887777765

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=92.75  E-value=0.32  Score=44.34  Aligned_cols=129  Identities=8%  Similarity=-0.059  Sum_probs=70.3

Q ss_pred             CHHHHHHHHHHHH---hcCChhHHHHHHHHHHhCCC-CCChhhHHHHHHHHHhhcCHH-HHHHHHHHccccCCChhHHHH
Q 011236           68 SELELQRVIRQLR---SRKRFKHALQVSEWMSGQGL-AFSVHDHAVQLDLIGKVRGLE-SAETYFNSLNDEDKVDKLYGA  142 (490)
Q Consensus        68 ~~~~~~~ll~~~~---~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~-~A~~~~~~~~~~~p~~~~~~~  142 (490)
                      |...+..++....   ..|+.+.|.+.++.+...-- ++=+...         ...+- ....-+++..     ..+...
T Consensus       111 D~~~f~~l~~~~~~~~~~~~~~~a~~~l~~Al~L~rG~~L~~~~---------~~~w~~~~r~~l~~~~-----~~a~~~  176 (388)
T 2ff4_A          111 DLGRFVAEKTAGVHAAAAGRFEQASRHLSAALREWRGPVLDDLR---------DFQFVEPFATALVEDK-----VLAHTA  176 (388)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTGGGT---------TSTTHHHHHHHHHHHH-----HHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCCC---------chhHHHHHHHHHHHHH-----HHHHHH
Confidence            4444555554432   35788888888888877532 1111110         01111 1111111111     123445


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHH-----CCCCCCHHHHH
Q 011236          143 LLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKE-----NGVPPDNFSYR  211 (490)
Q Consensus       143 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~~  211 (490)
                      ++..+...|++++|+..+..+....+- +...|..+|.++.+.|+..+|++.|+.+.+     .|+.|...+-.
T Consensus       177 ~~~~~l~~g~~~~a~~~l~~~~~~~P~-~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          177 KAEAEIACGRASAVIAELEALTFEHPY-REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            566666777777777777766655332 556677777777777777777777766543     36777666543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=92.66  E-value=1  Score=44.63  Aligned_cols=53  Identities=17%  Similarity=-0.013  Sum_probs=40.4

Q ss_pred             HHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHH
Q 011236          322 GSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEI  375 (490)
Q Consensus       322 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m  375 (490)
                      +-|...|+++.|..+-++.... .+-+-.+|..|..+|...|+++.|+-.++.+
T Consensus       345 ~FLl~K~~~elAL~~Ak~AV~~-aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          345 NFLLNRGDYELALGVSNTSTEL-ALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH-CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             HHHhccCcHHHHHHHHHHHHhc-CchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence            3455678888888888888775 3335668888888888888888888877766

>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=91.95  E-value=2.4  Score=31.16  Aligned_cols=64  Identities=13%  Similarity=0.142  Sum_probs=46.8

Q ss_pred             CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHH
Q 011236          399 NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAH  467 (490)
Q Consensus       399 ~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~  467 (490)
                      |.-+..+-++....     ..+.|++......+++|.+.+|+..|.++|+-++..... ..+|..+++-+
T Consensus        68 D~wElrrglN~l~~-----~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~~~~~iY~y~lqEl  132 (152)
T 2y69_E           68 DAWELRKGMNTLVG-----YDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQEL  132 (152)
T ss_dssp             CHHHHHHHHHHHTT-----SSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhc-----cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCchhhHHHHHHHH
Confidence            34445556666655     667888888888888888888888888888888776655 56677666554

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=91.23  E-value=3.8  Score=43.37  Aligned_cols=22  Identities=23%  Similarity=0.149  Sum_probs=12.9

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHH
Q 011236          248 TVANYYIIAGLKEKAIIYLKKC  269 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~  269 (490)
                      .+..+|...|++++|.+.|.+.
T Consensus       847 l~g~~~L~~ge~~~A~~~F~ka  868 (1139)
T 4fhn_B          847 LKALIYLKSKEAVKAVRCFKTT  868 (1139)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHTC
T ss_pred             HHHHHHHhcCCHHHHHHHHHHH
Confidence            3455566666666666666553

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=91.23  E-value=7.2  Score=34.18  Aligned_cols=168  Identities=12%  Similarity=0.053  Sum_probs=87.5

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHH----HHHHHHCCCCCCHHHHHHHHH
Q 011236          140 YGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDV----LLDMKENGVPPDNFSYRICIN  215 (490)
Q Consensus       140 ~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~----~~~m~~~~~~p~~~~~~~li~  215 (490)
                      |.++..-|.+.+++++|++++..-..               .+.+.|+...+-++    ++-..+.++++|......++.
T Consensus        38 ~RTi~~Ry~~~k~y~eAidLL~~GA~---------------~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~  102 (336)
T 3lpz_A           38 TRLVAARYSKQGNWAAAVDILASVSQ---------------TLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLG  102 (336)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHHHHH---------------HHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            44455556667777777766543211               12233443333322    233444556666666666666


Q ss_pred             HHhccCChH-HHHHHHHHHH----h-CCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHH
Q 011236          216 SYGARSELS-SMENVLQEME----S-QSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHY  289 (490)
Q Consensus       216 ~~~~~g~~~-~a~~~~~~~~----~-~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  289 (490)
                      .+.....-+ .=..+.+++.    . .....-|......+...|.+.+++.+|...|-.    +.. ++...|..++.-+
T Consensus       103 L~~~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~il----g~~-~s~~~~a~mL~ew  177 (336)
T 3lpz_A          103 CLRLFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLVL----GTK-ESPEVLARMEYEW  177 (336)
T ss_dssp             HHTTSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHTT----SCT-THHHHHHHHHHHH
T ss_pred             HHHhCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHh----cCC-chHHHHHHHHHHH
Confidence            555443211 1122222222    0 222335677778899999999999999888742    322 3335665555444


Q ss_pred             HhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          290 ASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       290 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      ...+...+              ++...-.+++. |...++...|..+++...+
T Consensus       178 ~~~~~~~e--------------~dlfiaRaVL~-yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          178 YKQDESHT--------------APLYCARAVLP-YLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HHTSCGGG--------------HHHHHHHHHHH-HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhcCCcc--------------HHHHHHHHHHH-HHHhCCHHHHHHHHHHHHH
Confidence            44333222              12222223333 4456788888887766553

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=90.67  E-value=7.9  Score=33.66  Aligned_cols=181  Identities=13%  Similarity=0.064  Sum_probs=100.2

Q ss_pred             HHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHH
Q 011236          113 LIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIP  192 (490)
Q Consensus       113 ~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~  192 (490)
                      .....|++=+|.+.             |.++..-|.+.+++++|++++..-..               .+.+.|+...|-
T Consensus        22 ~~I~~G~yYEAhQ~-------------~Rtl~~Ry~~~~~~~eAidlL~~ga~---------------~ll~~~Q~~sa~   73 (312)
T 2wpv_A           22 NKIKAGDYYEAHQT-------------LRTIANRYVRSKSYEHAIELISQGAL---------------SFLKAKQGGSGT   73 (312)
T ss_dssp             HHHHHTCHHHHHHH-------------HHHHHHHHHHTTCHHHHHHHHHHHHH---------------HHHHTTCHHHHH
T ss_pred             HHhhccChHHHHHH-------------HHHHHHHHHHhcCHHHHHHHHHHHHH---------------HHHHCCCcchHH
Confidence            33445555555554             55666677778888888877654322               233445444433


Q ss_pred             H----HHHHHHHCCCCCCHHHHHHHHHHHhccCChH-HHHHHHHHHH----hCCC-CCCCHHHHHHHHHHHHHcCCHHHH
Q 011236          193 D----VLLDMKENGVPPDNFSYRICINSYGARSELS-SMENVLQEME----SQSH-ISMDWGTYSTVANYYIIAGLKEKA  262 (490)
Q Consensus       193 ~----~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~-~a~~~~~~~~----~~~~-~~~~~~~~~~li~~~~~~~~~~~a  262 (490)
                      +    +.+-..+.+++++......++..+.....-+ .=.++++++.    ...+ ..-++..+..+...|.+.|++.+|
T Consensus        74 DLa~llvev~~~~~~~~~~~~~~rl~~l~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A  153 (312)
T 2wpv_A           74 DLIFYLLEVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEA  153 (312)
T ss_dssp             HHHHHHHHHHHHTTCCCSHHHHHHHHHHHTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHH
Confidence            3    3444455677777777777776665533211 1123333332    1111 235678888899999999999999


Q ss_pred             HHHHHHHhhhhccCCChhhHHHHHHHHHhc---CChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHH
Q 011236          263 IIYLKKCEDIVSKSKDALGYNHLISHYASL---GNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEE  339 (490)
Q Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  339 (490)
                      ...|-.    +.. .|...+..++.-+...   |...++--              ..-.+++. |...|+...|..+++.
T Consensus       154 ~~H~i~----~~~-~s~~~~a~~l~~w~~~~~~~~~~e~dl--------------f~~RaVL~-yL~l~n~~~A~~~~~~  213 (312)
T 2wpv_A          154 ERYFML----GTH-DSMIKYVDLLWDWLCQVDDIEDSTVAE--------------FFSRLVFN-YLFISNISFAHESKDI  213 (312)
T ss_dssp             HHHHHT----SCH-HHHHHHHHHHHHHHHHTTCCCHHHHHH--------------HHHHHHHH-HHHTTBHHHHHHHHHH
T ss_pred             HHHHHh----CCC-ccHHHHHHHHHHHHHhcCCCCcchHHH--------------HHHHHHHH-HHHhcCHHHHHHHHHH
Confidence            887763    211 1344555555444333   33322211              11222222 4456888888888886


Q ss_pred             HH
Q 011236          340 WE  341 (490)
Q Consensus       340 ~~  341 (490)
                      ..
T Consensus       214 f~  215 (312)
T 2wpv_A          214 FL  215 (312)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=90.64  E-value=10  Score=40.18  Aligned_cols=52  Identities=6%  Similarity=-0.040  Sum_probs=29.5

Q ss_pred             HHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHH
Q 011236          109 VQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKM  163 (490)
Q Consensus       109 ~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m  163 (490)
                      .++..+...+..+.+.++......   +...--.+..++...|++++|.+.|.+.
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~~~---~~~~~yl~g~~~L~~ge~~~A~~~F~ka  868 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWLNS---DPIAVYLKALIYLKSKEAVKAVRCFKTT  868 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHSCC---CHHHHHHHHHHHHHTTCHHHHHHHHHTC
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccC---CcHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            345555566666666665544432   3323334456666777777777777653

>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=90.55  E-value=2.2  Score=31.44  Aligned_cols=73  Identities=8%  Similarity=-0.041  Sum_probs=50.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCh---hHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC
Q 011236           64 GQKISELELQRVIRQLRSRKRF---KHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV  136 (490)
Q Consensus        64 ~~~~~~~~~~~ll~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~  136 (490)
                      +..|+..+--....++.+....   ..++.+++.+.+.+.....+..-.+.-++.+.|+++.|++..+.+.+..|+
T Consensus        35 ~~~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP~  110 (134)
T 3o48_A           35 GPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  110 (134)
T ss_dssp             GGGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCTT
T ss_pred             CCCCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCCC
Confidence            5566777777777777766543   467788888777653233455555666777888888888888888887774

>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=89.60  E-value=4.9  Score=29.61  Aligned_cols=69  Identities=10%  Similarity=-0.004  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHHhccCC---HHHHHHHHHHHHHhhhcCcCCCc--chhhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          381 TPTPNSWSIIAAGYADKNN---MEKAFECMKEALAVHEENKFWRP--KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       381 ~p~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~p--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                      .|+..+--.+..++.+..+   ..+++.++++...     .+  |  ....+..+.-++.+.|+++.|.+..+.+.+..|
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~-----~~--~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP  109 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYK-----EA--ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHER  109 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHH-----HC--GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCT
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHh-----cC--cchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCC
Confidence            3444444444444444443   2345555555544     12  2  123333444455556666666666666555555


Q ss_pred             c
Q 011236          456 K  456 (490)
Q Consensus       456 ~  456 (490)
                      .
T Consensus       110 ~  110 (134)
T 3o48_A          110 N  110 (134)
T ss_dssp             T
T ss_pred             C
Confidence            4

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.57  E-value=4.9  Score=37.09  Aligned_cols=98  Identities=16%  Similarity=0.041  Sum_probs=59.8

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC--hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC-CCCchhHHHH-
Q 011236          280 LGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL--NRDYITMLGSLVKIGELEEAEKMLEEWELSCY-CYDFRVPNII-  355 (490)
Q Consensus       280 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l-  355 (490)
                      .+...+...|.+.|+++.|.+.|.++......+.  ...+...++.+...+++..+...+.++...-. .++....+.+ 
T Consensus       132 ~~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk  211 (429)
T 4b4t_R          132 QAWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYK  211 (429)
T ss_dssp             SCCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHH
Confidence            3566788888888888888888887777654332  24566677777778888888888777654311 1222221111 


Q ss_pred             ---HHHHHhcCCHHHHHHHHHHHHH
Q 011236          356 ---LLGYSQKGMIEKADAVLKEIVK  377 (490)
Q Consensus       356 ---~~~~~~~g~~~~A~~~~~~m~~  377 (490)
                         ...+...+++..|...|-+...
T Consensus       212 ~~~gl~~l~~r~f~~Aa~~f~e~~~  236 (429)
T 4b4t_R          212 TYYGIHCLAVRNFKEAAKLLVDSLA  236 (429)
T ss_dssp             HHHHHGGGGTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhChHHHHHHHHHHHhc
Confidence               1112345667777666665544

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=89.44  E-value=3.4  Score=31.81  Aligned_cols=101  Identities=7%  Similarity=0.044  Sum_probs=57.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcC-CCCCH-------HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhc---C-----
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKKG-KTPTP-------NSWSIIAAGYADKNNMEKAFECMKEALAVHEE---N-----  417 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~~-~~p~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~-----  417 (490)
                      .-+..+...|.++.|+-+.+.+.... ..|+.       .++..+.+++...+++.+|...|+++++....   .     
T Consensus        25 dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s~~~  104 (167)
T 3ffl_A           25 DHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSKVRP  104 (167)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC--------
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCCccc
Confidence            34455566667777666655543321 12221       24555666777777777777777776552210   0     


Q ss_pred             -----------cCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Q 011236          418 -----------KFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKV  454 (490)
Q Consensus       418 -----------~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  454 (490)
                                 ....++...-.-+..+|.+.|++++|..+++.+....
T Consensus       105 ~~~~~ss~p~s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k~  152 (167)
T 3ffl_A          105 STGNSASTPQSQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSRQ  152 (167)
T ss_dssp             ------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGGG
T ss_pred             cccccCCCcccccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCchh
Confidence                       0111222344456778889999999999988765443

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=89.43  E-value=3.9  Score=28.31  Aligned_cols=62  Identities=8%  Similarity=-0.047  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHH
Q 011236          223 LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLIS  287 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  287 (490)
                      .-+..+-++.+- ..++.|++....+.+.+|.+.+++.-|.++|+.++.....  ...+|..+++
T Consensus        26 ~~e~rrglN~l~-~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~--~~~iY~~~lq   87 (109)
T 1v54_E           26 AWELRKGMNTLV-GYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGP--HKEIYPYVIQ   87 (109)
T ss_dssp             HHHHHHHHHHHT-TSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTT--CTTHHHHHHH
T ss_pred             HHHHHHHHHHHh-ccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcC--chhhHHHHHH
Confidence            334555555555 5566666666666666666666666666666666654432  2334544443

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=88.85  E-value=5.9  Score=29.59  Aligned_cols=46  Identities=11%  Similarity=0.131  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          367 KADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       367 ~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +++.+++.+...+..-.....-.|.-++.+.|++++|.++.+.+++
T Consensus        60 ~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~  105 (144)
T 1y8m_A           60 LGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  105 (144)
T ss_dssp             HHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            3444454444433221223333444455555555555555555554

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=88.47  E-value=2.1  Score=36.09  Aligned_cols=56  Identities=21%  Similarity=0.146  Sum_probs=38.3

Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011236          323 SLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG  379 (490)
Q Consensus       323 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  379 (490)
                      .+.+.|+++++.+....-++. -+-|...-..|+..+|-.|++++|.+-++...+..
T Consensus         6 ~ll~~g~L~~al~~~~~~VR~-~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~   61 (273)
T 1zbp_A            6 NALSEGQLQQALELLIEAIKA-SPKDASLRSSFIELLCIDGDFERADEQLMQSIKLF   61 (273)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHT-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHhCCCHHHHHHHHHHHHHh-CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC
Confidence            455677777777777766665 23355566667777777777777777777776653

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.66  E-value=5.6  Score=36.73  Aligned_cols=97  Identities=15%  Similarity=0.042  Sum_probs=50.0

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC--chhHHHHHHHHHhcCCHHHHHHHHHHHHHc---CCCCCHHH--HH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYD--FRVPNIILLGYSQKGMIEKADAVLKEIVKK---GKTPTPNS--WS  388 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~---~~~p~~~~--~~  388 (490)
                      +...+...|.+.|+++.|.+.+.++......+.  ...+-.+++.+...+++..+...+.++...   +..|+...  ..
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk~  212 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYKT  212 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHHH
Confidence            455666666666666666666666665432222  234445555666666666666666655332   22222211  11


Q ss_pred             HHHHHHhccCCHHHHHHHHHHHHH
Q 011236          389 IIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       389 ~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .-+..+...+++..|.+.|-++..
T Consensus       213 ~~gl~~l~~r~f~~Aa~~f~e~~~  236 (429)
T 4b4t_R          213 YYGIHCLAVRNFKEAAKLLVDSLA  236 (429)
T ss_dssp             HHHHGGGGTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhChHHHHHHHHHHHhc
Confidence            112223445666666666666555

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=86.47  E-value=2.7  Score=35.38  Aligned_cols=59  Identities=10%  Similarity=-0.023  Sum_probs=42.1

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCC
Q 011236           77 RQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKV  136 (490)
Q Consensus        77 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~  136 (490)
                      ..+.+.|++++|++....-++.. |-+...-..++..+|-.|+++.|..-++...+.+|+
T Consensus         5 ~~ll~~g~L~~al~~~~~~VR~~-P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~   63 (273)
T 1zbp_A            5 KNALSEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE   63 (273)
T ss_dssp             HHHTTTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCch
Confidence            34456677777777777777766 567777777777777777877777777777666654

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=86.45  E-value=8  Score=28.46  Aligned_cols=61  Identities=8%  Similarity=-0.042  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHH
Q 011236          224 SSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLIS  287 (490)
Q Consensus       224 ~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  287 (490)
                      -+..+-++.+. ..++.|++....+.+.+|.+.+++.-|.++|+.++.+..  +....|..+++
T Consensus        70 wElrrglN~l~-~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~--~~~~iY~y~lq  130 (152)
T 2y69_E           70 WELRKGMNTLV-GYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVIQ  130 (152)
T ss_dssp             HHHHHHHHHHT-TSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHHH
T ss_pred             HHHHHHHHHHh-ccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcC--CchhhHHHHHH
Confidence            34555555555 666667777777777777777777777777777666554  23444555543

>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=86.27  E-value=6.4  Score=27.15  Aligned_cols=81  Identities=19%  Similarity=0.122  Sum_probs=56.4

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHH
Q 011236           81 SRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLM  160 (490)
Q Consensus        81 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  160 (490)
                      -.+..++|..+-+++...+.  ...+...-+..+...|++++|..+.+...  -||...|-+|..  .+.|-.+++..-+
T Consensus        19 G~H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c--~pdlepw~ALce--~rlGl~s~le~rL   92 (116)
T 2p58_C           19 GNHYHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLA--YPDLEPWLALCE--YRLGLGSALESRL   92 (116)
T ss_dssp             TTTCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSC--CGGGHHHHHHHH--HHHTCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCC--CchHHHHHHHHH--HhcccHHHHHHHH
Confidence            44667888888888888762  23233333556678889999988888776  478777776654  4667777777777


Q ss_pred             HHHHhcC
Q 011236          161 QKMKEMG  167 (490)
Q Consensus       161 ~~m~~~~  167 (490)
                      .++...|
T Consensus        93 ~~la~sg   99 (116)
T 2p58_C           93 NRLARSQ   99 (116)
T ss_dssp             HHHTTCC
T ss_pred             HHHHhCC
Confidence            6776664

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=86.26  E-value=19  Score=32.57  Aligned_cols=132  Identities=9%  Similarity=0.047  Sum_probs=64.7

Q ss_pred             HHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCH---HHHHHHHHHHHHc-CCHHHHHHHHHHHhhhhccCCChhhH-
Q 011236          208 FSYRICINSYGARSELSSMENVLQEMESQSHISMDW---GTYSTVANYYIIA-GLKEKAIIYLKKCEDIVSKSKDALGY-  282 (490)
Q Consensus       208 ~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~---~~~~~li~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~-  282 (490)
                      .....|...|.+.|+.++..+++....+-.+..+-.   .....+++.+... +..+.-.++..+..+...  .+..+| 
T Consensus        20 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~--~~~r~fl   97 (394)
T 3txn_A           20 QGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAK--QEKRTFL   97 (394)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHH--HTTCHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHH--HHHHHHH
Confidence            344556667777777777777776664211211211   2233445555443 233333444444433222  122233 


Q ss_pred             -----HHHHHHHHhcCChhHHHHHHHHHHHhcCCCChh-----hHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          283 -----NHLISHYASLGNKDEMMKFWGLQKIKCKKQLNR-----DYITMLGSLVKIGELEEAEKMLEEWE  341 (490)
Q Consensus       283 -----~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-----~~~~l~~~~~~~~~~~~a~~~~~~~~  341 (490)
                           .-++..|...|++.+|..++..+.......|..     .+..-++.|...+++.++...+....
T Consensus        98 r~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~  166 (394)
T 3txn_A           98 RQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSAR  166 (394)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence                 134555666666666666666655554433322     23344455555666666666665544

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=86.19  E-value=6.2  Score=27.18  Aligned_cols=81  Identities=12%  Similarity=0.118  Sum_probs=57.4

Q ss_pred             hcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHH
Q 011236           81 SRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLM  160 (490)
Q Consensus        81 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~  160 (490)
                      -.+..++|..+-+++...+.  ...+...-+..+...|++++|..+.+...  .||...|-+|..  .+.|-.+++..-+
T Consensus        18 G~H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c--~pdlepw~ALce--~rlGl~s~le~rL   91 (115)
T 2uwj_G           18 GQHCHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNP--WPALEPWFALCE--WHLGLGAALDRRL   91 (115)
T ss_dssp             TTTCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCC--CGGGHHHHHHHH--HHTTCHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCC--CchHHHHHHHHH--HhcccHHHHHHHH
Confidence            44667888888888888762  23333333556678899999988887776  478777776654  4778888888777


Q ss_pred             HHHHhcC
Q 011236          161 QKMKEMG  167 (490)
Q Consensus       161 ~~m~~~~  167 (490)
                      .++...|
T Consensus        92 ~~la~sg   98 (115)
T 2uwj_G           92 AGLGGSS   98 (115)
T ss_dssp             HHHHTCS
T ss_pred             HHHHhCC
Confidence            7777665

>4g8k_A 2-5A-dependent ribonuclease; ankyrin-repeat domain, single-stranded RNA, hydrolase; 2.40A {Homo sapiens} PDB: 4g8l_A*

Probab=86.12  E-value=9.5  Score=33.58  Aligned_cols=19  Identities=11%  Similarity=0.034  Sum_probs=10.3

Q ss_pred             HHHHHhhcCHHHHHHHHHH
Q 011236          111 LDLIGKVRGLESAETYFNS  129 (490)
Q Consensus       111 ~~~~~~~~~~~~A~~~~~~  129 (490)
                      +...+..|+.+-+.-+++.
T Consensus        63 Lh~A~~~g~~~iv~~Ll~~   81 (337)
T 4g8k_A           63 LHNAVQMSREDIVELLLRH   81 (337)
T ss_dssp             HHHHHHTTCHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHc
Confidence            3444556666655555543

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=84.32  E-value=3.8  Score=34.87  Aligned_cols=19  Identities=11%  Similarity=0.034  Sum_probs=9.7

Q ss_pred             HHHHHhhcCHHHHHHHHHH
Q 011236          111 LDLIGKVRGLESAETYFNS  129 (490)
Q Consensus       111 ~~~~~~~~~~~~A~~~~~~  129 (490)
                      +...+..|+.+-+..+++.
T Consensus        43 L~~A~~~g~~~~v~~Ll~~   61 (285)
T 1wdy_A           43 LHNAVQMSREDIVELLLRH   61 (285)
T ss_dssp             HHHHHHTTCHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHc
Confidence            4444555665555555443

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=82.80  E-value=13  Score=27.80  Aligned_cols=81  Identities=10%  Similarity=-0.002  Sum_probs=58.0

Q ss_pred             CCCCHHHHHHHHHHHhccCC---HHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          380 KTPTPNSWSIIAAGYADKNN---MEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       380 ~~p~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ..|+..+--.+..++.+..+   ..+++.++++...     .+-.-.......+.-++.+.|++++|.++.+.+.+..|.
T Consensus        35 ~~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~-----~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~eP~  109 (144)
T 1y8m_A           35 PTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYK-----EAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERN  109 (144)
T ss_dssp             TTSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHH-----HCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTCCC
T ss_pred             CCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHh-----cCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCC
Confidence            35777777777888888765   4578888888877     221112344556667899999999999999999999987


Q ss_pred             ---hhhhHHHHH
Q 011236          457 ---RNMYHALTE  465 (490)
Q Consensus       457 ---~~~~~~l~~  465 (490)
                         ......+|.
T Consensus       110 n~QA~~Lk~~Ie  121 (144)
T 1y8m_A          110 NKQVGALKSMVE  121 (144)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHH
Confidence               444444443

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=82.76  E-value=14  Score=28.38  Aligned_cols=61  Identities=5%  Similarity=-0.076  Sum_probs=37.7

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh-------hhHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA-------LGYNHLISHYASLGNKDEMMKFWGLQKIK  308 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  308 (490)
                      .-+..+...|.++.|+-+.+.+.......++.       .++..+.+++...+++..|...|++.+..
T Consensus        25 dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~   92 (167)
T 3ffl_A           25 DHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQ   92 (167)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHH
Confidence            34556667777777777666654433211331       24566677777788888888887765443

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=80.40  E-value=33  Score=30.98  Aligned_cols=167  Identities=10%  Similarity=-0.032  Sum_probs=109.0

Q ss_pred             cchHHHHHHHHHhcCCcCcHHHHHHHHHHC-CCCCC---HHHHHHHHHHHhccC-ChHHHHHHHHHHHhCCCCCCCHHHH
Q 011236          172 ALNYNGIMCLYTNTGQHEKIPDVLLDMKEN-GVPPD---NFSYRICINSYGARS-ELSSMENVLQEMESQSHISMDWGTY  246 (490)
Q Consensus       172 ~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~-~~~p~---~~~~~~li~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~~~~  246 (490)
                      ......|...|.+.|+.++..+++...... +.-|-   ......++..+.... ..+.-.++..+.. +..- -...+|
T Consensus        19 e~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~-~~a~-~~~r~f   96 (394)
T 3txn_A           19 EQGILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCI-EWAK-QEKRTF   96 (394)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHH-HHHH-HTTCHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHH-HHHH-HHHHHH
Confidence            345677889999999999999888876432 11122   234667788887643 4444555555554 2211 122222


Q ss_pred             ------HHHHHHHHHcCCHHHHHHHHHHHhhhhccCCCh-----hhHHHHHHHHHhcCChhHHHHHHHHHHHhcC--CCC
Q 011236          247 ------STVANYYIIAGLKEKAIIYLKKCEDIVSKSKDA-----LGYNHLISHYASLGNKDEMMKFWGLQKIKCK--KQL  313 (490)
Q Consensus       247 ------~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~--~~~  313 (490)
                            .-++..|...|++.+|..++.++.+.... .|.     ..+..-++.|...+++.++...+........  .++
T Consensus        97 lr~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~-~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~  175 (394)
T 3txn_A           97 LRQSLEARLIALYFDTALYTEALALGAQLLRELKK-LDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCP  175 (394)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTT-SSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCC
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhc-cccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCC
Confidence                  15788999999999999999999886654 333     3355667778889999999999987654432  133


Q ss_pred             hhhH----HHHHHHHH-hcCCHHHHHHHHHHHH
Q 011236          314 NRDY----ITMLGSLV-KIGELEEAEKMLEEWE  341 (490)
Q Consensus       314 ~~~~----~~l~~~~~-~~~~~~~a~~~~~~~~  341 (490)
                      +...    ..-...+. ..+++..|...|-+..
T Consensus       176 p~i~a~i~~~~Gi~~l~~~rdyk~A~~~F~eaf  208 (394)
T 3txn_A          176 PKVQGALDLQSGILHAADERDFKTAFSYFYEAF  208 (394)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHhccCHHHHHHHHHHHH
Confidence            3322    12233345 7889999988887764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	490
d1w3ba_	388	a.118.8.1 (A:) O-GlcNAc transferase p110 subunit,	5e-08

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]} Length = 388

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (124), Expect = 5e-08
 Identities = 27/176 (15%), Positives = 63/176 (35%), Gaps = 5/176 (2%)

Query: 242 DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKF 301
               Y  + N    A + ++A+    +   +         + +L   Y   G  D  +  
Sbjct: 202 FLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVV--HGNLACVYYEQGLIDLAIDT 259

Query: 302 WGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ 361
           +  + I+ +      Y  +  +L + G + EAE       L          N +     +
Sbjct: 260 Y-RRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTA-LRLCPTHADSLNNLANIKRE 317

Query: 362 KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEEN 417
           +G IE+A  + ++ ++        + S +A+    +  +++A    KEA+ +    
Sbjct: 318 QGNIEEAVRLYRKALEVFPE-FAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTF 372

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	490
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.95
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.94
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.69
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.68
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.41
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.37
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.35
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.31
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.29
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.28
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.26
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.22
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.22
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.18
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.81
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.76
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.75
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.71
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.7
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.66
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.65
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.63
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.53
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.52
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.52
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.5
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.43
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.4
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.38
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.35
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.35
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.32
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.29
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.28
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.24
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.19
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.18
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.12
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.11
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.07
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.06
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.99
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.97
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.9
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.89
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.88
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.87
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.8
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.77
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.76
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.74
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.68
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.6
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.94
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.18
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	95.79
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	95.66
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	94.52
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	94.13
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	93.81
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	93.51
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.47
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	93.26
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	88.76

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.9e-24  Score=198.47  Aligned_cols=380  Identities=11%  Similarity=0.007  Sum_probs=320.9

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCCh
Q 011236           75 VIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLV  153 (490)
Q Consensus        75 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~  153 (490)
                      +...+.+.|++++|++.++++.+.. |-++..+..+..++...|++++|...|+...+.+| +..+|..+...+.+.|++
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~~~g~~   83 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQL   83 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHhhhhccc
Confidence            3455678899999999999999876 45778888899999999999999999999998888 578899999999999999


Q ss_pred             hHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 011236          154 DESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEM  233 (490)
Q Consensus       154 ~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  233 (490)
                      ++|+..+......... +...+..........+....+............ ................+....+...+...
T Consensus        84 ~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (388)
T d1w3ba_          84 QEAIEHYRHALRLKPD-FIDGYINLAAALVAAGDMEGAVQAYVSALQYNP-DLYCVRSDLGNLLKALGRLEEAKACYLKA  161 (388)
T ss_dssp             HHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             cccccccccccccccc-ccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhhhHHHHHHh
Confidence            9999999999887544 455555566666667777777777766655433 34445555666677788888888888877


Q ss_pred             HhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCC
Q 011236          234 ESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQL  313 (490)
Q Consensus       234 ~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  313 (490)
                      . .... .+...+..+...+...|++++|...+++.....+  .+..++..+...+...|++++|...++......+ .+
T Consensus       162 ~-~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~  236 (388)
T d1w3ba_         162 I-ETQP-NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP--NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP-NH  236 (388)
T ss_dssp             H-HHCT-TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT-TC
T ss_pred             h-ccCc-chhHHHHhhcccccccCcHHHHHHHHHHHHHhCc--ccHHHHHHHhhhhhccccHHHHHHHHHHhHHHhh-hH
Confidence            6 3333 4567788889999999999999999999887665  5778899999999999999999999998887765 67


Q ss_pred             hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 011236          314 NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG  393 (490)
Q Consensus       314 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~  393 (490)
                      ...+..+...+.+.|++++|...+++..+.. +-+..++..+...|...|++++|...++......+. +...+..+...
T Consensus       237 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~  314 (388)
T d1w3ba_         237 AVVHGNLACVYYEQGLIDLAIDTYRRAIELQ-PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPT-HADSLNNLANI  314 (388)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTC-SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTT-CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCc-cchhhhHHHHH
Confidence            7788889999999999999999999998863 335668888999999999999999999999887544 78889999999


Q ss_pred             HhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC
Q 011236          394 YADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG  471 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g  471 (490)
                      +...|++++|+..|+++++       +.|+ ..++..+..++.+.|++++|...|+++.+..|. +..|..++.+|.+.|
T Consensus       315 ~~~~~~~~~A~~~~~~al~-------~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~lg~~~~~~~  387 (388)
T d1w3ba_         315 KREQGNIEEAVRLYRKALE-------VFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQ  387 (388)
T ss_dssp             HHTTTCHHHHHHHHHHHTT-------SCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTC
T ss_pred             HHHCCCHHHHHHHHHHHHH-------hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC
Confidence            9999999999999999987       3455 467888999999999999999999999999999 999999999998766

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=1.1e-22  Score=187.60  Aligned_cols=363  Identities=13%  Similarity=0.057  Sum_probs=305.3

Q ss_pred             HHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCc
Q 011236          110 QLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQH  188 (490)
Q Consensus       110 l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  188 (490)
                      +...+.+.|++++|.+.|+++.+..| +..++..+...+.+.|++++|+..|++..+..+. +..+|..+..++...|++
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~l~~~~~~~g~~   83 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPL-LAEAYSNLGNVYKERGQL   83 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHhhhhccc
Confidence            34567788999999999999998888 5888999999999999999999999999988644 677899999999999999


Q ss_pred             CcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Q 011236          189 EKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKK  268 (490)
Q Consensus       189 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  268 (490)
                      ++|...+....+... .+..............+....+........ .... ................+....+...+..
T Consensus        84 ~~A~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (388)
T d1w3ba_          84 QEAIEHYRHALRLKP-DFIDGYINLAAALVAAGDMEGAVQAYVSAL-QYNP-DLYCVRSDLGNLLKALGRLEEAKACYLK  160 (388)
T ss_dssp             HHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHSCSSHHHHHHHHHH-HHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             ccccccccccccccc-cccccccccccccccccccccccccccccc-cccc-ccccccccccccccccchhhhhHHHHHH
Confidence            999999999988643 344455555555556666666666666554 3333 4445555677778888889999988888


Q ss_pred             HhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC
Q 011236          269 CEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD  348 (490)
Q Consensus       269 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  348 (490)
                      .....+  .+...+..+...+...|++++|...+++.....+ .+...+..+...+...|++++|...++.....+ +.+
T Consensus       161 ~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~  236 (388)
T d1w3ba_         161 AIETQP--NFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDP-NFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNH  236 (388)
T ss_dssp             HHHHCT--TCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTC
T ss_pred             hhccCc--chhHHHHhhcccccccCcHHHHHHHHHHHHHhCc-ccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhH
Confidence            877655  5778888999999999999999999998888765 567788999999999999999999999998863 345


Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHH
Q 011236          349 FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVS  428 (490)
Q Consensus       349 ~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~  428 (490)
                      ...+..+...+.+.|++++|...|++..+..+. +..+|..+...+...|++++|.+.++.+..      ..+.+...+.
T Consensus       237 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~------~~~~~~~~~~  309 (388)
T d1w3ba_         237 AVVHGNLACVYYEQGLIDLAIDTYRRAIELQPH-FPDAYCNLANALKEKGSVAEAEDCYNTALR------LCPTHADSLN  309 (388)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHH------HCTTCHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHhhhc------cCCccchhhh
Confidence            667788899999999999999999999997655 778899999999999999999999999987      2335567888


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHHHhCCCCCC
Q 011236          429 SILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESMKADDIDED  489 (490)
Q Consensus       429 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m~~~~~~pd  489 (490)
                      .+...+...|++++|...+++..+..|. +.+|..++.+|.+.|  ++|.+.+++..+.  .|+
T Consensus       310 ~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l--~P~  371 (388)
T d1w3ba_         310 NLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPT  371 (388)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT--CTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCC
Confidence            8999999999999999999999999999 999999999999999  9999999998764  454

>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=99.69  E-value=1.5e-14  Score=129.19  Aligned_cols=241  Identities=11%  Similarity=-0.012  Sum_probs=116.8

Q ss_pred             HHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhH
Q 011236           77 RQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDE  155 (490)
Q Consensus        77 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~  155 (490)
                      ..+.+.|++++|+..|+.+++.. |-++..+..+..++...|++++|...|++.....| +...|..+...|...|++++
T Consensus        27 ~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~  105 (323)
T d1fcha_          27 LRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQ  105 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccccccc
Confidence            33445555555555555555544 23344445555555555555555555555544444 34445555555555555555


Q ss_pred             HHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHh
Q 011236          156 SLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMES  235 (490)
Q Consensus       156 a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~  235 (490)
                      |.+.+++......  +.............                   ..+.......+..+...+.+.+|...|.+...
T Consensus       106 A~~~~~~~~~~~~--~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~  164 (323)
T d1fcha_         106 ACEILRDWLRYTP--AYAHLVTPAEEGAG-------------------GAGLGPSKRILGSLLSDSLFLEVKELFLAAVR  164 (323)
T ss_dssp             HHHHHHHHHHTST--TTGGGCC----------------------------------CTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccchhhHHHhcc--chHHHHHhhhhhhh-------------------hcccccchhhHHHHHHhhHHHHHHHHHHHHHH
Confidence            5555555444321  11000000000000                   00000000111122233445555555555441


Q ss_pred             CCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChh
Q 011236          236 QSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNR  315 (490)
Q Consensus       236 ~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  315 (490)
                      ...-..+..++..+...+...|++++|+..|++.....+  .+..+|..+..+|...|++++|.+.|++.....+ .+..
T Consensus       165 ~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p--~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~  241 (323)
T d1fcha_         165 LDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRP--NDYLLWNKLGATLANGNQSEEAVAAYRRALELQP-GYIR  241 (323)
T ss_dssp             HSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHH
T ss_pred             HhhcccccccchhhHHHHHHHHHHhhhhccccccccccc--ccccchhhhhhcccccccchhHHHHHHHHHHHhh-ccHH
Confidence            111123455555666666666666666666666655443  3555666666666666666666666666555543 3445


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHh
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWEL  342 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~  342 (490)
                      ++..+..+|.+.|++++|...|++.++
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            566666666666666666666666554

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.4e-14  Score=129.43  Aligned_cols=249  Identities=11%  Similarity=-0.052  Sum_probs=154.6

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCC
Q 011236          143 LLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSE  222 (490)
Q Consensus       143 li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~  222 (490)
                      ....+.+.|++++|+..|+++.+..+. +..+|..+..++...|++++|...|.+..+... -+...+..+..++...|+
T Consensus        25 ~g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          25 EGLRRLQEGDLPNAVLLFEAAVQQDPK-HMEAWQYLGTTQAENEQELLAISALRRCLELKP-DNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCChHHHHHHHHhhhcccc-cccccccccccccccccc
Confidence            344556666666666666666665433 455666666666666666666666666655321 234455556666666666


Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHH
Q 011236          223 LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFW  302 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~  302 (490)
                      +++|.+.+++.. ...  |+..............                    .+.......+..+...+...++...+
T Consensus       103 ~~~A~~~~~~~~-~~~--~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~~~~~a~~~~  159 (323)
T d1fcha_         103 QRQACEILRDWL-RYT--PAYAHLVTPAEEGAGG--------------------AGLGPSKRILGSLLSDSLFLEVKELF  159 (323)
T ss_dssp             HHHHHHHHHHHH-HTS--TTTGGGCC-----------------------------------CTTHHHHHHHHHHHHHHHH
T ss_pred             ccccccchhhHH-Hhc--cchHHHHHhhhhhhhh--------------------cccccchhhHHHHHHhhHHHHHHHHH
Confidence            666666666655 222  1111000000000000                    00001111122233445566777777


Q ss_pred             HHHHHhcC-CCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          303 GLQKIKCK-KQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       303 ~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      .......+ ..+...+..+...+...|++++|...+++..... +-+...|..+...|...|++++|...|++.++..+.
T Consensus       160 ~~al~~~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~  238 (323)
T d1fcha_         160 LAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPG  238 (323)
T ss_dssp             HHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHhhcccccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHHhhc
Confidence            77666554 3455667778888888888999988888887753 235667788888888999999999999988887544


Q ss_pred             CCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCc
Q 011236          382 PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENK  418 (490)
Q Consensus       382 p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~  418 (490)
                       +..+|..+..+|.+.|++++|+..|+++++..|+..
T Consensus       239 -~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~  274 (323)
T d1fcha_         239 -YIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSR  274 (323)
T ss_dssp             -CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC-
T ss_pred             -cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCh
Confidence             677888888899999999999999999888665443

>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=99.41  E-value=3.9e-11  Score=105.56  Aligned_cols=163  Identities=7%  Similarity=0.019  Sum_probs=77.2

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcC-ChhHHHHHHHHHHHhcCCCChhhHHHHHHH
Q 011236          245 TYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLG-NKDEMMKFWGLQKIKCKKQLNRDYITMLGS  323 (490)
Q Consensus       245 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  323 (490)
                      .|+.+...+.+.+.+++|+..++++....|  .+...|+....++...| ++++|+..++......+ -+..+|..+...
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP--~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p-~~~~a~~~~~~~  121 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIELNA--ANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQP-KNYQVWHHRRVL  121 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHCT--TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHHCC--CChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHH-hhhhHHHHHhHH
Confidence            333444444445555555555555554443  34444454444444433 24555555554444443 344445555555


Q ss_pred             HHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC----
Q 011236          324 LVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN----  399 (490)
Q Consensus       324 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~----  399 (490)
                      +.+.|++++|...++++.+. -+.+...|..+...+.+.|++++|+..++++++.++. +...|+.+...+.+.+.    
T Consensus       122 ~~~l~~~~eAl~~~~kal~~-dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~-n~~a~~~r~~~l~~~~~~~~~  199 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQ-DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVR-NNSVWNQRYFVISNTTGYNDR  199 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCSCSH
T ss_pred             HHhhccHHHHHHHHhhhhhh-hhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCc-cHHHHHHHHHHHHHccccchh
Confidence            55555555555555555543 1223444555555555555555555555555554433 44444444443333322    


Q ss_pred             --HHHHHHHHHHHHH
Q 011236          400 --MEKAFECMKEALA  412 (490)
Q Consensus       400 --~~~a~~~~~~~~~  412 (490)
                        +++|++.+.++++
T Consensus       200 ~~~~~ai~~~~~al~  214 (315)
T d2h6fa1         200 AVLEREVQYTLEMIK  214 (315)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             hhhHHhHHHHHHHHH
Confidence              3445555555554

>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=99.37  E-value=1.9e-10  Score=101.09  Aligned_cols=148  Identities=7%  Similarity=-0.000  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhc-CHHHHHHHHHHccccCC-ChhHHHHHHHH
Q 011236           69 ELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVR-GLESAETYFNSLNDEDK-VDKLYGALLNC  146 (490)
Q Consensus        69 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~p-~~~~~~~li~~  146 (490)
                      ...++.+-..+.+.+.+++|+++++++++.+ |-+...+.....++...| ++++|+..++......| +..+|+.+...
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~  121 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVL  121 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHH
Confidence            3455555566667777777777777777776 445556666666666555 46777777777766665 46667777777


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhc
Q 011236          147 YVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGA  219 (490)
Q Consensus       147 ~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  219 (490)
                      +.+.|++++|+..++++.+..+. +...|..+...+...|++++|.+.++.+++.+. -+...|+.+..++.+
T Consensus       122 ~~~l~~~~eAl~~~~kal~~dp~-n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p-~n~~a~~~r~~~l~~  192 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQDAK-NYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDV-RNNSVWNQRYFVISN  192 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCT-TCHHHHHHHHHHHHH
T ss_pred             HHhhccHHHHHHHHhhhhhhhhc-chHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCC-ccHHHHHHHHHHHHH
Confidence            77777777777777777766544 566677777777777777777777777766432 244455544444433

>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=99.35  E-value=9.1e-10  Score=98.70  Aligned_cols=167  Identities=10%  Similarity=-0.044  Sum_probs=73.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHHhcCCC----ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCC----C--CchhHHH
Q 011236          285 LISHYASLGNKDEMMKFWGLQKIKCKKQ----LNRDYITMLGSLVKIGELEEAEKMLEEWELSCYC----Y--DFRVPNI  354 (490)
Q Consensus       285 l~~~~~~~~~~~~a~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~----~--~~~~~~~  354 (490)
                      +...+...|+++.+...+..........    ....+......+...++...+...+.+.......    +  ....+..
T Consensus       139 la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~  218 (366)
T d1hz4a_         139 RAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKV  218 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHH
T ss_pred             HHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHH
Confidence            3444444555555555554444332211    1122333334444455555555444443321100    0  0112333


Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCC---HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVKKGKTPT---PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSI  430 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~~~~~p~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l  430 (490)
                      +...+...|++++|...+++..+.....+   ...+..+...+...|++++|...+++++..... .+..|+. ..+..+
T Consensus       219 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~~~l  297 (366)
T d1hz4a_         219 RVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARS-LRLMSDLNRNLLLL  297 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHH
T ss_pred             HHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhh-cccChHHHHHHHHH
Confidence            44445555556666555555443322211   223344455555566666666666555432211 1222322 344555


Q ss_pred             HHHHHcCCCHHHHHHHHHHHHh
Q 011236          431 LDWLGDNRDVEEVEAFVSSLKI  452 (490)
Q Consensus       431 ~~~~~~~g~~~~a~~~~~~~~~  452 (490)
                      ...+.+.|++++|.+.+++..+
T Consensus       298 a~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         298 NQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH
Confidence            5555566666666666555443

>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=99.31  E-value=6.8e-10  Score=99.55  Aligned_cols=300  Identities=12%  Similarity=0.003  Sum_probs=177.9

Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCC----cchHHHHHHHHHhcCCcCcHHHHHHHHHHCC----CCC-CHHHHHHHH
Q 011236          144 LNCYVREGLVDESLSLMQKMKEMGSFGS----ALNYNGIMCLYTNTGQHEKIPDVLLDMKENG----VPP-DNFSYRICI  214 (490)
Q Consensus       144 i~~~~~~g~~~~a~~~~~~m~~~~~~p~----~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~----~~p-~~~~~~~li  214 (490)
                      ...+...|++++|++++++..+.....+    ..++..+...+...|++++|...|++..+..    ..+ ....+..+.
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            4445556666666666666555422111    1234455556666666666666666554321    111 122344555


Q ss_pred             HHHhccCChHHHHHHHHHHHh---CCCC--CC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccC---CChhhHHHH
Q 011236          215 NSYGARSELSSMENVLQEMES---QSHI--SM-DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKS---KDALGYNHL  285 (490)
Q Consensus       215 ~~~~~~g~~~~a~~~~~~~~~---~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~~l  285 (490)
                      ..+...|++..+...+.+...   ....  .+ ....+..+...+...|+++.+...+..........   ....++..+
T Consensus        99 ~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  178 (366)
T d1hz4a_          99 EILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAML  178 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence            666677777777777665431   1111  11 12344556677888888888888887776543321   223445556


Q ss_pred             HHHHHhcCChhHHHHHHHHHHHhcCCCC------hhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC---chhHHHHH
Q 011236          286 ISHYASLGNKDEMMKFWGLQKIKCKKQL------NRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD---FRVPNIIL  356 (490)
Q Consensus       286 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~~~~~l~  356 (490)
                      ...+...++...+...+...........      ...+..+...+...|+++.|...+..........+   ...+..+.
T Consensus       179 ~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la  258 (366)
T d1hz4a_         179 IQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIA  258 (366)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHH
Confidence            6667778888888887776555433111      12355566677888999999988887765432222   23445577


Q ss_pred             HHHHhcCCHHHHHHHHHHHHH----cCCCCC-HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc----chhhH
Q 011236          357 LGYSQKGMIEKADAVLKEIVK----KGKTPT-PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP----KPSLV  427 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~----~~~~p~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p----~~~~~  427 (490)
                      ..+...|++++|...+++...    .+..|+ ..++..+...|...|++++|.+.+++++++.+. .|...    ....+
T Consensus       259 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~~~-~~~~~~~~~~~~~~  337 (366)
T d1hz4a_         259 RAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANR-TGFISHFVIEGEAM  337 (366)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH-HCCCHHHHTTHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhh-cCcHHHHHHHHHHH
Confidence            888999999999999988764    233333 346788888999999999999999998874321 12111    11233


Q ss_pred             HHHHHHHHcCCCHHHHH
Q 011236          428 SSILDWLGDNRDVEEVE  444 (490)
Q Consensus       428 ~~l~~~~~~~g~~~~a~  444 (490)
                      ..++..+...+..+++.
T Consensus       338 ~~~~~~l~~~~~l~e~e  354 (366)
T d1hz4a_         338 AQQLRQLIQLNTLPELE  354 (366)
T ss_dssp             HHHHHHHHHTTCSCHHH
T ss_pred             HHHHHHHHhcCCChHHH
Confidence            44455555556555544

>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=99.29  E-value=7.5e-10  Score=97.09  Aligned_cols=193  Identities=10%  Similarity=0.004  Sum_probs=148.1

Q ss_pred             CCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHH
Q 011236          257 GLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKM  336 (490)
Q Consensus       257 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  336 (490)
                      +..++|..+|++.....++ .+...|...+..+...|+.+.|..+|+.+....+......|...+..+.+.|+.+.|.++
T Consensus        78 ~~~~~a~~i~~ral~~~~p-~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i  156 (308)
T d2onda1          78 LFSDEAANIYERAISTLLK-KNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMI  156 (308)
T ss_dssp             HHHHHHHHHHHHHHTTTTT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHH
Confidence            3457888888888765554 566778888888888999999999999887765534445788888888899999999999


Q ss_pred             HHHHHhcCCCCCchhHHHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhh
Q 011236          337 LEEWELSCYCYDFRVPNIILLG-YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHE  415 (490)
Q Consensus       337 ~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  415 (490)
                      |+.+.+.+. .+...|...... +...|+.+.|..+|+.+.+..+. +...|...+..+.+.|+.+.|..+|++++..  
T Consensus       157 ~~~al~~~~-~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~-~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~--  232 (308)
T d2onda1         157 FKKAREDAR-TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGD-IPEYVLAYIDYLSHLNEDNNTRVLFERVLTS--  232 (308)
T ss_dssp             HHHHHTSTT-CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHS--
T ss_pred             HHHHHHhCC-CcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhh-hHHHHHHHHHHHHHcCChHHHHHHHHHHHHh--
Confidence            999887632 344444444433 34468899999999999887544 6788999999999999999999999999882  


Q ss_pred             cCcCCCcc--hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          416 ENKFWRPK--PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       416 ~~~~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                        .+..|.  ...|...+..-...|+.+.+.++++++.+..|.
T Consensus       233 --~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~~  273 (308)
T d2onda1         233 --GSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFRE  273 (308)
T ss_dssp             --SSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTT
T ss_pred             --CCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcc
Confidence              223443  246778887777889999999999988887665

>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=99.28  E-value=9.6e-10  Score=96.40  Aligned_cols=215  Identities=9%  Similarity=0.024  Sum_probs=163.5

Q ss_pred             HHHHHHHHHHhhhhccCCChhhHHHHHHHHHh--------------cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHH
Q 011236          260 EKAIIYLKKCEDIVSKSKDALGYNHLISHYAS--------------LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLV  325 (490)
Q Consensus       260 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--------------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  325 (490)
                      +.+..+|+++....+  .+...|...+..+..              .+..++|..+|++......+.+...+...+..+.
T Consensus        33 ~Rv~~vyerAl~~~~--~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~  110 (308)
T d2onda1          33 KRVMFAYEQCLLVLG--HHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHHT--TCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            445566777766555  455556555544322              2345788899998887655455667888888889


Q ss_pred             hcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HhccCCHHHHH
Q 011236          326 KIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAG-YADKNNMEKAF  404 (490)
Q Consensus       326 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~-~~~~~~~~~a~  404 (490)
                      +.|+++.|..+++.+.+........+|...+..+.+.|+++.|..+|+++++.++. +...|...... +...|+.+.|.
T Consensus       111 ~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~  189 (308)
T d2onda1         111 SRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART-RHHVYVTAALMEYYCSKDKSVAF  189 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHH
T ss_pred             hcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHhccCHHHHH
Confidence            99999999999999988633333447889999999999999999999999987654 44455444443 34568999999


Q ss_pred             HHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-----hhhhHHHHHHHHhcC--CcHHHH
Q 011236          405 ECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-----RNMYHALTEAHIRSG--QEVDGL  477 (490)
Q Consensus       405 ~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g--~~a~~~  477 (490)
                      .+|+.++...      ..+...|...+..+.+.|+.+.|+.+|++..+..+.     ...|...+..-...|  +.+..+
T Consensus       190 ~i~e~~l~~~------p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~  263 (308)
T d2onda1         190 KIFELGLKKY------GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKV  263 (308)
T ss_dssp             HHHHHHHHHH------TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             HHHHHHHHhh------hhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9999999833      244578999999999999999999999999887653     457888888888889  888888


Q ss_pred             HHHHHh
Q 011236          478 LESMKA  483 (490)
Q Consensus       478 ~~~m~~  483 (490)
                      .+++.+
T Consensus       264 ~~r~~~  269 (308)
T d2onda1         264 EKRRFT  269 (308)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            888765

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.26  E-value=1.9e-11  Score=109.04  Aligned_cols=231  Identities=7%  Similarity=-0.021  Sum_probs=129.5

Q ss_pred             CChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCC--cCcHHHHHHHHHHCCCCCCHHHH-HHHHHHHhccCChHHHH
Q 011236          151 GLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQ--HEKIPDVLLDMKENGVPPDNFSY-RICINSYGARSELSSME  227 (490)
Q Consensus       151 g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~--~~~a~~~~~~m~~~~~~p~~~~~-~~li~~~~~~g~~~~a~  227 (490)
                      |++++|+.+++...+..++ +...|..+..++...++  ++++...++.+.+... ++...+ ......+...+.++.|.
T Consensus        87 ~~~~~al~~~~~~l~~~pk-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~-~~~~~~~~~~~~~~~~~~~~~~Al  164 (334)
T d1dcea1          87 ALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSRLPEPNWARELELCARFLEADE-RNFHCWDYRRFVAAQAAVAPAEEL  164 (334)
T ss_dssp             HHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTCCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCC-cHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhCc-hhhhhhhhHHHHHHHhccccHHHH
Confidence            3455666666666655433 44455555555544443  4566666666655422 233333 23335555667777777


Q ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHH
Q 011236          228 NVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKI  307 (490)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  307 (490)
                      ..++.+. ..++ -+...|+.+..++...|++++|...+.......+.  +    ..+...+...+..+++...+.....
T Consensus       165 ~~~~~~i-~~~p-~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~--~----~~~~~~~~~l~~~~~a~~~~~~~l~  236 (334)
T d1dcea1         165 AFTDSLI-TRNF-SNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLK--E----LELVQNAFFTDPNDQSAWFYHRWLL  236 (334)
T ss_dssp             HHHHTTT-TTTC-CCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHH--H----HHHHHHHHHHCSSCSHHHHHHHHHH
T ss_pred             HHHHHHH-HcCC-CCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhHHH--H----HHHHHHHHHhcchhHHHHHHHHHHH
Confidence            7777776 5554 55666777777777777777666555544433221  1    1122233445556666666665555


Q ss_pred             hcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHH
Q 011236          308 KCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSW  387 (490)
Q Consensus       308 ~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~  387 (490)
                      ..+ ++...+..+...+...++..+|...+.+..+.. +.+...+..+...|.+.|+.++|.+.+++.++.++. +..-|
T Consensus       237 ~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~-~~~y~  313 (334)
T d1dcea1         237 GRA-EPLFRCELSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPM-RAAYL  313 (334)
T ss_dssp             SCC-CCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGG-GHHHH
T ss_pred             hCc-chhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhC-chHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcc-cHHHH
Confidence            443 444555555666666677777777776665542 123445666666777777777777777777765322 33344


Q ss_pred             HHHHHHH
Q 011236          388 SIIAAGY  394 (490)
Q Consensus       388 ~~l~~~~  394 (490)
                      ..+...+
T Consensus       314 ~~L~~~~  320 (334)
T d1dcea1         314 DDLRSKF  320 (334)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5444443

>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=99.22  E-value=5.8e-10  Score=95.21  Aligned_cols=220  Identities=12%  Similarity=-0.010  Sum_probs=132.8

Q ss_pred             hHHHHHHHHHHHhCCCCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHH
Q 011236          223 LSSMENVLQEMESQSHISM--DWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMK  300 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  300 (490)
                      .+.++..+++........+  ...+|..+..+|.+.|++++|+..|++.....+  .+..+|..+..+|...|++++|+.
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p--~~~~a~~~lg~~~~~~g~~~~A~~   92 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRP--DMPEVFNYLGIYLTQAGNFDAAYE   92 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCC--CCHHHHhhhchHHHHHHHHHHhhh
Confidence            3445555556552222211  134555667778888888888888888777655  567778888888888888888888


Q ss_pred             HHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCC
Q 011236          301 FWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGK  380 (490)
Q Consensus       301 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  380 (490)
                      .|++.....+ .+..++..+..++...|++++|...++...+.. +.+......+..++.+.+..+.+..+.........
T Consensus        93 ~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (259)
T d1xnfa_          93 AFDSVLELDP-TYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDK  170 (259)
T ss_dssp             HHHHHHHHCT-TCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCC
T ss_pred             hhhHHHHHHh-hhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccch
Confidence            8887777665 455677777778888888888888888877753 22333333344445555555555555555544322


Q ss_pred             CCCHHHHHHHHHHHhccCC----HHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          381 TPTPNSWSIIAAGYADKNN----MEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       381 ~p~~~~~~~l~~~~~~~~~----~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                        +...++ ++..+.....    .+.+...+.....       ..|+. .+|..+...+...|++++|.+.|++..+..|
T Consensus       171 --~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  240 (259)
T d1xnfa_         171 --EQWGWN-IVEFYLGNISEQTLMERLKADATDNTS-------LAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNV  240 (259)
T ss_dssp             --CSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHH-------HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             --hhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhh-------cCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence              222222 2222222222    2222222222222       22333 4566677788888888888888888888777


Q ss_pred             c
Q 011236          456 K  456 (490)
Q Consensus       456 ~  456 (490)
                      .
T Consensus       241 ~  241 (259)
T d1xnfa_         241 H  241 (259)
T ss_dssp             T
T ss_pred             C
Confidence            6

>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=99.22  E-value=1.2e-10  Score=99.55  Aligned_cols=148  Identities=13%  Similarity=-0.004  Sum_probs=92.5

Q ss_pred             hhHHHHHHHHHHhCCCCC---ChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcCChhHHHHHH
Q 011236           85 FKHALQVSEWMSGQGLAF---SVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREGLVDESLSLM  160 (490)
Q Consensus        85 ~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g~~~~a~~~~  160 (490)
                      .+.++.-+++........   ....+..+..+|.+.|++++|+..|++....+| ++.+|+.+..++.+.|++++|+..|
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~   94 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAF   94 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhh
Confidence            344555555555443211   123444556677777888888888887777776 4677777888888888888888888


Q ss_pred             HHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHH
Q 011236          161 QKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEME  234 (490)
Q Consensus       161 ~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~  234 (490)
                      ++..+..+. +..+|..+..++...|++++|.+.|+...+... .+......+..++.+.+..+.+..+.....
T Consensus        95 ~~al~~~p~-~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  166 (259)
T d1xnfa_          95 DSVLELDPT-YNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDP-NDPFRSLWLYLAEQKLDEKQAKEVLKQHFE  166 (259)
T ss_dssp             HHHHHHCTT-CTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             hHHHHHHhh-hhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhcc-ccHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence            887776543 556677777777777888888888777766432 233333333344444454444444444443

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.18  E-value=8.1e-11  Score=104.88  Aligned_cols=275  Identities=7%  Similarity=-0.088  Sum_probs=194.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHH---HH-------HHhhcCHHHHHHHHHHccccCC-ChhHH
Q 011236           72 LQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQL---DL-------IGKVRGLESAETYFNSLNDEDK-VDKLY  140 (490)
Q Consensus        72 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~---~~-------~~~~~~~~~A~~~~~~~~~~~p-~~~~~  140 (490)
                      +..++.........++|+++++..++.. |-+...+...-   ..       +...|.+++|+.+++......| +..+|
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~~-P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~  110 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTW  110 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHH
Confidence            3444444444444589999999999876 23333333222   22       2334557889999999988887 67788


Q ss_pred             HHHHHHHHhcCC--hhHHHHHHHHHHhcCCCCCcchHH-HHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011236          141 GALLNCYVREGL--VDESLSLMQKMKEMGSFGSALNYN-GIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSY  217 (490)
Q Consensus       141 ~~li~~~~~~g~--~~~a~~~~~~m~~~~~~p~~~~~~-~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  217 (490)
                      ..+..++...++  +++|+..++++.+.... +...+. .....+...+.+++|+..++...+.+. -+...|+.+..++
T Consensus       111 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~-~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p-~~~~a~~~l~~~~  188 (334)
T d1dcea1         111 HHRCWLLSRLPEPNWARELELCARFLEADER-NFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWHYRSCLL  188 (334)
T ss_dssp             HHHHHHHHTCSSCCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTC-CCHHHHHHHHHHH
T ss_pred             HHhhHHHHHhccccHHHHHHHHHHHHhhCch-hhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCC-CCHHHHHHHHHHH
Confidence            888777777664  78999999999887543 455544 445677778999999999999888654 3677888888999


Q ss_pred             hccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhH
Q 011236          218 GARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDE  297 (490)
Q Consensus       218 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  297 (490)
                      ...|++++|...++... ...  |.   .......+...+..+++...+.......+  ++...+..+...+...++.++
T Consensus       189 ~~~~~~~~A~~~~~~~~-~~~--~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~~--~~~~~~~~l~~~~~~~~~~~~  260 (334)
T d1dcea1         189 PQLHPQPDSGPQGRLPE-NVL--LK---ELELVQNAFFTDPNDQSAWFYHRWLLGRA--EPLFRCELSVEKSTVLQSELE  260 (334)
T ss_dssp             HHHSCCCCSSSCCSSCH-HHH--HH---HHHHHHHHHHHCSSCSHHHHHHHHHHSCC--CCSSSCCCCHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHhH-HhH--HH---HHHHHHHHHHhcchhHHHHHHHHHHHhCc--chhhHHHHHHHHHHHHhhHHH
Confidence            99999887765554433 110  11   12244456667788888888888776554  566667777888888899999


Q ss_pred             HHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCC-chhHHHHHHHHH
Q 011236          298 MMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYD-FRVPNIILLGYS  360 (490)
Q Consensus       298 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~  360 (490)
                      |...+.+.....+ .+...+..+..++...|+.++|.+.++++.+.  .|+ ...|..|...+.
T Consensus       261 a~~~~~~~~~~~p-~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l--dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         261 SCKELQELEPENK-WCLLTIILLMRALDPLLYEKETLQYFSTLKAV--DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             HHHHHHHHCTTCH-HHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH--CGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCc-hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CcccHHHHHHHHHHHh
Confidence            9999887665554 45677888999999999999999999999885  454 345555555444

>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=98.81  E-value=3.5e-07  Score=78.80  Aligned_cols=207  Identities=10%  Similarity=-0.033  Sum_probs=135.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHhhhhccCCC----hhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCC-C----hhhHHH
Q 011236          249 VANYYIIAGLKEKAIIYLKKCEDIVSKSKD----ALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQ-L----NRDYIT  319 (490)
Q Consensus       249 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~----~~~~~~  319 (490)
                      ....|...|++++|...|.+.........+    ..+|..+..+|.+.|++++|.+.++......... +    ..++..
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            345688888999999888887654322122    3578888889999999999999988766543311 1    234556


Q ss_pred             HHHHHHh-cCCHHHHHHHHHHHHhc----CCCC-CchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCH------HHH
Q 011236          320 MLGSLVK-IGELEEAEKMLEEWELS----CYCY-DFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTP------NSW  387 (490)
Q Consensus       320 l~~~~~~-~~~~~~a~~~~~~~~~~----~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~------~~~  387 (490)
                      +...|.. .|++++|.+.+++..+.    +.++ -..++..+...|...|++++|...|+++.........      ..+
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            6666644 69999999999887643    1111 1235677888899999999999999998876433211      123


Q ss_pred             HHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc--CCCHHHHHHHHHHHHhcccc
Q 011236          388 SIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD--NRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       388 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~--~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ...+..+...|+++.|...++++.+..|.-. -.........++.++..  .+.+++|...|+.+.+.++.
T Consensus       203 ~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~-~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~~lD~~  272 (290)
T d1qqea_         203 LKKGLCQLAATDAVAAARTLQEGQSEDPNFA-DSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKW  272 (290)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHGGGCC----------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCHH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHHHHhCCCcc-chHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCHH
Confidence            4555567788999999999999877321000 00012345666666654  34578888888766655543

>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=98.76  E-value=2e-07  Score=80.42  Aligned_cols=198  Identities=9%  Similarity=-0.105  Sum_probs=136.6

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcC-CC----ChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-----CchhHH
Q 011236          284 HLISHYASLGNKDEMMKFWGLQKIKCK-KQ----LNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY-----DFRVPN  353 (490)
Q Consensus       284 ~l~~~~~~~~~~~~a~~~~~~~~~~~~-~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-----~~~~~~  353 (490)
                      .....|...+++++|.+.|.+...... ..    ...+|..+..+|.+.|++++|...+++..+.-...     ...++.
T Consensus        42 ~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~  121 (290)
T d1qqea_          42 QAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKF  121 (290)
T ss_dssp             HHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHH
Confidence            345668889999999999998776432 11    23578889999999999999999999876531111     133455


Q ss_pred             HHHHHHHh-cCCHHHHHHHHHHHHHc----CCCC-CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hh
Q 011236          354 IILLGYSQ-KGMIEKADAVLKEIVKK----GKTP-TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SL  426 (490)
Q Consensus       354 ~l~~~~~~-~g~~~~A~~~~~~m~~~----~~~p-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~  426 (490)
                      .+...|.. .|++++|...+++..+.    +..+ -..+|..+...+...|++++|+..|+++....+......... ..
T Consensus       122 ~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~  201 (290)
T d1qqea_         122 ELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDY  201 (290)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHH
T ss_pred             HHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHH
Confidence            66666644 69999999999988653    1111 134578889999999999999999999988544333333333 23


Q ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhcccc-h-----hhhHHHHHHHHhcC----CcHHHHHHHH
Q 011236          427 VSSILDWLGDNRDVEEVEAFVSSLKIKVQK-R-----NMYHALTEAHIRSG----QEVDGLLESM  481 (490)
Q Consensus       427 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~-----~~~~~l~~~~~~~g----~~a~~~~~~m  481 (490)
                      +...+..+...|+++.|...+++..+..|. .     .....++.++....    ++|+..|+++
T Consensus       202 ~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~  266 (290)
T d1qqea_         202 FLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNF  266 (290)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            345555667889999999999999888765 2     24466777776543    4566555443

>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=98.75  E-value=1.6e-07  Score=68.37  Aligned_cols=100  Identities=18%  Similarity=0.051  Sum_probs=55.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc
Q 011236          357 LGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD  436 (490)
Q Consensus       357 ~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~  436 (490)
                      ..+.+.|++++|+..|++.++..+. +...|..+..+|...|++++|+..++++++..      +.+...|..+..++..
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~------p~~~~~~~~~g~~~~~   83 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLDPH-NHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK------PDWGKGYSRKAAALEF   83 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC------TTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCc-chhhhhcccccccccccccccchhhhhHHHhc------cchhhHHHHHHHHHHH
Confidence            3455556666666666666555443 55556666666666666666666666665522      1233455555556666


Q ss_pred             CCCHHHHHHHHHHHHhcccc-hhhhHHH
Q 011236          437 NRDVEEVEAFVSSLKIKVQK-RNMYHAL  463 (490)
Q Consensus       437 ~g~~~~a~~~~~~~~~~~~~-~~~~~~l  463 (490)
                      .|++++|...+++..+..|. +..+..+
T Consensus        84 ~~~~~~A~~~~~~a~~~~p~~~~~~~~l  111 (117)
T d1elwa_          84 LNRFEEAKRTYEEGLKHEANNPQLKEGL  111 (117)
T ss_dssp             TTCHHHHHHHHHHHHTTCTTCHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            66666666666666655555 4444443

>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=98.71  E-value=9.4e-07  Score=70.60  Aligned_cols=124  Identities=16%  Similarity=0.014  Sum_probs=63.3

Q ss_pred             HHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHH
Q 011236          252 YYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELE  331 (490)
Q Consensus       252 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  331 (490)
                      .+...|++++|++.|+++    .+ ++..+|..+..+|...|++++|++.|++.+...+ .....|..+..++.+.|+++
T Consensus        14 ~~~~~~d~~~Al~~~~~i----~~-~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp-~~~~a~~~~g~~~~~~g~~~   87 (192)
T d1hh8a_          14 LAADKKDWKGALDAFSAV----QD-PHSRICFNIGCMYTILKNMTEAEKAFTRSINRDK-HLAVAYFQRGMLYYQTEKYD   87 (192)
T ss_dssp             HHHHTTCHHHHHHHHHTS----SS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHCCCHHHHHHHHHhc----CC-CCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhh-hhhhhHHHHHHHHHhhccHH
Confidence            344455555555555432    11 3444455555555555555555555555554443 34444555555555555555


Q ss_pred             HHHHHHHHHHhcCC------------CCC---chhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          332 EAEKMLEEWELSCY------------CYD---FRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       332 ~a~~~~~~~~~~~~------------~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      +|...|++......            ...   ..++..+..+|.+.|++++|.+.+....+..+.
T Consensus        88 ~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~  152 (192)
T d1hh8a_          88 LAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  152 (192)
T ss_dssp             HHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            55555555443210            000   123344566677777777777777777665433

>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=98.70  E-value=6.4e-07  Score=71.58  Aligned_cols=131  Identities=11%  Similarity=0.010  Sum_probs=95.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCH
Q 011236          321 LGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNM  400 (490)
Q Consensus       321 ~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~  400 (490)
                      ...+...|+++.|.+.|.++    .+|+..+|..+..+|...|++++|+..|++.++.++. +...|..+..+|.+.|++
T Consensus        12 g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~-~~~a~~~~g~~~~~~g~~   86 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKH-LAVAYFQRGMLYYQTEKY   86 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhh-hhhhHHHHHHHHHhhccH
Confidence            34456678888888887754    3456677777888888888888888888888887665 677888888888888888


Q ss_pred             HHHHHHHHHHHHhhhcCc-------C--CCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          401 EKAFECMKEALAVHEENK-------F--WRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       401 ~~a~~~~~~~~~~~~~~~-------~--~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      ++|+..|++++...+...       |  ..++ ..++..+..++.+.|++++|.+.++...+..+.
T Consensus        87 ~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~  152 (192)
T d1hh8a_          87 DLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  152 (192)
T ss_dssp             HHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            888888888876321110       1  1111 245566777888899999999999988877665

>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=98.66  E-value=8.3e-08  Score=77.86  Aligned_cols=102  Identities=10%  Similarity=-0.033  Sum_probs=88.2

Q ss_pred             CChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHH
Q 011236          312 QLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIA  391 (490)
Q Consensus       312 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~  391 (490)
                      |+...+......+.+.|++++|...|.+.++.. +.+...|..+..+|.+.|++++|+..|++.++..+. +..+|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~-~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQ-SVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTT-CHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCC-cHHHHHHHH
Confidence            677778888899999999999999999988863 446778888999999999999999999999887654 678899999


Q ss_pred             HHHhccCCHHHHHHHHHHHHHhhh
Q 011236          392 AGYADKNNMEKAFECMKEALAVHE  415 (490)
Q Consensus       392 ~~~~~~~~~~~a~~~~~~~~~~~~  415 (490)
                      .+|...|++++|+..|+++++..|
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~l~p  103 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYSLAK  103 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCc
Confidence            999999999999999999988543

>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=98.65  E-value=3.5e-07  Score=70.83  Aligned_cols=92  Identities=13%  Similarity=-0.023  Sum_probs=45.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC
Q 011236          319 TMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKN  398 (490)
Q Consensus       319 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~  398 (490)
                      .....|.+.|++++|...|++..+.. +-+...|..+..+|...|++++|...|++.++.++. +..+|..++.+|...|
T Consensus        15 ~~gn~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~-~~~a~~~~g~~~~~~g   92 (159)
T d1a17a_          15 TQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKK-YIKGYYRRAASNMALG   92 (159)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHccc-chHHHHHHHHHHHHcC
Confidence            33444445555555555555555442 223344444555555555555555555555544333 4444555555555555


Q ss_pred             CHHHHHHHHHHHHH
Q 011236          399 NMEKAFECMKEALA  412 (490)
Q Consensus       399 ~~~~a~~~~~~~~~  412 (490)
                      ++++|...+++++.
T Consensus        93 ~~~eA~~~~~~a~~  106 (159)
T d1a17a_          93 KFRAALRDYETVVK  106 (159)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            55555555555544

>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=98.63  E-value=6.8e-07  Score=64.87  Aligned_cols=91  Identities=19%  Similarity=0.067  Sum_probs=70.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC
Q 011236          320 MLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN  399 (490)
Q Consensus       320 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~  399 (490)
                      -...+.+.|++++|...|++.++. -+.+...|..+..+|...|++++|+..+.+.++.++. +...|..+..++...|+
T Consensus         9 ~g~~~~~~g~~~eAi~~~~~al~~-~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~-~~~~~~~~g~~~~~~~~   86 (117)
T d1elwa_           9 KGNKALSVGNIDDALQCYSEAIKL-DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPD-WGKGYSRKAAALEFLNR   86 (117)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhc-CCcchhhhhcccccccccccccccchhhhhHHHhccc-hhhHHHHHHHHHHHccC
Confidence            355667778888888888888776 3335667777888888888888888888888877655 77778888888888888


Q ss_pred             HHHHHHHHHHHHH
Q 011236          400 MEKAFECMKEALA  412 (490)
Q Consensus       400 ~~~a~~~~~~~~~  412 (490)
                      +++|+..|+++++
T Consensus        87 ~~~A~~~~~~a~~   99 (117)
T d1elwa_          87 FEEAKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHH
Confidence            8888888888877

>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=98.53  E-value=2.6e-07  Score=74.86  Aligned_cols=99  Identities=10%  Similarity=-0.099  Sum_probs=89.2

Q ss_pred             CChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCC-CchhHHHH
Q 011236          277 KDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCY-DFRVPNII  355 (490)
Q Consensus       277 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~~~l  355 (490)
                      |+...+......+.+.|++++|+..|.+.+...+ .+...|..+..+|.+.|++++|...+++.++.  .| +...|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p-~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l--~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNP-LVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS-CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHh--CCCcHHHHHHH
Confidence            7777888889999999999999999999998876 77888999999999999999999999999875  44 46678899


Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHc
Q 011236          356 LLGYSQKGMIEKADAVLKEIVKK  378 (490)
Q Consensus       356 ~~~~~~~g~~~~A~~~~~~m~~~  378 (490)
                      ..+|.+.|++++|+..|++..+.
T Consensus        79 g~~~~~l~~~~~A~~~~~~al~l  101 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAYSL  101 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh
Confidence            99999999999999999998775

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.52  E-value=0.00017  Score=61.93  Aligned_cols=135  Identities=13%  Similarity=0.129  Sum_probs=65.0

Q ss_pred             ChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHH
Q 011236          103 SVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLY  182 (490)
Q Consensus       103 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~  182 (490)
                      +......+...|.+.|.++.|..+|..+..       |..++..+.+.++++.|.+++.+..      +..+|..+...+
T Consensus        13 n~~d~~~i~~~c~~~~lye~A~~lY~~~~d-------~~rl~~~~v~l~~~~~avd~~~k~~------~~~~~k~~~~~l   79 (336)
T d1b89a_          13 NNAHIQQVGDRCYDEKMYDAAKLLYNNVSN-------FGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVCFAC   79 (336)
T ss_dssp             ----------------CTTTHHHHHHHTTC-------HHHHHHHHHTTTCHHHHHHHHHHHT------CHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHCCCHHHHHHHHHhCCC-------HHHHHHHHHhhccHHHHHHHHHHcC------CHHHHHHHHHHH
Confidence            334444455566666666666666665543       5566666666666666666554331      445666666666


Q ss_pred             HhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcC
Q 011236          183 TNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSHISMDWGTYSTVANYYIIAG  257 (490)
Q Consensus       183 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~  257 (490)
                      ........+     .+...+...+......++..|-..|.+++...+++... ... ..+...++-++.+|++.+
T Consensus        80 ~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~-~~~-~~~~~~~~~L~~lyak~~  147 (336)
T d1b89a_          80 VDGKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAAL-GLE-RAHMGMFTELAILYSKFK  147 (336)
T ss_dssp             HHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHT-TST-TCCHHHHHHHHHHHHTTC
T ss_pred             HhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHH-cCC-ccchHHHHHHHHHHHHhC
Confidence            654433221     12222233344445556666666666666666666654 322 245555666666666543

>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=98.52  E-value=2.8e-06  Score=65.46  Aligned_cols=91  Identities=18%  Similarity=0.087  Sum_probs=48.5

Q ss_pred             HHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCC
Q 011236          250 ANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGE  329 (490)
Q Consensus       250 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  329 (490)
                      ...|.+.|++++|+..|++..+..+  .+...|..+..+|...|++++|...|++.+...+ .+..+|..+..++...|+
T Consensus        17 gn~~~~~~~y~~A~~~~~~al~~~p--~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p-~~~~a~~~~g~~~~~~g~   93 (159)
T d1a17a_          17 ANDYFKAKDYENAIKFYSQAIELNP--SNAIYYGNRSLAYLRTECYGYALGDATRAIELDK-KYIKGYYRRAASNMALGK   93 (159)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHST--TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHhhhccccch--hhhhhhhhhHHHHHhccccchHHHHHHHHHHHcc-cchHHHHHHHHHHHHcCC
Confidence            3445555555555555555555443  3455555555555555555555555555554443 344455555555555555


Q ss_pred             HHHHHHHHHHHHhc
Q 011236          330 LEEAEKMLEEWELS  343 (490)
Q Consensus       330 ~~~a~~~~~~~~~~  343 (490)
                      +++|...+++....
T Consensus        94 ~~eA~~~~~~a~~~  107 (159)
T d1a17a_          94 FRAALRDYETVVKV  107 (159)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc
Confidence            55555555555553

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.50  E-value=1.7e-06  Score=63.86  Aligned_cols=102  Identities=15%  Similarity=0.011  Sum_probs=71.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILD  432 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~  432 (490)
                      .+...|.+.|++++|+..|.+.++.++. +..+|..+..+|.+.|++++|++.++++++..+......+.. .+|..+..
T Consensus         9 ~~G~~~~~~~~y~~Ai~~y~~al~~~p~-~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~lg~   87 (128)
T d1elra_           9 ELGNDAYKKKDFDTALKHYDKAKELDPT-NMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARIGN   87 (128)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCcc-cHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence            4556677778888888888887777654 677777788888888888888888888777555433333332 46666777


Q ss_pred             HHHcCCCHHHHHHHHHHHHhcccc
Q 011236          433 WLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       433 ~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .+...+++++|...|++.....+.
T Consensus        88 ~~~~~~~~~~A~~~~~kal~~~~~  111 (128)
T d1elra_          88 SYFKEEKYKDAIHFYNKSLAEHRT  111 (128)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCCC
T ss_pred             HHHHhCCHHHHHHHHHHHHhcCCC
Confidence            777778888888887776655444

>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=98.43  E-value=1e-06  Score=63.27  Aligned_cols=88  Identities=11%  Similarity=0.134  Sum_probs=55.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcc-hhhHHHHHHH
Q 011236          355 ILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPK-PSLVSSILDW  433 (490)
Q Consensus       355 l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~  433 (490)
                      +...+.+.|++++|...|++.++..+. +..+|..+..++.+.|++++|+..++++++       +.|+ ...+..+...
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~p~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~-------~~p~~~~a~~~la~~   93 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKEPE-REEAWRSLGLTQAENEKDGLAIIALNHARM-------LDPKDIAVHAALAVS   93 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccccc-cchhhhhhhhhhhhhhhHHHhhcccccccc-------cccccccchHHHHHH
Confidence            445566666666666666666665544 566666666666666666666666666666       2233 3566666666


Q ss_pred             HHcCCCHHHHHHHHHHH
Q 011236          434 LGDNRDVEEVEAFVSSL  450 (490)
Q Consensus       434 ~~~~g~~~~a~~~~~~~  450 (490)
                      |...|++++|.+.+++.
T Consensus        94 y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          94 HTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHH
Confidence            66666666666666654

>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=98.40  E-value=2.2e-06  Score=62.35  Aligned_cols=97  Identities=12%  Similarity=0.014  Sum_probs=58.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCC---HHHHHHHHHHHHHhhhcCcCCCcch-hhHHH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNN---MEKAFECMKEALAVHEENKFWRPKP-SLVSS  429 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~  429 (490)
                      .++..+...+++++|.+.|++.+..++. ++.++..+..++.+.++   +++|+.++++++.     ..-.|+. .++..
T Consensus         4 ~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~-~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~-----~~~~~~~~~~~~~   77 (122)
T d1nzna_           4 AVLNELVSVEDLLKFEKKFQSEKAAGSV-SKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLP-----KGSKEEQRDYVFY   77 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHSCC-CHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTT-----TSCHHHHHHHHHH
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHHhhCCC-CHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHh-----ccCCchHHHHHHH
Confidence            4555666666677777777776666544 66666666666665443   3456666666655     2212221 24556


Q ss_pred             HHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          430 ILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       430 l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      +..+|.+.|++++|.+.|+++.+..|.
T Consensus        78 Lg~~y~~~g~~~~A~~~~~~aL~~~P~  104 (122)
T d1nzna_          78 LAVGNYRLKEYEKALKYVRGLLQTEPQ  104 (122)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHhCcC
Confidence            666666777777777777777666665

>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=98.38  E-value=0.00014  Score=61.03  Aligned_cols=47  Identities=15%  Similarity=0.045  Sum_probs=26.4

Q ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHHHHHHHHHH
Q 011236          363 GMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAFECMKEALA  412 (490)
Q Consensus       363 g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~  412 (490)
                      .++++|...|++..+.|   ++..+..|...|.+    ..+.++|.++|+++.+
T Consensus       196 ~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~  246 (265)
T d1ouva_         196 KNFKEALARYSKACELE---NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCK  246 (265)
T ss_dssp             CCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHH
T ss_pred             cchhhhhhhHhhhhccc---CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHH
Confidence            45666666666666654   34445555555543    2355666666666655

>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=98.35  E-value=6.9e-06  Score=63.92  Aligned_cols=80  Identities=15%  Similarity=-0.013  Sum_probs=65.8

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHH
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHA  462 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~  462 (490)
                      .+|+.+..+|.+.|++++|+..+++++.       +.| +...+..+..++...|++++|...|+++.+..|. +.+...
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~-------~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~  135 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALE-------LDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQ  135 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhh-------ccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            3577788889999999999999999998       335 5578888899999999999999999999999988 777666


Q ss_pred             HHHHHHhcC
Q 011236          463 LTEAHIRSG  471 (490)
Q Consensus       463 l~~~~~~~g  471 (490)
                      +.....+.+
T Consensus       136 l~~~~~~~~  144 (170)
T d1p5qa1         136 LAVCQQRIR  144 (170)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            666655444

>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=98.35  E-value=2.3e-06  Score=61.34  Aligned_cols=90  Identities=13%  Similarity=-0.016  Sum_probs=57.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccC
Q 011236          319 TMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKN  398 (490)
Q Consensus       319 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~  398 (490)
                      .+...+.+.|++++|...+++..+.. +-+...|..+..++.+.|++++|+..|++.++..+. +...|..+...|...|
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~-~~~a~~~la~~y~~~g   98 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPK-DIAVHAALAVSHTNEH   98 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccccc-cccchHHHHHHHHHCC
Confidence            34455566667777777776666652 224556666666677777777777777776666544 5666666777777777


Q ss_pred             CHHHHHHHHHHH
Q 011236          399 NMEKAFECMKEA  410 (490)
Q Consensus       399 ~~~~a~~~~~~~  410 (490)
                      ++++|.+.+++.
T Consensus        99 ~~~~A~~~l~~~  110 (112)
T d1hxia_          99 NANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            777777766654

>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=98.32  E-value=1.7e-06  Score=62.86  Aligned_cols=94  Identities=19%  Similarity=0.189  Sum_probs=60.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCC---HHHHHHHHHHHHHcCCCCC-HHHHHHHHHH
Q 011236          318 ITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGM---IEKADAVLKEIVKKGKTPT-PNSWSIIAAG  393 (490)
Q Consensus       318 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~m~~~~~~p~-~~~~~~l~~~  393 (490)
                      ..++..+...+++++|++.|++....+ +.+..++..+..++.+.++   +++|+.+|+++...+..|+ ..+|..+..+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            345666667777777777777777653 2355566666666665443   3457777777766544333 2356677777


Q ss_pred             HhccCCHHHHHHHHHHHHH
Q 011236          394 YADKNNMEKAFECMKEALA  412 (490)
Q Consensus       394 ~~~~~~~~~a~~~~~~~~~  412 (490)
                      |.+.|++++|++.|+++++
T Consensus        82 y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHH
Confidence            7777777777777777777

>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=98.29  E-value=1.5e-05  Score=61.99  Aligned_cols=112  Identities=8%  Similarity=-0.048  Sum_probs=77.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHH
Q 011236          281 GYNHLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYS  360 (490)
Q Consensus       281 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  360 (490)
                      .+......+.+.|++++|+..|.+.+...+......              ..-......+       -..+|+.+..+|.
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~--------------~~~~~~~~~~-------~~~~~~nla~~y~   73 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFS--------------NEEAQKAQAL-------RLASHLNLAMCHL   73 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCC--------------SHHHHHHHHH-------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccc--------------hHHHhhhchh-------HHHHHHHHHHHHH
Confidence            344555667777777777777776665543111100              0000011111       1135667888899


Q ss_pred             hcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhh
Q 011236          361 QKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVH  414 (490)
Q Consensus       361 ~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  414 (490)
                      +.|++++|+..++..++.++. ++.+|..+..+|...|++++|+..|+++++..
T Consensus        74 k~~~~~~A~~~~~~al~~~p~-~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~  126 (170)
T d1p5qa1          74 KLQAFSAAIESCNKALELDSN-NEKGLSRRGEAHLAVNDFELARADFQKVLQLY  126 (170)
T ss_dssp             HTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             hhhhcccccchhhhhhhcccc-chhhhHHHHHHHHHhhhHHHHHHHHHHHHHhC
Confidence            999999999999999998765 88899999999999999999999999999833

>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=98.28  E-value=0.00031  Score=58.79  Aligned_cols=225  Identities=12%  Similarity=-0.034  Sum_probs=126.0

Q ss_pred             hhHHHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHh----cCCcCcHHHHHHHHHHCCCCCCHHHHHH
Q 011236          137 DKLYGALLNCYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTN----TGQHEKIPDVLLDMKENGVPPDNFSYRI  212 (490)
Q Consensus       137 ~~~~~~li~~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~  212 (490)
                      +..+..|...+.+.+++++|++.|++..+.|   +...+..|...|..    ..+...+...+......+.   ......
T Consensus         2 p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~---~~a~~~   75 (265)
T d1ouva_           2 PKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNY---SNGCHL   75 (265)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---HHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccc---cchhhc
Confidence            3445555555666666777777776666654   44455555555554    3355556666666555432   222222


Q ss_pred             HHHHHh----ccCChHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHH----cCCHHHHHHHHHHHhhhhccCCChhhHHH
Q 011236          213 CINSYG----ARSELSSMENVLQEMESQSHISMDWGTYSTVANYYII----AGLKEKAIIYLKKCEDIVSKSKDALGYNH  284 (490)
Q Consensus       213 li~~~~----~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  284 (490)
                      +...+.    ...+.+.|...++... ..+. +  .....+...+..    ......+...+.....   . .+...+..
T Consensus        76 l~~~~~~~~~~~~~~~~a~~~~~~a~-~~g~-~--~a~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~---~-~~~~~~~~  147 (265)
T d1ouva_          76 LGNLYYSGQGVSQNTNKALQYYSKAC-DLKY-A--EGCASLGGIYHDGKVVTRDFKKAVEYFTKACD---L-NDGDGCTI  147 (265)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHH-HTTC-H--HHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH---T-TCHHHHHH
T ss_pred             cccccccccccchhhHHHHHHHhhhh-hhhh-h--hHHHhhcccccCCCcccchhHHHHHHhhhhhc---c-cccchhhh
Confidence            222222    2445666777777665 4443 1  122223333332    2334455555554332   2 45556666


Q ss_pred             HHHHHHh----cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHh----cCCHHHHHHHHHHHHhcCCCCCchhHHHHH
Q 011236          285 LISHYAS----LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVK----IGELEEAEKMLEEWELSCYCYDFRVPNIIL  356 (490)
Q Consensus       285 l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  356 (490)
                      +...+..    ..+...+...++.....   .+......+...+..    ..+.+.|...|....+.|   ++..+..|.
T Consensus       148 L~~~~~~~~~~~~~~~~~~~~~~~a~~~---g~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG  221 (265)
T d1ouva_         148 LGSLYDAGRGTPKDLKKALASYDKACDL---KDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLG  221 (265)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             hhhhhccCCCcccccccchhhhhccccc---cccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHH
Confidence            6666664    34455666666644433   345555555555544    567888999998888875   344556677


Q ss_pred             HHHHh----cCCHHHHHHHHHHHHHcCCC
Q 011236          357 LGYSQ----KGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       357 ~~~~~----~g~~~~A~~~~~~m~~~~~~  381 (490)
                      ..|.+    ..+.++|.+.|++..+.|..
T Consensus       222 ~~y~~G~g~~~n~~~A~~~~~kAa~~g~~  250 (265)
T d1ouva_         222 AMQYNGEGVTRNEKQAIENFKKGCKLGAK  250 (265)
T ss_dssp             HHHHTTSSSSCCSTTHHHHHHHHHHHTCH
T ss_pred             HHHHcCCCCccCHHHHHHHHHHHHHCcCH
Confidence            77765    34788899999988887744

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.24  E-value=0.0011  Score=56.83  Aligned_cols=282  Identities=10%  Similarity=-0.000  Sum_probs=151.4

Q ss_pred             CCCHHHHHHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHH
Q 011236           66 KISELELQRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLN  145 (490)
Q Consensus        66 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~  145 (490)
                      .|+..-...+.+.|.+.|.++.|..+|..+         ..+..++..+.+.++++.|.+++....    +..+|..+..
T Consensus        11 ~~n~~d~~~i~~~c~~~~lye~A~~lY~~~---------~d~~rl~~~~v~l~~~~~avd~~~k~~----~~~~~k~~~~   77 (336)
T d1b89a_          11 GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGARKAN----STRTWKEVCF   77 (336)
T ss_dssp             CC----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHHHHHT----CHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHCCCHHHHHHHHHhC---------CCHHHHHHHHHhhccHHHHHHHHHHcC----CHHHHHHHHH
Confidence            345566667778888889999999888743         335567778888889998888876552    5668888888


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHH
Q 011236          146 CYVREGLVDESLSLMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSS  225 (490)
Q Consensus       146 ~~~~~g~~~~a~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~  225 (490)
                      .+.+......+.     +.......++.....++..|-..|.+++...+++..... -.++...++.++..|++.+ .++
T Consensus        78 ~l~~~~e~~la~-----i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~-~~k  150 (336)
T d1b89a_          78 ACVDGKEFRLAQ-----MCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK-PQK  150 (336)
T ss_dssp             HHHHTTCHHHHH-----HTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTC-HHH
T ss_pred             HHHhCcHHHHHH-----HHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhC-hHH
Confidence            888877665432     223333345556677888888899999988888877643 2456677888888888764 344


Q ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhh---------hccCCChhhHHHHHHHHHhcCChh
Q 011236          226 MENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDI---------VSKSKDALGYNHLISHYASLGNKD  296 (490)
Q Consensus       226 a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~~~~~~l~~~~~~~~~~~  296 (490)
                      ..+.+....   + ..+...   ++..|-..+-++++.-++.++...         .+  ++..-....+..+.+..+.+
T Consensus       151 l~e~l~~~s---~-~y~~~k---~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~--~~~~~~~~f~e~~~k~~N~e  221 (336)
T d1b89a_         151 MREHLELFW---S-RVNIPK---VLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHP--TDAWKEGQFKDIITKVANVE  221 (336)
T ss_dssp             HHHHHHHHS---T-TSCHHH---HHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHST--TTTCCHHHHHHHHHHCSSTH
T ss_pred             HHHHHHhcc---c-cCCHHH---HHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcc--hhhhhHHHHHHHHHccCChH
Confidence            444443332   1 122222   344444444444444444432211         11  22223333444445555554


Q ss_pred             HHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHH
Q 011236          297 EMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIV  376 (490)
Q Consensus       297 ~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  376 (490)
                      ...++........    +...+.++......-+.                      ..++....+.+++.-....++...
T Consensus       222 ~~~~~i~~yL~~~----p~~i~~lL~~v~~~~d~----------------------~r~V~~~~k~~~l~li~p~Le~v~  275 (336)
T d1b89a_         222 LYYRAIQFYLEFK----PLLLNDLLMVLSPRLDH----------------------TRAVNYFSKVKQLPLVKPYLRSVQ  275 (336)
T ss_dssp             HHHHHHHHHHHHC----GGGHHHHHHHHGGGCCH----------------------HHHHHHHHHTTCTTTTHHHHHHHH
T ss_pred             HHHHHHHHHHHcC----HHHHHHHHHHhccCCCH----------------------HHHHHHHHhcCCcHHHHHHHHHHH
Confidence            4444444333221    12223333332222222                      234444455556666666666655


Q ss_pred             HcCCCCCHHHHHHHHHHHhccCCHHHHHH
Q 011236          377 KKGKTPTPNSWSIIAAGYADKNNMEKAFE  405 (490)
Q Consensus       377 ~~~~~p~~~~~~~l~~~~~~~~~~~~a~~  405 (490)
                      +.|   +..+.+++...|...++++.-.+
T Consensus       276 ~~n---~~~vn~al~~lyie~~d~~~l~~  301 (336)
T d1b89a_         276 NHN---NKSVNESLNNLFITEEDYQALRT  301 (336)
T ss_dssp             TTC---CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HcC---hHHHHHHHHHHHhCcchhHHHHH
Confidence            544   34577888888888887655333

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.19  E-value=2.2e-05  Score=61.35  Aligned_cols=129  Identities=11%  Similarity=0.051  Sum_probs=91.1

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcC
Q 011236          284 HLISHYASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKG  363 (490)
Q Consensus       284 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  363 (490)
                      .........|++++|.+.|.........+ ....       ...+.+  +...-..+...    ....+..+...+.+.|
T Consensus        16 ~~g~~~~~~g~~e~A~~~~~~AL~l~rG~-~l~~-------~~~~~w--~~~~r~~l~~~----~~~a~~~la~~~~~~g   81 (179)
T d2ff4a2          16 TAGVHAAAAGRFEQASRHLSAALREWRGP-VLDD-------LRDFQF--VEPFATALVED----KVLAHTAKAEAEIACG   81 (179)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCSS-TTGG-------GTTSTT--HHHHHHHHHHH----HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhCccc-cccc-------CcchHH--HHHHHHHHHHH----HHHHHHHHHHHHHHCC
Confidence            34456677888888888888877654311 1000       001111  11111111111    2345677889999999


Q ss_pred             CHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhH
Q 011236          364 MIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLV  427 (490)
Q Consensus       364 ~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~  427 (490)
                      ++++|+..++++++..+. +...|..++.+|...|+..+|++.|+++.....+..|+.|+..+-
T Consensus        82 ~~~~Al~~~~~al~~~P~-~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~  144 (179)
T d2ff4a2          82 RASAVIAELEALTFEHPY-REPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  144 (179)
T ss_dssp             CHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             CchHHHHHHHHHHHhCCc-cHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHH
Confidence            999999999999998766 889999999999999999999999999987666668999988653

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=7.3e-07  Score=83.06  Aligned_cols=225  Identities=9%  Similarity=-0.058  Sum_probs=103.1

Q ss_pred             cHHHHHHHHHHCCCCCCH-HHHHHHHHHHhccCChHHHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHH
Q 011236          190 KIPDVLLDMKENGVPPDN-FSYRICINSYGARSELSSMENVLQEMESQSHISMD-WGTYSTVANYYIIAGLKEKAIIYLK  267 (490)
Q Consensus       190 ~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~  267 (490)
                      +|.+.|++..+  ++||. ..+..+..++...|++++|   |+++. ..+  |+ ...++..... . ...+..+.+.++
T Consensus         4 eA~q~~~qA~~--l~p~~a~a~~~la~~~~~~~~l~ea---ye~~i-~~d--p~~a~~~~~e~~L-w-~~~y~~~ie~~r   73 (497)
T d1ya0a1           4 QSAQYLRQAEV--LKADMTDSKLGPAEVWTSRQALQDL---YQKML-VTD--LEYALDKKVEQDL-W-NHAFKNQITTLQ   73 (497)
T ss_dssp             HHHHHHHHHHH--HHGGGTCSSSCSSSSHHHHHHHHHH---HHHHH-HHC--HHHHHHHTHHHHH-H-HHHTHHHHHHHH
T ss_pred             HHHHHHHHHHH--cCCCCHHHHhhHHHHHHHHchHHHH---HHHHH-HcC--hhhHHHHhHHHHH-H-HHHHHHHHHHHH
Confidence            46667777665  34443 2444455566666666654   55544 212  11 1111111111 1 112344555565


Q ss_pred             HHhhhhccCCChhhHHHHHHHH--HhcCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCC
Q 011236          268 KCEDIVSKSKDALGYNHLISHY--ASLGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCY  345 (490)
Q Consensus       268 ~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  345 (490)
                      ...+.... ++..-.......+  ...+.++.++..+....... .++...+..+...+.+.|+.+.|...+....... 
T Consensus        74 ~~~k~~~~-~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-  150 (497)
T d1ya0a1          74 GQAKNRAN-PNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVD-LPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI-  150 (497)
T ss_dssp             HHHSCSSC-TTTTHHHHHHHHHHHHHHHHHHHHHHHHTC--------------------------------CCHHHHHH-
T ss_pred             HhcccccC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-hhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC-
Confidence            55443322 3322222222111  12333444444443332222 2445556667777777777777777766655421 


Q ss_pred             CCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchh
Q 011236          346 CYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPS  425 (490)
Q Consensus       346 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~  425 (490)
                       | ..++..+...+...|++++|...|++..+..+. +...|+.|...+...|+..+|...|.+++.      --.|-..
T Consensus       151 -~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~-~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~------~~~~~~~  221 (497)
T d1ya0a1         151 -C-QHCLVHLGDIARYRNQTSQAESYYRHAAQLVPS-NGQPYNQLAILASSKGDHLTTIFYYCRSIA------VKFPFPA  221 (497)
T ss_dssp             -H-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-BSHHHHHHHHHHHHTTCHHHHHHHHHHHHS------SSBCCHH
T ss_pred             -H-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCC-chHHHHHHHHHHHHcCCHHHHHHHHHHHHh------CCCCCHH
Confidence             1 245666777777788888888888888776544 566788888888888888888888888776      2235556


Q ss_pred             hHHHHHHHHHc
Q 011236          426 LVSSILDWLGD  436 (490)
Q Consensus       426 ~~~~l~~~~~~  436 (490)
                      ++..|...+.+
T Consensus       222 a~~nL~~~~~~  232 (497)
T d1ya0a1         222 ASTNLQKALSK  232 (497)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            67777666544

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.12  E-value=5e-05  Score=57.63  Aligned_cols=61  Identities=15%  Similarity=0.048  Sum_probs=40.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      +|+.+..+|.+.|++++|+..+++.++.++. +..+|..+..++...|++++|+..|+++++
T Consensus        69 ~~~Nla~~~~~l~~~~~Al~~~~~al~~~p~-~~ka~~~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          69 CNLNLATCYNKNKDYPKAIDHASKVLKIDKN-NVKALYKLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHhcccchhhhhhhccccccch-hhhhhHHhHHHHHHcCCHHHHHHHHHHHHH
Confidence            4455666666667777777777666666543 566666666667777777777777766666

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.11  E-value=2.2e-05  Score=57.57  Aligned_cols=95  Identities=14%  Similarity=0.147  Sum_probs=69.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-CC-----HHHHHHH
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT-PT-----PNSWSII  390 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~-p~-----~~~~~~l  390 (490)
                      +..+...+.+.|++++|...|.+.++.+ +.+...+..+..+|.+.|++++|+..++++++..+. +.     ..+|..+
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~l   85 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHH
Confidence            3456667777888888888888887763 335667777888888888888888888887764321 11     1356677


Q ss_pred             HHHHhccCCHHHHHHHHHHHHH
Q 011236          391 AAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       391 ~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...+...+++++|++.|++.+.
T Consensus        86 g~~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          86 GNSYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHh
Confidence            7778888889999999888876

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=98.07  E-value=8.2e-05  Score=56.42  Aligned_cols=76  Identities=9%  Similarity=-0.030  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCc-chhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHH
Q 011236          385 NSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRP-KPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHA  462 (490)
Q Consensus       385 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~  462 (490)
                      .+|..+..+|.+.|++++|++.++++++.       .| +..+|..+..++...|++++|...|++..+..|. ..+...
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~al~~-------~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~~~~~~  140 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKVLKI-------DKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNS  140 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-------STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhccccc-------cchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            47888999999999999999999999983       35 4589999999999999999999999999999998 666665


Q ss_pred             HHHHH
Q 011236          463 LTEAH  467 (490)
Q Consensus       463 l~~~~  467 (490)
                      +..+.
T Consensus       141 l~~~~  145 (153)
T d2fbna1         141 YELCV  145 (153)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            54443

>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=98.06  E-value=5.6e-05  Score=58.44  Aligned_cols=80  Identities=11%  Similarity=0.056  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHH
Q 011236          386 SWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALT  464 (490)
Q Consensus       386 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~  464 (490)
                      +|..+..+|.+.|++++|+..+++++...|      .+...|..+..++...|++++|...|+++.+..|. ..++..+.
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p------~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~  139 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLDS------ANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIF  139 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCT------TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhccc------chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            456677777888888888888888877331      33467777777888888888888888888887777 66666655


Q ss_pred             HHHHhcC
Q 011236          465 EAHIRSG  471 (490)
Q Consensus       465 ~~~~~~g  471 (490)
                      ....+.+
T Consensus       140 ~~~~~~~  146 (168)
T d1kt1a1         140 MCQKKAK  146 (168)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5554444

>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=97.99  E-value=4.6e-06  Score=77.49  Aligned_cols=226  Identities=8%  Similarity=-0.133  Sum_probs=129.6

Q ss_pred             HHHHHHHHHHhCCCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHH
Q 011236          225 SMENVLQEMESQSHISMD-WGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWG  303 (490)
Q Consensus       225 ~a~~~~~~~~~~~~~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~  303 (490)
                      +|.+.|++.. ..  .|+ ...+..+..+|...|++++|   |+++....+.  .....+.  ........+..+.+.++
T Consensus         4 eA~q~~~qA~-~l--~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~dp~--~a~~~~~--e~~Lw~~~y~~~ie~~r   73 (497)
T d1ya0a1           4 QSAQYLRQAE-VL--KADMTDSKLGPAEVWTSRQALQDL---YQKMLVTDLE--YALDKKV--EQDLWNHAFKNQITTLQ   73 (497)
T ss_dssp             HHHHHHHHHH-HH--HGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHCHH--HHHHHTH--HHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHH-Hc--CCCCHHHHhhHHHHHHHHchHHHH---HHHHHHcChh--hHHHHhH--HHHHHHHHHHHHHHHHH
Confidence            6778888876 32  233 34455677788888888876   5665543321  1111111  11111122455667777


Q ss_pred             HHHHhcCCCChhhHHHHHHHH--HhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC
Q 011236          304 LQKIKCKKQLNRDYITMLGSL--VKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKT  381 (490)
Q Consensus       304 ~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  381 (490)
                      ........++..-.......+  ...+.++.+...+....+. ..++...+..+...+.+.|+.++|...++......  
T Consensus        74 ~~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l-~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--  150 (497)
T d1ya0a1          74 GQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNV-DLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI--  150 (497)
T ss_dssp             HHHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC--------------------------------CCHHHHHH--
T ss_pred             HhcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC--
Confidence            555544444443333222222  2234455555555444332 13355667778888999999999998888776542  


Q ss_pred             CCHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhh
Q 011236          382 PTPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNM  459 (490)
Q Consensus       382 p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~  459 (490)
                       ...++..+...+...|++++|...|+++.+       +.|+. ..|+.+...+...|+..+|...|.+.....++ +.+
T Consensus       151 -~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~-------l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a  222 (497)
T d1ya0a1         151 -CQHCLVHLGDIARYRNQTSQAESYYRHAAQ-------LVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAA  222 (497)
T ss_dssp             -HHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-------HCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHH
T ss_pred             -HHHHHHHHHHHHHHcccHHHHHHHHHHHHH-------HCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHH
Confidence             235788889999999999999999999998       44666 79999999999999999999999999999999 999


Q ss_pred             hHHHHHHHHhcC
Q 011236          460 YHALTEAHIRSG  471 (490)
Q Consensus       460 ~~~l~~~~~~~g  471 (490)
                      +..|...|.+..
T Consensus       223 ~~nL~~~~~~~~  234 (497)
T d1ya0a1         223 STNLQKALSKAL  234 (497)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhh
Confidence            999999987765

>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=97.97  E-value=6.2e-05  Score=58.29  Aligned_cols=61  Identities=13%  Similarity=0.007  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          351 VPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       351 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .+..+..+|.+.|++++|+..++++++..+. ++.+|..+..+|...|++++|++.|+++++
T Consensus        79 ~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~-~~~a~~~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          79 CVLNIGACKLKMSDWQGAVDSCLEALEIDPS-NTKALYRRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchhhhhhhhhhhhhhh-hhhHHHhHHHHHHHccCHHHHHHHHHHHHH
Confidence            4444555666666666666666666665443 555666666666666666666666666666

>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=97.90  E-value=0.00013  Score=56.31  Aligned_cols=77  Identities=10%  Similarity=-0.095  Sum_probs=42.5

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Q 011236          316 DYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGY  394 (490)
Q Consensus       316 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~  394 (490)
                      .+..+..++.+.|++++|+..+..+++.. +.+...|..+..+|.+.|++++|+..|++.++..+. +...+..+..+.
T Consensus        79 ~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~-n~~~~~~l~~~~  155 (169)
T d1ihga1          79 CVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE-DKAIQAELLKVK  155 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            44455555666666666666666665542 224445555666666666666666666666665433 444444444443

>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=97.89  E-value=0.00047  Score=53.02  Aligned_cols=62  Identities=8%  Similarity=-0.043  Sum_probs=31.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Q 011236          317 YITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKG  379 (490)
Q Consensus       317 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  379 (490)
                      |..+..+|.+.|++++|...++..++.. +.+...|..+..+|...|++++|...|+++++..
T Consensus        67 ~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~  128 (168)
T d1kt1a1          67 FLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVN  128 (168)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC
T ss_pred             HHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            3344444555555555555555555431 2234444555555555555555555555555543

>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=97.88  E-value=7.8e-05  Score=58.07  Aligned_cols=56  Identities=13%  Similarity=0.027  Sum_probs=34.8

Q ss_pred             hHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcC--CcHHHHHHHH
Q 011236          426 LVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSG--QEVDGLLESM  481 (490)
Q Consensus       426 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g--~~a~~~~~~m  481 (490)
                      .+..+..++.+.|++++|...++++.+..|. ...|..++.+|.+.|  .+|++.|+++
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            3455555666666666666666666666666 666666666666666  5566666654

>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=97.87  E-value=0.00011  Score=50.32  Aligned_cols=82  Identities=11%  Similarity=0.001  Sum_probs=62.9

Q ss_pred             CHHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhh
Q 011236          383 TPNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMY  460 (490)
Q Consensus       383 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~  460 (490)
                      +...+-.+...+.+.|++++|+..|+++++..+......++. .++..+..++.+.|++++|...++++.+..|. +.++
T Consensus         4 saddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~~~~a~   83 (95)
T d1tjca_           4 TAEDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRAN   83 (95)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcCCHHHH
Confidence            344455677888889999999999999888665444444443 67888888999999999999999999998888 7776


Q ss_pred             HHHH
Q 011236          461 HALT  464 (490)
Q Consensus       461 ~~l~  464 (490)
                      +.+.
T Consensus        84 ~Nl~   87 (95)
T d1tjca_          84 GNLK   87 (95)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6654

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.80  E-value=0.00014  Score=55.23  Aligned_cols=100  Identities=15%  Similarity=0.052  Sum_probs=73.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCC-CC----------HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcch
Q 011236          356 LLGYSQKGMIEKADAVLKEIVKKGKT-PT----------PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKP  424 (490)
Q Consensus       356 ~~~~~~~g~~~~A~~~~~~m~~~~~~-p~----------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~  424 (490)
                      ...+.+.|++++|+..|++.++.... |+          ..+|+.+..+|...|++++|...+++++...++.....++.
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~   95 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDE   95 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccc
Confidence            34456678888888888877763221 11          35788899999999999999999999988654333333332


Q ss_pred             -----hhHHHHHHHHHcCCCHHHHHHHHHHHHhccc
Q 011236          425 -----SLVSSILDWLGDNRDVEEVEAFVSSLKIKVQ  455 (490)
Q Consensus       425 -----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  455 (490)
                           ..+..+..+|...|++++|...|++..+..+
T Consensus        96 ~~~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~  131 (156)
T d2hr2a1          96 GKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIE  131 (156)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             cchhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence                 2567778899999999999999998877644

>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=97.77  E-value=0.00065  Score=51.41  Aligned_cols=107  Identities=12%  Similarity=-0.041  Sum_probs=70.1

Q ss_pred             HHHhcCCHHHHHHHHHHHHhcCCC-C----------CchhHHHHHHHHHhcCCHHHHHHHHHHHHHc-----CCCCC---
Q 011236          323 SLVKIGELEEAEKMLEEWELSCYC-Y----------DFRVPNIILLGYSQKGMIEKADAVLKEIVKK-----GKTPT---  383 (490)
Q Consensus       323 ~~~~~~~~~~a~~~~~~~~~~~~~-~----------~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~-----~~~p~---  383 (490)
                      .+.+.|++++|...|++.++.... |          ....|+.+..+|...|++++|...+++.++.     ...++   
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~   97 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGK   97 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccc
Confidence            344556666666666655542110 1          1245667778888888888888888777642     11222   


Q ss_pred             --HHHHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHH
Q 011236          384 --PNSWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSS  429 (490)
Q Consensus       384 --~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~  429 (490)
                        ...|..+..+|...|++++|+..|++++++.++..+-.+....+..
T Consensus        98 ~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~~~~~~~~~~~~~~~  145 (156)
T d2hr2a1          98 LWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGETPGKERMME  145 (156)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSCCTTHHHHHH
T ss_pred             hhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHhhchHHHHHHHHH
Confidence              2256778899999999999999999999977766666555544433

>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=97.76  E-value=8.4e-05  Score=55.68  Aligned_cols=115  Identities=11%  Similarity=0.091  Sum_probs=81.7

Q ss_pred             HHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhcc----------CCHHHHHHHHHHHHHhhhcCcCCCcch-hhH
Q 011236          359 YSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADK----------NNMEKAFECMKEALAVHEENKFWRPKP-SLV  427 (490)
Q Consensus       359 ~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~----------~~~~~a~~~~~~~~~~~~~~~~~~p~~-~~~  427 (490)
                      |-+.+.+++|...|+..++..+. ++.++..+..+|...          +.+++|+..|+++++       +.|+. .+|
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~P~-~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~-------l~P~~~~a~   78 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSNPL-DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALL-------IDPKKDEAV   78 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhCCc-chHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHH-------hcchhhHHH
Confidence            44566788888888888887655 777777777777643          446789999999988       44554 678


Q ss_pred             HHHHHHHHcCC-----------CHHHHHHHHHHHHhcccc-hhhhHHHHHHHHhcCCcHHHHHHHHHhCCC
Q 011236          428 SSILDWLGDNR-----------DVEEVEAFVSSLKIKVQK-RNMYHALTEAHIRSGQEVDGLLESMKADDI  486 (490)
Q Consensus       428 ~~l~~~~~~~g-----------~~~~a~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~a~~~~~~m~~~~~  486 (490)
                      ..+..+|...|           .++.|.+.|++..+..|. ...+..|...     .+|.+++.+..+.|+
T Consensus        79 ~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~~~-----~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1          79 WCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT-----AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH-----HTHHHHHHHHHHSSS
T ss_pred             hhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHHHH-----HHHHHHHHHHHHHhc
Confidence            88888876654           368899999999999988 5544444433     345666666666554

>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=97.74  E-value=9.1e-05  Score=55.47  Aligned_cols=112  Identities=15%  Similarity=0.037  Sum_probs=68.4

Q ss_pred             cCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHh----------cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc
Q 011236          327 IGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQ----------KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD  396 (490)
Q Consensus       327 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----------~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~  396 (490)
                      .+.+++|...++...+.. +.+..++..+..+|..          .+.+++|+..|++.++.++. +..+|..+..+|..
T Consensus        10 ~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~-~~~a~~~lG~~y~~   87 (145)
T d1zu2a1          10 ILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPK-KDEAVWCIGNAYTS   87 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHH
T ss_pred             HccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcch-hhHHHhhHHHHHHH
Confidence            334555555555554431 2233344444444432          23457788888888887655 67788888887766


Q ss_pred             cC-----------CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhc
Q 011236          397 KN-----------NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIK  453 (490)
Q Consensus       397 ~~-----------~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  453 (490)
                      .|           .+++|.+.|+++++       +.|+...+..-+..+      ..|.+++.++.+.
T Consensus        88 ~g~~~~~~~~~~~~~~~A~~~~~kal~-------l~P~~~~~~~~L~~~------~ka~~~~~e~~k~  142 (145)
T d1zu2a1          88 FAFLTPDETEAKHNFDLATQFFQQAVD-------EQPDNTHYLKSLEMT------AKAPQLHAEAYKQ  142 (145)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHHHHHH-------HCTTCHHHHHHHHHH------HTHHHHHHHHHHS
T ss_pred             cccchhhHHHHHHhHHHhhhhhhcccc-------cCCCHHHHHHHHHHH------HHHHHHHHHHHHH
Confidence            54           36888999999988       668887776655544      3455555555443

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.68  E-value=2.2e-05  Score=65.59  Aligned_cols=124  Identities=15%  Similarity=0.005  Sum_probs=65.1

Q ss_pred             HhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHH
Q 011236          325 VKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAF  404 (490)
Q Consensus       325 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~  404 (490)
                      .+.|++++|...+++.++. -+-|...+..+...|+..|++++|...|+...+..+. +...+..+...+...+..+++.
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~   84 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKA-SPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE-YLPGASQLRHLVKAAQARKDFA   84 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHT-CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG-GHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHhccccHHHH
Confidence            3557777777777777665 2335566677777777777777777777777665432 3333433333332222222211


Q ss_pred             HHHHHHHHhhhcCcCCCcc-hhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc
Q 011236          405 ECMKEALAVHEENKFWRPK-PSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       405 ~~~~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  456 (490)
                      .-......     .+ .|+ ...+......+...|+.++|...++++.+..|.
T Consensus        85 ~~~~~~~~-----~~-~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p~  131 (264)
T d1zbpa1          85 QGAATAKV-----LG-ENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQE  131 (264)
T ss_dssp             TSCCCEEC-----CC-SCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC
T ss_pred             HHhhhhhc-----cc-CchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCC
Confidence            11100000     01 122 123333444566677777777777777666554

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.60  E-value=4.3e-05  Score=63.74  Aligned_cols=52  Identities=15%  Similarity=0.003  Sum_probs=26.5

Q ss_pred             HcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHhcCChhHHHHHHHHHHHh
Q 011236          255 IAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYASLGNKDEMMKFWGLQKIK  308 (490)
Q Consensus       255 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  308 (490)
                      +.|++++|+..+++..+..+  .|...+..+...++..|++++|...++.....
T Consensus         8 ~~G~l~eAl~~l~~al~~~P--~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l   59 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKASP--KDASLRSSFIELLCIDGDFERADEQLMQSIKL   59 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTCT--TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHCC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            34555555555555544444  34455555555555555555555555544444

>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=96.94  E-value=0.0066  Score=40.97  Aligned_cols=63  Identities=5%  Similarity=-0.065  Sum_probs=31.6

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHhhhhccCC-----ChhhHHHHHHHHHhcCChhHHHHHHHHHHHhcC
Q 011236          248 TVANYYIIAGLKEKAIIYLKKCEDIVSKSK-----DALGYNHLISHYASLGNKDEMMKFWGLQKIKCK  310 (490)
Q Consensus       248 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  310 (490)
                      .+...+.+.|++++|+..|++..+..+..+     ...++..+..++.+.|++++|+..+++.+...|
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P   77 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDP   77 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCc
Confidence            455555555566665555555543322100     123455555555555555555555555555443

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=96.18  E-value=0.11  Score=37.24  Aligned_cols=84  Identities=10%  Similarity=-0.077  Sum_probs=45.6

Q ss_pred             cCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----cCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHc-
Q 011236          362 KGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYAD----KNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGD-  436 (490)
Q Consensus       362 ~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~-  436 (490)
                      ..+.++|...+++..+.|   ++.....|...|..    ..+.++|.++|+++.+     .|.   +.....|...|.. 
T Consensus        36 ~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa~-----~g~---~~a~~~Lg~~y~~G  104 (133)
T d1klxa_          36 QINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAAQYYSKACG-----LND---QDGCLILGYKQYAG  104 (133)
T ss_dssp             TSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHH-----TTC---HHHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHHHHHhhhhc-----cCc---chHHHHHHHHHHcC
Confidence            345666666666666654   44444444444443    3456677777777666     331   2223333333333 


Q ss_pred             ---CCCHHHHHHHHHHHHhcccc
Q 011236          437 ---NRDVEEVEAFVSSLKIKVQK  456 (490)
Q Consensus       437 ---~g~~~~a~~~~~~~~~~~~~  456 (490)
                         ..+.++|.++|++..+.+..
T Consensus       105 ~gv~~d~~~A~~~~~~Aa~~G~~  127 (133)
T d1klxa_         105 KGVVKNEKQAVKTFEKACRLGSE  127 (133)
T ss_dssp             SSSCCCHHHHHHHHHHHHHTTCH
T ss_pred             CccCCCHHHHHHHHHHHHHCCCH
Confidence               34666777777766665543

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=95.79  E-value=0.093  Score=37.58  Aligned_cols=16  Identities=19%  Similarity=0.052  Sum_probs=9.9

Q ss_pred             ChhHHHHHHHHHHhCC
Q 011236           84 RFKHALQVSEWMSGQG   99 (490)
Q Consensus        84 ~~~~a~~~~~~~~~~~   99 (490)
                      ++++|++.|++..+.|
T Consensus         8 d~~~A~~~~~kaa~~g   23 (133)
T d1klxa_           8 DLKKAIQYYVKACELN   23 (133)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHCC
Confidence            4566666666666655

>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=95.66  E-value=0.66  Score=41.09  Aligned_cols=116  Identities=7%  Similarity=-0.071  Sum_probs=58.6

Q ss_pred             CChhHHHHHHHHHHHhcCCCChhhHHH----HHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 011236          293 GNKDEMMKFWGLQKIKCKKQLNRDYIT----MLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKA  368 (490)
Q Consensus       293 ~~~~~a~~~~~~~~~~~~~~~~~~~~~----l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  368 (490)
                      .+.+.+..++........ .+......    +...+...+..+.+...+......+  .+.......+......+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQQ-LNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHTT-CCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhccc-ccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccc--cchHHHHHHHHHHHHcCChHHH
Confidence            456666666665544433 22222221    2222223455566666665555432  2333333344445556677777


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          369 DAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       369 ~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ...++.|.... .-...-.--+..++...|+.+.|...|..+..
T Consensus       305 ~~~~~~l~~~~-~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~  347 (450)
T d1qsaa1         305 NTWLARLPMEA-KEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (450)
T ss_dssp             HHHHHHSCTTG-GGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHhcCccc-ccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc
Confidence            66666653321 11223334555666777777777777776644

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=94.52  E-value=0.44  Score=32.86  Aligned_cols=58  Identities=19%  Similarity=0.131  Sum_probs=24.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          354 IILLGYSQKGMIEKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       354 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      .-++.+..+|+-+.-.++++.+.+. -+|++...-.+..+|.+.|...++.+++.++.+
T Consensus        91 lALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe  148 (161)
T d1wy6a1          91 KALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACK  148 (161)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence            3334444444444444444443332 233444444444444444444444444444444

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.13  E-value=0.37  Score=33.40  Aligned_cols=47  Identities=11%  Similarity=0.131  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHhccCCHHHHHHHHHHHHH
Q 011236          366 EKADAVLKEIVKKGKTPTPNSWSIIAAGYADKNNMEKAFECMKEALA  412 (490)
Q Consensus       366 ~~A~~~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  412 (490)
                      ++++.+|+++.+.++.-....+-.|..+|.+.|++++|.++++.+++
T Consensus        55 ~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~  101 (124)
T d2pqrb1          55 RLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  101 (124)
T ss_dssp             HHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHc
Confidence            34444554444432110112334444445555555555555555544

>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=93.81  E-value=0.64  Score=32.15  Aligned_cols=70  Identities=10%  Similarity=0.001  Sum_probs=54.0

Q ss_pred             CCCCHHHHHHHHHHHhccC---CHHHHHHHHHHHHHhhhcCcCCCc-ch-hhHHHHHHHHHcCCCHHHHHHHHHHHHhcc
Q 011236          380 KTPTPNSWSIIAAGYADKN---NMEKAFECMKEALAVHEENKFWRP-KP-SLVSSILDWLGDNRDVEEVEAFVSSLKIKV  454 (490)
Q Consensus       380 ~~p~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~p-~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  454 (490)
                      ..|...|--....++.++.   +.++++.+|++...     .  .| +. ..+..|.-+|.+.|+++.|.+.++.+.+..
T Consensus        31 ~~~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~-----~--~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ie  103 (124)
T d2pqrb1          31 PTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYK-----E--AESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHE  103 (124)
T ss_dssp             GGSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHH-----H--CGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             CCCCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHh-----c--CchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccC
Confidence            3456666666677777654   46789999999887     1  24 33 466677788999999999999999999999


Q ss_pred             cc
Q 011236          455 QK  456 (490)
Q Consensus       455 ~~  456 (490)
                      |.
T Consensus       104 P~  105 (124)
T d2pqrb1         104 RN  105 (124)
T ss_dssp             TT
T ss_pred             CC
Confidence            88

>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=93.51  E-value=0.56  Score=30.53  Aligned_cols=63  Identities=13%  Similarity=0.154  Sum_probs=45.2

Q ss_pred             CHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHHHHHHHHhcccc-hhhhHHHHHH
Q 011236          399 NMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEAFVSSLKIKVQK-RNMYHALTEA  466 (490)
Q Consensus       399 ~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~l~~~  466 (490)
                      +.-++.+-++.+..     ..+.|++....+.+++|.+..|+..|.++|+.++..... ...|..+++-
T Consensus        21 D~we~rrgmN~l~~-----~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~~~k~~y~yilqe   84 (105)
T d1v54e_          21 DAWELRKGMNTLVG-----YDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGPHKEIYPYVIQE   84 (105)
T ss_dssp             CHHHHHHHHHHHTT-----SSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCTTHHHHHHHH
T ss_pred             cHHHHHHHHHHHhc-----cccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            45556666666665     667788888888888888888888888888877766544 5566655544

>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=93.47  E-value=0.73  Score=31.72  Aligned_cols=140  Identities=5%  Similarity=-0.077  Sum_probs=74.4

Q ss_pred             HHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCCChhHHHHHHHHHHhcCChhHHHH
Q 011236           79 LRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDKVDKLYGALLNCYVREGLVDESLS  158 (490)
Q Consensus        79 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~li~~~~~~g~~~~a~~  158 (490)
                      +.-.|..++..++..+...+.   +..-++.++.-....-+-+...++++.+-... |.          ..+++......
T Consensus        12 ~ildG~ve~Gveii~k~~~ss---~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~F-Dl----------s~C~Nlk~vv~   77 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSYF-DL----------DKCQNLKSVVE   77 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGS-CG----------GGCSCTHHHHH
T ss_pred             HHHhhhHHhHHHHHHHHcccC---CccccceeeeecccccchHHHHHHHHHHhhhc-Cc----------hhhhcHHHHHH
Confidence            344577777777777776654   45666666655555555566666665554321 10          11222222222


Q ss_pred             HHHHHHhcCCCCCcchHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHHhccCChHHHHHHHHHHHhCCC
Q 011236          159 LMQKMKEMGSFGSALNYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSYGARSELSSMENVLQEMESQSH  238 (490)
Q Consensus       159 ~~~~m~~~~~~p~~~~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  238 (490)
                      .+-.+-     .+...++..++.....|+-+...++++++.+. -+|++...-.+..+|.+.|+..++.+++.+.- +.|
T Consensus        78 C~~~~n-----~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~AC-e~G  150 (161)
T d1wy6a1          78 CGVINN-----TLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEAC-KKG  150 (161)
T ss_dssp             HHHHTT-----CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HTT
T ss_pred             HHHHhc-----chHHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHH-HHh
Confidence            221111     13334445555566666666666666665553 34555566666666666666666666666655 444


Q ss_pred             C
Q 011236          239 I  239 (490)
Q Consensus       239 ~  239 (490)
                      +
T Consensus       151 ~  151 (161)
T d1wy6a1         151 E  151 (161)
T ss_dssp             C
T ss_pred             H
Confidence            4

>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=93.26  E-value=2.5  Score=37.18  Aligned_cols=339  Identities=9%  Similarity=0.019  Sum_probs=160.3

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCCCCCChhhHHHHHHHHHhhcCHHHHHHHHHHccccCC-ChhHHHHHHHHHHhcC
Q 011236           73 QRVIRQLRSRKRFKHALQVSEWMSGQGLAFSVHDHAVQLDLIGKVRGLESAETYFNSLNDEDK-VDKLYGALLNCYVREG  151 (490)
Q Consensus        73 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~li~~~~~~g  151 (490)
                      ..-+..+.+.++++..+..+.     ..+.+...-.....+....|+.+.|...+..+=..+. .+...+.+...+.+.|
T Consensus        76 ~~~l~~L~~~~~w~~~~~~~~-----~~p~~~~~~c~~~~A~~~~g~~~~a~~~~~~lW~~~~~~p~~c~~l~~~~~~~~  150 (450)
T d1qsaa1          76 SRFVNELARREDWRGLLAFSP-----EKPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPNACDKLFSVWRASG  150 (450)
T ss_dssp             HHHHHHHHHTTCHHHHHHHCC-----SCCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCSSCCCTHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhccCHHHHHHhcc-----CCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCCchHHHHHHHHHHhcC
Confidence            344566777777766544331     2244566666677777788888887777665544332 2334455555554444


Q ss_pred             ChhHH--HHHHHHHHhcC-----------CCCCcc-hHHHHHHHHHhcCCcCcHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 011236          152 LVDES--LSLMQKMKEMG-----------SFGSAL-NYNGIMCLYTNTGQHEKIPDVLLDMKENGVPPDNFSYRICINSY  217 (490)
Q Consensus       152 ~~~~a--~~~~~~m~~~~-----------~~p~~~-~~~~l~~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  217 (490)
                      .....  .+-+..+...|           ++++.. .....+...   .+...+.....   .  ..++......+..++
T Consensus       151 ~lt~~~~~~R~~~~l~~~~~~~a~~l~~~l~~~~~~~~~a~~~l~---~~p~~~~~~~~---~--~~~~~~~~~~~~~~l  222 (450)
T d1qsaa1         151 KQDPLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLA---NNPNTVLTFAR---T--TGATDFTRQMAAVAF  222 (450)
T ss_dssp             CSCHHHHHHHHHHHHHTTCHHHHHHHHHTCCGGGHHHHHHHHHHH---HCGGGHHHHHH---H--SCCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCChhhHHHHHhhCChhHHHHHHHHHHHH---hChHhHHHHHh---c--CCCChhhhHHHHHHH
Confidence            43221  11122221111           111111 111122111   12222222211   1  112333333333333


Q ss_pred             hc--cCChHHHHHHHHHHHhCCCCCCCHHHHHH----HHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHHHHHHh
Q 011236          218 GA--RSELSSMENVLQEMESQSHISMDWGTYST----VANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLISHYAS  291 (490)
Q Consensus       218 ~~--~g~~~~a~~~~~~~~~~~~~~~~~~~~~~----li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  291 (490)
                      .+  ..+.+.|...+.........  +..-...    +...+...+..+.+...+.......   .+.....-.+.....
T Consensus       223 ~rla~~d~~~a~~~l~~~~~~~~~--~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~~w~~~~al~  297 (450)
T d1qsaa1         223 ASVARQDAENARLMIPSLAQAQQL--NEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS---QSTSLIERRVRMALG  297 (450)
T ss_dssp             HHHHHHCHHHHHHHHHHHHHHTTC--CHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC---CCHHHHHHHHHHHHH
T ss_pred             HHHhccChhHHHHHHHhhhhcccc--cHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccc---cchHHHHHHHHHHHH
Confidence            22  34677777777776522222  2222221    2222233455666766666544322   333333344455566


Q ss_pred             cCChhHHHHHHHHHHHhcCCCChhhHHHHHHHHHhcCCHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhcCCHHHHHHH
Q 011236          292 LGNKDEMMKFWGLQKIKCKKQLNRDYITMLGSLVKIGELEEAEKMLEEWELSCYCYDFRVPNIILLGYSQKGMIEKADAV  371 (490)
Q Consensus       292 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  371 (490)
                      .+++..+...++.+... ........--+.+++...|+.+.|...|..+...   ++  -|. ++.+- +.|..-.    
T Consensus       298 ~~~~~~~~~~~~~l~~~-~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~~---~~--fYG-~LAa~-~Lg~~~~----  365 (450)
T d1qsaa1         298 TGDRRGLNTWLARLPME-AKEKDEWRYWQADLLLERGREAEAKEILHQLMQQ---RG--FYP-MVAAQ-RIGEEYE----  365 (450)
T ss_dssp             HTCHHHHHHHHHHSCTT-GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS---CS--HHH-HHHHH-HTTCCCC----
T ss_pred             cCChHHHHHHHHhcCcc-cccHHHHHHHHHHHHHHcCChhhHHHHHHHHhcC---CC--hHH-HHHHH-HcCCCCC----
Confidence            77888887777755322 1122334456677778888888888888877542   21  222 22111 1111000    


Q ss_pred             HHHHHHcCC--CCCH-H---HHHHHHHHHhccCCHHHHHHHHHHHHHhhhcCcCCCcchhhHHHHHHHHHcCCCHHHHHH
Q 011236          372 LKEIVKKGK--TPTP-N---SWSIIAAGYADKNNMEKAFECMKEALAVHEENKFWRPKPSLVSSILDWLGDNRDVEEVEA  445 (490)
Q Consensus       372 ~~~m~~~~~--~p~~-~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~  445 (490)
                         +....+  .++. .   .-..-+..+...|....|...|..+..     ..   +......+.....+.|.++.|..
T Consensus       366 ---~~~~~~~~~~~~~~~~~~~~~ra~~L~~~g~~~~A~~e~~~l~~-----~~---~~~~~~~la~lA~~~g~~~~aI~  434 (450)
T d1qsaa1         366 ---LKIDKAPQNVDSALTQGPEMARVRELMYWNLDNTARSEWANLVK-----SK---SKTEQAQLARYAFNNQWWDLSVQ  434 (450)
T ss_dssp             ---CCCCCCCSCCCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHHHT-----TC---CHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             ---CCcCCCCccHHHhhhcChHHHHHHHHHHcCCchHHHHHHHHHHh-----CC---CHHHHHHHHHHHHHCCChhHHHH
Confidence               000000  0000 0   011224456667777777777776665     32   23345566666777777777777


Q ss_pred             HHHHHHh
Q 011236          446 FVSSLKI  452 (490)
Q Consensus       446 ~~~~~~~  452 (490)
                      ...+...
T Consensus       435 a~~~~~~  441 (450)
T d1qsaa1         435 ATIAGKL  441 (450)
T ss_dssp             HHHHTTC
T ss_pred             HHHHHHc
Confidence            6665543

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=88.76  E-value=2  Score=27.87  Aligned_cols=61  Identities=8%  Similarity=-0.049  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhhhhccCCChhhHHHHH
Q 011236          223 LSSMENVLQEMESQSHISMDWGTYSTVANYYIIAGLKEKAIIYLKKCEDIVSKSKDALGYNHLI  286 (490)
Q Consensus       223 ~~~a~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  286 (490)
                      .-++.+-++.+- ..++.|++....+.+.+|.+.+++.-|.++|+.++....  .+...|..++
T Consensus        22 ~we~rrgmN~l~-~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~--~~k~~y~yil   82 (105)
T d1v54e_          22 AWELRKGMNTLV-GYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVI   82 (105)
T ss_dssp             HHHHHHHHHHHT-TSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHH
T ss_pred             HHHHHHHHHHHh-ccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--CcHHHHHHHH
Confidence            334555555555 556666666666666666666666666666666655443  2333444443